From ff94904574c51eeb7aecb327d6f2679fa4a60fb4 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 28 May 2020 20:24:01 -0500 Subject: Added lines calling proxy for publish datasets + added some resource redis queries and a missing import for the hmac functions --- wqflask/utility/redis_tools.py | 54 ++++++++++++++++++++++++++++++++++++++---- 1 file changed, 49 insertions(+), 5 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index ca42f7b7..15841032 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -1,17 +1,25 @@ from __future__ import print_function, division, absolute_import +import uuid import simplejson as json import redis # used for collections -Redis = redis.StrictRedis() import logging from flask import (render_template, flash) +from utility import hmac + from utility.logger import getLogger logger = getLogger(__name__) +def get_redis_conn(): + Redis = redis.StrictRedis(port=6380) + return Redis + +Redis = get_redis_conn() + def is_redis_available(): try: Redis.ping() @@ -70,14 +78,15 @@ def check_verification_code(code): email_address = None user_details = None email_address = Redis.hget("verification_codes", code) - return email_address if email_address: user_details = get_user_by_unique_column('email_address', email_address) - return user_details + if user_details: + return user_details + else: + return None else: return None - flash("Invalid code: Password reset code does not exist or might have expired!", "error") def get_user_groups(user_id): #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups @@ -167,4 +176,39 @@ def change_group_name(user_id, group_id, new_name): group_info["name"] = new_name return group_info else: - return None \ No newline at end of file + return None + +def get_resources(): + resource_list = Redis.hgetall("resources") + return resource_list + +def get_resource_id(dataset_type, dataset_id, trait_id = None, all_resources = None): + if not all_resources: + all_resources = get_resources() + + resource_list = [[key, json.loads(value)] for key, value in all_resources.items()] + + if not trait_id: + matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id] + else: + matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id and resource[1]['data']['trait'] == trait_id] + + if len(matched_resources): + return matched_resources[0] + else: + return False + +def get_resource_info(resource_id): + resource_info = Redis.hget("resources", resource_id) + return json.loads(resource_info) + +def add_resource(resource_info): + + if 'trait' in resource_info['data']: + resource_id = hmac.data_hmac('{}:{}'.format(str(resource_info['data']['dataset']), str(resource_info['data']['trait']))) + else: + resource_id = hmac.data_hmac('{}'.format(str(resource_info['data']['dataset']))) + + Redis.hset("resources", resource_id, json.dumps(resource_info)) + + return resource_info -- cgit v1.2.3 From 1a663f987bf3a640d21c2c89402318d5433efd9e Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 4 Jun 2020 14:23:30 -0500 Subject: Really should have split this into many more commits: - Now use proxy to pull trait data and hide traits/results that the user doesn't have view permission for - Created a factory method for creating trait ob so it can return None when user doesn't have view permissions (this is why such a large number of files are changed) - Added metadata to permutation export - Added current group management code - Added fixed password verification e-mail code --- wqflask/base/trait.py | 177 ++++---- wqflask/utility/helper_functions.py | 11 +- wqflask/utility/redis_tools.py | 58 +-- wqflask/wqflask/api/correlation.py | 472 ++++++++++----------- wqflask/wqflask/api/gen_menu.py | 11 +- wqflask/wqflask/api/mapping.py | 4 +- wqflask/wqflask/collect.py | 15 +- .../comparison_bar_chart/comparison_bar_chart.py | 4 +- wqflask/wqflask/correlation/corr_scatter_plot.py | 8 +- wqflask/wqflask/correlation/show_corr_results.py | 8 +- .../wqflask/correlation_matrix/show_corr_matrix.py | 22 +- wqflask/wqflask/ctl/ctl_analysis.py | 10 +- wqflask/wqflask/do_search.py | 11 +- wqflask/wqflask/gsearch.py | 13 +- .../marker_regression/display_mapping_results.py | 6 + wqflask/wqflask/marker_regression/gemma_mapping.py | 4 +- wqflask/wqflask/marker_regression/rqtl_mapping.py | 64 ++- wqflask/wqflask/marker_regression/run_mapping.py | 3 +- wqflask/wqflask/network_graph/network_graph.py | 4 +- wqflask/wqflask/search_results.py | 106 ++--- wqflask/wqflask/show_trait/export_trait_data.py | 4 +- wqflask/wqflask/show_trait/show_trait.py | 21 +- wqflask/wqflask/templates/admin/group_manager.html | 45 +- wqflask/wqflask/templates/correlation_page.html | 1 + wqflask/wqflask/templates/email/verification.txt | 7 - wqflask/wqflask/templates/gsearch_pheno.html | 2 +- wqflask/wqflask/templates/mapping_results.html | 31 +- wqflask/wqflask/user_login.py | 43 +- wqflask/wqflask/user_session.py | 18 +- wqflask/wqflask/views.py | 71 +++- 30 files changed, 637 insertions(+), 617 deletions(-) delete mode 100644 wqflask/wqflask/templates/email/verification.txt (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 1b7cb23c..b133bf21 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -11,6 +11,7 @@ from base.data_set import create_dataset from db import webqtlDatabaseFunction from utility import webqtlUtil from utility import hmac +from utility.authentication_tools import check_resource_availability from utility.tools import GN2_BASE_URL from utility.redis_tools import get_redis_conn Redis = get_redis_conn() @@ -21,11 +22,33 @@ import simplejson as json from MySQLdb import escape_string as escape from pprint import pformat as pf -from flask import Flask, g, request, url_for +from flask import Flask, g, request, url_for, redirect from utility.logger import getLogger logger = getLogger(__name__ ) +def create_trait(**kw): + assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; + + permitted = True + if kw.get('name'): + if kw.get('dataset_name'): + if kw.get('dataset_name') != "Temp": + dataset = create_dataset(kw.get('dataset_name')) + else: + dataset = kw.get('dataset') + + if kw.get('dataset_name') != "Temp": + if dataset.type == 'Publish': + permitted = check_resource_availability(dataset, kw.get('name')) + else: + permitted = check_resource_availability(dataset) + + if permitted: + return GeneralTrait(**kw) + else: + return None + class GeneralTrait(object): """ Trait class defines a trait in webqtl, can be either Microarray, @@ -50,6 +73,7 @@ class GeneralTrait(object): self.haveinfo = kw.get('haveinfo', False) self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet self.data = kw.get('data', {}) + self.view = True # Sets defaults self.locus = None @@ -77,6 +101,7 @@ class GeneralTrait(object): # So we could add a simple if statement to short-circuit this if necessary if self.dataset.type != "Temp": self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info) + if get_sample_info != False: self = retrieve_sample_data(self, self.dataset) @@ -212,26 +237,28 @@ def get_sample_data(): trait = params['trait'] dataset = params['dataset'] - trait_ob = GeneralTrait(name=trait, dataset_name=dataset) - - trait_dict = {} - trait_dict['name'] = trait - trait_dict['db'] = dataset - trait_dict['type'] = trait_ob.dataset.type - trait_dict['group'] = trait_ob.dataset.group.name - trait_dict['tissue'] = trait_ob.dataset.tissue - trait_dict['species'] = trait_ob.dataset.group.species - trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset) - trait_dict['description'] = trait_ob.description_display - if trait_ob.dataset.type == "ProbeSet": - trait_dict['symbol'] = trait_ob.symbol - trait_dict['location'] = trait_ob.location_repr - elif trait_ob.dataset.type == "Publish": - if trait_ob.pubmed_id: - trait_dict['pubmed_link'] = trait_ob.pubmed_link - trait_dict['pubmed_text'] = trait_ob.pubmed_text - - return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) + trait_ob = create_trait(name=trait, dataset_name=dataset) + if trait_ob: + trait_dict = {} + trait_dict['name'] = trait + trait_dict['db'] = dataset + trait_dict['type'] = trait_ob.dataset.type + trait_dict['group'] = trait_ob.dataset.group.name + trait_dict['tissue'] = trait_ob.dataset.tissue + trait_dict['species'] = trait_ob.dataset.group.species + trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset) + trait_dict['description'] = trait_ob.description_display + if trait_ob.dataset.type == "ProbeSet": + trait_dict['symbol'] = trait_ob.symbol + trait_dict['location'] = trait_ob.location_repr + elif trait_ob.dataset.type == "Publish": + if trait_ob.pubmed_id: + trait_dict['pubmed_link'] = trait_ob.pubmed_link + trait_dict['pubmed_text'] = trait_ob.pubmed_text + + return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) + else: + return None def jsonable(trait): """Return a dict suitable for using as json @@ -350,91 +377,36 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): assert dataset, "Dataset doesn't exist" if dataset.type == 'Publish': - resource_id = hmac.data_hmac("{}:{}".format(dataset.id, trait.name)) - - the_url = "http://localhost:8080/run_action/?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id) - trait_data = json.loads(requests.get("http://localhost:8080/run_action/?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id))) - - query = """ - SELECT - PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID, - Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, - Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean, - Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, - Publication.Authors, Publication.Title, Publication.Abstract, - Publication.Journal, Publication.Volume, Publication.Pages, - Publication.Month, Publication.Year, PublishXRef.Sequence, - Phenotype.Units, PublishXRef.comments - FROM - PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet - WHERE - PublishXRef.Id = %s AND - Phenotype.Id = PublishXRef.PhenotypeId AND - Publication.Id = PublishXRef.PublicationId AND - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishXRef.InbredSetId = InbredSet.Id AND - PublishFreeze.Id = %s - """ % (trait.name, dataset.id) - - logger.sql(query) - trait_info = g.db.execute(query).fetchone() - - - #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name - #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. + resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait.name)) + the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id) elif dataset.type == 'ProbeSet': - display_fields_string = ', ProbeSet.'.join(dataset.display_fields) - display_fields_string = 'ProbeSet.' + display_fields_string - query = """ - SELECT %s - FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' - """ % (escape(display_fields_string), - escape(dataset.name), - escape(str(trait.name))) - logger.sql(query) - trait_info = g.db.execute(query).fetchone() - #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name - # to avoid the problem of same marker name from different species. - elif dataset.type == 'Geno': - display_fields_string = string.join(dataset.display_fields,',Geno.') - display_fields_string = 'Geno.' + display_fields_string - query = """ - SELECT %s - FROM Geno, GenoFreeze, GenoXRef - WHERE - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoXRef.GenoId = Geno.Id AND - GenoFreeze.Name = '%s' AND - Geno.Name = '%s' - """ % (escape(display_fields_string), - escape(dataset.name), - escape(trait.name)) - logger.sql(query) - trait_info = g.db.execute(query).fetchone() - else: #Temp type - query = """SELECT %s FROM %s WHERE Name = %s""" - logger.sql(query) - trait_info = g.db.execute(query, - (string.join(dataset.display_fields,','), - dataset.type, trait.name)).fetchone() + resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id)) + the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name) + else: + resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id)) + the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name) + + try: + response = requests.get(the_url).content + if response.strip() == "no-access": + trait.view = False + return trait + except: + resource_info = get_resource_info(resource_id) + default_permissions = resource_info['default_mask']['data'] + if 'view' not in default_persmissions: + trait.view = False + return trait + + trait_info = json.loads(response) if trait_info: trait.haveinfo = True - #XZ: assign SQL query result to trait attributes. for i, field in enumerate(dataset.display_fields): holder = trait_info[i] - # if isinstance(trait_info[i], basestring): - # logger.debug("HOLDER:", holder) - # logger.debug("HOLDER2:", holder.decode(encoding='latin1')) - # holder = unicode(trait_info[i], "utf-8", "ignore") - if isinstance(trait_info[i], basestring): - holder = holder.encode('latin1') + #if isinstance(trait_info[i], basestring): + # holder = holder.encode('latin1') setattr(trait, field, holder) if dataset.type == 'Publish': @@ -453,13 +425,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait.confidential: trait.abbreviation = trait.pre_publication_abbreviation trait.description_display = trait.pre_publication_description - - #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( - # privilege=self.dataset.privilege, - # userName=self.dataset.userName, - # authorized_users=self.authorized_users): - # - # description = self.pre_publication_description else: trait.abbreviation = trait.post_publication_abbreviation if description: diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index e7c04fef..9ce809b6 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -1,7 +1,7 @@ from __future__ import absolute_import, print_function, division -from base.trait import GeneralTrait from base import data_set +from base.trait import create_trait from base.species import TheSpecies from utility import hmac @@ -11,7 +11,6 @@ from flask import Flask, g import logging logger = logging.getLogger(__name__ ) - def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" if "temp_trait" in start_vars.keys(): @@ -24,7 +23,7 @@ def get_species_dataset_trait(self, start_vars): logger.debug("After creating dataset") self.species = TheSpecies(dataset=self.dataset) logger.debug("After creating species") - self.this_trait = GeneralTrait(dataset=self.dataset, + self.this_trait = create_trait(dataset=self.dataset, name=start_vars['trait_id'], cellid=None, get_qtl_info=True) @@ -34,7 +33,6 @@ def get_species_dataset_trait(self, start_vars): #self.dataset.group.read_genotype_file() #self.genotype = self.dataset.group.genotype - def get_trait_db_obs(self, trait_db_list): if isinstance(trait_db_list, basestring): trait_db_list = trait_db_list.split(",") @@ -49,10 +47,11 @@ def get_trait_db_obs(self, trait_db_list): dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2]) else: dataset_ob = data_set.create_dataset(dataset_name) - trait_ob = GeneralTrait(dataset=dataset_ob, + trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) - self.trait_list.append((trait_ob, dataset_ob)) + if trait_ob: + self.trait_list.append((trait_ob, dataset_ob)) def get_species_groups(): diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 15841032..0ad96879 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -2,6 +2,7 @@ from __future__ import print_function, division, absolute_import import uuid import simplejson as json +import datetime import redis # used for collections @@ -96,15 +97,22 @@ def get_user_groups(user_id): for key in groups_list: group_ob = json.loads(groups_list[key]) group_admins = set(group_ob['admins']) - group_users = set(group_ob['users']) + group_members = set(group_ob['members']) if user_id in group_admins: admin_group_ids.append(group_ob['id']) - elif user_id in group_users: + elif user_id in group_members: user_group_ids.append(group_ob['id']) else: continue - return admin_group_ids, user_group_ids + admin_groups = [] + user_groups = [] + for the_id in admin_group_ids: + admin_groups.append(get_group_info(the_id)) + for the_id in user_group_ids: + user_groups.append(get_group_info(the_id)) + + return admin_groups, user_groups def get_group_info(group_id): group_json = Redis.hget("groups", group_id) @@ -114,18 +122,18 @@ def get_group_info(group_id): return group_info -def create_group(admin_member_ids, user_member_ids = [], group_name = ""): +def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"): group_id = str(uuid.uuid4()) new_group = { "id" : group_id, - "admins": admin_member_ids, - "users" : user_member_ids, + "admins": admin_user_ids, + "members" : member_user_ids, "name" : group_name, "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') } - Redis.hset("groups", group_id, new_group) + Redis.hset("groups", group_id, json.dumps(new_group)) return new_group @@ -144,7 +152,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS if admins: group_users = set(group_info["admins"]) else: - group_users = set(group_info["users"]) + group_users = set(group_info["members"]) for email in user_emails: user_id = get_user_id("email_address", email) @@ -153,7 +161,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS if admins: group_info["admins"] = list(group_users) else: - group_info["users"] = list(group_users) + group_info["members"] = list(group_users) group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') Redis.hset("groups", group_id, json.dumps(group_info)) @@ -161,7 +169,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS else: return None -def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "users"): #ZS: User type is because I assume admins can remove other admins +def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins group_info = get_group_info(group_id) if user_id in group_info["admins"]: group_users = set(group_info[user_type]) @@ -174,6 +182,7 @@ def change_group_name(user_id, group_id, new_name): group_info = get_group_info(group_id) if user_id in group_info["admins"]: group_info["name"] = new_name + Redis.hset("groups", group_id, json.dumps(group_info)) return group_info else: return None @@ -182,22 +191,21 @@ def get_resources(): resource_list = Redis.hgetall("resources") return resource_list -def get_resource_id(dataset_type, dataset_id, trait_id = None, all_resources = None): - if not all_resources: - all_resources = get_resources() - - resource_list = [[key, json.loads(value)] for key, value in all_resources.items()] - - if not trait_id: - matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id] - else: - matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id and resource[1]['data']['trait'] == trait_id] - - if len(matched_resources): - return matched_resources[0] +def get_resource_id(dataset, trait_id=None): + if dataset.type == "Publish": + if trait_id: + resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id)) + else: + return False + elif dataset.type == "ProbeSet": + resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id)) + elif dataset.type == "Geno": + resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id)) else: return False + return resource_id + def get_resource_info(resource_id): resource_info = Redis.hget("resources", resource_id) return json.loads(resource_info) @@ -205,9 +213,9 @@ def get_resource_info(resource_id): def add_resource(resource_info): if 'trait' in resource_info['data']: - resource_id = hmac.data_hmac('{}:{}'.format(str(resource_info['data']['dataset']), str(resource_info['data']['trait']))) + resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait']))) else: - resource_id = hmac.data_hmac('{}'.format(str(resource_info['data']['dataset']))) + resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']))) Redis.hset("resources", resource_id, json.dumps(resource_info)) diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index 66eb94ac..7f5312c1 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -1,237 +1,237 @@ -from __future__ import absolute_import, division, print_function - -import collections - -import scipy - -from MySQLdb import escape_string as escape - -from flask import g - -from base import data_set -from base.trait import GeneralTrait, retrieve_sample_data - -from wqflask.correlation.show_corr_results import generate_corr_json -from wqflask.correlation import correlation_functions - -from utility import webqtlUtil, helper_functions, corr_result_helpers -from utility.benchmark import Bench - -import utility.logger -logger = utility.logger.getLogger(__name__ ) - -def do_correlation(start_vars): - assert('db' in start_vars) - assert('target_db' in start_vars) - assert('trait_id' in start_vars) - - this_dataset = data_set.create_dataset(dataset_name = start_vars['db']) - target_dataset = data_set.create_dataset(dataset_name = start_vars['target_db']) - this_trait = GeneralTrait(dataset = this_dataset, name = start_vars['trait_id']) - this_trait = retrieve_sample_data(this_trait, this_dataset) - - corr_params = init_corr_params(start_vars) - - corr_results = calculate_results(this_trait, this_dataset, target_dataset, corr_params) - #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) - - final_results = [] - for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]): - if corr_params['type'] == "tissue": - [sample_r, num_overlap, sample_p, symbol] = corr_results[trait] - result_dict = { - "trait" : trait, - "sample_r" : sample_r, - "#_strains" : num_overlap, - "p_value" : sample_p, - "symbol" : symbol - } - elif corr_params['type'] == "literature" or corr_params['type'] == "lit": - [gene_id, sample_r] = corr_results[trait] - result_dict = { - "trait" : trait, - "sample_r" : sample_r, - "gene_id" : gene_id - } - else: - [sample_r, sample_p, num_overlap] = corr_results[trait] - result_dict = { - "trait" : trait, - "sample_r" : sample_r, - "#_strains" : num_overlap, - "p_value" : sample_p - } - - final_results.append(result_dict) - - # json_corr_results = generate_corr_json(final_corr_results, this_trait, this_dataset, target_dataset, for_api = True) - - return final_results - -def calculate_results(this_trait, this_dataset, target_dataset, corr_params): - corr_results = {} - - target_dataset.get_trait_data() - - if corr_params['type'] == "tissue": - trait_symbol_dict = this_dataset.retrieve_genes("Symbol") - corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params) - sorted_results = collections.OrderedDict(sorted(corr_results.items(), - key=lambda t: -abs(t[1][1]))) - elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature" - trait_geneid_dict = this_dataset.retrieve_genes("GeneId") - corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params) - sorted_results = collections.OrderedDict(sorted(corr_results.items(), - key=lambda t: -abs(t[1][1]))) - else: - for target_trait, target_vals in target_dataset.trait_data.iteritems(): - result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) - if result is not None: - corr_results[target_trait] = result - - sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) - - return sorted_results - -def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1): - #Gets tissue expression values for the primary trait - primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list = [this_trait.symbol]) - - if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()] - - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values()) - - tissue_corr_data = {} - for trait, symbol in trait_symbol_dict.iteritems(): - if symbol and symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] - - result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, - this_trait_tissue_values, - corr_params['method']) - - tissue_corr_data[trait] = [result[0], result[1], result[2], symbol] - - return tissue_corr_data - -def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params): - input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid) - - lit_corr_data = {} - for trait, gene_id in trait_geneid_dict.iteritems(): - mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id) - - if mouse_gene_id and str(mouse_gene_id).find(";") == -1: - result = g.db.execute( - """SELECT value - FROM LCorrRamin3 - WHERE GeneId1='%s' and - GeneId2='%s' - """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id)) - ).fetchone() - if not result: - result = g.db.execute("""SELECT value - FROM LCorrRamin3 - WHERE GeneId2='%s' and - GeneId1='%s' - """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id)) - ).fetchone() - if result: - lit_corr = result.value - lit_corr_data[trait] = [gene_id, lit_corr] - else: - lit_corr_data[trait] = [gene_id, 0] - else: - lit_corr_data[trait] = [gene_id, 0] - - return lit_corr_data - -def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type): - """ - Calculates the sample r (or rho) and p-value - - Given a primary trait and a target trait's sample values, - calculates either the pearson r or spearman rho and the p-value - using the corresponding scipy functions. - """ - - this_trait_vals = [] - shared_target_vals = [] - for i, sample in enumerate(target_dataset.group.samplelist): - if sample in this_trait.data: - this_sample_value = this_trait.data[sample].value - target_sample_value = target_vals[i] - this_trait_vals.append(this_sample_value) - shared_target_vals.append(target_sample_value) - - this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, shared_target_vals) - - if type == 'pearson': - sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, shared_target_vals) - else: - sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, shared_target_vals) - - if num_overlap > 5: - if scipy.isnan(sample_r): - return None - else: - return [sample_r, sample_p, num_overlap] - -def convert_to_mouse_gene_id(species=None, gene_id=None): - """If the species is rat or human, translate the gene_id to the mouse geneid - - If there is no input gene_id or there's no corresponding mouse gene_id, return None - - """ - if not gene_id: - return None - - mouse_gene_id = None - - if species == 'mouse': - mouse_gene_id = gene_id - - elif species == 'rat': - - query = """SELECT mouse - FROM GeneIDXRef - WHERE rat='%s'""" % escape(gene_id) - - result = g.db.execute(query).fetchone() - if result != None: - mouse_gene_id = result.mouse - - elif species == 'human': - - query = """SELECT mouse - FROM GeneIDXRef - WHERE human='%s'""" % escape(gene_id) - - result = g.db.execute(query).fetchone() - if result != None: - mouse_gene_id = result.mouse - - return mouse_gene_id - -def init_corr_params(start_vars): - method = "pearson" - if 'method' in start_vars: - method = start_vars['method'] - - type = "sample" - if 'type' in start_vars: - type = start_vars['type'] - - return_count = 500 - if 'return_count' in start_vars: - assert(start_vars['return_count'].isdigit()) - return_count = int(start_vars['return_count']) - - corr_params = { - 'method' : method, - 'type' : type, - 'return_count' : return_count - } - +from __future__ import absolute_import, division, print_function + +import collections + +import scipy + +from MySQLdb import escape_string as escape + +from flask import g + +from base import data_set +from base.trait import create_trait, retrieve_sample_data + +from wqflask.correlation.show_corr_results import generate_corr_json +from wqflask.correlation import correlation_functions + +from utility import webqtlUtil, helper_functions, corr_result_helpers +from utility.benchmark import Bench + +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def do_correlation(start_vars): + assert('db' in start_vars) + assert('target_db' in start_vars) + assert('trait_id' in start_vars) + + this_dataset = data_set.create_dataset(dataset_name = start_vars['db']) + target_dataset = data_set.create_dataset(dataset_name = start_vars['target_db']) + this_trait = create_trait(dataset = this_dataset, name = start_vars['trait_id']) + this_trait = retrieve_sample_data(this_trait, this_dataset) + + corr_params = init_corr_params(start_vars) + + corr_results = calculate_results(this_trait, this_dataset, target_dataset, corr_params) + #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) + + final_results = [] + for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]): + if corr_params['type'] == "tissue": + [sample_r, num_overlap, sample_p, symbol] = corr_results[trait] + result_dict = { + "trait" : trait, + "sample_r" : sample_r, + "#_strains" : num_overlap, + "p_value" : sample_p, + "symbol" : symbol + } + elif corr_params['type'] == "literature" or corr_params['type'] == "lit": + [gene_id, sample_r] = corr_results[trait] + result_dict = { + "trait" : trait, + "sample_r" : sample_r, + "gene_id" : gene_id + } + else: + [sample_r, sample_p, num_overlap] = corr_results[trait] + result_dict = { + "trait" : trait, + "sample_r" : sample_r, + "#_strains" : num_overlap, + "p_value" : sample_p + } + + final_results.append(result_dict) + + # json_corr_results = generate_corr_json(final_corr_results, this_trait, this_dataset, target_dataset, for_api = True) + + return final_results + +def calculate_results(this_trait, this_dataset, target_dataset, corr_params): + corr_results = {} + + target_dataset.get_trait_data() + + if corr_params['type'] == "tissue": + trait_symbol_dict = this_dataset.retrieve_genes("Symbol") + corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params) + sorted_results = collections.OrderedDict(sorted(corr_results.items(), + key=lambda t: -abs(t[1][1]))) + elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature" + trait_geneid_dict = this_dataset.retrieve_genes("GeneId") + corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params) + sorted_results = collections.OrderedDict(sorted(corr_results.items(), + key=lambda t: -abs(t[1][1]))) + else: + for target_trait, target_vals in target_dataset.trait_data.iteritems(): + result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) + if result is not None: + corr_results[target_trait] = result + + sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) + + return sorted_results + +def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1): + #Gets tissue expression values for the primary trait + primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list = [this_trait.symbol]) + + if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: + primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()] + + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values()) + + tissue_corr_data = {} + for trait, symbol in trait_symbol_dict.iteritems(): + if symbol and symbol.lower() in corr_result_tissue_vals_dict: + this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] + + result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, + this_trait_tissue_values, + corr_params['method']) + + tissue_corr_data[trait] = [result[0], result[1], result[2], symbol] + + return tissue_corr_data + +def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params): + input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid) + + lit_corr_data = {} + for trait, gene_id in trait_geneid_dict.iteritems(): + mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id) + + if mouse_gene_id and str(mouse_gene_id).find(";") == -1: + result = g.db.execute( + """SELECT value + FROM LCorrRamin3 + WHERE GeneId1='%s' and + GeneId2='%s' + """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id)) + ).fetchone() + if not result: + result = g.db.execute("""SELECT value + FROM LCorrRamin3 + WHERE GeneId2='%s' and + GeneId1='%s' + """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id)) + ).fetchone() + if result: + lit_corr = result.value + lit_corr_data[trait] = [gene_id, lit_corr] + else: + lit_corr_data[trait] = [gene_id, 0] + else: + lit_corr_data[trait] = [gene_id, 0] + + return lit_corr_data + +def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type): + """ + Calculates the sample r (or rho) and p-value + + Given a primary trait and a target trait's sample values, + calculates either the pearson r or spearman rho and the p-value + using the corresponding scipy functions. + """ + + this_trait_vals = [] + shared_target_vals = [] + for i, sample in enumerate(target_dataset.group.samplelist): + if sample in this_trait.data: + this_sample_value = this_trait.data[sample].value + target_sample_value = target_vals[i] + this_trait_vals.append(this_sample_value) + shared_target_vals.append(target_sample_value) + + this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, shared_target_vals) + + if type == 'pearson': + sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, shared_target_vals) + else: + sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, shared_target_vals) + + if num_overlap > 5: + if scipy.isnan(sample_r): + return None + else: + return [sample_r, sample_p, num_overlap] + +def convert_to_mouse_gene_id(species=None, gene_id=None): + """If the species is rat or human, translate the gene_id to the mouse geneid + + If there is no input gene_id or there's no corresponding mouse gene_id, return None + + """ + if not gene_id: + return None + + mouse_gene_id = None + + if species == 'mouse': + mouse_gene_id = gene_id + + elif species == 'rat': + + query = """SELECT mouse + FROM GeneIDXRef + WHERE rat='%s'""" % escape(gene_id) + + result = g.db.execute(query).fetchone() + if result != None: + mouse_gene_id = result.mouse + + elif species == 'human': + + query = """SELECT mouse + FROM GeneIDXRef + WHERE human='%s'""" % escape(gene_id) + + result = g.db.execute(query).fetchone() + if result != None: + mouse_gene_id = result.mouse + + return mouse_gene_id + +def init_corr_params(start_vars): + method = "pearson" + if 'method' in start_vars: + method = start_vars['method'] + + type = "sample" + if 'type' in start_vars: + type = start_vars['type'] + + return_count = 500 + if 'return_count' in start_vars: + assert(start_vars['return_count'].isdigit()) + return_count = int(start_vars['return_count']) + + corr_params = { + 'method' : method, + 'type' : type, + 'return_count' : return_count + } + return corr_params \ No newline at end of file diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index c7bcb65d..bdcc3bf7 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -126,9 +126,7 @@ def build_types(species, group): InbredSet.Name = '{1}' AND ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND - ProbeSetFreeze.public > 0 AND - ProbeSetFreeze.confidentiality < 1 + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name""".format(species, group) results = [] @@ -194,9 +192,7 @@ def build_datasets(species, group, type_name): FROM InfoFiles, GenoFreeze, InbredSet WHERE InbredSet.Name = '{}' AND GenoFreeze.InbredSetId = InbredSet.Id AND - InfoFiles.InfoPageName = GenoFreeze.ShortName AND - GenoFreeze.public > 0 AND - GenoFreeze.confidentiality < 1 + InfoFiles.InfoPageName = GenoFreeze.ShortName ORDER BY GenoFreeze.CreateTime DESC""".format(group)).fetchone() if results != None: @@ -214,8 +210,7 @@ def build_datasets(species, group, type_name): Species.Id = InbredSet.SpeciesId AND InbredSet.Name = '{1}' AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '{2}' AND - ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id AND - ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 + ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id ORDER BY ProbeSetFreeze.CreateTime DESC""".format(species, group, type_name)).fetchall() datasets = [] diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index d830cefc..92c27c9b 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -4,7 +4,7 @@ import string from base import data_set from base import webqtlConfig -from base.trait import GeneralTrait, retrieve_sample_data +from base.trait import create_trait, retrieve_sample_data from utility import helper_functions from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping @@ -18,7 +18,7 @@ def do_mapping_for_api(start_vars): dataset = data_set.create_dataset(dataset_name = start_vars['db']) dataset.group.get_markers() - this_trait = GeneralTrait(dataset = dataset, name = start_vars['trait_id']) + this_trait = create_trait(dataset = dataset, name = start_vars['trait_id']) this_trait = retrieve_sample_data(this_trait, dataset) samples = [] diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index b22e0004..4fb8e69b 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -14,9 +14,6 @@ import urlparse import simplejson as json -import redis -Redis = redis.StrictRedis() - from flask import (Flask, g, render_template, url_for, request, make_response, redirect, flash, jsonify) @@ -30,8 +27,10 @@ from wqflask import model from utility import Bunch, Struct, hmac from utility.formatting import numify +from utility.redis_tools import get_redis_conn +Redis = get_redis_conn() -from base import trait +from base.trait import create_trait, retrieve_trait_info, jsonable from base.data_set import create_dataset import logging @@ -208,14 +207,14 @@ def view_collection(): if dataset_name == "Temp": group = name.split("_")[2] dataset = create_dataset(dataset_name, dataset_type = "Temp", group_name = group) - trait_ob = trait.GeneralTrait(name=name, dataset=dataset) + trait_ob = create_trait(name=name, dataset=dataset) else: dataset = create_dataset(dataset_name) - trait_ob = trait.GeneralTrait(name=name, dataset=dataset) - trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True) + trait_ob = create_trait(name=name, dataset=dataset) + trait_ob = retrieve_trait_info(trait_ob, dataset, get_qtl_info=True) trait_obs.append(trait_ob) - json_version.append(trait.jsonable(trait_ob)) + json_version.append(jsonable(trait_ob)) collection_info = dict(trait_obs=trait_obs, uc = uc) diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index 21eb1493..5d74dc9d 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -37,7 +37,7 @@ from pprint import pformat as pf import reaper -from base.trait import GeneralTrait +from base.trait import create_trait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers from db import webqtlDatabaseFunction @@ -108,7 +108,7 @@ class ComparisonBarChart(object): trait_name, dataset_name = trait_db.split(":") #print("dataset_name:", dataset_name) dataset_ob = data_set.create_dataset(dataset_name) - trait_ob = GeneralTrait(dataset=dataset_ob, + trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) self.trait_list.append((trait_ob, dataset_ob)) diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index dfb81c54..04ec427d 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -4,7 +4,7 @@ import math from flask import g -from base.trait import GeneralTrait +from base.trait import create_trait from base import data_set from utility import corr_result_helpers from scipy import stats @@ -20,9 +20,9 @@ class CorrScatterPlot(object): self.data_set_1 = data_set.create_dataset(params['dataset_1']) self.data_set_2 = data_set.create_dataset(params['dataset_2']) #self.data_set_3 = data_set.create_dataset(params['dataset_3']) - self.trait_1 = GeneralTrait(name=params['trait_1'], dataset=self.data_set_1) - self.trait_2 = GeneralTrait(name=params['trait_2'], dataset=self.data_set_2) - #self.trait_3 = GeneralTrait(name=params['trait_3'], dataset=self.data_set_3) + self.trait_1 = create_trait(name=params['trait_1'], dataset=self.data_set_1) + self.trait_2 = create_trait(name=params['trait_2'], dataset=self.data_set_2) + #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.data_set_3) samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index b099b83d..7eab7184 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -47,7 +47,7 @@ import reaper from base import webqtlConfig from utility.THCell import THCell from utility.TDCell import TDCell -from base.trait import GeneralTrait +from base.trait import create_trait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers, hmac from db import webqtlDatabaseFunction @@ -97,7 +97,7 @@ class CorrelationResults(object): if start_vars['dataset'] == "Temp": self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) self.trait_id = start_vars['trait_id'] - self.this_trait = GeneralTrait(dataset=self.dataset, + self.this_trait = create_trait(dataset=self.dataset, name=self.trait_id, cellid=None) else: @@ -199,7 +199,9 @@ class CorrelationResults(object): range_chr_as_int = order_id for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): - trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) + trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) + if not trait_object: + continue if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert trait chromosome to an int for the location range option diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index b5c45d05..2b9467d1 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -43,14 +43,16 @@ from pprint import pformat as pf import reaper -import redis -Redis = redis.StrictRedis() +from utility.redis_tools import get_redis_conn +Redis = get_redis_conn() +THIRTY_DAYS = 60 * 60 * 24 * 30 from utility.THCell import THCell from utility.TDCell import TDCell from base.trait import GeneralTrait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers + from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions @@ -204,20 +206,6 @@ class CorrelationMatrix(object): samples = self.all_sample_list, sample_data = self.sample_data,) # corr_results = [result[1] for result in result_row for result_row in self.corr_results]) - - def get_trait_db_obs(self, trait_db_list): - - self.trait_list = [] - for i, trait_db in enumerate(trait_db_list): - if i == (len(trait_db_list) - 1): - break - trait_name, dataset_name = trait_db.split(":") - #print("dataset_name:", dataset_name) - dataset_ob = data_set.create_dataset(dataset_name) - trait_ob = GeneralTrait(dataset=dataset_ob, - name=trait_name, - cellid=None) - self.trait_list.append((trait_ob, dataset_ob)) def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors): base = importr('base') @@ -257,7 +245,7 @@ class CorrelationMatrix(object): this_vals_string += "x " this_vals_string = this_vals_string[:-1] - Redis.set(trait_id, this_vals_string) + Redis.set(trait_id, this_vals_string, ex=THIRTY_DAYS) self.pca_trait_ids.append(trait_id) return pca diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 4415b86a..35067036 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -17,7 +17,7 @@ import csv import itertools from base import data_set -from base import trait as TRAIT +from base.trait import create_trait, retrieve_sample_data from utility import helper_functions from utility.tools import locate, GN2_BRANCH_URL @@ -122,8 +122,8 @@ class CTL(object): logger.debug("retrieving data for", trait) if trait != "": ts = trait.split(':') - gt = TRAIT.GeneralTrait(name = ts[0], dataset_name = ts[1]) - gt = TRAIT.retrieve_sample_data(gt, dataset, individuals) + gt = create_trait(name = ts[0], dataset_name = ts[1]) + gt = retrieve_sample_data(gt, dataset, individuals) for ind in individuals: if ind in gt.data.keys(): traits.append(gt.data[ind].value) @@ -180,8 +180,8 @@ class CTL(object): logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console tsS = significant[0][x].split(':') # Source tsT = significant[2][x].split(':') # Target - gtS = TRAIT.GeneralTrait(name = tsS[0], dataset_name = tsS[1]) # Retrieve Source info from the DB - gtT = TRAIT.GeneralTrait(name = tsT[0], dataset_name = tsT[1]) # Retrieve Target info from the DB + gtS = create_trait(name = tsS[0], dataset_name = tsS[1]) # Retrieve Source info from the DB + gtT = create_trait(name = tsT[0], dataset_name = tsT[1]) # Retrieve Target info from the DB self.addNode(gtS) self.addNode(gtT) self.addEdge(gtS, gtT, significant, x) diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index b0ca5ced..1e15d28f 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -34,10 +34,7 @@ class DoSearch(object): self.search_type = search_type if self.dataset: - logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) - logger.debug("self.dataset.group is: ", pf(self.dataset.group)) #Get group information for dataset and the species id - self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) def execute(self, query): @@ -54,10 +51,6 @@ class DoSearch(object): return keyword - #def escape(self, stringy): - # """Shorter name than self.db_conn.escape_string""" - # return escape(str(stringy)) - def mescape(self, *items): """Multiple escape""" escaped = [escape(str(item)) for item in items] @@ -71,8 +64,6 @@ class DoSearch(object): @classmethod def get_search(cls, search_type): - logger.debug("search_types are:", pf(cls.search_types)) - search_type_string = search_type['dataset_type'] if 'key' in search_type and search_type['key'] != None: search_type_string += '_' + search_type['key'] @@ -648,7 +639,7 @@ class CisTransLrsSearch(DoSearch): escape(self.dataset.type), chromosome) else: - location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type)) + location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type)) where_clause = sub_clause + """ %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 04e3d578..c65a1415 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -4,7 +4,7 @@ import json from flask import Flask, g from base.data_set import create_dataset -from base.trait import GeneralTrait +from base.trait import create_trait from db import webqtlDatabaseFunction from base import webqtlConfig @@ -96,7 +96,9 @@ class GSearch(object): #dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False) #trait_id = line[4] #with Bench("Building trait object"): - trait_ob = GeneralTrait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) + trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) + if not trait_ob: + continue max_lrs_text = "N/A" if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": max_lrs_text = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb) @@ -210,13 +212,12 @@ class GSearch(object): if line[11] != "" and line[11] != None: this_trait['additive'] = '%.3f' % line[11] - #dataset = create_dataset(line[2], "Publish") - #trait_id = line[3] - #this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) this_trait['max_lrs_text'] = "N/A" + trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) + if not trait_ob: + continue if this_trait['dataset'] == this_trait['group'] + "Publish": try: - trait_ob = GeneralTrait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": this_trait['max_lrs_text'] = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb) except: diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index a648667b..74fa4329 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -246,6 +246,12 @@ class DisplayMappingResults(object): if 'output_files' in start_vars: self.output_files = ",".join(start_vars['output_files']) + self.categorical_vars = "" + self.perm_strata = "" + if 'perm_strata' in start_vars.keys() and 'categorical_vars' in start_vars.keys(): + self.categorical_vars = start_vars['categorical_vars'] + self.perm_strata = start_vars['perm_strata'] + self.selectedChr = int(start_vars['selected_chr']) self.strainlist = start_vars['samples'] diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index e2b15c26..88d27517 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -1,7 +1,7 @@ import os, math, string, random, json from base import webqtlConfig -from base.trait import GeneralTrait +from base.trait import create_trait from base.data_set import create_dataset from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, WEBSERVER_MODE @@ -129,7 +129,7 @@ def gen_covariates_file(this_dataset, covariates, samples): this_covariate_data = [] trait_name = covariate.split(":")[0] dataset_ob = create_dataset(covariate.split(":")[1]) - trait_ob = GeneralTrait(dataset=dataset_ob, + trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index e4a4d127..c5590a85 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -6,7 +6,7 @@ import json from flask import g from base.webqtlConfig import TMPDIR -from base.trait import GeneralTrait +from base.trait import create_trait from base.data_set import create_dataset from utility import webqtlUtil from utility.tools import locate, TEMPDIR @@ -86,7 +86,6 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype cross_object = add_names(cross_object, names_string, "the_names") # Add the phenotype logger.info("Added pheno and names"); - # Scan for QTLs marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers logger.info("Marker covars done"); if cofactors != "": @@ -115,6 +114,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec else: if do_control == "true" or cofactors != "": logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method) + ro.r('save.image(file = "/home/zas1024/gn2-zach/itp_cofactor_test.RData")') else: logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method) @@ -295,7 +295,7 @@ def add_cofactors(cross, this_dataset, covariates, samples): covar_as_string = "c(" trait_name = covariate.split(":")[0] dataset_ob = create_dataset(covariate.split(":")[1]) - trait_ob = GeneralTrait(dataset=dataset_ob, + trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) @@ -321,27 +321,27 @@ def add_cofactors(cross, this_dataset, covariates, samples): datatype = get_trait_data_type(covariate) logger.info("Covariate: " + covariate + " is of type: " + datatype); if(datatype == "categorical"): # Cat variable - logger.info("call of add_categorical_covar"); - cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross - logger.info("add_categorical_covar returned"); - for z, col_name in enumerate(col_names): # Go through the additional covar names + logger.info("call of add_categorical_covar"); + cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross + logger.info("add_categorical_covar returned"); + for z, col_name in enumerate(col_names): # Go through the additional covar names + if i < (len(covariate_list) - 1): + covar_name_string += '"' + col_name + '", ' + else: + if(z < (len(col_names) -1)): + covar_name_string += '"' + col_name + '", ' + else: + covar_name_string += '"' + col_name + '"' + + logger.info("covar_name_string:" + covar_name_string) + else: + col_name = "covar_" + str(i) + cross = add_phenotype(cross, covar_as_string, col_name) if i < (len(covariate_list) - 1): - covar_name_string += '"' + col_name + '", ' - else: - if(z < (len(col_names) -1)): covar_name_string += '"' + col_name + '", ' - else: + else: covar_name_string += '"' + col_name + '"' - logger.info("covar_name_string:" + covar_name_string); - else: - col_name = "covar_" + str(i) - cross = add_phenotype(cross, covar_as_string, col_name) - if i < (len(covariate_list) - 1): - covar_name_string += '"' + col_name + '", ' - else: - covar_name_string += '"' + col_name + '"' - covar_name_string += ")" logger.info("covar_name_string:" + covar_name_string); covars_ob = pull_var("trait_covars", cross, covar_name_string) @@ -350,9 +350,13 @@ def add_cofactors(cross, this_dataset, covariates, samples): def create_marker_covariates(control_marker, cross): ro.globalenv["the_cross"] = cross ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix - userinputS = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user - covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS) - ro.r('covnames <- c(' + covariate_names + ')') + userinput_sanitized = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user + logger.debug(userinput_sanitized) + if len(userinput_sanitized) > 0: + covariate_names = ', '.join('"{0}"'.format(w) for w in userinput_sanitized) + ro.r('covnames <- c(' + covariate_names + ')') + else: + ro.r('covnames <- c()') ro.r('covInGeno <- which(covnames %in% colnames(genotypes))') ro.r('covnames <- covnames[covInGeno]') ro.r("cat('covnames (purged): ', covnames,'\n')") @@ -404,16 +408,4 @@ def process_rqtl_results(result, species_name): # TODO: how to make this marker['lod_score'] = output[i][2] qtl_results.append(marker) - return qtl_results - -def get_trait_data_type(trait_db_string): - # Get a trait's type (numeric, categorical, etc) from the DB - the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'" - results_json = g.db.execute(the_query).fetchone() - - results_ob = json.loads(results_json[0]) - - if trait_db_string in results_ob: - return results_ob[trait_db_string] - else: - return "numeric" + return qtl_results \ No newline at end of file diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 5f7710ab..0711b852 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -161,7 +161,7 @@ class RunMapping(object): self.num_perm = 0 self.perm_output = [] self.bootstrap_results = [] - self.covariates = start_vars['covariates'] if "covariates" in start_vars else None + self.covariates = start_vars['covariates'] if "covariates" in start_vars else "" #ZS: This is passed to GN1 code for single chr mapping self.selected_chr = -1 @@ -467,6 +467,7 @@ class RunMapping(object): #mapping_scale = self.mapping_scale, #chromosomes = chromosome_mb_lengths, #qtl_results = self.qtl_results, + categorical_vars = self.categorical_vars, chr_lengths = chr_lengths, num_perm = self.num_perm, perm_results = self.perm_output, diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index 152e4168..f41f3017 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -44,7 +44,7 @@ import reaper from utility.THCell import THCell from utility.TDCell import TDCell -from base.trait import GeneralTrait +from base.trait import create_trait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers from utility.tools import GN2_BRANCH_URL @@ -217,7 +217,7 @@ class NetworkGraph(object): break trait_name, dataset_name = trait_db.split(":") dataset_ob = data_set.create_dataset(dataset_name) - trait_ob = GeneralTrait(dataset=dataset_ob, + trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) self.trait_list.append((trait_ob, dataset_ob)) \ No newline at end of file diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 8f702d58..de4b01eb 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -1,15 +1,9 @@ -# from __future__ import absolute_import, print_function, division +from __future__ import absolute_import, print_function, division - -import os -import cPickle import re import uuid from math import * import time -import math -import datetime -import collections import re import requests @@ -18,18 +12,16 @@ from pprint import pformat as pf import json from base.data_set import create_dataset -from base import trait +from base.trait import create_trait from wqflask import parser from wqflask import do_search -from utility import webqtlUtil,tools from db import webqtlDatabaseFunction -from flask import render_template, Flask, g +from flask import Flask, g -from utility import formatting -from utility import hmac +from utility import hmac, helper_functions from utility.tools import GN2_BASE_URL -from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string +from utility.type_checking import is_str from utility.logger import getLogger logger = getLogger(__name__ ) @@ -86,7 +78,7 @@ views.py). try: self.search() except: - self.search_term_exists = False + self.search_term_exists = False if self.search_term_exists: self.gen_search_result() @@ -113,50 +105,49 @@ views.py). trait_dict = {} trait_id = result[0] - trait_dict['index'] = index + 1 - this_trait = trait.GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) - trait_dict['name'] = this_trait.name - if this_trait.dataset.type == "Publish": - trait_dict['display_name'] = this_trait.display_name - else: - trait_dict['display_name'] = this_trait.name - trait_dict['dataset'] = this_trait.dataset.name - trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) - if this_trait.dataset.type == "ProbeSet": - trait_dict['symbol'] = this_trait.symbol - trait_dict['description'] = this_trait.description_display.decode('utf-8', 'replace') - trait_dict['location'] = this_trait.location_repr - trait_dict['mean'] = "N/A" - trait_dict['additive'] = "N/A" - if this_trait.mean != "" and this_trait.mean != None: - trait_dict['mean'] = '%.3f' % this_trait.mean - trait_dict['lrs_score'] = this_trait.LRS_score_repr - trait_dict['lrs_location'] = this_trait.LRS_location_repr - if this_trait.additive != "": - trait_dict['additive'] = '%.3f' % this_trait.additive - elif this_trait.dataset.type == "Geno": - trait_dict['location'] = this_trait.location_repr - elif this_trait.dataset.type == "Publish": - trait_dict['description'] = this_trait.description_display - trait_dict['authors'] = this_trait.authors - trait_dict['pubmed_id'] = "N/A" - if this_trait.pubmed_id: - trait_dict['pubmed_id'] = this_trait.pubmed_id - trait_dict['pubmed_link'] = this_trait.pubmed_link - trait_dict['pubmed_text'] = this_trait.pubmed_text - trait_dict['mean'] = "N/A" - if this_trait.mean != "" and this_trait.mean != None: - trait_dict['mean'] = '%.3f' % this_trait.mean - trait_dict['lrs_score'] = this_trait.LRS_score_repr - trait_dict['lrs_location'] = this_trait.LRS_location_repr - trait_dict['additive'] = "N/A" - if this_trait.additive != "": - trait_dict['additive'] = '%.3f' % this_trait.additive - trait_list.append(trait_dict) - #json_trait_list.append(trait.jsonable_table_row(this_trait, self.dataset.name, index + 1)) + this_trait = create_trait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) + if this_trait: + trait_dict['index'] = index + 1 + trait_dict['name'] = this_trait.name + if this_trait.dataset.type == "Publish": + trait_dict['display_name'] = this_trait.display_name + else: + trait_dict['display_name'] = this_trait.name + trait_dict['dataset'] = this_trait.dataset.name + trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) + if this_trait.dataset.type == "ProbeSet": + trait_dict['symbol'] = this_trait.symbol + trait_dict['description'] = this_trait.description_display.decode('utf-8', 'replace') + trait_dict['location'] = this_trait.location_repr + trait_dict['mean'] = "N/A" + trait_dict['additive'] = "N/A" + if this_trait.mean != "" and this_trait.mean != None: + trait_dict['mean'] = '%.3f' % this_trait.mean + trait_dict['lrs_score'] = this_trait.LRS_score_repr + trait_dict['lrs_location'] = this_trait.LRS_location_repr + if this_trait.additive != "": + trait_dict['additive'] = '%.3f' % this_trait.additive + elif this_trait.dataset.type == "Geno": + trait_dict['location'] = this_trait.location_repr + elif this_trait.dataset.type == "Publish": + trait_dict['description'] = this_trait.description_display + trait_dict['authors'] = this_trait.authors + trait_dict['pubmed_id'] = "N/A" + if this_trait.pubmed_id: + trait_dict['pubmed_id'] = this_trait.pubmed_id + trait_dict['pubmed_link'] = this_trait.pubmed_link + trait_dict['pubmed_text'] = this_trait.pubmed_text + trait_dict['mean'] = "N/A" + if this_trait.mean != "" and this_trait.mean != None: + trait_dict['mean'] = '%.3f' % this_trait.mean + trait_dict['lrs_score'] = this_trait.LRS_score_repr + trait_dict['lrs_location'] = this_trait.LRS_location_repr + trait_dict['additive'] = "N/A" + if this_trait.additive != "": + trait_dict['additive'] = '%.3f' % this_trait.additive + trait_list.append(trait_dict) self.trait_list = json.dumps(trait_list) - #self.json_trait_list = json.dumps(json_trait_list) def search(self): """ @@ -234,7 +225,6 @@ views.py). self.header_fields = the_search.header_fields def get_search_ob(self, a_search): - logger.debug("[kodak] item is:", pf(a_search)) search_term = a_search['search_term'] search_operator = a_search['separator'] search_type = {} @@ -243,12 +233,10 @@ views.py). search_type['key'] = a_search['key'].upper() else: search_type['key'] = None - logger.debug("search_type is:", pf(search_type)) search_ob = do_search.DoSearch.get_search(search_type) if search_ob: search_class = getattr(do_search, search_ob) - logger.debug("search_class is: ", pf(search_class)) the_search = search_class(search_term, search_operator, self.dataset, diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 107f87c6..253c887b 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -4,7 +4,7 @@ import simplejson as json from pprint import pformat as pf -from base.trait import GeneralTrait +from base.trait import create_trait from base import data_set def export_sample_table(targs): @@ -26,7 +26,7 @@ def export_sample_table(targs): def get_export_metadata(trait_id, dataset_name): dataset = data_set.create_dataset(dataset_name) - this_trait = GeneralTrait(dataset=dataset, + this_trait = create_trait(dataset=dataset, name=trait_id, cellid=None, get_qtl_info=False) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 29b2f77e..c77e247f 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -10,9 +10,6 @@ import json as json from collections import OrderedDict -import redis -Redis = redis.StrictRedis() - import numpy as np import scipy.stats as ss @@ -21,11 +18,15 @@ from flask import Flask, g from base import webqtlConfig from base import webqtlCaseData from wqflask.show_trait.SampleList import SampleList -from utility import webqtlUtil, Plot, Bunch, helper_functions -from utility.tools import locate_ignore_error -from base.trait import GeneralTrait +from base.trait import create_trait from base import data_set from db import webqtlDatabaseFunction +from utility import webqtlUtil, Plot, Bunch, helper_functions +from utility.authentication_tools import check_owner +from utility.tools import locate_ignore_error +from utility.redis_tools import get_redis_conn, get_resource_id +Redis = get_redis_conn() +ONE_YEAR = 60 * 60 * 24 * 365 from pprint import pformat as pf @@ -55,9 +56,9 @@ class ShowTrait(object): self.temp_group = kw['group'] self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group) # Put values in Redis so they can be looked up later if added to a collection - Redis.set(self.trait_id, kw['trait_paste']) + Redis.set(self.trait_id, kw['trait_paste'], ex=ONE_YEAR) self.trait_vals = kw['trait_paste'].split() - self.this_trait = GeneralTrait(dataset=self.dataset, + self.this_trait = create_trait(dataset=self.dataset, name=self.trait_id, cellid=None) else: @@ -66,11 +67,13 @@ class ShowTrait(object): self.temp_species = self.trait_id.split("_")[1] self.temp_group = self.trait_id.split("_")[2] self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group) - self.this_trait = GeneralTrait(dataset=self.dataset, + self.this_trait = create_trait(dataset=self.dataset, name=self.trait_id, cellid=None) self.trait_vals = Redis.get(self.trait_id).split() + self.resource_id = check_owner(self.dataset, self.trait_id) + #ZS: Get verify/rna-seq link URLs try: blatsequence = self.this_trait.sequence diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index ac5c1350..b7df1aad 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -2,17 +2,25 @@ {% block title %}Group Manager{% endblock %} {% block content %} - {{ header("List of groups", "" )}} -

Manage Groups

+
-
+ +
+ {% if admin_groups|length == 0 and user_groups|length == 0 %} +

You currently aren't a member or admin of any groups.

+
+ + {% else %}

Admin Groups

- + {% if admin_groups|length == 0 %} +

You currently aren't the administrator of any groups.

+ {% else %} +
@@ -26,7 +34,7 @@ {% for group in admin_groups %} - + @@ -36,12 +44,16 @@ {% endfor %}
{{ loop.index }} {{ group.name }} {{ group.admins|length + group.users|length }}
+ {% endif %}

User Groups

- + {% if user_groups|length == 0 %} +

You currently aren't a member of any groups.

+ {% else %} +
@@ -65,12 +77,12 @@ {% endfor %}
+ {% endif %} + {% endif %}
- - {% endblock %} @@ -79,7 +91,6 @@ - {% endblock %} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 1c84239c..71705390 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -1,4 +1,5 @@ {% extends "base.html" %} +{% block title %}Correlation Results{% endblock %} {% block css %} diff --git a/wqflask/wqflask/templates/email/verification.txt b/wqflask/wqflask/templates/email/verification.txt deleted file mode 100644 index 76149a3a..00000000 --- a/wqflask/wqflask/templates/email/verification.txt +++ /dev/null @@ -1,7 +0,0 @@ -Thank you for signing up for GeneNetwork. - -We need to verify your email address. - -To do that please click the following link, or cut and paste it into your browser window: - -{{ url_for_hmac("verify_email", code = verification_code, _external=True )}} diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 05b2f988..04b45659 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -31,7 +31,7 @@

-
+
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index b4429b46..c5d49168 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -41,7 +41,8 @@ - + + @@ -464,13 +465,27 @@ {% if mapping_method != "gemma" and mapping_method != "plink" %} $('#download_perm').click(function(){ - var num_perm, perm_data; - num_perm = js_data.num_perm - perm_data = js_data.perm_results - json_perm_data = JSON.stringify(perm_data); - $('input[name=perm_results]').val(json_perm_data); - $('#marker_regression_form').attr('action', '/export_perm_data'); - return $('#marker_regression_form').submit(); + perm_info_dict = { + perm_data: js_data.perm_results, + num_perm: "{{ nperm }}", + trait_name: "{{ this_trait.display_name }}", + trait_description: "{{ this_trait.description_display }}", + cofactors: "{{ covariates }}", + n_samples: {{ n_samples }}, + n_genotypes: {{ qtl_results|length }}, + {% if genofile_string is defined %} + genofile: "{{ genofile_string }}", + {% else %} + genofile: "", + {% endif %} + units_linkage: "{{ LRS_LOD }}", + strat_cofactors: js_data.categorical_vars + } + json_perm_data = JSON.stringify(perm_info_dict); + + $('input[name=perm_info]').val(json_perm_data); + $('#marker_regression_form').attr('action', '/export_perm_data'); + return $('#marker_regression_form').submit(); }); modebar_options = { diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index edd272c2..cfee0079 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -12,9 +12,6 @@ import requests import simplejson as json -import redis # used for collections -Redis = redis.StrictRedis() - from flask import (Flask, g, render_template, url_for, request, make_response, redirect, flash, abort) @@ -23,7 +20,8 @@ from wqflask import pbkdf2 from wqflask.user_session import UserSession from utility import hmac -from utility.redis_tools import is_redis_available, get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections +from utility.redis_tools import is_redis_available, get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections +Redis = get_redis_conn() from utility.logger import getLogger logger = getLogger(__name__) @@ -127,7 +125,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): server.quit() logger.info("Successfully sent email to "+toaddr) -def send_verification_email(user_details, template_name = "email/verification.txt", key_prefix = "verification_code", subject = "GeneNetwork email verification"): +def send_verification_email(user_details, template_name = "email/user_verification.txt", key_prefix = "verification_code", subject = "GeneNetwork e-mail verification"): verification_code = str(uuid.uuid4()) key = key_prefix + ":" + verification_code @@ -141,6 +139,21 @@ def send_verification_email(user_details, template_name = "email/verification.tx send_email(recipient, subject, body) return {"recipient": recipient, "subject": subject, "body": body} +@app.route("/manage/verify_email") +def verify_email(): + if 'code' in request.args: + user_details = check_verification_code(request.args['code']) + if user_details: + # As long as they have access to the email account + # We might as well log them in + session_id_signed = get_signed_session_id(user_details) + flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success") + response = make_response(redirect(url_for('index_page', import_collections = import_col, anon_id = anon_id))) + response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) + return response + else: + flash("Invalid code: Password reset code does not exist or might have expired!", "error") + @app.route("/n/login", methods=('GET', 'POST')) def login(): params = request.form if request.form else request.args @@ -204,7 +217,7 @@ def login(): response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) return response else: - email_ob = send_verification_email(user_details) + email_ob = send_verification_email(user_details, template_name = "email/user_verification.txt") return render_template("newsecurity/verification_still_needed.html", subject=email_ob['subject']) else: # Incorrect password #ZS: It previously seemed to store that there was an incorrect log-in attempt here, but it did so in the MySQL DB so this might need to be reproduced with Redis @@ -374,16 +387,13 @@ def password_reset(): hmac = request.args.get('hm') if verification_code: - user_email = check_verification_code(verification_code) - if user_email: - user_details = get_user_by_unique_column('email_address', user_email) - if user_details: - return render_template( - "new_security/password_reset.html", user_encode=user_details["email_address"]) - else: - flash("Invalid code: User no longer exists!", "error") + user_details = check_verification_code(verification_code) + if user_details: + return render_template( + "new_security/password_reset.html", user_encode=user_details["email_address"]) else: flash("Invalid code: Password reset code does not exist or might have expired!", "error") + return redirect(url_for("login")) else: return redirect(url_for("login")) @@ -394,6 +404,7 @@ def password_reset_step2(): errors = [] user_email = request.form['user_encode'] + user_id = get_user_id("email_address", user_email) password = request.form['password'] encoded_password = set_password(password) @@ -401,9 +412,7 @@ def password_reset_step2(): set_user_attribute(user_id, "password", encoded_password) flash("Password changed successfully. You can now sign in.", "alert-info") - response = make_response(redirect(url_for('login'))) - - return response + return redirect(url_for('login')) def register_user(params): thank_you_mode = False diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index 50419146..ec6d4ae3 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -6,10 +6,6 @@ import uuid import simplejson as json -import redis # used for collections -Redis = redis.StrictRedis() - - from flask import (Flask, g, render_template, url_for, request, make_response, redirect, flash, abort) @@ -17,7 +13,8 @@ from wqflask import app from utility import hmac #from utility.elasticsearch_tools import get_elasticsearch_connection -from utility.redis_tools import get_user_id, get_user_by_unique_column, get_user_collections, save_collections +from utility.redis_tools import get_redis_conn, get_user_id, get_user_collections, save_collections +Redis = get_redis_conn() from utility.logger import getLogger logger = getLogger(__name__) @@ -29,6 +26,11 @@ THIRTY_DAYS = 60 * 60 * 24 * 30 def get_user_session(): logger.info("@app.before_request get_session") g.user_session = UserSession() + #ZS: I think this should solve the issue of deleting the cookie and redirecting to the home page when a user's session has expired + if not g.user_session: + response = make_response(redirect(url_for('login'))) + response.set_cookie('session_id_v2', '', expires=0) + return response @app.after_request def set_user_session(response): @@ -37,7 +39,6 @@ def set_user_session(response): response.set_cookie(g.user_session.cookie_name, g.user_session.cookie) return response - def verify_cookie(cookie): the_uuid, separator, the_signature = cookie.partition(':') assert len(the_uuid) == 36, "Is session_id a uuid?" @@ -88,14 +89,11 @@ class UserSession(object): user_id = str(uuid.uuid4())) Redis.hmset(self.redis_key, self.record) Redis.expire(self.redis_key, THIRTY_DAYS) - response = make_response(redirect(url_for('login'))) - response.set_cookie(self.user_cookie_name, '', expires=0) ########### Grrr...this won't work because of the way flask handles cookies # Delete the cookie flash("Due to inactivity your session has expired. If you'd like please login again.") - return response - #return + return None else: self.record = dict(login_time = time.time(), user_type = "anon", diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 938570f3..24a4dcee 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -23,16 +23,13 @@ import uuid import simplejson as json import yaml -#Switching from Redis to StrictRedis; might cause some issues -import redis -Redis = redis.StrictRedis() - import flask import base64 import array import sqlalchemy from wqflask import app -from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect +from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for +from wqflask import group_manager from wqflask import search_results from wqflask import export_traits from wqflask import gsearch @@ -55,11 +52,13 @@ from wqflask.correlation import corr_scatter_plot from wqflask.wgcna import wgcna_analysis from wqflask.ctl import ctl_analysis from wqflask.snp_browser import snp_browser -#from wqflask.trait_submission import submit_trait from utility import temp_data from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH from utility.helper_functions import get_species_groups +from utility.authentication_tools import check_resource_availability +from utility.redis_tools import get_redis_conn +Redis = get_redis_conn() from base.webqtlConfig import GENERATED_IMAGE_DIR from utility.benchmark import Bench @@ -87,6 +86,24 @@ def connect_db(): g.db = g._database = sqlalchemy.create_engine(SQL_URI, encoding="latin1") logger.debug(g.db) +@app.before_request +def check_access_permissions(): + logger.debug("@app.before_request check_access_permissions") + if "temp_trait" in request.args: + if request.args['temp_trait'] == "True": + pass + else: + if 'dataset' in request.args: + dataset = create_dataset(request.args['dataset']) + logger.debug("USER:", Redis.hget("users")) + if 'trait_id' in request.args: + available = check_resource_availability(dataset, request.args['trait_id']) + else: + available = check_resource_availability(dataset) + + if not available: + return redirect(url_for("no_access_page")) + @app.teardown_appcontext def shutdown_session(exception=None): db = getattr(g, '_database', None) @@ -120,6 +137,10 @@ def handle_bad_request(e): resp.set_cookie(err_msg[:32],animation) return resp +@app.route("/authentication_needed") +def no_access_page(): + return render_template("new_security/not_authenticated.html") + @app.route("/") def index_page(): logger.info("Sending index_page") @@ -401,25 +422,43 @@ def export_traits_csv(): def export_perm_data(): """CSV file consisting of the permutation data for the mapping results""" logger.info(request.url) - num_perm = float(request.form['num_perm']) - perm_data = json.loads(request.form['perm_results']) + perm_info = json.loads(request.form['perm_info']) + + now = datetime.datetime.now() + time_str = now.strftime('%H:%M_%d%B%Y') + + file_name = "Permutation_" + perm_info['num_perm'] + "_" + perm_info['trait_name'] + "_" + time_str + + the_rows = [ + ["#Permutation Test"], + ["#File_name: " + file_name], + ["#Metadata: From GeneNetwork.org"], + ["#Trait_ID: " + perm_info['trait_name']], + ["#Trait_description: " + perm_info['trait_description']], + ["#N_permutations: " + str(perm_info['num_perm'])], + ["#Cofactors: " + perm_info['cofactors']], + ["#N_cases: " + str(perm_info['n_samples'])], + ["#N_genotypes: " + str(perm_info['n_genotypes'])], + ["#Genotype_file: " + perm_info['genofile']], + ["#Units_linkage: " + perm_info['units_linkage']], + ["#Permutation_stratified_by: " + ", ".join([ str(cofactor) for cofactor in perm_info['strat_cofactors']])], + ["#RESULTS_1: Suggestive LRS(p=0.63) = " + str(np.percentile(np.array(perm_info['perm_data']), 67))], + ["#RESULTS_2: Significant LRS(p=0.05) = " + str(np.percentile(np.array(perm_info['perm_data']), 95))], + ["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str(np.percentile(np.array(perm_info['perm_data']), 99))], + ["#Comment: Results sorted from low to high peak linkage"] + ] buff = StringIO.StringIO() writer = csv.writer(buff) - writer.writerow(["Suggestive LRS (p=0.63) = " + str(np.percentile(np.array(perm_data), 67))]) - writer.writerow(["Significant LRS (p=0.05) = " + str(np.percentile(np.array(perm_data), 95))]) - writer.writerow(["Highly Significant LRS (p=0.01) = " + str(np.percentile(np.array(perm_data), 99))]) - writer.writerow("") - writer.writerow([str(num_perm) + " Permutations"]) - writer.writerow("") - for item in perm_data: + writer.writerows(the_rows) + for item in perm_info['perm_data']: writer.writerow([item]) csv_data = buff.getvalue() buff.close() return Response(csv_data, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=perm_data.csv"}) + headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"}) @app.route("/show_temp_trait", methods=('POST',)) def show_temp_trait_page(): -- cgit v1.2.3 From a302a2b0ac0e7c0f26a0d063c3f2b057f61d47f1 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 5 Jun 2020 16:52:56 -0500 Subject: Commiting other current group/resource management code, plus the new files --- wqflask/base/trait.py | 2 + wqflask/maintenance/set_resource_defaults.py | 155 +++++++++++++++++++++ wqflask/utility/authentication_tools.py | 46 ++++++ wqflask/utility/redis_tools.py | 37 +++-- wqflask/wqflask/group_manager.py | 77 ++++++++++ wqflask/wqflask/resource_manager.py | 72 ++++++++++ .../wqflask/static/new/javascript/group_manager.js | 38 +++++ wqflask/wqflask/templates/admin/create_group.html | 89 ++++++++++++ wqflask/wqflask/templates/admin/group_manager.html | 68 ++++----- .../wqflask/templates/admin/manage_resource.html | 92 ++++++++++++ .../wqflask/templates/admin/search_for_groups.html | 64 +++++++++ .../templates/admin/select_group_to_add.html | 54 +++++++ .../templates/new_security/not_authenticated.html | 11 ++ wqflask/wqflask/templates/show_trait_details.html | 5 + wqflask/wqflask/views.py | 3 +- 15 files changed, 764 insertions(+), 49 deletions(-) create mode 100644 wqflask/maintenance/set_resource_defaults.py create mode 100644 wqflask/utility/authentication_tools.py create mode 100644 wqflask/wqflask/group_manager.py create mode 100644 wqflask/wqflask/resource_manager.py create mode 100644 wqflask/wqflask/static/new/javascript/group_manager.js create mode 100644 wqflask/wqflask/templates/admin/create_group.html create mode 100644 wqflask/wqflask/templates/admin/manage_resource.html create mode 100644 wqflask/wqflask/templates/admin/search_for_groups.html create mode 100644 wqflask/wqflask/templates/admin/select_group_to_add.html create mode 100644 wqflask/wqflask/templates/new_security/not_authenticated.html (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 405c4ebf..2a945588 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -391,6 +391,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if response.strip() == "no-access": trait.view = False return trait + else: + trait_info = json.loads(response) except: resource_info = get_resource_info(resource_id) default_permissions = resource_info['default_mask']['data'] diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py new file mode 100644 index 00000000..ba102d9c --- /dev/null +++ b/wqflask/maintenance/set_resource_defaults.py @@ -0,0 +1,155 @@ +""" + +Script that sets default resource access masks for use with the DB proxy + +Defaults will be: +Owner - omni_gn +Mask - Public/non-confidential: { data: "view", + metadata: "view", + admin: "not-admin" } + Private/confidentia: { data: "no-access", + metadata: "no-access", + admin: "not-admin" } + +To run: +./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py + +""" + +from __future__ import print_function, division + +import sys +import json + +# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead +sys.path.insert(0,'./') + +# NEW: import app to avoid a circular dependency on utility.tools +from wqflask import app + +from utility.tools import SQL_URI +from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources +Redis = get_redis_conn() + +import MySQLdb + +import urlparse + +from utility.logger import getLogger +logger = getLogger(__name__) + +def parse_db_uri(): + """Converts a database URI to the db name, host name, user name, and password""" + + parsed_uri = urlparse.urlparse(SQL_URI) + + db_conn_info = dict( + db = parsed_uri.path[1:], + host = parsed_uri.hostname, + user = parsed_uri.username, + passwd = parsed_uri.password) + + print(db_conn_info) + return db_conn_info + +def insert_probeset_resources(default_owner_id): + current_resources = Redis.hgetall("resources") + Cursor.execute(""" SELECT + ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.confidentiality, ProbeSetFreeze.public + FROM + ProbeSetFreeze""") + + resource_results = Cursor.fetchall() + for i, resource in enumerate(resource_results): + if i % 20 == 0: + print(i) + resource_ob = {} + resource_ob['name'] = resource[1] + resource_ob['owner_id'] = default_owner_id + resource_ob['data'] = { "dataset" : str(resource[0])} + resource_ob['type'] = "dataset-probeset" + if resource[2] < 1 and resource[3] > 0: + resource_ob['default_mask'] = { "data": ["no-access", "view"] } + else: + resource_ob['default_mask'] = { "data": ["no-access"] } + resource_ob['group_masks'] = {} + + add_resource(resource_ob) + +def insert_publish_resources(default_owner_id): + current_resources = Redis.hgetall("resources") + Cursor.execute(""" SELECT + PublishXRef.Id, PublishFreeze.Id, InbredSet.InbredSetCode + FROM + PublishXRef, PublishFreeze, InbredSet, Publication + WHERE + PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND + InbredSet.Id = PublishXRef.InbredSetId AND + Publication.Id = PublishXRef.PublicationId""") + + resource_results = Cursor.fetchall() + for resource in resource_results: + if resource[2]: + resource_ob = {} + if resource[2]: + resource_ob['name'] = resource[2] + "_" + str(resource[0]) + else: + resource_ob['name'] = str(resource[0]) + resource_ob['owner_id'] = default_owner_id + resource_ob['data'] = { "dataset" : str(resource[1]) , + "trait" : str(resource[0])} + resource_ob['type'] = "dataset-publish" + resource_ob['default_mask'] = { "data": "view" } + + resource_ob['group_masks'] = {} + + add_resource(resource_ob) + else: + continue + +def insert_geno_resources(default_owner_id): + current_resources = Redis.hgetall("resources") + Cursor.execute(""" SELECT + GenoFreeze.Id, GenoFreeze.ShortName, GenoFreeze.confidentiality + FROM + GenoFreeze""") + + resource_results = Cursor.fetchall() + for i, resource in enumerate(resource_results): + if i % 20 == 0: + print(i) + resource_ob = {} + resource_ob['name'] = resource[1] + resource_ob['owner_id'] = default_owner_id + resource_ob['data'] = { "dataset" : str(resource[0]) } + resource_ob['type'] = "dataset-geno" + if resource[2] < 1: + resource_ob['default_mask'] = { "data": "view" } + else: + resource_ob['default_mask'] = { "data": "no-access" } + resource_ob['group_masks'] = {} + + add_resource(resource_ob) + +def insert_resources(default_owner_id): + current_resources = get_resources() + print("START") + insert_publish_resources(default_owner_id) + print("AFTER PUBLISH") + insert_geno_resources(default_owner_id) + print("AFTER GENO") + insert_probeset_resources(default_owner_id) + print("AFTER PROBESET") + +def main(): + """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" + + Redis.delete("resources") + + owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com") + insert_resources(owner_id) + +if __name__ == '__main__': + Conn = MySQLdb.Connect(**parse_db_uri()) + Cursor = Conn.cursor() + main() \ No newline at end of file diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py new file mode 100644 index 00000000..537881a5 --- /dev/null +++ b/wqflask/utility/authentication_tools.py @@ -0,0 +1,46 @@ +from __future__ import absolute_import, print_function, division + +import json +import requests + +from base import data_set + +from utility import hmac +from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id + +from flask import Flask, g, redirect, url_for + +import logging +logger = logging.getLogger(__name__ ) + +def check_resource_availability(dataset, trait_id=None): + resource_id = get_resource_id(dataset, trait_id) + + if resource_id: + the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) + try: + response = json.loads(requests.get(the_url).content)['data'] + except: + resource_info = get_resource_info(resource_id) + response = resource_info['default_mask']['data'] + + if 'view' in response: + return True + else: + return redirect(url_for("no_access_page")) + + return True + +def check_owner(dataset=None, trait_id=None, resource_id=None): + if resource_id: + resource_info = get_resource_info(resource_id) + if g.user_session.user_id == resource_info['owner_id']: + return resource_id + else: + resource_id = get_resource_id(dataset, trait_id) + if resource_id: + resource_info = get_resource_info(resource_id) + if g.user_session.user_id == resource_info['owner_id']: + return resource_id + + return False \ No newline at end of file diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 0ad96879..bc30a0af 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -95,14 +95,17 @@ def get_user_groups(user_id): user_group_ids = [] #ZS: Group IDs where user is a regular user groups_list = Redis.hgetall("groups") for key in groups_list: - group_ob = json.loads(groups_list[key]) - group_admins = set(group_ob['admins']) - group_members = set(group_ob['members']) - if user_id in group_admins: - admin_group_ids.append(group_ob['id']) - elif user_id in group_members: - user_group_ids.append(group_ob['id']) - else: + try: + group_ob = json.loads(groups_list[key]) + group_admins = set(group_ob['admins']) + group_members = set(group_ob['members']) + if user_id in group_admins: + admin_group_ids.append(group_ob['id']) + elif user_id in group_members: + user_group_ids.append(group_ob['id']) + else: + continue + except: continue admin_groups = [] @@ -122,6 +125,24 @@ def get_group_info(group_id): return group_info +def get_group_by_unique_column(column_name, column_value): + """ Get group by column; not sure if there's a faster way to do this """ + + matched_groups = [] + + all_group_list = Redis.hgetall("groups") + for key in all_group_list: + group_info = json.loads(all_group_list[key]) + if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list + if column_value in group_info[column_name]: + matched_groups.append(group_info) + else: + if group_info[column_name] == column_value: + matched_groups.append(group_info) + + return matched_groups + + def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"): group_id = str(uuid.uuid4()) new_group = { diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py new file mode 100644 index 00000000..f41ae56d --- /dev/null +++ b/wqflask/wqflask/group_manager.py @@ -0,0 +1,77 @@ + +from __future__ import print_function, division, absolute_import + +from flask import (Flask, g, render_template, url_for, request, make_response, + redirect, flash) + +from wqflask import app +from wqflask.user_login import send_verification_email + +from utility.redis_tools import get_user_groups, get_group_info, create_group, delete_group, add_users_to_group, remove_users_from_group, \ + change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column + +from utility.logger import getLogger +logger = getLogger(__name__) + +@app.route("/groups/manage", methods=('GET', 'POST')) +def manage_groups(): + params = request.form if request.form else request.args + if "add_new_group" in params: + return redirect(url_for('add_group')) + else: + admin_groups, user_groups = get_user_groups(g.user_session.user_id) + return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups) + +@app.route("/groups/remove", methods=('POST',)) +def remove_groups(): + group_ids_to_remove = request.form['selected_group_ids'] + for group_id in group_ids_to_remove.split(":"): + delete_group(g.user_session.user_id, group_id) + + return redirect(url_for('manage_groups')) + +@app.route("/groups/create", methods=('GET', 'POST')) +def add_group(): + params = request.form if request.form else request.args + if "group_name" in params: + member_user_ids = set() + admin_user_ids = set() + admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin + if "admin_emails" in params: + admin_emails = params['admin_emails_to_add'].split(",") + for email in admin_emails: + user_details = get_user_by_unique_column("email_address", email) + if user_details: + admin_user_ids.add(user_details['user_id']) + #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins") + if "user_emails" in params: + member_emails = params['member_emails_to_add'].split(",") + for email in member_emails: + user_details = get_user_by_unique_column("email_address", email) + if user_details: + member_user_ids.add(user_details['user_id']) + #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") + + create_group(list(admin_user_ids), list(member_user_ids), params['group_name']) + return redirect(url_for('manage_groups')) + else: + return render_template("admin/create_group.html") + +#ZS: Will integrate this later, for now just letting users be added directly +def send_group_invites(group_id, user_email_list = [], user_type="members"): + for user_email in user_email_list: + user_details = get_user_by_unique_column("email_address", user_email) + if user_details: + group_info = get_group_info(group_id) + #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here, + # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something + if group_info: + #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user, + # but do add them if they're a regular user and are added as an admin + if (user_details['user_id'] in group_info['admins']) or \ + ((user_type == "members") and (user_details['user_id'] in group_info['members'])): + continue + else: + send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group") + +#@app.route() \ No newline at end of file diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py new file mode 100644 index 00000000..7d88b8ed --- /dev/null +++ b/wqflask/wqflask/resource_manager.py @@ -0,0 +1,72 @@ +from __future__ import print_function, division, absolute_import + +from flask import (Flask, g, render_template, url_for, request, make_response, + redirect, flash) + +from wqflask import app + +from utility.authentication_tools import check_owner +from utility.redis_tools import get_resource_info, get_group_info, get_group_by_unique_column, get_user_id + +from utility.logger import getLogger +logger = getLogger(__name__) + +@app.route("/resources/manage", methods=('GET', 'POST')) +def view_resource(): + params = request.form if request.form else request.args + if 'resource_id' in request.args: + resource_id = request.args['resource_id'] + if check_owner(resource_id=resource_id): + resource_info = get_resource_info(resource_id) + group_masks = resource_info['group_masks'] + group_masks_with_names = get_group_names(group_masks) + default_mask = resource_info['default_mask']['data'] + return render_template("admin/manage_resource.html", resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names) + else: + return redirect(url_for("no_access_page")) + +@app.route("/resources/add_group", methods=('POST',)) +def add_group_to_resource(): + resource_id = request.form['resource_id'] + if check_owner(resource_id=resource_id): + if all(key in request.form for key in ('group_id', 'group_name', 'user_name', 'user_email')): + group_list = [] + if request.form['group_id'] != "": + the_group = get_group_info(request.form['group_id']) + if the_group: + group_list.append(the_group) + if request.form['group_name'] != "": + matched_groups = get_group_by_unique_column("name", request.form['group_name']) + for group in matched_groups: + group_list.append(group) + if request.form['user_name'] != "": + user_id = get_user_id("user_name", request.form['user_name']) + if user_id: + matched_groups = get_group_by_unique_column("admins", user_id) + matched_groups += get_group_by_unique_column("members", user_id) + for group in matched_groups: + group_list.append(group) + if request.form['user_email'] != "": + user_id = get_user_id("email_address", request.form['user_email']) + if user_id: + matched_groups = get_group_by_unique_column("admins", user_id) + matched_groups += get_group_by_unique_column("members", user_id) + for group in matched_groups: + group_list.append(group) + return render_template("admin/select_group_to_add.html", group_list=group_list, resource_id = resource_id) + elif 'selected_group' in request.form: + group_id = request.form['selected_group'] + return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id) + else: + return render_template("admin/search_for_groups.html", resource_id = resource_id) + else: + return redirect(url_for("no_access_page")) + +def get_group_names(group_masks): + group_masks_with_names = {} + for group_id, group_mask in group_masks.iteritems(): + this_mask = group_mask + group_name = get_group_info(group_id)['name'] + this_mask['name'] = group_name + + return group_masks_with_names \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/group_manager.js b/wqflask/wqflask/static/new/javascript/group_manager.js new file mode 100644 index 00000000..5e82d104 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/group_manager.js @@ -0,0 +1,38 @@ +$('#add_to_admins').click(function() { + add_emails('admin') +}) + +$('#add_to_members').click(function() { + add_emails('member') +}) + +$('#clear_admins').click(function(){ + clear_emails('admin') +}) + +$('#clear_members').click(function(){ + clear_emails('member') +}) + + +function add_emails(user_type){ + var email_address = $('input[name=user_email]').val(); + var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val() + console.log(email_list_string) + if (email_list_string == ""){ + var email_set = new Set(); + } else { + var email_set = new Set(email_list_string.split(",")) + } + email_set.add(email_address) + + $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(',')) + + var emails_display_string = Array.from(email_set).join('\n') + $('.added_' + user_type + 's').val(emails_display_string) +} + +function clear_emails(user_type){ + $('input[name=' + user_type + '_emails_to_add]').val("") + $('.added_' + user_type + 's').val("") +} \ No newline at end of file diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html new file mode 100644 index 00000000..55c3fa0b --- /dev/null +++ b/wqflask/wqflask/templates/admin/create_group.html @@ -0,0 +1,89 @@ +{% extends "base.html" %} +{% block title %}Group Manager{% endblock %} +{% block content %} + +
+
+

Create Group

+
+
+ + +
+
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+
+
+
+ +
+ + + + + +{% endblock %} + +{% block js %} + + + + + +{% endblock %} diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index b7df1aad..23d8205a 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -1,15 +1,23 @@ {% extends "base.html" %} {% block title %}Group Manager{% endblock %} +{% block css %} + + + +{% endblock %} {% block content %}

Manage Groups

- +
+ + +
-
+
{% if admin_groups|length == 0 and user_groups|length == 0 %}

You currently aren't a member or admin of any groups.


@@ -20,7 +28,7 @@ {% if admin_groups|length == 0 %}

You currently aren't the administrator of any groups.

{% else %} -

Loading...
+
@@ -29,17 +37,19 @@ + {% for group in admin_groups %} - + - + + {% endfor %} @@ -47,13 +57,13 @@ {% endif %}
-
+

User Groups

{% if user_groups|length == 0 %}

You currently aren't a member of any groups.

{% else %} -
# Members Created Last ChangedGroup ID
{{ loop.index }}{{ loop.index }} {{ group.name }}{{ group.admins|length + group.users|length }}{{ group.admins|length + group.users|length }} {{ group.created_timestamp }} {{ group.changed_timestamp }}{{ group.id }}
+
@@ -88,48 +98,26 @@ {% endblock %} {% block js %} - - - + + + + +{% endblock %} diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html new file mode 100644 index 00000000..89eb11dd --- /dev/null +++ b/wqflask/wqflask/templates/admin/search_for_groups.html @@ -0,0 +1,64 @@ +{% extends "base.html" %} +{% block title %}Resource Manager{% endblock %} +{% block content %} + +
+
+

Find Groups

+
+ + +
+
+
+
+

Search by:

+
+
+ +
+ +
+
+
+ +
+ +
+
+
+ +
+ +
+
+
+ +
+ +
+
+
+ +
+ +
+
+
+
+
+ +
+ + + +{% endblock %} + +{% block js %} + + + + + +{% endblock %} diff --git a/wqflask/wqflask/templates/admin/select_group_to_add.html b/wqflask/wqflask/templates/admin/select_group_to_add.html new file mode 100644 index 00000000..df70fb2f --- /dev/null +++ b/wqflask/wqflask/templates/admin/select_group_to_add.html @@ -0,0 +1,54 @@ +{% extends "base.html" %} +{% block title %}Matched Groups{% endblock %} +{% block css %} + + + +{% endblock %} +{% block content %} + +
+

The following groups were found:

+
+
+ +
+ {% if group_list|length > 0 %} + +
+ + + + + + + + + + {% for group in group_list %} + + + + + + + {% endfor %} + +
NameCreatedLast Changed
{% if 'name' in group %}{{ group.name }}{% else %}N/A{% endif %}{% if 'created_timestamp' in group %}{{ group.created_timestamp }}{% else %}N/A{% endif %}{% if 'changed_timestamp' in group %}{{ group.changed_timestamp }}{% else %}N/A{% endif %}
+ {% else %} +

No matching groups were found.

+ {% endif %} +
+ +
+ + + +{% endblock %} + +{% block js %} + + +{% endblock %} diff --git a/wqflask/wqflask/templates/new_security/not_authenticated.html b/wqflask/wqflask/templates/new_security/not_authenticated.html new file mode 100644 index 00000000..7d0d3060 --- /dev/null +++ b/wqflask/wqflask/templates/new_security/not_authenticated.html @@ -0,0 +1,11 @@ +{% extends "base.html" %} +{% block title %}Authentication Needed{% endblock %} +{% block content %} +
+
+

You lack the permissions to view this data.

+
+

Please contact the data's owner or GN administrators if you believe you should have access to this data.

+
+ +{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 878b6ced..5c315878 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -248,6 +248,11 @@ + {% if resource_id %} + + + + {% endif %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 24a4dcee..ee827ba3 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -30,6 +30,7 @@ import sqlalchemy from wqflask import app from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for from wqflask import group_manager +from wqflask import resource_manager from wqflask import search_results from wqflask import export_traits from wqflask import gsearch @@ -89,13 +90,13 @@ def connect_db(): @app.before_request def check_access_permissions(): logger.debug("@app.before_request check_access_permissions") + available = True if "temp_trait" in request.args: if request.args['temp_trait'] == "True": pass else: if 'dataset' in request.args: dataset = create_dataset(request.args['dataset']) - logger.debug("USER:", Redis.hget("users")) if 'trait_id' in request.args: available = check_resource_availability(dataset, request.args['trait_id']) else: -- cgit v1.2.3 From ea47eb228b1224ea83e3f50a056bf715b3bf5ec6 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Jun 2020 14:49:40 -0500 Subject: Adding all the authentication stuff --- wqflask/base/data_set.py | 36 +-- wqflask/base/trait.py | 5 +- wqflask/maintenance/set_resource_defaults.py | 307 ++++++++++----------- wqflask/utility/authentication_tools.py | 132 ++++++--- wqflask/utility/redis_tools.py | 67 ++++- wqflask/wqflask/docs.py | 4 +- wqflask/wqflask/group_manager.py | 220 ++++++++++----- wqflask/wqflask/resource_manager.py | 204 +++++++++----- .../wqflask/static/new/javascript/group_manager.js | 74 ++--- .../static/new/javascript/search_results.js | 1 - .../templates/admin/change_resource_owner.html | 116 ++++++++ wqflask/wqflask/templates/admin/create_group.html | 178 ++++++------ wqflask/wqflask/templates/admin/group_manager.html | 18 +- .../wqflask/templates/admin/manage_resource.html | 200 ++++++++------ .../wqflask/templates/admin/search_for_groups.html | 198 ++++++++----- .../templates/admin/select_group_to_add.html | 54 ---- .../templates/admin/set_group_privileges.html | 102 +++++++ wqflask/wqflask/templates/admin/view_group.html | 238 ++++++++++++++++ wqflask/wqflask/templates/base.html | 5 + .../wqflask/templates/set_group_privileges.html | 77 ++++++ wqflask/wqflask/templates/show_trait_details.html | 4 +- wqflask/wqflask/views.py | 2 +- 22 files changed, 1516 insertions(+), 726 deletions(-) create mode 100644 wqflask/wqflask/templates/admin/change_resource_owner.html delete mode 100644 wqflask/wqflask/templates/admin/select_group_to_add.html create mode 100644 wqflask/wqflask/templates/admin/set_group_privileges.html create mode 100644 wqflask/wqflask/templates/admin/view_group.html create mode 100644 wqflask/wqflask/templates/set_group_privileges.html (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1457ba8d..92dc8615 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -486,25 +486,18 @@ class DatasetGroup(object): def datasets(group_name, this_group = None): key = "group_dataset_menu:v2:" + group_name - logger.debug("key is2:", key) dataset_menu = [] - logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) - logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) the_results = fetchall(''' (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name FROM PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s' - and PublishFreeze.public > %s - and PublishFreeze.confidentiality < 1 ORDER BY PublishFreeze.Id ASC) UNION (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze, InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id - and InbredSet.Name = '%s' - and GenoFreeze.public > %s - and GenoFreeze.confidentiality < 1) + and InbredSet.Name = '%s') UNION (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue @@ -512,12 +505,10 @@ def datasets(group_name, this_group = None): and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s - and ProbeSetFreeze.public > %s - and ProbeSetFreeze.confidentiality < 1 ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC) - ''' % (group_name, webqtlConfig.PUBLICTHRESH, - group_name, webqtlConfig.PUBLICTHRESH, - "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) + ''' % (group_name, + group_name, + "'" + group_name + "'")) sorted_results = sorted(the_results, key=lambda kv: kv[0]) @@ -637,29 +628,25 @@ class DataSet(object): """ - try: if self.type == "ProbeSet": query_args = tuple(escape(x) for x in ( - str(webqtlConfig.PUBLICTHRESH), self.name, self.name, self.name)) self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1(""" -SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name -FROM ProbeSetFreeze, ProbeFreeze, Tissue -WHERE ProbeSetFreeze.public > %s -AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id -AND ProbeFreeze.TissueId = Tissue.Id -AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') + SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name + FROM ProbeSetFreeze, ProbeFreeze, Tissue + WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id + AND ProbeFreeze.TissueId = Tissue.Id + AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') """ % (query_args),"/dataset/"+self.name+".json", lambda r: (r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"]) ) else: query_args = tuple(escape(x) for x in ( (self.type + "Freeze"), - str(webqtlConfig.PUBLICTHRESH), self.name, self.name, self.name)) @@ -668,9 +655,8 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre self.id, self.name, self.fullname, self.shortname = fetchone(""" SELECT Id, Name, FullName, ShortName FROM %s - WHERE public > %s AND - (Name = '%s' OR FullName = '%s' OR ShortName = '%s') - """ % (query_args)) + WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s') + """ % (query_args)) except TypeError: logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name)) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 2a945588..7700ecd5 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -46,9 +46,10 @@ def create_trait(**kw): else: permitted = check_resource_availability(dataset) - if permitted: + if permitted != "no-access": the_trait = GeneralTrait(**kw) if the_trait.dataset.type != "Temp": + the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info')) return the_trait else: @@ -383,7 +384,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if dataset.type == 'Publish': the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id) else: - the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name) try: @@ -424,7 +424,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): logger.sql(query) trait_info = g.db.execute(query).fetchone() - #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. elif dataset.type == 'ProbeSet': diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index ba102d9c..344e6a23 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -1,155 +1,154 @@ -""" - -Script that sets default resource access masks for use with the DB proxy - -Defaults will be: -Owner - omni_gn -Mask - Public/non-confidential: { data: "view", - metadata: "view", - admin: "not-admin" } - Private/confidentia: { data: "no-access", - metadata: "no-access", - admin: "not-admin" } - -To run: -./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py - -""" - -from __future__ import print_function, division - -import sys -import json - -# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') - -# NEW: import app to avoid a circular dependency on utility.tools -from wqflask import app - -from utility.tools import SQL_URI -from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources -Redis = get_redis_conn() - -import MySQLdb - -import urlparse - -from utility.logger import getLogger -logger = getLogger(__name__) - -def parse_db_uri(): - """Converts a database URI to the db name, host name, user name, and password""" - - parsed_uri = urlparse.urlparse(SQL_URI) - - db_conn_info = dict( - db = parsed_uri.path[1:], - host = parsed_uri.hostname, - user = parsed_uri.username, - passwd = parsed_uri.password) - - print(db_conn_info) - return db_conn_info - -def insert_probeset_resources(default_owner_id): - current_resources = Redis.hgetall("resources") - Cursor.execute(""" SELECT - ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.confidentiality, ProbeSetFreeze.public - FROM - ProbeSetFreeze""") - - resource_results = Cursor.fetchall() - for i, resource in enumerate(resource_results): - if i % 20 == 0: - print(i) - resource_ob = {} - resource_ob['name'] = resource[1] - resource_ob['owner_id'] = default_owner_id - resource_ob['data'] = { "dataset" : str(resource[0])} - resource_ob['type'] = "dataset-probeset" - if resource[2] < 1 and resource[3] > 0: - resource_ob['default_mask'] = { "data": ["no-access", "view"] } - else: - resource_ob['default_mask'] = { "data": ["no-access"] } - resource_ob['group_masks'] = {} - - add_resource(resource_ob) - -def insert_publish_resources(default_owner_id): - current_resources = Redis.hgetall("resources") - Cursor.execute(""" SELECT - PublishXRef.Id, PublishFreeze.Id, InbredSet.InbredSetCode - FROM - PublishXRef, PublishFreeze, InbredSet, Publication - WHERE - PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND - InbredSet.Id = PublishXRef.InbredSetId AND - Publication.Id = PublishXRef.PublicationId""") - - resource_results = Cursor.fetchall() - for resource in resource_results: - if resource[2]: - resource_ob = {} - if resource[2]: - resource_ob['name'] = resource[2] + "_" + str(resource[0]) - else: - resource_ob['name'] = str(resource[0]) - resource_ob['owner_id'] = default_owner_id - resource_ob['data'] = { "dataset" : str(resource[1]) , - "trait" : str(resource[0])} - resource_ob['type'] = "dataset-publish" - resource_ob['default_mask'] = { "data": "view" } - - resource_ob['group_masks'] = {} - - add_resource(resource_ob) - else: - continue - -def insert_geno_resources(default_owner_id): - current_resources = Redis.hgetall("resources") - Cursor.execute(""" SELECT - GenoFreeze.Id, GenoFreeze.ShortName, GenoFreeze.confidentiality - FROM - GenoFreeze""") - - resource_results = Cursor.fetchall() - for i, resource in enumerate(resource_results): - if i % 20 == 0: - print(i) - resource_ob = {} - resource_ob['name'] = resource[1] - resource_ob['owner_id'] = default_owner_id - resource_ob['data'] = { "dataset" : str(resource[0]) } - resource_ob['type'] = "dataset-geno" - if resource[2] < 1: - resource_ob['default_mask'] = { "data": "view" } - else: - resource_ob['default_mask'] = { "data": "no-access" } - resource_ob['group_masks'] = {} - - add_resource(resource_ob) - -def insert_resources(default_owner_id): - current_resources = get_resources() - print("START") - insert_publish_resources(default_owner_id) - print("AFTER PUBLISH") - insert_geno_resources(default_owner_id) - print("AFTER GENO") - insert_probeset_resources(default_owner_id) - print("AFTER PROBESET") - -def main(): - """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" - - Redis.delete("resources") - - owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com") - insert_resources(owner_id) - -if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri()) - Cursor = Conn.cursor() +""" + +Script that sets default resource access masks for use with the DB proxy + +Defaults will be: +Owner - omni_gn +Mask - Public/non-confidential: { data: "view", + metadata: "view", + admin: "not-admin" } + Private/confidentia: { data: "no-access", + metadata: "no-access", + admin: "not-admin" } + +To run: +./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py + +""" + +from __future__ import print_function, division + +import sys +import json + +# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead +sys.path.insert(0,'./') + +# NEW: import app to avoid a circular dependency on utility.tools +from wqflask import app + +from utility.tools import SQL_URI +from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources +Redis = get_redis_conn() + +import MySQLdb + +import urlparse + +from utility.logger import getLogger +logger = getLogger(__name__) + +def parse_db_uri(): + """Converts a database URI to the db name, host name, user name, and password""" + + parsed_uri = urlparse.urlparse(SQL_URI) + + db_conn_info = dict( + db = parsed_uri.path[1:], + host = parsed_uri.hostname, + user = parsed_uri.username, + passwd = parsed_uri.password) + + print(db_conn_info) + return db_conn_info + +def insert_probeset_resources(default_owner_id): + current_resources = Redis.hgetall("resources") + Cursor.execute(""" SELECT + ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.confidentiality, ProbeSetFreeze.public + FROM + ProbeSetFreeze""") + + resource_results = Cursor.fetchall() + for i, resource in enumerate(resource_results): + resource_ob = {} + resource_ob['name'] = resource[1] + resource_ob['owner_id'] = default_owner_id + resource_ob['data'] = { "dataset" : str(resource[0])} + resource_ob['type'] = "dataset-probeset" + if resource[2] < 1 and resource[3] > 0: + resource_ob['default_mask'] = { "data": "view" } + else: + resource_ob['default_mask'] = { "data": "no-access" } + resource_ob['group_masks'] = {} + + add_resource(resource_ob) + +def insert_publish_resources(default_owner_id): + current_resources = Redis.hgetall("resources") + Cursor.execute(""" SELECT + PublishXRef.Id, PublishFreeze.Id, InbredSet.InbredSetCode + FROM + PublishXRef, PublishFreeze, InbredSet, Publication + WHERE + PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND + InbredSet.Id = PublishXRef.InbredSetId AND + Publication.Id = PublishXRef.PublicationId""") + + resource_results = Cursor.fetchall() + for resource in resource_results: + if resource[2]: + resource_ob = {} + if resource[2]: + resource_ob['name'] = resource[2] + "_" + str(resource[0]) + else: + resource_ob['name'] = str(resource[0]) + resource_ob['owner_id'] = default_owner_id + resource_ob['data'] = { "dataset" : str(resource[1]) , + "trait" : str(resource[0])} + resource_ob['type'] = "dataset-publish" + resource_ob['default_mask'] = { "data": "view" } + + resource_ob['group_masks'] = {} + + add_resource(resource_ob) + else: + continue + +def insert_geno_resources(default_owner_id): + current_resources = Redis.hgetall("resources") + Cursor.execute(""" SELECT + GenoFreeze.Id, GenoFreeze.ShortName, GenoFreeze.confidentiality + FROM + GenoFreeze""") + + resource_results = Cursor.fetchall() + for i, resource in enumerate(resource_results): + resource_ob = {} + resource_ob['name'] = resource[1] + if resource[1] == "HET3-ITPGeno": + resource_ob['owner_id'] = "73a3f093-ca13-4ae0-a179-9a446f709f6e" + else: + resource_ob['owner_id'] = default_owner_id + resource_ob['data'] = { "dataset" : str(resource[0]) } + resource_ob['type'] = "dataset-geno" + if resource[2] < 1: + resource_ob['default_mask'] = { "data": "view" } + else: + resource_ob['default_mask'] = { "data": "no-access" } + resource_ob['group_masks'] = {} + + add_resource(resource_ob) + +def insert_resources(default_owner_id): + current_resources = get_resources() + print("START") + insert_publish_resources(default_owner_id) + print("AFTER PUBLISH") + insert_geno_resources(default_owner_id) + print("AFTER GENO") + insert_probeset_resources(default_owner_id) + print("AFTER PROBESET") + +def main(): + """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" + + Redis.delete("resources") + + owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com") + insert_resources(owner_id) + +if __name__ == '__main__': + Conn = MySQLdb.Connect(**parse_db_uri()) + Cursor = Conn.cursor() main() \ No newline at end of file diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 537881a5..07ceacc0 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -1,46 +1,86 @@ -from __future__ import absolute_import, print_function, division - -import json -import requests - -from base import data_set - -from utility import hmac -from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id - -from flask import Flask, g, redirect, url_for - -import logging -logger = logging.getLogger(__name__ ) - -def check_resource_availability(dataset, trait_id=None): - resource_id = get_resource_id(dataset, trait_id) - - if resource_id: - the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) - try: - response = json.loads(requests.get(the_url).content)['data'] - except: - resource_info = get_resource_info(resource_id) - response = resource_info['default_mask']['data'] - - if 'view' in response: - return True - else: - return redirect(url_for("no_access_page")) - - return True - -def check_owner(dataset=None, trait_id=None, resource_id=None): - if resource_id: - resource_info = get_resource_info(resource_id) - if g.user_session.user_id == resource_info['owner_id']: - return resource_id - else: - resource_id = get_resource_id(dataset, trait_id) - if resource_id: - resource_info = get_resource_info(resource_id) - if g.user_session.user_id == resource_info['owner_id']: - return resource_id - - return False \ No newline at end of file +from __future__ import absolute_import, print_function, division + +import json +import requests + +from base import data_set + +from utility import hmac +from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id + +from flask import Flask, g, redirect, url_for + +import logging +logger = logging.getLogger(__name__ ) + +def check_resource_availability(dataset, trait_id=None): + resource_id = get_resource_id(dataset, trait_id) + + response = None + if resource_id: + resource_info = get_resource_info(resource_id) + + the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) + try: + response = json.loads(requests.get(the_url).content)['data'] + except: + response = resource_info['default_mask']['data'] + + if 'edit' in response: + return "edit" + elif 'view' in response: + return "view" + else: + return "no-access" + + return False + +def check_admin(resource_id=None): + + return "not-admin" + + # ZS: commented out until proxy can return this + # the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) + # try: + # response = json.loads(requests.get(the_url).content) + # except: + # response = resource_info['default_mask']['admin'] + + # if 'edit-admins' in response: + # return "edit-admins" + # elif 'edit-access' in response: + # return "edit-access" + # else: + # return "not-admin" + +def check_owner(dataset=None, trait_id=None, resource_id=None): + if resource_id: + resource_info = get_resource_info(resource_id) + if g.user_session.user_id == resource_info['owner_id']: + return resource_id + else: + resource_id = get_resource_id(dataset, trait_id) + if resource_id: + resource_info = get_resource_info(resource_id) + if g.user_session.user_id == resource_info['owner_id']: + return resource_id + + return False + +def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None): + if resource_id: + resource_info = get_resource_info(resource_id) + if g.user_session.user_id == resource_info['owner_id']: + return [resource_id, "owner"] + else: + return [resource_id, check_admin(resource_id)] + else: + resource_id = get_resource_id(dataset, trait_id) + if resource_id: + resource_info = get_resource_info(resource_id) + if g.user_session.user_id == resource_info['owner_id']: + return [resource_id, "owner"] + else: + return [resource_id, check_admin(resource_id)] + + return [resource_id, "not-admin"] \ No newline at end of file diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index bc30a0af..c6d221ff 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -16,7 +16,7 @@ from utility.logger import getLogger logger = getLogger(__name__) def get_redis_conn(): - Redis = redis.StrictRedis(port=6380) + Redis = redis.StrictRedis(port=6379) return Redis Redis = get_redis_conn() @@ -51,6 +51,27 @@ def get_user_by_unique_column(column_name, column_value): return item_details +def get_users_like_unique_column(column_name, column_value): + """ + Like previous function, but this only checks if the input is a subset of a field and can return multiple results + """ + matched_users = [] + + if column_value != "": + user_list = Redis.hgetall("users") + if column_name != "user_id": + for key in user_list: + user_ob = json.loads(user_list[key]) + if column_name in user_ob: + if column_value in user_ob[column_name]: + matched_users.append(user_ob) + else: + matched_users.append(json.loads(user_list[column_value])) + + return matched_users + +# def search_users_by_unique_column(column_name, column_value): + def set_user_attribute(user_id, column_name, column_value): user_info = json.loads(Redis.hget("users", user_id)) user_info[column_name] = column_value @@ -142,6 +163,28 @@ def get_group_by_unique_column(column_name, column_value): return matched_groups +def get_groups_like_unique_column(column_name, column_value): + """ + Like previous function, but this only checks if the input is a subset of a field and can return multiple results + """ + matched_groups = [] + + if column_value != "": + group_list = Redis.hgetall("groups") + if column_name != "group_id": + for key in group_list: + group_info = json.loads(group_list[key]) + if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list + if column_value in group_info[column_name]: + matched_groups.append(group_info) + else: + if column_name in group_info: + if column_value in group_info[column_name]: + matched_groups.append(group_info) + else: + matched_groups.append(json.loads(group_list[column_value])) + + return matched_groups def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"): group_id = str(uuid.uuid4()) @@ -192,9 +235,13 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins group_info = get_group_info(group_id) + if user_id in group_info["admins"]: + users_to_remove_set = set(users_to_remove_ids) + if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less + users_to_remove_set.remove(user_id) group_users = set(group_info[user_type]) - group_users -= set(users_to_remove_ids) + group_users -= users_to_remove_set group_info[user_type] = list(group_users) group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') Redis.hset("groups", group_id, json.dumps(group_info)) @@ -232,7 +279,6 @@ def get_resource_info(resource_id): return json.loads(resource_info) def add_resource(resource_info): - if 'trait' in resource_info['data']: resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait']))) else: @@ -241,3 +287,18 @@ def add_resource(resource_info): Redis.hset("resources", resource_id, json.dumps(resource_info)) return resource_info + +def add_access_mask(resource_id, group_id, access_mask): + the_resource = get_resource_info(resource_id) + the_resource['group_masks'][group_id] = access_mask + + Redis.hset("resources", resource_id, json.dumps(the_resource)) + + return the_resource + +def change_resource_owner(resource_id, new_owner_id): + the_resource= get_resource_info(resource_id) + the_resource['owner_id'] = new_owner_id + + Redis.delete("resource") + Redis.hset("resources", resource_id, json.dumps(the_resource)) \ No newline at end of file diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 0187f32e..78407e22 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -1,5 +1,7 @@ from __future__ import absolute_import, print_function, division +import codecs + from flask import g from utility.logger import getLogger @@ -20,7 +22,7 @@ class Docs(object): self.content = "" else: self.title = result[0] - self.content = result[1] + self.content = result[1].encode("latin1") self.editable = "false" # ZS: Removing option to edit to see if text still gets vandalized diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index f41ae56d..9afc016b 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -1,77 +1,145 @@ - -from __future__ import print_function, division, absolute_import - -from flask import (Flask, g, render_template, url_for, request, make_response, - redirect, flash) - -from wqflask import app -from wqflask.user_login import send_verification_email - -from utility.redis_tools import get_user_groups, get_group_info, create_group, delete_group, add_users_to_group, remove_users_from_group, \ - change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column - -from utility.logger import getLogger -logger = getLogger(__name__) - -@app.route("/groups/manage", methods=('GET', 'POST')) -def manage_groups(): - params = request.form if request.form else request.args - if "add_new_group" in params: - return redirect(url_for('add_group')) - else: - admin_groups, user_groups = get_user_groups(g.user_session.user_id) - return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups) - -@app.route("/groups/remove", methods=('POST',)) -def remove_groups(): - group_ids_to_remove = request.form['selected_group_ids'] - for group_id in group_ids_to_remove.split(":"): - delete_group(g.user_session.user_id, group_id) - - return redirect(url_for('manage_groups')) - -@app.route("/groups/create", methods=('GET', 'POST')) -def add_group(): - params = request.form if request.form else request.args - if "group_name" in params: - member_user_ids = set() - admin_user_ids = set() - admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin - if "admin_emails" in params: - admin_emails = params['admin_emails_to_add'].split(",") - for email in admin_emails: - user_details = get_user_by_unique_column("email_address", email) - if user_details: - admin_user_ids.add(user_details['user_id']) - #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins") - if "user_emails" in params: - member_emails = params['member_emails_to_add'].split(",") - for email in member_emails: - user_details = get_user_by_unique_column("email_address", email) - if user_details: - member_user_ids.add(user_details['user_id']) - #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") - - create_group(list(admin_user_ids), list(member_user_ids), params['group_name']) - return redirect(url_for('manage_groups')) - else: - return render_template("admin/create_group.html") - -#ZS: Will integrate this later, for now just letting users be added directly -def send_group_invites(group_id, user_email_list = [], user_type="members"): - for user_email in user_email_list: - user_details = get_user_by_unique_column("email_address", user_email) - if user_details: - group_info = get_group_info(group_id) - #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here, - # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something - if group_info: - #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user, - # but do add them if they're a regular user and are added as an admin - if (user_details['user_id'] in group_info['admins']) or \ - ((user_type == "members") and (user_details['user_id'] in group_info['members'])): - continue - else: - send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group") - + +from __future__ import print_function, division, absolute_import + +from flask import (Flask, g, render_template, url_for, request, make_response, + redirect, flash) + +from wqflask import app +from wqflask.user_login import send_verification_email + +from utility.redis_tools import get_user_groups, get_group_info, create_group, delete_group, add_users_to_group, remove_users_from_group, \ + change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column, get_resources, get_resource_info + +from utility.logger import getLogger +logger = getLogger(__name__) + +@app.route("/groups/manage", methods=('GET', 'POST')) +def manage_groups(): + params = request.form if request.form else request.args + if "add_new_group" in params: + return redirect(url_for('add_group')) + else: + admin_groups, user_groups = get_user_groups(g.user_session.user_id) + return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups) + +@app.route("/groups/view", methods=('GET', 'POST')) +def view_group(): + params = request.form if request.form else request.args + group_id = params['id'] + group_info = get_group_info(group_id) + admins_info = [] + user_is_admin = False + if g.user_session.user_id in group_info['admins']: + user_is_admin = True + for user_id in group_info['admins']: + if user_id: + user_info = get_user_by_unique_column("user_id", user_id) + admins_info.append(user_info) + members_info = [] + for user_id in group_info['members']: + if user_id: + user_info = get_user_by_unique_column("user_id", user_id) + members_info.append(user_info) + + #ZS: This whole part might not scale well with many resources + resources_info = [] + all_resources = get_resources() + for resource_id in all_resources: + resource_info = get_resource_info(resource_id) + group_masks = resource_info['group_masks'] + if group_id in group_masks: + this_resource = {} + privileges = group_masks[group_id] + this_resource['id'] = resource_id + this_resource['name'] = resource_info['name'] + this_resource['data'] = privileges['data'] + this_resource['metadata'] = privileges['metadata'] + this_resource['admin'] = privileges['admin'] + resources_info.append(this_resource) + + return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info) + +@app.route("/groups/remove", methods=('POST',)) +def remove_groups(): + group_ids_to_remove = request.form['selected_group_ids'] + for group_id in group_ids_to_remove.split(":"): + delete_group(g.user_session.user_id, group_id) + + return redirect(url_for('manage_groups')) + +@app.route("/groups/remove_users", methods=('POST',)) +def remove_users(): + group_id = request.form['group_id'] + admin_ids_to_remove = request.form['selected_admin_ids'] + member_ids_to_remove = request.form['selected_member_ids'] + + remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(":"), group_id, user_type="admins") + remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(":"), group_id, user_type="members") + + return redirect(url_for('view_group', id=group_id)) + +@app.route("/groups/add_", methods=('POST',)) +def add_users(user_type='members'): + group_id = request.form['group_id'] + if user_type == "admins": + user_emails = request.form['admin_emails_to_add'].split(",") + add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = True) + elif user_type == "members": + user_emails = request.form['member_emails_to_add'].split(",") + add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = False) + + return redirect(url_for('view_group', id=group_id)) + +@app.route("/groups/change_name", methods=('POST',)) +def change_name(): + group_id = request.form['group_id'] + new_name = request.form['new_name'] + group_info = change_group_name(g.user_session.user_id, group_id, new_name) + + return new_name + +@app.route("/groups/create", methods=('GET', 'POST')) +def add_or_edit_group(): + params = request.form if request.form else request.args + if "group_name" in params: + member_user_ids = set() + admin_user_ids = set() + admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin + if "admin_emails_to_add" in params: + admin_emails = params['admin_emails_to_add'].split(",") + for email in admin_emails: + user_details = get_user_by_unique_column("email_address", email) + if user_details: + admin_user_ids.add(user_details['user_id']) + #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins") + if "member_emails_to_add" in params: + member_emails = params['member_emails_to_add'].split(",") + for email in member_emails: + user_details = get_user_by_unique_column("email_address", email) + if user_details: + member_user_ids.add(user_details['user_id']) + #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") + + create_group(list(admin_user_ids), list(member_user_ids), params['group_name']) + return redirect(url_for('manage_groups')) + else: + return render_template("admin/create_group.html") + +#ZS: Will integrate this later, for now just letting users be added directly +def send_group_invites(group_id, user_email_list = [], user_type="members"): + for user_email in user_email_list: + user_details = get_user_by_unique_column("email_address", user_email) + if user_details: + group_info = get_group_info(group_id) + #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here, + # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something + if group_info: + #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user, + # but do add them if they're a regular user and are added as an admin + if (user_details['user_id'] in group_info['admins']) or \ + ((user_type == "members") and (user_details['user_id'] in group_info['members'])): + continue + else: + send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group") + #@app.route() \ No newline at end of file diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 7d88b8ed..0f9f5c9d 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -1,72 +1,134 @@ -from __future__ import print_function, division, absolute_import - -from flask import (Flask, g, render_template, url_for, request, make_response, - redirect, flash) - -from wqflask import app - -from utility.authentication_tools import check_owner -from utility.redis_tools import get_resource_info, get_group_info, get_group_by_unique_column, get_user_id - -from utility.logger import getLogger -logger = getLogger(__name__) - -@app.route("/resources/manage", methods=('GET', 'POST')) -def view_resource(): - params = request.form if request.form else request.args - if 'resource_id' in request.args: - resource_id = request.args['resource_id'] - if check_owner(resource_id=resource_id): - resource_info = get_resource_info(resource_id) - group_masks = resource_info['group_masks'] - group_masks_with_names = get_group_names(group_masks) - default_mask = resource_info['default_mask']['data'] - return render_template("admin/manage_resource.html", resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names) - else: - return redirect(url_for("no_access_page")) - -@app.route("/resources/add_group", methods=('POST',)) -def add_group_to_resource(): - resource_id = request.form['resource_id'] - if check_owner(resource_id=resource_id): - if all(key in request.form for key in ('group_id', 'group_name', 'user_name', 'user_email')): - group_list = [] - if request.form['group_id'] != "": - the_group = get_group_info(request.form['group_id']) - if the_group: - group_list.append(the_group) - if request.form['group_name'] != "": - matched_groups = get_group_by_unique_column("name", request.form['group_name']) - for group in matched_groups: - group_list.append(group) - if request.form['user_name'] != "": - user_id = get_user_id("user_name", request.form['user_name']) - if user_id: - matched_groups = get_group_by_unique_column("admins", user_id) - matched_groups += get_group_by_unique_column("members", user_id) - for group in matched_groups: - group_list.append(group) - if request.form['user_email'] != "": - user_id = get_user_id("email_address", request.form['user_email']) - if user_id: - matched_groups = get_group_by_unique_column("admins", user_id) - matched_groups += get_group_by_unique_column("members", user_id) - for group in matched_groups: - group_list.append(group) - return render_template("admin/select_group_to_add.html", group_list=group_list, resource_id = resource_id) - elif 'selected_group' in request.form: - group_id = request.form['selected_group'] - return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id) - else: - return render_template("admin/search_for_groups.html", resource_id = resource_id) - else: - return redirect(url_for("no_access_page")) - -def get_group_names(group_masks): - group_masks_with_names = {} - for group_id, group_mask in group_masks.iteritems(): - this_mask = group_mask - group_name = get_group_info(group_id)['name'] - this_mask['name'] = group_name - +from __future__ import print_function, division, absolute_import + +import json + +from flask import (Flask, g, render_template, url_for, request, make_response, + redirect, flash) + +from wqflask import app + +from utility.authentication_tools import check_owner_or_admin +from utility.redis_tools import get_resource_info, get_group_info, get_groups_like_unique_column, get_user_id, get_user_by_unique_column, get_users_like_unique_column, add_access_mask, add_resource, change_resource_owner + +from utility.logger import getLogger +logger = getLogger(__name__) + +@app.route("/resources/manage", methods=('GET', 'POST')) +def manage_resource(): + params = request.form if request.form else request.args + if 'resource_id' in request.args: + resource_id = request.args['resource_id'] + admin_status = check_owner_or_admin(resource_id=resource_id)[1] + + resource_info = get_resource_info(resource_id) + group_masks = resource_info['group_masks'] + group_masks_with_names = get_group_names(group_masks) + default_mask = resource_info['default_mask']['data'] + owner_id = resource_info['owner_id'] + owner_info = get_user_by_unique_column("user_id", owner_id) + + if 'name' in owner_info: + owner_display_name = owner_info['full_name'] + elif 'user_name' in owner_info: + owner_display_name = owner_info['user_name'] + elif 'email_address' in owner_info: + owner_display_name = owner_info['email_address'] + else: + owner_display_name = None + + return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status) + +@app.route("/search_for_users", methods=('POST',)) +def search_for_user(): + params = request.form + user_list = [] + user_list += get_users_like_unique_column("full_name", params['user_name']) + user_list += get_users_like_unique_column("email_address", params['user_email']) + + return json.dumps(user_list) + +@app.route("/search_for_groups", methods=('POST',)) +def search_for_groups(): + params = request.form + group_list = [] + group_list += get_groups_like_unique_column("id", params['group_id']) + group_list += get_groups_like_unique_column("name", params['group_name']) + + user_list = [] + user_list += get_users_like_unique_column("full_name", params['user_name']) + user_list += get_users_like_unique_column("email_address", params['user_email']) + for user in user_list: + group_list += get_groups_like_unique_column("admins", user['user_id']) + group_list += get_groups_like_unique_column("members", user['user_id']) + + return json.dumps(group_list) + +@app.route("/resources/change_owner", methods=('POST',)) +def change_owner(): + resource_id = request.form['resource_id'] + if 'new_owner' in request.form: + admin_status = check_owner_or_admin(resource_id=resource_id)[1] + if admin_status == "owner": + new_owner_id = request.form['new_owner'] + change_resource_owner(resource_id, new_owner_id) + flash("The resource's owner has beeen changed.", "alert-info") + return redirect(url_for("manage_resource", resource_id=resource_id)) + else: + flash("You lack the permissions to make this change.", "error") + return redirect(url_for("manage_resource", resource_id=resource_id)) + else: + return render_template("admin/change_resource_owner.html", resource_id = resource_id) + +@app.route("/resources/change_default_privileges", methods=('POST',)) +def change_default_privileges(): + resource_id = request.form['resource_id'] + admin_status = check_owner_or_admin(resource_id=resource_id) + if admin_status == "owner" or admin_status == "edit-admins": + resource_info = get_resource_info(resource_id) + default_mask = resource_info['default_mask'] + if request.form['open_to_public'] == "True": + default_mask['data'] = 'view' + else: + default_mask['data'] = 'no-access' + resource_info['default_mask'] = default_mask + add_resource(resource_info) + flash("Your changes have been saved.", "alert-info") + return redirect(url_for("manage_resource", resource_id=resource_id)) + else: + return redirect(url_for("no_access_page")) + +@app.route("/resources/add_group", methods=('POST',)) +def add_group_to_resource(): + resource_id = request.form['resource_id'] + admin_status = check_owner_or_admin(resource_id=resource_id)[1] + if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access": + if 'selected_group' in request.form: + group_id = request.form['selected_group'] + resource_info = get_resource_info(resource_id) + default_privileges = resource_info['default_mask'] + return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id, default_privileges = default_privileges) + elif all(key in request.form for key in ('data_privilege', 'metadata_privilege', 'admin_privilege')): + group_id = request.form['group_id'] + group_name = get_group_info(group_id)['name'] + access_mask = { + 'data': request.form['data_privilege'], + 'metadata': request.form['metadata_privilege'], + 'admin': request.form['admin_privilege'] + } + add_access_mask(resource_id, group_id, access_mask) + flash("Privileges have been added for group {}.".format(group_name), "alert-info") + return redirect(url_for("manage_resource", resource_id=resource_id)) + else: + return render_template("admin/search_for_groups.html", resource_id = resource_id) + else: + return redirect(url_for("no_access_page")) + +def get_group_names(group_masks): + group_masks_with_names = {} + for group_id, group_mask in group_masks.iteritems(): + this_mask = group_mask + group_name = get_group_info(group_id)['name'] + this_mask['name'] = group_name + group_masks_with_names[group_id] = this_mask + return group_masks_with_names \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/group_manager.js b/wqflask/wqflask/static/new/javascript/group_manager.js index 5e82d104..4c172cbf 100644 --- a/wqflask/wqflask/static/new/javascript/group_manager.js +++ b/wqflask/wqflask/static/new/javascript/group_manager.js @@ -1,38 +1,38 @@ -$('#add_to_admins').click(function() { - add_emails('admin') -}) - -$('#add_to_members').click(function() { - add_emails('member') -}) - -$('#clear_admins').click(function(){ - clear_emails('admin') -}) - -$('#clear_members').click(function(){ - clear_emails('member') -}) - - -function add_emails(user_type){ - var email_address = $('input[name=user_email]').val(); - var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val() - console.log(email_list_string) - if (email_list_string == ""){ - var email_set = new Set(); - } else { - var email_set = new Set(email_list_string.split(",")) - } - email_set.add(email_address) - - $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(',')) - - var emails_display_string = Array.from(email_set).join('\n') - $('.added_' + user_type + 's').val(emails_display_string) -} - -function clear_emails(user_type){ - $('input[name=' + user_type + '_emails_to_add]').val("") - $('.added_' + user_type + 's').val("") +$('#add_to_admins').click(function() { + add_emails('admin') +}) + +$('#add_to_members').click(function() { + add_emails('member') +}) + +$('#clear_admins').click(function(){ + clear_emails('admin') +}) + +$('#clear_members').click(function(){ + clear_emails('member') +}) + + +function add_emails(user_type){ + var email_address = $('input[name=user_email]').val(); + var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val().trim() + console.log(email_list_string) + if (email_list_string == ""){ + var email_set = new Set(); + } else { + var email_set = new Set(email_list_string.split(",")) + } + email_set.add(email_address) + + $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(',')) + + var emails_display_string = Array.from(email_set).join('\n') + $('.added_' + user_type + 's').val(emails_display_string) +} + +function clear_emails(user_type){ + $('input[name=' + user_type + '_emails_to_add]').val("") + $('.added_' + user_type + 's').val("") } \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js index 8fa698b4..115dac13 100644 --- a/wqflask/wqflask/static/new/javascript/search_results.js +++ b/wqflask/wqflask/static/new/javascript/search_results.js @@ -296,7 +296,6 @@ $(function() { $("#deselect_all").click(deselect_all); $("#invert").click(invert); $("#add").click(add); - $("#remove").click(remove); $("#submit_bnw").click(submit_bnw); $("#export_traits").click(export_traits); $('.trait_checkbox, .btn').click(change_buttons); diff --git a/wqflask/wqflask/templates/admin/change_resource_owner.html b/wqflask/wqflask/templates/admin/change_resource_owner.html new file mode 100644 index 00000000..ae9409b0 --- /dev/null +++ b/wqflask/wqflask/templates/admin/change_resource_owner.html @@ -0,0 +1,116 @@ +{% extends "base.html" %} +{% block title %}Resource Manager{% endblock %} +{% block css %} + + +{% endblock %} +{% block content %} + +
+
+

Search for user to assign ownership to:

+
+
+ +
+
+
+
+

Search for user by either name or e-mail:

+
+
+ +
+ +
+
+
+ +
+ +
+
+
+ +
+ + +
+
+
+
+
+
+
+
+
+
+ + + +{% endblock %} + +{% block js %} + + + +{% endblock %} diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html index 55c3fa0b..5a6929fb 100644 --- a/wqflask/wqflask/templates/admin/create_group.html +++ b/wqflask/wqflask/templates/admin/create_group.html @@ -1,89 +1,89 @@ -{% extends "base.html" %} -{% block title %}Group Manager{% endblock %} -{% block content %} - -
-
-

Create Group

-
-
- - -
-
-
- -
-
- -
-
-
-
- -
-
- -
-
-
-
- -
-
- -
-
- -
-
-
-
- -
-
- -
-
- -
-
-
-
- -
-
- -
-
- -
-
-
-
- -
-
- -
-
-
-
-
-
-
- - - - - -{% endblock %} - -{% block js %} - - - - - -{% endblock %} +{% extends "base.html" %} +{% block title %}Group Manager{% endblock %} +{% block content %} + +
+
+

Create Group

+
+
+ + +
+
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+ +
+
+
+
+ +
+
+ +
+
+
+
+
+
+
+ + + + + +{% endblock %} + +{% block js %} + + + + + +{% endblock %} diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index 23d8205a..70d55684 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -23,7 +23,7 @@
{% else %} -

Admin Groups

+

Admin Groups

{% if admin_groups|length == 0 %}

You currently aren't the administrator of any groups.

@@ -45,8 +45,8 @@ {{ loop.index }} - {{ group.name }} - {{ group.admins|length + group.users|length }} + {{ group.name }} + {{ group.admins|length + group.members|length }} {{ group.created_timestamp }} {{ group.changed_timestamp }} {{ group.id }} @@ -58,7 +58,7 @@
-

User Groups

+

User Groups

{% if user_groups|length == 0 %}

You currently aren't a member of any groups.

@@ -80,7 +80,7 @@ {{ loop.index }} {{ group.name }} - {{ group.admins|length + group.users|length }} + {{ group.admins|length + group.members|length }} {{ group.created_timestamp }} {{ group.changed_timestamp }} @@ -103,10 +103,14 @@ - - - - -{% endblock %} +{% extends "base.html" %} +{% block title %}Resource Manager{% endblock %} +{% block css %} + + +{% endblock %} +{% block content %} + +
+ {{ flash_me() }} +
+

Resource Manager

+

{% if owner_name is not none %}Current Owner: {{ owner_name }}{% endif %} {% if admin_status == "owner" %}{% endif %}

+
+
+ +
+
+
+
+ +
+ {{ resource_info.name }} +
+
+ {% if admin_status == "owner" %} +
+ +
+ + +
+
+
+ +
+ +
+
+ {% endif %} +
+
+
+ {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} +
+
+ +
+ {% if group_masks|length > 0 %} +

Current Group Permissions

+
+ + + + + + + + + + + {% for key, value in group_masks.iteritems() %} + + + + + + + {% endfor %} + +
NameDataMetadataAdmin
{{ value.name }}{{ value.data }}{{ value.metadata }}{{ value.admin }}
+ {% else %} +

No groups are currently added to this resource.

+ {% endif %} +
+ {% endif %} +
+
+ + + + + +{% endblock %} + +{% block js %} + + + +{% endblock %} diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html index 89eb11dd..f304a172 100644 --- a/wqflask/wqflask/templates/admin/search_for_groups.html +++ b/wqflask/wqflask/templates/admin/search_for_groups.html @@ -1,64 +1,134 @@ -{% extends "base.html" %} -{% block title %}Resource Manager{% endblock %} -{% block content %} - -
-
-

Find Groups

-
-
- -
-
-
-
-

Search by:

-
-
- -
- -
-
-
- -
- -
-
-
- -
- -
-
-
- -
- -
-
-
- -
- -
-
-
-
-
-
-
- - - -{% endblock %} - -{% block js %} - - - - - -{% endblock %} +{% extends "base.html" %} +{% block title %}Resource Manager{% endblock %} +{% block css %} + + +{% endblock %} +{% block content %} + +
+
+

Find Groups

+
+
+ +
+
+
+
+

Search by:

+
+
+ +
+ +
+
+
+ +
+ +
+
+
+ +
+ +
+
+
+ +
+ +
+
+
+ +
+ + +
+
+
+
+
+
+
+
+
+
+ + + +{% endblock %} + +{% block js %} + + + + + +{% endblock %} diff --git a/wqflask/wqflask/templates/admin/select_group_to_add.html b/wqflask/wqflask/templates/admin/select_group_to_add.html deleted file mode 100644 index df70fb2f..00000000 --- a/wqflask/wqflask/templates/admin/select_group_to_add.html +++ /dev/null @@ -1,54 +0,0 @@ -{% extends "base.html" %} -{% block title %}Matched Groups{% endblock %} -{% block css %} - - - -{% endblock %} -{% block content %} - -
-

The following groups were found:

-
-
- -
- {% if group_list|length > 0 %} - - - - - - - - - - - - {% for group in group_list %} - - - - - - - {% endfor %} - -
NameCreatedLast Changed
{% if 'name' in group %}{{ group.name }}{% else %}N/A{% endif %}{% if 'created_timestamp' in group %}{{ group.created_timestamp }}{% else %}N/A{% endif %}{% if 'changed_timestamp' in group %}{{ group.changed_timestamp }}{% else %}N/A{% endif %}
- {% else %} -

No matching groups were found.

- {% endif %} -
-
-
- - - -{% endblock %} - -{% block js %} - - -{% endblock %} diff --git a/wqflask/wqflask/templates/admin/set_group_privileges.html b/wqflask/wqflask/templates/admin/set_group_privileges.html new file mode 100644 index 00000000..bc52788f --- /dev/null +++ b/wqflask/wqflask/templates/admin/set_group_privileges.html @@ -0,0 +1,102 @@ +{% extends "base.html" %} +{% block title %}Set Group Privileges{% endblock %} +{% block css %} + + + +{% endblock %} +{% block content %} + +
+

Group Privileges

+
+
+ + +
+ +
+

Data and Metadata Privileges

+ + + + + + + + + + + + + {% if 'data' in default_privileges %} + + + + {% else %} + + + + {% endif %} + + + + {% if 'metadata' in default_privileges %} + + + + {% else %} + + + + {% endif %} + + +
No-AccessViewEdit
Data:
Metadata:
+
+

Admin Privileges

+ + + + + + + + + + + + + {% if 'admin' in default_privileges %} + + + + {% else %} + + + + {% endif %} + + +
Not AdminEdit AccessEdit Admins
Admin:
+
+
+
+ + + +{% endblock %} + +{% block js %} + + +{% endblock %} diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html new file mode 100644 index 00000000..b797cd70 --- /dev/null +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -0,0 +1,238 @@ +{% extends "base.html" %} +{% block title %}View and Edit Group{% endblock %} +{% block css %} + + + +{% endblock %} +{% block content %} + +
+
+

+ {{ group_info.name }} + + +

+ {% if user_is_admin == true %} +
+ +
+ {% endif %} +
+
+ + + +
+
+
+

Admins

+
+ + + + + + + + + + + + {% for admin in admins %} + + + + + + + + {% endfor %} + +
IndexNameEmail AddressOrganization
{{ loop.index }}{% if 'full_name' in admin %}{{ admin.full_name }}{% else %}N/A{% endif %}{% if 'email_address' in admin %}{{ admin.email_address }}{% else %}N/A{% endif %}{% if 'organization' in admin %}{{ admin.organization }}{% else %}N/A{% endif %}
+ {% if user_is_admin == true %} +
+ E-mail of user to add to admins (multiple e-mails can be added separated by commas): + +
+
+ +
+ {% endif %} +
+
+
+ {% if members|length > 0 %} +

Members

+
+ + + + + + + + + + + + {% for member in members %} + + + + + + + + {% endfor %} + +
IndexNameEmail AddressOrganization
{{ loop.index }}{% if 'full_name' in member %}{{ member.full_name }}{% else %}N/A{% endif %}{% if 'email_address' in member %}{{ member.email_address }}{% else %}N/A{% endif %}{% if 'organization' in member %}{{ member.organization }}{% else %}N/A{% endif %}
+ {% if user_is_admin == true %} +
+ E-mail of user to add to members (multiple e-mails can be added separated by commas): + +
+
+ +
+ {% endif %} + {% else %} + There are currently no members in this group. + {% endif %} +
+
+
+

Resources

+
+ {% if resources|length > 0 %} + + + + + + + + + + + + {% for resource in resources %} + + + + + + + + {% endfor %} + +
IndexNameDataMetadataAdmin
{{ loop.index }}{% if 'name' in resource %}{{ resource.name }}{% else %}N/A{% endif %}{% if 'data' in resource %}{{ resource.data }}{% else %}N/A{% endif %}{% if 'metadata' in resource %}{{ resource.metadata }}{% else %}N/A{% endif %}{% if 'admin' in resource %}{{ resource.admin }}{% else %}N/A{% endif %}
+ {% else %} + There are currently no resources associated with this group. + {% endif %} +
+
+
+
+ + + +{% endblock %} + +{% block js %} + + + +{% endblock %} diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 07c1b48e..262d9ee5 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -94,6 +94,11 @@ Sign in {% endif %} + {% if g.user_session.logged_in %} +
  • + Manage Groups +
    • + {% endif %} {% endif %} +
    +

    Group Privileges

    +
    +
    + +
    + +
    +

    Data and Metadata Privileges

    + + + + + + + + + + + + + + + + + + + + + + + +
    No-AccessViewEdit
    Data:
    Metadata:
    +
    +

    Admin Privileges

    + + + + + + + + + + + + + + + + + +
    Not AdminEdit AccessEdit Admins
    Admin:
    +
    +
    +
    + + + +{% endblock %} + +{% block js %} + + +{% endblock %} diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 5c315878..5e0bae79 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -248,8 +248,8 @@ - {% if resource_id %} - + {% if admin_status[1] == "owner" or admin_status[1] == "edit-admins" or admin_status[1] == "edit-access" %} + {% endif %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index ee827ba3..dc431aa9 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -102,7 +102,7 @@ def check_access_permissions(): else: available = check_resource_availability(dataset) - if not available: + if available == "no-access": return redirect(url_for("no_access_page")) @app.teardown_appcontext -- cgit v1.2.3 From fcb3cb1105cf2a1d97c1a08fa636b118ed231ffa Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Jun 2020 16:28:15 -0500 Subject: A user's id is now set as a parameter if it doesn't already exist --- wqflask/maintenance/set_resource_defaults.py | 8 +++--- wqflask/utility/authentication_tools.py | 30 ++++++++++++---------- wqflask/utility/redis_tools.py | 4 +++ wqflask/wqflask/group_manager.py | 4 +-- wqflask/wqflask/templates/admin/group_manager.html | 16 +++++++----- 5 files changed, 36 insertions(+), 26 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 344e6a23..0c221bbf 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -27,8 +27,9 @@ sys.path.insert(0,'./') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app +from utility import hmac from utility.tools import SQL_URI -from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources +from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources, get_resource_info Redis = get_redis_conn() import MySQLdb @@ -117,7 +118,7 @@ def insert_geno_resources(default_owner_id): resource_ob = {} resource_ob['name'] = resource[1] if resource[1] == "HET3-ITPGeno": - resource_ob['owner_id'] = "73a3f093-ca13-4ae0-a179-9a446f709f6e" + resource_ob['owner_id'] = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae" else: resource_ob['owner_id'] = default_owner_id resource_ob['data'] = { "dataset" : str(resource[0]) } @@ -145,7 +146,8 @@ def main(): Redis.delete("resources") - owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com") + owner_id = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae" + insert_resources(owner_id) if __name__ == '__main__': diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 07ceacc0..dfa0e2d9 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -7,6 +7,7 @@ from base import data_set from utility import hmac from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id +Redis = get_redis_conn() from flask import Flask, g, redirect, url_for @@ -14,8 +15,12 @@ import logging logger = logging.getLogger(__name__ ) def check_resource_availability(dataset, trait_id=None): - resource_id = get_resource_id(dataset, trait_id) + #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy + if g.user_session.user_id in Redis.smembers("super_users"): + return "edit" + + resource_id = get_resource_id(dataset, trait_id) response = None if resource_id: resource_info = get_resource_info(resource_id) @@ -68,19 +73,16 @@ def check_owner(dataset=None, trait_id=None, resource_id=None): return False def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None): - if resource_id: - resource_info = get_resource_info(resource_id) - if g.user_session.user_id == resource_info['owner_id']: - return [resource_id, "owner"] - else: - return [resource_id, check_admin(resource_id)] - else: + if not resource_id: resource_id = get_resource_id(dataset, trait_id) - if resource_id: - resource_info = get_resource_info(resource_id) - if g.user_session.user_id == resource_info['owner_id']: - return [resource_id, "owner"] - else: - return [resource_id, check_admin(resource_id)] + + if g.user_session.user_id in Redis.smembers("super_users"): + return [resource_id, "owner"] + + resource_info = get_resource_info(resource_id) + if g.user_session.user_id == resource_info['owner_id']: + return [resource_id, "owner"] + else: + return [resource_id, check_admin(resource_id)] return [resource_id, "not-admin"] \ No newline at end of file diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index c6d221ff..9d09a66b 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -30,6 +30,7 @@ def is_redis_available(): def get_user_id(column_name, column_value): user_list = Redis.hgetall("users") + key_list = [] for key in user_list: user_ob = json.loads(user_list[key]) if column_name in user_ob and user_ob[column_name] == column_value: @@ -62,6 +63,9 @@ def get_users_like_unique_column(column_name, column_value): if column_name != "user_id": for key in user_list: user_ob = json.loads(user_list[key]) + if "user_id" not in user_ob: + set_user_attribute(key, "user_id", key) + user_ob["user_id"] = key if column_name in user_ob: if column_value in user_ob[column_name]: matched_users.append(user_ob) diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 9afc016b..24848ed8 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -19,8 +19,8 @@ def manage_groups(): if "add_new_group" in params: return redirect(url_for('add_group')) else: - admin_groups, user_groups = get_user_groups(g.user_session.user_id) - return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups) + admin_groups, member_groups = get_user_groups(g.user_session.user_id) + return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups) @app.route("/groups/view", methods=('GET', 'POST')) def view_group(): diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index 70d55684..c8ed6851 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -10,18 +10,20 @@

    Manage Groups

    + {% if admin_groups|length != 0 or member_groups|length != 0 %}
    + {% endif %}
    - {% if admin_groups|length == 0 and user_groups|length == 0 %} + {% if admin_groups|length == 0 and member_groups|length == 0 %}

    You currently aren't a member or admin of any groups.


    - + {% else %}

    Admin Groups

    @@ -60,10 +62,10 @@

    User Groups

    - {% if user_groups|length == 0 %} + {% if member_groups|length == 0 %}

    You currently aren't a member of any groups.

    {% else %} - +
    @@ -75,7 +77,7 @@ - {% for group in user_groups %} + {% for group in member_groups %} @@ -107,8 +109,8 @@ 'sDom': 'tr' }); {% endif %} - {% if user_groups|length != 0 %} - $('#user_groups').dataTable({ + {% if member_groups|length != 0 %} + $('#member_groups').dataTable({ 'sDom': 'tr' }); {% endif %} -- cgit v1.2.3 From 645c07b98aae9508e8a0aeedd8eaca815d5daf54 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 24 Jun 2020 17:13:45 -0500 Subject: Temporary partial fix to issue of resources without info; need to add something that automatically inserts resources with default privileges --- wqflask/base/trait.py | 12 ++++-------- wqflask/utility/authentication_tools.py | 11 +++++++---- wqflask/utility/redis_tools.py | 5 ++++- wqflask/wqflask/correlation/show_corr_results.py | 7 +++---- wqflask/wqflask/templates/correlation_page.html | 4 ++++ 5 files changed, 22 insertions(+), 17 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 0e26ca2c..7fc016f3 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -386,13 +386,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name) - response = requests.get(the_url).content - if response.strip() == "no-access": - trait.view = False - return trait - else: - trait_info = json.loads(response) - try: response = requests.get(the_url).content if response.strip() == "no-access": @@ -402,7 +395,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait_info = json.loads(response) except: resource_info = get_resource_info(resource_id) - default_permissions = resource_info['default_mask']['data'] + if resource_info: + default_permissions = resource_info['default_mask']['data'] + else: + default_permissions = webqtlConfig.DEFAULT_PRIVILEGES if 'view' not in default_permissions: trait.view = False return trait diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 06b2854a..f9028f32 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -32,6 +32,8 @@ def check_resource_availability(dataset, trait_id=None): if resource_id: resource_info = get_resource_info(resource_id) + if not resource_info: + return webqtlConfig.DEFAULT_PRIVILEGES else: return response #ZS: Need to substitute in something that creates the resource in Redis later @@ -85,9 +87,10 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None): return "owner" resource_info = get_resource_info(resource_id) - if g.user_session.user_id == resource_info['owner_id']: - return "owner" - else: - return check_admin(resource_id) + if resource_info: + if g.user_session.user_id == resource_info['owner_id']: + return "owner" + else: + return check_admin(resource_id) return "not-admin" \ No newline at end of file diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 9d09a66b..8a5f95ee 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -280,7 +280,10 @@ def get_resource_id(dataset, trait_id=None): def get_resource_info(resource_id): resource_info = Redis.hget("resources", resource_id) - return json.loads(resource_info) + if resource_info: + return json.loads(resource_info) + else: + return None def add_resource(resource_info): if 'trait' in resource_info['data']: diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 7eab7184..bc2912f2 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -200,8 +200,6 @@ class CorrelationResults(object): for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) - if not trait_object: - continue if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert trait chromosome to an int for the location range option @@ -237,9 +235,8 @@ class CorrelationResults(object): trait_object.tissue_pvalue = tissue_corr_data[trait][2] elif self.corr_type == "lit": trait_object.lit_corr = lit_corr_data[trait][1] - self.correlation_results.append(trait_object) - self.target_dataset.get_trait_info(self.correlation_results, self.target_dataset.group.species) + self.correlation_results.append(trait_object) if self.corr_type != "lit" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet": self.do_lit_correlation_for_trait_list() @@ -498,6 +495,8 @@ def do_bicor(this_trait_vals, target_trait_vals): def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api = False): results_list = [] for i, trait in enumerate(corr_results): + if trait.view == False: + continue results_dict = {} if not for_api: results_dict['checkbox'] = "" diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index f429948d..3d750bea 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -169,7 +169,11 @@ {% endif %} + {% if trait.authors %} + {% else %} + + {% endif %}
    {{ loop.index }}N/A{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}N/A {{ trait.pubmed_text }} -- cgit v1.2.3 From 0a0d733af4b6c61c381a1c4ec9fa162182a057e9 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 6 Jul 2020 14:47:04 -0500 Subject: Fixed some of the logic with how traits are authenticated to avoid situation where a trait is authenticated twice --- wqflask/base/trait.py | 30 ++++++++-------------------- wqflask/maintenance/set_resource_defaults.py | 6 +++--- wqflask/utility/redis_tools.py | 5 +++-- 3 files changed, 14 insertions(+), 27 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7fc016f3..4c3e790c 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -49,7 +49,6 @@ def create_trait(**kw): if "view" in permissions['data']: the_trait = GeneralTrait(**kw) if the_trait.dataset.type != "Temp": - the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info')) return the_trait else: @@ -144,6 +143,7 @@ class GeneralTrait(object): formatted = self.post_publication_description else: formatted = "Not available" + return formatted @property @@ -388,27 +388,14 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): try: response = requests.get(the_url).content - if response.strip() == "no-access": - trait.view = False - return trait - else: - trait_info = json.loads(response) - except: - resource_info = get_resource_info(resource_id) - if resource_info: - default_permissions = resource_info['default_mask']['data'] - else: - default_permissions = webqtlConfig.DEFAULT_PRIVILEGES - if 'view' not in default_permissions: - trait.view = False - return trait - + trait_info = json.loads(response) + except: #ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait if dataset.type == 'Publish': query = """ SELECT - PublishXRef.Id, Publication.PubMed_ID, + PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID, Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, - Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, + Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, Publication.Authors, Publication.Title, Publication.Abstract, Publication.Journal, Publication.Volume, Publication.Pages, @@ -472,11 +459,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait_info: trait.haveinfo = True - for i, field in enumerate(dataset.display_fields): - holder = trait_info[i] - #if isinstance(trait_info[i], basestring): - # holder = holder.encode('latin1') + holder = trait_info[i] + # if isinstance(trait_info[i], basestring): + # holder = unicode(holder.strip(codecs.BOM_UTF8), 'utf-8', "ignore") setattr(trait, field, holder) if dataset.type == 'Publish': diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index ddb3b17b..54fd8e7e 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -77,7 +77,7 @@ def insert_probeset_resources(default_owner_id): "admin": "not-admin"} resource_ob['group_masks'] = {} - add_resource(resource_ob) + add_resource(resource_ob, update=False) def insert_publish_resources(default_owner_id): current_resources = Redis.hgetall("resources") @@ -108,7 +108,7 @@ def insert_publish_resources(default_owner_id): resource_ob['group_masks'] = {} - add_resource(resource_ob) + add_resource(resource_ob, update=False) else: continue @@ -139,7 +139,7 @@ def insert_geno_resources(default_owner_id): "admin": "not-admin"} resource_ob['group_masks'] = {} - add_resource(resource_ob) + add_resource(resource_ob, update=False) def insert_resources(default_owner_id): current_resources = get_resources() diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 8a5f95ee..6c912a23 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -285,13 +285,14 @@ def get_resource_info(resource_id): else: return None -def add_resource(resource_info): +def add_resource(resource_info, update=True): if 'trait' in resource_info['data']: resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait']))) else: resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']))) - Redis.hset("resources", resource_id, json.dumps(resource_info)) + if not Redis.hexists("resources", resource_id): + Redis.hset("resources", resource_id, json.dumps(resource_info)) return resource_info -- cgit v1.2.3 From 81c35e99a7ff808bf2fcf1f5e19631adf07d42e8 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 22 Jul 2020 17:46:37 -0500 Subject: It should add new resources to Redis automatically now --- wqflask/utility/authentication_tools.py | 61 +++++++++++++++++++++++++-------- wqflask/utility/redis_tools.py | 5 +-- 2 files changed, 47 insertions(+), 19 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index f9028f32..ed7462d1 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -6,7 +6,7 @@ import requests from base import data_set, webqtlConfig from utility import hmac -from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id +from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource Redis = get_redis_conn() from flask import Flask, g, redirect, url_for @@ -16,13 +16,7 @@ logger = logging.getLogger(__name__ ) def check_resource_availability(dataset, trait_id=None): - #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy - if g.user_session.user_id in Redis.smembers("super_users"): - return webqtlConfig.SUPER_PRIVILEGES - - response = None - - #At least for now assume temporary entered traits are accessible#At least for now assume temporary entered traits are accessible + #At least for now assume temporary entered traits are accessible if type(dataset) == str: return webqtlConfig.DEFAULT_PRIVILEGES if dataset.type == "Temp": @@ -33,9 +27,13 @@ def check_resource_availability(dataset, trait_id=None): if resource_id: resource_info = get_resource_info(resource_id) if not resource_info: - return webqtlConfig.DEFAULT_PRIVILEGES - else: - return response #ZS: Need to substitute in something that creates the resource in Redis later + resource_info = add_new_resource(dataset, trait_id) + + #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy + if g.user_session.user_id in Redis.smembers("super_users"): + return webqtlConfig.SUPER_PRIVILEGES + + response = None the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) try: @@ -43,10 +41,43 @@ def check_resource_availability(dataset, trait_id=None): except: response = resource_info['default_mask'] - if response: - return response - else: #ZS: No idea how this would happen, but just in case - return False + return response + +def add_new_resource(dataset, trait_id=None): + resource_ob = { + 'owner_id' : webqtlConfig.DEFAULT_OWNER_ID, + 'default_mask': webqtlConfig.DEFAULT_PRIVILEGES, + 'group_masks' : {} + } + + if dataset.type == "Publish": + resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id) + resource_ob['data'] = { + 'dataset': dataset.id, + 'trait' : trait_id + } + resource_ob['type'] = 'dataset-publish' + elif dataset.type == "Geno": + resource_ob['name'] = dataset.name + resource_ob['data'] = { + 'dataset': dataset.id + } + resource_ob['type'] = 'dataset-geno' + else: + resource_ob['name'] = dataset.name + resource_ob['data'] = { + 'dataset': dataset.id + } + resource_ob['type'] = 'dataset-probeset' + + resource_info = add_resource(resource_ob, update=False) + + return resource_info + +def get_group_code(dataset): + results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone() + + return results[0] def check_admin(resource_id=None): the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 6c912a23..1377a564 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -264,17 +264,14 @@ def get_resources(): return resource_list def get_resource_id(dataset, trait_id=None): + resource_id = False if dataset.type == "Publish": if trait_id: resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id)) - else: - return False elif dataset.type == "ProbeSet": resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id)) elif dataset.type == "Geno": resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id)) - else: - return False return resource_id -- cgit v1.2.3 From 303e4b71c2172da5be19c84d4be5a062329ac013 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 19:12:33 +0300 Subject: Remove "from __future__ import new_feature" statements See: --- test/requests/link_checker.py | 1 - test/requests/main_web_functionality.py | 22 ++++++++++++---------- test/requests/mapping_tests.py | 1 - test/requests/navigation_tests.py | 1 - test/requests/test-website.py | 2 +- webtests/browser_run.py | 4 +--- webtests/correlation_matrix_test.py | 2 -- webtests/correlation_test.py | 2 -- webtests/marker_regression_test.py | 2 -- webtests/show_trait_js_test.py | 2 -- webtests/test_runner.py | 4 +--- wqflask/base/data_set.py | 1 - wqflask/base/mrna_assay_tissue_data.py | 4 +--- wqflask/base/species.py | 4 +--- wqflask/base/trait.py | 2 -- wqflask/maintenance/convert_dryad_to_bimbam.py | 3 +-- wqflask/maintenance/convert_geno_to_bimbam.py | 3 +-- wqflask/maintenance/gen_select_dataset.py | 10 +--------- .../maintenance/generate_kinship_from_bimbam.py | 3 +-- .../maintenance/generate_probesetfreeze_file.py | 2 -- wqflask/maintenance/geno_to_json.py | 3 +-- wqflask/maintenance/get_group_samplelists.py | 2 -- wqflask/maintenance/print_benchmark.py | 4 +--- wqflask/maintenance/quantile_normalize.py | 7 +------ wqflask/maintenance/set_resource_defaults.py | 4 +--- wqflask/utility/Plot.py | 2 -- wqflask/utility/after.py | 4 +--- wqflask/utility/authentication_tools.py | 2 -- wqflask/utility/benchmark.py | 2 -- wqflask/utility/chunks.py | 2 -- wqflask/utility/db_tools.py | 2 -- wqflask/utility/gen_geno_ob.py | 4 +--- wqflask/utility/genofile_parser.py | 1 - wqflask/utility/helper_functions.py | 2 -- wqflask/utility/hmac.py | 4 +--- wqflask/utility/redis_tools.py | 4 +--- wqflask/utility/temp_data.py | 1 - wqflask/wqflask/__init__.py | 2 -- wqflask/wqflask/api/correlation.py | 4 +--- wqflask/wqflask/api/gen_menu.py | 2 -- wqflask/wqflask/api/mapping.py | 2 -- wqflask/wqflask/api/router.py | 4 +--- wqflask/wqflask/collect.py | 3 --- .../comparison_bar_chart/comparison_bar_chart.py | 1 - wqflask/wqflask/correlation/corr_scatter_plot.py | 4 +--- .../wqflask/correlation/correlation_functions.py | 4 +--- wqflask/wqflask/correlation/show_corr_results.py | 2 -- .../wqflask/correlation_matrix/show_corr_matrix.py | 2 -- wqflask/wqflask/do_search.py | 2 -- wqflask/wqflask/docs.py | 4 +--- wqflask/wqflask/export_traits.py | 4 +--- wqflask/wqflask/external_tools/send_to_bnw.py | 4 +--- .../wqflask/external_tools/send_to_geneweaver.py | 4 +--- .../wqflask/external_tools/send_to_webgestalt.py | 4 +--- wqflask/wqflask/group_manager.py | 5 +---- wqflask/wqflask/gsearch.py | 2 -- wqflask/wqflask/heatmap/heatmap.py | 2 -- wqflask/wqflask/interval_analyst/GeneUtil.py | 2 -- wqflask/wqflask/marker_regression/run_mapping.py | 4 +--- wqflask/wqflask/model.py | 4 +--- wqflask/wqflask/network_graph/network_graph.py | 2 -- wqflask/wqflask/news.py | 1 - wqflask/wqflask/parser.py | 2 -- wqflask/wqflask/resource_manager.py | 4 +--- wqflask/wqflask/search_results.py | 2 -- wqflask/wqflask/send_mail.py | 2 -- wqflask/wqflask/show_trait/SampleList.py | 2 -- wqflask/wqflask/show_trait/export_trait_data.py | 4 +--- wqflask/wqflask/show_trait/show_trait.py | 2 -- wqflask/wqflask/snp_browser/snp_browser.py | 2 -- wqflask/wqflask/submit_bnw.py | 4 +--- wqflask/wqflask/update_search_results.py | 2 -- wqflask/wqflask/user_login.py | 4 +--- wqflask/wqflask/user_manager.py | 2 -- wqflask/wqflask/user_session.py | 2 -- wqflask/wqflask/views.py | 2 -- 76 files changed, 45 insertions(+), 190 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py index 5e16a5cd..949a33c8 100644 --- a/test/requests/link_checker.py +++ b/test/requests/link_checker.py @@ -1,4 +1,3 @@ -from __future__ import print_function import re import requests from lxml.html import parse diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py index d070dab9..78030307 100644 --- a/test/requests/main_web_functionality.py +++ b/test/requests/main_web_functionality.py @@ -1,9 +1,7 @@ -from __future__ import print_function -import re import requests from lxml.html import parse from link_checker import check_page -from requests.exceptions import ConnectionError + def check_home(url): doc = parse(url).getroot() @@ -11,20 +9,23 @@ def check_home(url): assert(search_button[0].value == "Search") print("OK") + def check_search_page(host): data = dict( - species="mouse" - , group="BXD" - , type="Hippocampus mRNA" - , dataset="HC_M2_0606_P" - , search_terms_or="" - , search_terms_and="MEAN=(15 16) LRS=(23 46)") + species="mouse", + group="BXD", + type="Hippocampus mRNA", + dataset="HC_M2_0606_P", + search_terms_or="", + search_terms_and="MEAN=(15 16) LRS=(23 46)") result = requests.get(host+"/search", params=data) found = result.text.find("records are shown below") assert(found >= 0) assert(result.status_code == 200) print("OK") - check_traits_page(host, "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P") + check_traits_page(host, ("/show_trait?trait_id=1435395_" + "s_at&dataset=HC_M2_0606_P")) + def check_traits_page(host, traits_url): doc = parse(host+traits_url).getroot() @@ -33,6 +34,7 @@ def check_traits_page(host, traits_url): print("OK") check_page(host, host+traits_url) + def check_main_web_functionality(args_obj, parser): print("") print("Checking main web functionality...") diff --git a/test/requests/mapping_tests.py b/test/requests/mapping_tests.py index 5748a2a3..19b22c21 100644 --- a/test/requests/mapping_tests.py +++ b/test/requests/mapping_tests.py @@ -1,4 +1,3 @@ -from __future__ import print_function import re import copy import json diff --git a/test/requests/navigation_tests.py b/test/requests/navigation_tests.py index eda27324..6b91c1fd 100644 --- a/test/requests/navigation_tests.py +++ b/test/requests/navigation_tests.py @@ -1,4 +1,3 @@ -from __future__ import print_function import re import requests from lxml.html import parse diff --git a/test/requests/test-website.py b/test/requests/test-website.py index f90d1843..8bfb47c2 100755 --- a/test/requests/test-website.py +++ b/test/requests/test-website.py @@ -3,7 +3,7 @@ # env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003 # # Mostly to pick up the Guix GN2_PROFILE and python modules -from __future__ import print_function + import argparse from link_checker import check_links from link_checker import check_packaged_js_files diff --git a/webtests/browser_run.py b/webtests/browser_run.py index 2ec299c5..7ee540b7 100644 --- a/webtests/browser_run.py +++ b/webtests/browser_run.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - __all__ = ('sleep', 'testmod', 'test') from doctest import testmod @@ -71,4 +69,4 @@ class Test(object): -test = Test() \ No newline at end of file +test = Test() diff --git a/webtests/correlation_matrix_test.py b/webtests/correlation_matrix_test.py index 8529c265..97114890 100644 --- a/webtests/correlation_matrix_test.py +++ b/webtests/correlation_matrix_test.py @@ -65,8 +65,6 @@ text: 0.608\n71 """ -from __future__ import absolute_import, division, print_function - from browser_run import * testmod() diff --git a/webtests/correlation_test.py b/webtests/correlation_test.py index aad3a69f..311bb847 100644 --- a/webtests/correlation_test.py +++ b/webtests/correlation_test.py @@ -44,8 +44,6 @@ text: 1.000 """ -from __future__ import absolute_import, division, print_function - from browser_run import * testmod() diff --git a/webtests/marker_regression_test.py b/webtests/marker_regression_test.py index c4f76f53..9b4a4acb 100644 --- a/webtests/marker_regression_test.py +++ b/webtests/marker_regression_test.py @@ -48,8 +48,6 @@ text: 11.511 """ -from __future__ import absolute_import, division, print_function - from browser_run import * testmod() diff --git a/webtests/show_trait_js_test.py b/webtests/show_trait_js_test.py index 0fd2c16c..34ffd3b7 100644 --- a/webtests/show_trait_js_test.py +++ b/webtests/show_trait_js_test.py @@ -35,8 +35,6 @@ style: display: none; """ -from __future__ import absolute_import, division, print_function - from browser_run import * testmod() diff --git a/webtests/test_runner.py b/webtests/test_runner.py index ef6d0d69..b5b590a6 100644 --- a/webtests/test_runner.py +++ b/webtests/test_runner.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import unittest import doctest import glob @@ -25,4 +23,4 @@ def main(): runner.run(suite) if __name__ == '__main__': - main() \ No newline at end of file + main() diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 39a8a2ed..8ac7a279 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -18,7 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division from db.call import fetchall, fetchone, fetch1 from utility.logger import getLogger from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 6fec5dcd..33ce12bd 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import collections from flask import g @@ -92,4 +90,4 @@ class MrnaAssayTissueData(object): else: symbol_values_dict[result.Symbol.lower()].append(result.value) - return symbol_values_dict \ No newline at end of file + return symbol_values_dict diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 6d99af65..e3f1bc4a 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import collections from flask import Flask, g @@ -59,4 +57,4 @@ class Chromosomes(object): results = g.db.execute(query).fetchall() for item in results: - self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) \ No newline at end of file + self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 09c41fa7..b20efd2a 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import os import string import resource diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py index e833b395..12ce35e9 100644 --- a/wqflask/maintenance/convert_dryad_to_bimbam.py +++ b/wqflask/maintenance/convert_dryad_to_bimbam.py @@ -6,7 +6,6 @@ Convert data dryad files to a BIMBAM _geno and _snps file """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") @@ -67,4 +66,4 @@ def convert_dryad_to_bimbam(filename): if __name__=="__main__": input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt" - convert_dryad_to_bimbam(input_filename) \ No newline at end of file + convert_dryad_to_bimbam(input_filename) diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 528b98cf..d49742f2 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -9,7 +9,6 @@ code """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -187,4 +186,4 @@ if __name__=="__main__": #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json") #convertob.convert() ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) - #ConvertGenoFiles(Geno_Directory) \ No newline at end of file + #ConvertGenoFiles(Geno_Directory) diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index fd65a52a..544e2fd1 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -30,14 +30,6 @@ It needs to be run manually when database has been changed. Run it as # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import print_function, division - -#from flask import config -# -#cdict = {} -#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS') -#print("cdict is:", cdict) - import sys # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead @@ -319,4 +311,4 @@ def _test_it(): if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main() \ No newline at end of file + main() diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index b53f5dda..60257b28 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -8,7 +8,6 @@ and uses GEMMA to generate their corresponding kinship/relatedness matrix file """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -58,4 +57,4 @@ if __name__=="__main__": Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/""" GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory) - #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD \ No newline at end of file + #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index 4231cc7c..b1e41e9a 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -1,7 +1,5 @@ #!/usr/bin/python -from __future__ import absolute_import, print_function, division - import sys # sys.path.insert(0, "..") - why? diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index 9579812a..7e7fd241 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -9,7 +9,6 @@ code """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -194,4 +193,4 @@ if __name__=="__main__": ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) #ConvertGenoFiles(Geno_Directory) - #process_csv(Input_File, Output_File) \ No newline at end of file + #process_csv(Input_File, Output_File) diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py index fb22898a..3f9d0278 100644 --- a/wqflask/maintenance/get_group_samplelists.py +++ b/wqflask/maintenance/get_group_samplelists.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import os import glob import gzip diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py index ae327cf3..b24ce4f1 100644 --- a/wqflask/maintenance/print_benchmark.py +++ b/wqflask/maintenance/print_benchmark.py @@ -1,7 +1,5 @@ #!/usr/bin/python -from __future__ import absolute_import, print_function, division - import time from pprint import pformat as pf @@ -40,4 +38,4 @@ def new_main(): print(pf(TheCounter.Counters)) if __name__ == '__main__': - new_main() \ No newline at end of file + new_main() diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 4d6e03bf..701b2b50 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -1,10 +1,5 @@ -from __future__ import absolute_import, print_function, division - import sys sys.path.insert(0, './') - - - import MySQLdb import urllib.parse @@ -126,4 +121,4 @@ if __name__ == '__main__': } ) - print(response) \ No newline at end of file + print(response) diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index abd5416c..4177c124 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -16,8 +16,6 @@ To run: """ -from __future__ import print_function, division - import sys import json @@ -163,4 +161,4 @@ def main(): if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main() \ No newline at end of file + main() diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 48a5c7ba..61f408d2 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -24,8 +24,6 @@ # # Last updated by GeneNetwork Core Team 2010/10/20 -from __future__ import print_function - from PIL import ImageColor from PIL import ImageDraw from PIL import ImageFont diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py index b628a0a4..06091ecb 100644 --- a/wqflask/utility/after.py +++ b/wqflask/utility/after.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - """ See: http://flask.pocoo.org/docs/patterns/deferredcallbacks/#deferred-callbacks @@ -13,4 +11,4 @@ def after_this_request(f): if not hasattr(g, 'after_request_callbacks'): g.after_request_callbacks = [] g.after_request_callbacks.append(f) - return f \ No newline at end of file + return f diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index bc03eb55..0e499180 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import json import requests diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 221e5151..ea5a0ab6 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import collections import inspect import time diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py index d91b9bf4..9a7db102 100644 --- a/wqflask/utility/chunks.py +++ b/wqflask/utility/chunks.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import math import time diff --git a/wqflask/utility/db_tools.py b/wqflask/utility/db_tools.py index 4034f39c..92bde505 100644 --- a/wqflask/utility/db_tools.py +++ b/wqflask/utility/db_tools.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from MySQLdb import escape_string as escape def create_in_clause(items): diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index ae42f834..81085ffe 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -178,4 +176,4 @@ class Locus(object): if allele in list(geno_table.keys()): self.genotype.append(geno_table[allele]) else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown - self.genotype.append("U") \ No newline at end of file + self.genotype.append("U") diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index af306731..0b736176 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -1,7 +1,6 @@ # CTL analysis for GN2 # Author / Maintainer: Danny Arends -from __future__ import print_function, division, absolute_import import sys import os import glob diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 107c9ec6..7eb7f013 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from base import data_set from base.trait import create_trait from base.species import TheSpecies diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py index b08be97e..73e28790 100644 --- a/wqflask/utility/hmac.py +++ b/wqflask/utility/hmac.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import hmac import hashlib @@ -37,4 +35,4 @@ def url_for_hmac(endpoint, **values): return url + combiner + "hm=" + hm app.jinja_env.globals.update(url_for_hmac=url_for_hmac, - data_hmac=data_hmac) \ No newline at end of file + data_hmac=data_hmac) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 1377a564..13ac5cfe 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import uuid import simplejson as json import datetime @@ -306,4 +304,4 @@ def change_resource_owner(resource_id, new_owner_id): the_resource['owner_id'] = new_owner_id Redis.delete("resource") - Redis.hset("resources", resource_id, json.dumps(the_resource)) \ No newline at end of file + Redis.hset("resources", resource_id, json.dumps(the_resource)) diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 2f2726c6..4144ae00 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division, absolute_import from redis import Redis import simplejson as json diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index d729aef5..e73f833f 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import sys import jinja2 diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index eb05645e..7da13121 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import collections import scipy @@ -234,4 +232,4 @@ def init_corr_params(start_vars): 'return_count' : return_count } - return corr_params \ No newline at end of file + return corr_params diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index 41966f78..1dcafe1f 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division - from flask import g diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 92c27c9b..d59a69df 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import string from base import data_set diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 5f9b81b8..acf7ce4a 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -1,7 +1,5 @@ # GN2 API -from __future__ import absolute_import, division, print_function - import os, io, csv, json, datetime, requests, yaml import zlib from zipfile import ZipFile, ZIP_DEFLATED @@ -966,4 +964,4 @@ def get_group_id(group_name): if group_id: return group_id[0] else: - return None \ No newline at end of file + return None diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 06c00930..15383603 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -1,6 +1,3 @@ -from __future__ import print_function, division, absolute_import - - import os import hashlib import datetime diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index 16832621..92de6073 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -18,7 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division from pprint import pformat as pf from base.trait import create_trait diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 57a8d85f..929cd2c9 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import math from flask import g @@ -130,4 +128,4 @@ def get_intercept_coords(slope, intercept, x_range, y_range): intercept_coords.append([x1, y1]) intercept_coords.append([x2, y2]) - return intercept_coords \ No newline at end of file + return intercept_coords diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py index abaa212f..b883e361 100644 --- a/wqflask/wqflask/correlation/correlation_functions.py +++ b/wqflask/wqflask/correlation/correlation_functions.py @@ -24,8 +24,6 @@ # # Last updated by NL 2011/03/23 -from __future__ import absolute_import, print_function, division - import math import rpy2.robjects import string @@ -114,4 +112,4 @@ def get_trait_symbol_and_tissue_values(symbol_list=None): tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list) if len(tissue_data.gene_symbols): - return tissue_data.get_symbol_values_pairs() \ No newline at end of file + return tissue_data.get_symbol_values_pairs() diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 5ced30b6..e5b87c6a 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import collections import json import scipy diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index bd5aca1f..7b4bda31 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import datetime import math import numpy as np diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index cc9c1860..de8e1e78 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division - import string import requests import json diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 78407e22..8628b81d 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import codecs from flask import g @@ -42,4 +40,4 @@ def update_text(start_vars): sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(content, start_vars['entry_type']) g.db.execute(sql) except: - pass \ No newline at end of file + pass diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 2f4e9aac..3a886537 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division - import csv import xlsxwriter import io @@ -140,4 +138,4 @@ def sort_traits_by_group(trait_list=[]): traits_by_group[trait.dataset.group.name].append(trait) - return traits_by_group \ No newline at end of file + return traits_by_group diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py index 68efd10d..efa17f05 100644 --- a/wqflask/wqflask/external_tools/send_to_bnw.py +++ b/wqflask/wqflask/external_tools/send_to_bnw.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - from base.trait import GeneralTrait from utility import helper_functions, corr_result_helpers @@ -69,4 +67,4 @@ class SendToBNW(object): if has_none: continue self.form_value += ",".join(str(cell) for cell in row) - self.form_value += ";" \ No newline at end of file + self.form_value += ";" diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 9844bab4..93164233 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import string from flask import Flask, g @@ -109,4 +107,4 @@ def test_chip(trait_list): chip_name = '%s_NA' % result[0] return chip_name - return chip_name \ No newline at end of file + return chip_name diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index 30ca024f..b255ba95 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import string from flask import Flask, g @@ -123,4 +121,4 @@ def gen_gene_id_list(trait_list): trait_name_list.append(trait.name) retrieve_trait_info(trait, trait.dataset) gene_id_list.append(str(trait.geneid)) - return trait_name_list, gene_id_list \ No newline at end of file + return trait_name_list, gene_id_list diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 24848ed8..e6079c3e 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -1,6 +1,3 @@ - -from __future__ import print_function, division, absolute_import - from flask import (Flask, g, render_template, url_for, request, make_response, redirect, flash) @@ -142,4 +139,4 @@ def send_group_invites(group_id, user_email_list = [], user_type="members"): else: send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group") -#@app.route() \ No newline at end of file +#@app.route() diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index c65a1415..6d797a29 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import json from flask import Flask, g diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 1f1cdb90..cca5a4fc 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import string import os import random diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index a39e5d0f..17c8ccbf 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import string from flask import Flask, g diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 67512bc6..7ae84b16 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from base.trait import GeneralTrait from base import data_set #import create_dataset @@ -711,4 +709,4 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): list_to_numbers = [d[x] for x in perm_strata_strings] perm_strata = list_to_numbers - return perm_strata \ No newline at end of file + return perm_strata diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index a135761c..772f74e4 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import uuid import datetime @@ -168,4 +166,4 @@ def display_collapsible(number): def user_uuid(): """Unique cookie for a user""" - user_uuid = request.cookies.get('user_uuid') \ No newline at end of file + user_uuid = request.cookies.get('user_uuid') diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index 2a4c4a93..70e5dd58 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import scipy import simplejson as json from pprint import pformat as pf diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py index 20319756..0675ec4b 100644 --- a/wqflask/wqflask/news.py +++ b/wqflask/wqflask/news.py @@ -1,4 +1,3 @@ -from __future__ import absolute_import, print_function, division from flask import g class News(object): diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index 1ca5ecff..472dd30e 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -17,8 +17,6 @@ be acceptable.] """ -from __future__ import print_function, division - import re from pprint import pformat as pf diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 6b3e00fb..e883d5da 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import json from flask import (Flask, g, render_template, url_for, request, make_response, @@ -131,4 +129,4 @@ def get_group_names(group_masks): this_mask['name'] = group_name group_masks_with_names[group_id] = this_mask - return group_masks_with_names \ No newline at end of file + return group_masks_with_names diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index c07a7670..f6c677a8 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import re import uuid from math import * diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py index bf5d0dd8..86e8a558 100644 --- a/wqflask/wqflask/send_mail.py +++ b/wqflask/wqflask/send_mail.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import datetime import time diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index f17e825e..6fcf7cec 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from flask import Flask, g from base import webqtlCaseData diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 68c3ad7d..2d76b935 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division - import simplejson as json from pprint import pformat as pf @@ -71,4 +69,4 @@ def cmp_samples(a, b): else: return 1 else: - return -1 \ No newline at end of file + return -1 diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 6a74cada..e93b0289 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import string import os import datetime diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index b3d26caf..0db7e1fe 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from flask import Flask, g, url_for import string diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py index 59e60dfd..a0e84c8c 100644 --- a/wqflask/wqflask/submit_bnw.py +++ b/wqflask/wqflask/submit_bnw.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from base.trait import GeneralTrait from base import data_set from utility import helper_functions @@ -8,4 +6,4 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) def get_bnw_input(start_vars): - logger.debug("BNW VARS:", start_vars) \ No newline at end of file + logger.debug("BNW VARS:", start_vars) diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py index 68bea9d6..672f95b1 100644 --- a/wqflask/wqflask/update_search_results.py +++ b/wqflask/wqflask/update_search_results.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import json from flask import Flask, g diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index 04672b45..10cb7319 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import os import hashlib import datetime @@ -470,4 +468,4 @@ def register(): @app.errorhandler(401) def unauthorized(error): - return redirect(url_for('login')) \ No newline at end of file + return redirect(url_for('login')) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 3c41e2b8..24191a15 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import os import hashlib import datetime diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index 71c31c57..c1f38396 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import datetime import time import uuid diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 83d5202e..b0489e64 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -2,8 +2,6 @@ # # Main routing table for GN2 -from __future__ import absolute_import, division, print_function - import traceback # for error page import os # for error gifs import random # for random error gif -- cgit v1.2.3 From e754baaf51150156c159f59c8ba1fda0ba0a7269 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 31 Aug 2020 11:25:10 -0500 Subject: Fixed issue that was causing updating resource default privileges to not work * wqflask/utility/redis_tools.py - There was an issue where resources wouldn't be updated if they already existed. This is because the code didn't yet account for the "update" tag (that is meant to give the option of preventing updating resources when running the script to enter all resources into Redis). I changed the logic to add a resource if "update" is True or the resource doesn't already exist (so it won't if update is False and the resource exists). --- wqflask/utility/redis_tools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 1377a564..81ba04ea 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -288,7 +288,7 @@ def add_resource(resource_info, update=True): else: resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']))) - if not Redis.hexists("resources", resource_id): + if update or not Redis.hexists("resources", resource_id): Redis.hset("resources", resource_id, json.dumps(resource_info)) return resource_info -- cgit v1.2.3 From 75fe1adb2cfaf542bd22f33e8985938ca988661d Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 18 Sep 2020 02:45:26 +0300 Subject: Apply pep8 formatting --- wqflask/utility/redis_tools.py | 120 ++++++++++++++++++++++++++++------------- 1 file changed, 84 insertions(+), 36 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 81ba04ea..ef02268e 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -4,23 +4,21 @@ import uuid import simplejson as json import datetime -import redis # used for collections - -import logging - -from flask import (render_template, flash) - -from utility import hmac +import redis # used for collections +from utility.hmac import hmac_creation from utility.logger import getLogger logger = getLogger(__name__) + def get_redis_conn(): Redis = redis.StrictRedis(port=6379) return Redis + Redis = get_redis_conn() + def is_redis_available(): try: Redis.ping() @@ -28,6 +26,7 @@ def is_redis_available(): return False return True + def get_user_id(column_name, column_value): user_list = Redis.hgetall("users") key_list = [] @@ -38,6 +37,7 @@ def get_user_id(column_name, column_value): return None + def get_user_by_unique_column(column_name, column_value): item_details = None @@ -52,9 +52,11 @@ def get_user_by_unique_column(column_name, column_value): return item_details + def get_users_like_unique_column(column_name, column_value): - """ - Like previous function, but this only checks if the input is a subset of a field and can return multiple results + """Like previous function, but this only checks if the input is a + subset of a field and can return multiple results + """ matched_users = [] @@ -74,7 +76,6 @@ def get_users_like_unique_column(column_name, column_value): return matched_users -# def search_users_by_unique_column(column_name, column_value): def set_user_attribute(user_id, column_name, column_value): user_info = json.loads(Redis.hget("users", user_id)) @@ -82,6 +83,7 @@ def set_user_attribute(user_id, column_name, column_value): Redis.hset("users", user_id, json.dumps(user_info)) + def get_user_collections(user_id): collections = None collections = Redis.hget("collections", user_id) @@ -91,22 +93,27 @@ def get_user_collections(user_id): else: return [] + def save_user(user, user_id): Redis.hset("users", user_id, json.dumps(user)) + def save_collections(user_id, collections_ob): Redis.hset("collections", user_id, collections_ob) + def save_verification_code(user_email, code): Redis.hset("verification_codes", code, user_email) + def check_verification_code(code): email_address = None user_details = None email_address = Redis.hget("verification_codes", code) if email_address: - user_details = get_user_by_unique_column('email_address', email_address) + user_details = get_user_by_unique_column( + 'email_address', email_address) if user_details: return user_details else: @@ -114,10 +121,12 @@ def check_verification_code(code): else: return None + def get_user_groups(user_id): - #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups - admin_group_ids = [] #ZS: Group IDs where user is an admin - user_group_ids = [] #ZS: Group IDs where user is a regular user + # ZS: Get the groups where a user is an admin or a member and + # return lists corresponding to those two sets of groups + admin_group_ids = [] # ZS: Group IDs where user is an admin + user_group_ids = [] # ZS: Group IDs where user is a regular user groups_list = Redis.hgetall("groups") for key in groups_list: try: @@ -142,6 +151,7 @@ def get_user_groups(user_id): return admin_groups, user_groups + def get_group_info(group_id): group_json = Redis.hget("groups", group_id) group_info = None @@ -150,6 +160,7 @@ def get_group_info(group_id): return group_info + def get_group_by_unique_column(column_name, column_value): """ Get group by column; not sure if there's a faster way to do this """ @@ -158,7 +169,8 @@ def get_group_by_unique_column(column_name, column_value): all_group_list = Redis.hgetall("groups") for key in all_group_list: group_info = json.loads(all_group_list[key]) - if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list + # ZS: Since these fields are lists, search in the list + if column_name == "admins" or column_name == "members": if column_value in group_info[column_name]: matched_groups.append(group_info) else: @@ -167,9 +179,11 @@ def get_group_by_unique_column(column_name, column_value): return matched_groups + def get_groups_like_unique_column(column_name, column_value): - """ - Like previous function, but this only checks if the input is a subset of a field and can return multiple results + """Like previous function, but this only checks if the input is a + subset of a field and can return multiple results + """ matched_groups = [] @@ -178,7 +192,8 @@ def get_groups_like_unique_column(column_name, column_value): if column_name != "group_id": for key in group_list: group_info = json.loads(group_list[key]) - if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list + # ZS: Since these fields are lists, search in the list + if column_name == "admins" or column_name == "members": if column_value in group_info[column_name]: matched_groups.append(group_info) else: @@ -190,13 +205,15 @@ def get_groups_like_unique_column(column_name, column_value): return matched_groups -def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"): + +def create_group(admin_user_ids, member_user_ids=[], + group_name="Default Group Name"): group_id = str(uuid.uuid4()) new_group = { - "id" : group_id, + "id": group_id, "admins": admin_user_ids, - "members" : member_user_ids, - "name" : group_name, + "members": member_user_ids, + "name": group_name, "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') } @@ -205,8 +222,9 @@ def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Gro return new_group + def delete_group(user_id, group_id): - #ZS: If user is an admin of a group, remove it from the groups hash + # ZS: If user is an admin of a group, remove it from the groups hash group_info = get_group_info(group_id) if user_id in group_info["admins"]: Redis.hdel("groups", group_id) @@ -214,9 +232,15 @@ def delete_group(user_id, group_id): else: None -def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS "admins" is just to indicate whether the users should be added to the groups admins or regular users set + +# ZS "admins" is just to indicate whether the users should be added to +# the groups admins or regular users set +def add_users_to_group(user_id, group_id, user_emails=[], admins=False): group_info = get_group_info(group_id) - if user_id in group_info["admins"]: #ZS: Just to make sure that the user is an admin for the group, even though they shouldn't be able to reach this point unless they are + # ZS: Just to make sure that the user is an admin for the group, + # even though they shouldn't be able to reach this point unless + # they are + if user_id in group_info["admins"]: if admins: group_users = set(group_info["admins"]) else: @@ -231,25 +255,36 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS else: group_info["members"] = list(group_users) - group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') Redis.hset("groups", group_id, json.dumps(group_info)) return group_info else: return None -def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins + +# ZS: User type is because I assume admins can remove other admins +def remove_users_from_group(user_id, + users_to_remove_ids, + group_id, + user_type="members"): group_info = get_group_info(group_id) if user_id in group_info["admins"]: users_to_remove_set = set(users_to_remove_ids) - if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less + # ZS: Make sure an admin can't remove themselves from a group, + # since I imagine we don't want groups to be able to become + # admin-less + if user_type == "admins" and user_id in users_to_remove_set: users_to_remove_set.remove(user_id) group_users = set(group_info[user_type]) group_users -= users_to_remove_set group_info[user_type] = list(group_users) - group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') Redis.hset("groups", group_id, json.dumps(group_info)) + def change_group_name(user_id, group_id, new_name): group_info = get_group_info(group_id) if user_id in group_info["admins"]: @@ -259,22 +294,28 @@ def change_group_name(user_id, group_id, new_name): else: return None + def get_resources(): resource_list = Redis.hgetall("resources") return resource_list + def get_resource_id(dataset, trait_id=None): resource_id = False if dataset.type == "Publish": if trait_id: - resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id)) + resource_id = hmac_creation("{}:{}:{}".format( + 'dataset-publish', dataset.id, trait_id)) elif dataset.type == "ProbeSet": - resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id)) + resource_id = hmac_creation( + "{}:{}".format('dataset-probeset', dataset.id)) elif dataset.type == "Geno": - resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id)) + resource_id = hmac_creation( + "{}:{}".format('dataset-geno', dataset.id)) return resource_id + def get_resource_info(resource_id): resource_info = Redis.hget("resources", resource_id) if resource_info: @@ -282,17 +323,23 @@ def get_resource_info(resource_id): else: return None + def add_resource(resource_info, update=True): if 'trait' in resource_info['data']: - resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait']))) + resource_id = hmac_creation('{}:{}:{}'.format( + str(resource_info['type']), str( + resource_info['data']['dataset']), + str(resource_info['data']['trait']))) else: - resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']))) + resource_id = hmac_creation('{}:{}'.format( + str(resource_info['type']), str(resource_info['data']['dataset']))) if update or not Redis.hexists("resources", resource_id): Redis.hset("resources", resource_id, json.dumps(resource_info)) return resource_info + def add_access_mask(resource_id, group_id, access_mask): the_resource = get_resource_info(resource_id) the_resource['group_masks'][group_id] = access_mask @@ -301,9 +348,10 @@ def add_access_mask(resource_id, group_id, access_mask): return the_resource + def change_resource_owner(resource_id, new_owner_id): - the_resource= get_resource_info(resource_id) + the_resource = get_resource_info(resource_id) the_resource['owner_id'] = new_owner_id Redis.delete("resource") - Redis.hset("resources", resource_id, json.dumps(the_resource)) \ No newline at end of file + Redis.hset("resources", resource_id, json.dumps(the_resource)) -- cgit v1.2.3 From 04e981ba202a6bd9d969c05855a33040928d15d0 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 2 Nov 2020 13:21:40 -0600 Subject: Created function for encoding the column value as bytes when fetching from the JSON-formatted string pulled from Redis (since this was needed after the Python 3 switchover) * wqflask/utility/redis_tools.py - Created function load_json_from_redis that encodes the key (column_value) when fetching a value from the JSON pulled from Redis --- wqflask/utility/redis_tools.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index d855a7fa..236cc755 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -25,6 +25,10 @@ def is_redis_available(): return True +def load_json_from_redis(item_list, column_value): + return json.loads(item_list[str.encode(column_value)]) + + def get_user_id(column_name, column_value): user_list = Redis.hgetall("users") key_list = [] @@ -46,7 +50,7 @@ def get_user_by_unique_column(column_name, column_value): if column_name in user_ob and user_ob[column_name] == column_value: item_details = user_ob else: - item_details = json.loads(user_list[column_value]) + item_details = load_json_from_redis(user_list, column_value) return item_details @@ -70,7 +74,7 @@ def get_users_like_unique_column(column_name, column_value): if column_value in user_ob[column_name]: matched_users.append(user_ob) else: - matched_users.append(json.loads(user_list[column_value])) + matched_users.append(load_json_from_redis(user_list, column_value)) return matched_users @@ -199,7 +203,7 @@ def get_groups_like_unique_column(column_name, column_value): if column_value in group_info[column_name]: matched_groups.append(group_info) else: - matched_groups.append(json.loads(group_list[column_value])) + matched_groups.append(load_json_from_redis(group_list, column_value)) return matched_groups -- cgit v1.2.3 From 935d618da8986ad85292836f0762e435deb37108 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Feb 2021 19:24:57 +0000 Subject: Fixed error caused by user IDs being encoded as bytes --- wqflask/utility/redis_tools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 236cc755..f72d9110 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -26,7 +26,7 @@ def is_redis_available(): def load_json_from_redis(item_list, column_value): - return json.loads(item_list[str.encode(column_value)]) + return json.loads(item_list[str.encode(column_value.decode("utf-8"))]) def get_user_id(column_name, column_value): -- cgit v1.2.3 From cafdd7284f3c2f87e1dbb288e181f1e5aeeccc06 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 18 Feb 2021 18:37:16 +0000 Subject: Remove the deocde since it was throwing an error --- wqflask/utility/redis_tools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index f72d9110..236cc755 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -26,7 +26,7 @@ def is_redis_available(): def load_json_from_redis(item_list, column_value): - return json.loads(item_list[str.encode(column_value.decode("utf-8"))]) + return json.loads(item_list[str.encode(column_value)]) def get_user_id(column_name, column_value): -- cgit v1.2.3 From 02b14ccc55978742cd115f3c80bf8ef41ac77ae7 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 16 Mar 2021 17:23:45 +0000 Subject: Fixed encoding to make get_user_groups work properly, since the user IDs for groups in Redis are stored as strings --- wqflask/utility/redis_tools.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 236cc755..d05de923 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -133,8 +133,8 @@ def get_user_groups(user_id): for key in groups_list: try: group_ob = json.loads(groups_list[key]) - group_admins = set(group_ob['admins']) - group_members = set(group_ob['members']) + group_admins = set([this_admin.encode('utf-8') if this_admin else None for this_admin in group_ob['admins']]) + group_members = set([this_member.encode('utf-8') if this_member else None for this_member in group_ob['members']]) if user_id in group_admins: admin_group_ids.append(group_ob['id']) elif user_id in group_members: -- cgit v1.2.3 From 696585dda43ec238940b2e1cc239028e31684dc3 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 16 Mar 2021 17:25:14 +0000 Subject: Fixed encoding in load_json_from_redis to account for the first that column values are sometimes stored as bytes and sometimes as strings --- wqflask/utility/redis_tools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index d05de923..8052035f 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -26,7 +26,7 @@ def is_redis_available(): def load_json_from_redis(item_list, column_value): - return json.loads(item_list[str.encode(column_value)]) + return json.loads(item_list[column_value]) def get_user_id(column_name, column_value): -- cgit v1.2.3 From 03b6bcee689c1910bd850c6109cc37adc509cf5a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 30 Apr 2021 12:45:59 +0300 Subject: autopep8: Fix E501 --- wqflask/base/data_set.py | 6 +- wqflask/base/mrna_assay_tissue_data.py | 3 +- wqflask/base/species.py | 3 +- wqflask/base/webqtlCaseData.py | 6 +- wqflask/db/webqtlDatabaseFunction.py | 6 +- wqflask/maintenance/convert_geno_to_bimbam.py | 21 +- wqflask/maintenance/gen_select_dataset.py | 6 +- .../maintenance/generate_kinship_from_bimbam.py | 13 +- wqflask/maintenance/geno_to_json.py | 3 +- wqflask/maintenance/quantile_normalize.py | 3 +- .../test_display_mapping_results.py | 3 +- .../marker_regression/test_gemma_mapping.py | 15 +- .../marker_regression/test_qtlreaper_mapping.py | 6 +- .../wqflask/marker_regression/test_rqtl_mapping.py | 3 +- .../wqflask/marker_regression/test_run_mapping.py | 3 +- wqflask/tests/unit/wqflask/test_server_side.py | 9 +- wqflask/tests/wqflask/show_trait/testSampleList.py | 3 +- .../tests/wqflask/show_trait/test_show_trait.py | 3 +- wqflask/utility/Plot.py | 9 +- wqflask/utility/benchmark.py | 9 +- wqflask/utility/corestats.py | 3 +- wqflask/utility/elasticsearch_tools.py | 6 +- wqflask/utility/gen_geno_ob.py | 12 +- wqflask/utility/genofile_parser.py | 3 +- wqflask/utility/logger.py | 3 +- wqflask/utility/redis_tools.py | 9 +- wqflask/utility/startup_config.py | 6 +- wqflask/utility/svg.py | 60 ++- wqflask/utility/tools.py | 12 +- wqflask/wqflask/api/correlation.py | 54 +- wqflask/wqflask/api/mapping.py | 15 +- wqflask/wqflask/api/router.py | 48 +- wqflask/wqflask/collect.py | 15 +- .../comparison_bar_chart/comparison_bar_chart.py | 6 +- wqflask/wqflask/correlation/corr_scatter_plot.py | 33 +- wqflask/wqflask/correlation/show_corr_results.py | 75 ++- .../wqflask/correlation_matrix/show_corr_matrix.py | 64 ++- wqflask/wqflask/ctl/ctl_analysis.py | 72 ++- wqflask/wqflask/do_search.py | 69 ++- wqflask/wqflask/docs.py | 6 +- wqflask/wqflask/export_traits.py | 24 +- wqflask/wqflask/external_tools/send_to_bnw.py | 6 +- .../wqflask/external_tools/send_to_geneweaver.py | 3 +- .../wqflask/external_tools/send_to_webgestalt.py | 3 +- wqflask/wqflask/group_manager.py | 24 +- wqflask/wqflask/gsearch.py | 41 +- wqflask/wqflask/heatmap/heatmap.py | 19 +- wqflask/wqflask/interval_analyst/GeneUtil.py | 9 +- .../marker_regression/display_mapping_results.py | 548 ++++++++++++++------- wqflask/wqflask/marker_regression/gemma_mapping.py | 3 +- wqflask/wqflask/marker_regression/plink_mapping.py | 9 +- .../wqflask/marker_regression/qtlreaper_mapping.py | 27 +- wqflask/wqflask/marker_regression/rqtl_mapping.py | 103 ++-- wqflask/wqflask/marker_regression/run_mapping.py | 126 +++-- wqflask/wqflask/model.py | 30 +- wqflask/wqflask/resource_manager.py | 9 +- wqflask/wqflask/search_results.py | 33 +- wqflask/wqflask/show_trait/SampleList.py | 24 +- wqflask/wqflask/show_trait/export_trait_data.py | 21 +- wqflask/wqflask/snp_browser/snp_browser.py | 150 ++++-- wqflask/wqflask/update_search_results.py | 9 +- wqflask/wqflask/user_login.py | 87 ++-- wqflask/wqflask/user_manager.py | 96 ++-- wqflask/wqflask/user_session.py | 28 +- 64 files changed, 1431 insertions(+), 705 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index c14808d6..8ec0aaad 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -168,7 +168,8 @@ class DatasetType: results = g.db.execute(sql_query_mapping[t] % group_name).fetchone() if results: self.datasets[name] = dataset_name_mapping[t] - self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) + self.redis_instance.set( + "dataset_structure", json.dumps(self.datasets)) return True return None @@ -239,7 +240,8 @@ class Markers: for line in bimbam_fh: marker = {} marker['name'] = line.split(delimiter)[0].rstrip() - marker['Mb'] = float(line.split(delimiter)[1].rstrip()) / 1000000 + marker['Mb'] = float(line.split(delimiter)[ + 1].rstrip()) / 1000000 marker['chr'] = line.split(delimiter)[2].rstrip() markers.append(marker) diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index cbc05738..9bb29664 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -88,6 +88,7 @@ class MrnaAssayTissueData: if result.Symbol.lower() not in symbol_values_dict: symbol_values_dict[result.Symbol.lower()] = [result.value] else: - symbol_values_dict[result.Symbol.lower()].append(result.value) + symbol_values_dict[result.Symbol.lower()].append( + result.value) return symbol_values_dict diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 44f133b5..e3c29916 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -55,4 +55,5 @@ class Chromosomes: results = g.db.execute(query).fetchall() for item in results: - self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) + self.chromosomes[item.OrderId] = IndChromosome( + item.Name, item.Length) diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 2d07ab9d..25b6cb8a 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -34,12 +34,14 @@ class webqtlCaseData: def __init__(self, name, value=None, variance=None, num_cases=None, name2=None): self.name = name - self.name2 = name2 # Other name (for traits like BXD65a) + # Other name (for traits like BXD65a) + self.name2 = name2 self.value = value # Trait Value self.variance = variance # Trait Variance self.num_cases = num_cases # Number of individuals/cases self.extra_attributes = None - self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word) + # Set a sane default (can't be just "id" cause that's a reserved word) + self.this_id = None self.outlier = None # Not set to True/False until later def __repr__(self): diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index 50ac06fd..29112949 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -36,13 +36,15 @@ def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" """ - result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/" + group + ".json", lambda r: (r["species"],))[0] + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % ( + group), "/cross/" + group + ".json", lambda r: (r["species"],))[0] logger.debug("retrieve_species result:", result) return result def retrieve_species_id(group): - result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0] + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % ( + group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0] logger.debug("retrieve_species_id result:", result) return result diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 5b2369c9..a1712500 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -83,7 +83,8 @@ class ConvertGenoFile: genotypes = row_items[2:] for item_count, genotype in enumerate(genotypes): if genotype.upper().strip() in self.configurations: - this_marker.genotypes.append(self.configurations[genotype.upper().strip()]) + this_marker.genotypes.append( + self.configurations[genotype.upper().strip()]) else: this_marker.genotypes.append("NA") @@ -106,9 +107,11 @@ class ConvertGenoFile: with open(self.output_files[2], "w") as snp_fh: for marker in self.markers: if self.mb_exists: - snp_fh.write(marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n") + snp_fh.write( + marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n") else: - snp_fh.write(marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n") + snp_fh.write( + marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n") def get_sample_list(self, row_contents): self.sample_list = [] @@ -160,10 +163,14 @@ class ConvertGenoFile: group_name = ".".join(input_file.split('.')[:-1]) if group_name == "HSNIH-Palmer": continue - geno_output_file = os.path.join(new_directory, group_name + "_geno.txt") - pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt") - snp_output_file = os.path.join(new_directory, group_name + "_snps.txt") - output_files = [geno_output_file, pheno_output_file, snp_output_file] + geno_output_file = os.path.join( + new_directory, group_name + "_geno.txt") + pheno_output_file = os.path.join( + new_directory, group_name + "_pheno.txt") + snp_output_file = os.path.join( + new_directory, group_name + "_snps.txt") + output_files = [geno_output_file, + pheno_output_file, snp_output_file] print("%s -> %s" % ( os.path.join(old_directory, input_file), geno_output_file)) convertob = ConvertGenoFile(input_file, output_files) diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 583a06e1..484336a6 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -120,14 +120,16 @@ def get_types(groups): else: if not phenotypes_exist(group_name) and not genotypes_exist(group_name): types[species].pop(group_name, None) - groups[species] = tuple(group for group in groups[species] if group[0] != group_name) + groups[species] = tuple( + group for group in groups[species] if group[0] != group_name) else: # ZS: This whole else statement might be unnecessary, need to check types_list = build_types(species, group_name) if len(types_list) > 0: types[species][group_name] = types_list else: types[species].pop(group_name, None) - groups[species] = tuple(group for group in groups[species] if group[0] != group_name) + groups[species] = tuple( + group for group in groups[species] if group[0] != group_name) return types diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index 7cc60c9e..bed634fa 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -21,7 +21,9 @@ class GenerateKinshipMatrices: self.pheno_file = pheno_file def generate_kinship(self): - gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + " -p " + self.pheno_file + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name + gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \ + " -p " + self.pheno_file + \ + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name print("command:", gemma_command) os.system(gemma_command) @@ -34,9 +36,12 @@ class GenerateKinshipMatrices: group_name = ".".join(input_file.split('.')[:-1]) if group_name == "HSNIH-Palmer": continue - geno_input_file = os.path.join(bimbam_dir, group_name + "_geno.txt") - pheno_input_file = os.path.join(bimbam_dir, group_name + "_pheno.txt") - convertob = GenerateKinshipMatrices(group_name, geno_input_file, pheno_input_file) + geno_input_file = os.path.join( + bimbam_dir, group_name + "_geno.txt") + pheno_input_file = os.path.join( + bimbam_dir, group_name + "_pheno.txt") + convertob = GenerateKinshipMatrices( + group_name, geno_input_file, pheno_input_file) try: convertob.generate_kinship() except EmptyConfigurations as why: diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index ad3f2b72..7bdf2b53 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -100,7 +100,8 @@ class ConvertGenoFile: genotypes = row_items[2:] for item_count, genotype in enumerate(genotypes): if genotype.upper() in self.configurations: - this_marker.genotypes.append(self.configurations[genotype.upper()]) + this_marker.genotypes.append( + self.configurations[genotype.upper()]) else: this_marker.genotypes.append("NA") diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 1896bc52..ac7689f5 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -34,7 +34,8 @@ def create_dataframe(input_file): with open(input_file) as f: ncols = len(f.readline().split("\t")) - input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) + input_array = np.loadtxt(open( + input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) return pd.DataFrame(input_array) # This function taken from https://github.com/ShawnLYU/Quantile_Normalize diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py index 219a6a29..f4869c45 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py @@ -39,7 +39,8 @@ class TestHtmlGenWrapper(unittest.TestCase): cgi="/testing/", enctype='multipart/form-data', name="formName", - submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name') + submit=HtmlGenWrapper.create_input_tag( + type_='hidden', name='Default_Name') ) test_image = HtmlGenWrapper.create_image_tag( src="test.png", diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index f194c6c9..5cbaf0e0 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -70,7 +70,8 @@ class TestGemmaMapping(unittest.TestCase): ], vals=[], covariates="", use_loco=True) self.assertEqual(mock_os.system.call_count, 2) mock_gen_pheno_txt.assert_called_once() - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR", True) + mock_parse_loco.assert_called_once_with( + dataset, "GP1_GWA_RRRRRR", True) mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) self.assertEqual(mock_flat_files.call_count, 4) @@ -102,7 +103,8 @@ class TestGemmaMapping(unittest.TestCase): create_trait_side_effect = [] for i in range(4): - create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'})) + create_dataset_side_effect.append( + AttributeSetter({"name": f'name_{i}'})) create_trait_side_effect.append( AttributeSetter({"data": [f'data_{i}']})) @@ -160,9 +162,12 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") expected_results = [ - {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727}, - {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812}, - {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432}, + {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, + 'additive': 23.3, 'lod_score': 0.07058107428570727}, + {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, + 'additive': 24.0, 'lod_score': 0.3010299956639812}, + {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, + 'additive': 11.6, 'lod_score': 0.1549019599857432}, {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}] self.assertEqual(expected_results, results) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index 5cc8fd0f..c762982b 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -13,10 +13,12 @@ class TestQtlReaperMapping(unittest.TestCase): samples = ["S1", "S2", "S3", "S4","S5"] trait_filename = "trait_file" with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples, vals=vals, trait_filename=trait_filename) + gen_pheno_txt_file(samples=samples, vals=vals, + trait_filename=trait_filename) mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") filehandler = mock_open() - write_calls = [mock.call('Trait\t'), mock.call('S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] + write_calls = [mock.call('Trait\t'), mock.call( + 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] filehandler.write.assert_has_calls(write_calls) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index 6267ce9a..6996c275 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -20,7 +20,8 @@ class TestRqtlMapping(unittest.TestCase): def test_get_trait_data(self, mock_logger, mock_db): """test for getting trait data_type return True""" query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value = ["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + mock_db.db.execute.return_value.fetchone.return_value = [ + """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] results = get_trait_data_type("traid_id") mock_db.db.execute.assert_called_with(query_value) self.assertEqual(results, "fer434f") diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py index a29d8cfb..78cd3be9 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -187,7 +187,8 @@ class TestRunMapping(unittest.TestCase): mock.call('Time/Date: 09/01/19 / 10:12:12\n'), mock.call('Population: Human GP1_\n'), mock.call( 'Data Set: dataser_1\n'), - mock.call('N Samples: 100\n'), mock.call('Transform - Quantile Normalized\n'), + mock.call('N Samples: 100\n'), mock.call( + 'Transform - Quantile Normalized\n'), mock.call('Gene Symbol: IGFI\n'), mock.call( 'Location: X1 @ 123313 Mb\n'), mock.call('Cofactors (dataset - trait):\n'), diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py index 4f91d8ca..69977146 100644 --- a/wqflask/tests/unit/wqflask/test_server_side.py +++ b/wqflask/tests/unit/wqflask/test_server_side.py @@ -22,10 +22,13 @@ class TestServerSideTableTests(unittest.TestCase): {'first': 'c', 'second': 1, 'third': 'ss'}, ] headers = ['first', 'second', 'third'] - request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'} + request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', + 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'} - test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page() + test_page = ServerSideTable( + rows_count, table_rows, headers, request_args).get_page() self.assertEqual(test_page['sEcho'], '1') self.assertEqual(test_page['iTotalRecords'], 'nan') self.assertEqual(test_page['iTotalDisplayRecords'], '3') - self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}]) + self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, { + 'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}]) diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py index 441a88a7..305586ce 100644 --- a/wqflask/tests/wqflask/show_trait/testSampleList.py +++ b/wqflask/tests/wqflask/show_trait/testSampleList.py @@ -13,4 +13,5 @@ class TestSampleList(unittest.TestCase): sorted_list_a = natural_sort(characters_list) sorted_list_b = natural_sort(names_list) self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"]) - self.assertEqual(sorted_list_b, ["Dataset", "Sample", "publish", "temp1"]) + self.assertEqual( + sorted_list_b, ["Dataset", "Sample", "publish", "temp1"]) diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py index 24c3923e..63df2ba5 100644 --- a/wqflask/tests/wqflask/show_trait/test_show_trait.py +++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py @@ -72,7 +72,8 @@ class TestTraits(unittest.TestCase): mock_get.return_value = get_return_obj results = get_ncbi_summary(trait) mock_exists.assert_called_once() - mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json") + mock_get.assert_called_once_with( + f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json") self.assertEqual(results, "this is a summary of the geneid") diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index d35b2089..4f5691c1 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -178,7 +178,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab # draw drawing region im_drawer.rectangle( - xy=((xLeftOffset, yTopOffset), (xLeftOffset + plotWidth, yTopOffset + plotHeight)) + xy=((xLeftOffset, yTopOffset), + (xLeftOffset + plotWidth, yTopOffset + plotHeight)) ) # draw scale @@ -199,11 +200,13 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab y = yLow for i in range(int(stepY) + 1): yc = yTopOffset + plotHeight - (y - yLow) * yScale - im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor) + im_drawer.line( + xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor) strY = "%d" % y im_drawer.text( text=strY, - xy=(xLeftOffset - im_drawer.textsize(strY, font=scaleFont)[0] - 6, yc + 5), + xy=(xLeftOffset - im_drawer.textsize(strY, + font=scaleFont)[0] - 6, yc + 5), font=scaleFont) y += (yTop - yLow) / stepY diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 48ab1dc0..6ece2f21 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -19,7 +19,8 @@ class Bench: if self.name: logger.debug("Starting benchmark: %s" % (self.name)) else: - logger.debug("Starting benchmark at: %s [%i]" % (inspect.stack()[1][3], inspect.stack()[1][2])) + logger.debug("Starting benchmark at: %s [%i]" % ( + inspect.stack()[1][3], inspect.stack()[1][2])) self.start_time = time.time() def __exit__(self, type, value, traceback): @@ -33,11 +34,13 @@ class Bench: logger.info(" %s took: %f seconds" % (name, (time_taken))) if self.name: - Bench.entries[self.name] = Bench.entries.get(self.name, 0) + time_taken + Bench.entries[self.name] = Bench.entries.get( + self.name, 0) + time_taken @classmethod def report(cls): - total_time = sum((time_taken for time_taken in list(cls.entries.values()))) + total_time = sum( + (time_taken for time_taken in list(cls.entries.values()))) print("\nTiming report\n") for name, time_taken in list(cls.entries.items()): percent = int(round((time_taken / total_time) * 100)) diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py index 523280a1..da0a21db 100644 --- a/wqflask/utility/corestats.py +++ b/wqflask/utility/corestats.py @@ -65,7 +65,8 @@ class Stats: if len(self.sequence) < 1: value = None elif (percentile >= 100): - sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n' % percentile) + sys.stderr.write( + 'ERROR: percentile must be < 100. you supplied: %s\n' % percentile) value = None else: element_idx = int(len(self.sequence) * (percentile / 100.0)) diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 9415cef0..55907dd5 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -49,7 +49,8 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT def test_elasticsearch_connection(): - es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) + es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + \ + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) if not es.ping(): logger.warning("Elasticsearch is DOWN") @@ -88,7 +89,8 @@ def setup_users_index(es_connection): "type": "keyword"}}} es_connection.indices.create(index='users', ignore=400) - es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local") + es_connection.indices.put_mapping( + body=index_settings, index="users", doc_type="local") def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"): diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 24604e58..e619b7b6 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -38,13 +38,15 @@ class genotype: def read_rdata_output(self, qtl_results): # ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results - self.chromosomes = [] # ZS: Overwriting since the .geno file's contents are just placeholders + # ZS: Overwriting since the .geno file's contents are just placeholders + self.chromosomes = [] this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for marker in qtl_results: locus = Locus(self) - if (str(marker['chr']) != this_chr) and this_chr != "X": # ZS: This is really awkward but works as a temporary fix + # ZS: This is really awkward but works as a temporary fix + if (str(marker['chr']) != this_chr) and this_chr != "X": if this_chr != "": self.chromosomes.append(chr_ob) this_chr = str(marker['chr']) @@ -156,9 +158,11 @@ class Locus: try: self.cM = float(marker_row[geno_ob.cm_column]) except: - self.cM = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 + self.cM = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 try: - self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None + self.Mb = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None except: self.Mb = self.cM diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index 94a08c17..09100bd9 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -92,7 +92,8 @@ class ConvertGenoFile: genotypes = row_items[2:] for item_count, genotype in enumerate(genotypes): if genotype.upper().strip() in self.configurations: - this_marker.genotypes.append(self.configurations[genotype.upper().strip()]) + this_marker.genotypes.append( + self.configurations[genotype.upper().strip()]) else: print("WARNING:", genotype.upper()) this_marker.genotypes.append("NA") diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index 47079818..d706e32a 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -151,5 +151,6 @@ def getLogger(name, level=None): else: logger.setLevel(LOG_LEVEL) - logger.info("Log level of " + name + " set to " + logging.getLevelName(logger.getEffectiveLevel())) + logger.info("Log level of " + name + " set to " + \ + logging.getLevelName(logger.getEffectiveLevel())) return gnlogger diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 8052035f..96a4be12 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -133,8 +133,10 @@ def get_user_groups(user_id): for key in groups_list: try: group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin.encode('utf-8') if this_admin else None for this_admin in group_ob['admins']]) - group_members = set([this_member.encode('utf-8') if this_member else None for this_member in group_ob['members']]) + group_admins = set([this_admin.encode( + 'utf-8') if this_admin else None for this_admin in group_ob['admins']]) + group_members = set([this_member.encode( + 'utf-8') if this_member else None for this_member in group_ob['members']]) if user_id in group_admins: admin_group_ids.append(group_ob['id']) elif user_id in group_members: @@ -203,7 +205,8 @@ def get_groups_like_unique_column(column_name, column_value): if column_value in group_info[column_name]: matched_groups.append(group_info) else: - matched_groups.append(load_json_from_redis(group_list, column_value)) + matched_groups.append( + load_json_from_redis(group_list, column_value)) return matched_groups diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index 92f944bc..05f8a2b0 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -28,7 +28,8 @@ def app_config(): port = get_setting_int("SERVER_PORT") if get_setting_bool("USE_GN_SERVER"): - print(("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]")) + print( + ("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]")) import requests page = requests.get(get_setting("GN_SERVER_URL")) if page.status_code != 200: @@ -37,4 +38,5 @@ def app_config(): # import utility.elasticsearch_tools as es # es.test_elasticsearch_connection() - print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL")))) + print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % + (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL")))) diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index f5ef81e1..8d2e13ab 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -239,19 +239,23 @@ class pathdata: def smbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy absolut""" - self.path.append('S' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) + self.path.append('S' + str(x2) + ',' + str(y2) + \ + ' ' + str(x) + ',' + str(y)) def relsmbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy relative""" - self.path.append('s' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) + self.path.append('s' + str(x2) + ',' + str(y2) + \ + ' ' + str(x) + ',' + str(y)) def qbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy absolut""" - self.path.append('Q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y)) + self.path.append('Q' + str(x1) + ',' + str(y1) + \ + ' ' + str(x) + ',' + str(y)) def relqbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy relative""" - self.path.append('q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y)) + self.path.append('q' + str(x1) + ',' + str(y1) + \ + ' ' + str(x) + ',' + str(y)) def smqbezier(self, x, y): """smooth quadratic bezier to xy absolut""" @@ -447,7 +451,8 @@ class rect(SVGelement): if width == None or height == None: raise ValueError('both height and width are required') - SVGelement.__init__(self, 'rect', {'width': width, 'height': height}, **args) + SVGelement.__init__( + self, 'rect', {'width': width, 'height': height}, **args) if x != None: self.attributes['x'] = x if y != None: @@ -545,7 +550,8 @@ class polyline(SVGelement): """ def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args): - SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args) + SVGelement.__init__(self, 'polyline', { + 'points': _xypointlist(points)}, **args) if fill != None: self.attributes['fill'] = fill if stroke_width != None: @@ -561,7 +567,8 @@ class polygon(SVGelement): """ def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args): - SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args) + SVGelement.__init__( + self, 'polygon', {'points': _xypointlist(points)}, **args) if fill != None: self.attributes['fill'] = fill if stroke_width != None: @@ -745,7 +752,8 @@ class image(SVGelement): def __init__(self, url, x=None, y=None, width=None,height=None,**args): if width == None or height == None: raise ValueError('both height and width are required') - SVGelement.__init__(self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args) + SVGelement.__init__( + self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args) if x != None: self.attributes['x'] = x if y != None: @@ -886,7 +894,8 @@ class script(SVGelement): """ def __init__(self, type, cdata=None, **args): - SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args) + SVGelement.__init__( + self, 'script', {'type': type}, cdata=cdata, **args) class animate(SVGelement): @@ -896,7 +905,8 @@ class animate(SVGelement): """ def __init__(self, attribute, fr=None, to=None, dur=None,**args): - SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args) + SVGelement.__init__( + self, 'animate', {'attributeName': attribute}, **args) if fr != None: self.attributes['from'] = fr if to != None: @@ -926,7 +936,8 @@ class animateTransform(SVGelement): """ def __init__(self, type=None, fr=None, to=None, dur=None,**args): - SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args) + SVGelement.__init__(self, 'animateTransform', { + 'attributeName': 'transform'}, **args) # As far as I know the attributeName is always transform if type != None: self.attributes['type'] = type @@ -945,7 +956,8 @@ class animateColor(SVGelement): """ def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args): - SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args) + SVGelement.__init__(self, 'animateColor', { + 'attributeName': attribute}, **args) if type != None: self.attributes['type'] = type if fr != None: @@ -1020,11 +1032,13 @@ class drawing: import io xml = io.StringIO() xml.write("\n") - xml.write("\n" % (item, self.entity[item])) + xml.write("\n" % + (item, self.entity[item])) xml.write("]") xml.write(">\n") self.svg.toXml(0, xml) @@ -1042,7 +1056,8 @@ class drawing: else: if filename[-4:] == 'svgz': import gzip - f = gzip.GzipFile(filename=filename, mode="wb", compresslevel=9) + f = gzip.GzipFile(filename=filename, + mode="wb", compresslevel=9) f.write(xml.getvalue()) f.close() else: @@ -1057,7 +1072,8 @@ class drawing: writes a svg drawing to the screen or to a file compresses if filename ends with svgz or if compress is true """ - doctype = implementation.createDocumentType('svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') + doctype = implementation.createDocumentType( + 'svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') global root # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but @@ -1076,8 +1092,10 @@ class drawing: if element.text: textnode = root.createTextNode(element.text) e.appendChild(textnode) - for attribute in list(element.attributes.keys()): # in element.attributes is supported from python 2.2 - e.setAttribute(attribute, str(element.attributes[attribute])) + # in element.attributes is supported from python 2.2 + for attribute in list(element.attributes.keys()): + e.setAttribute(attribute, str( + element.attributes[attribute])) if element.elements: for el in element.elements: e = appender(el, e) @@ -1105,7 +1123,8 @@ class drawing: import io xml = io.StringIO() PrettyPrint(root, xml) - f = gzip.GzipFile(filename=filename, mode='wb', compresslevel=9) + f = gzip.GzipFile(filename=filename, + mode='wb', compresslevel=9) f.write(xml.getvalue()) f.close() else: @@ -1119,7 +1138,8 @@ class drawing: try: import xml.parsers.xmlproc.xmlval except: - raise exceptions.ImportError('PyXml is required for validating SVG') + raise exceptions.ImportError( + 'PyXml is required for validating SVG') svg = self.toXml() xv = xml.parsers.xmlproc.xmlval.XMLValidator() try: diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 4fe4db08..263c3948 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -64,7 +64,8 @@ def get_setting(command_id, guess=None): command = value(guess) if command is None or command == "": # print command - raise Exception(command_id + ' setting unknown or faulty (update default_settings.py?).') + raise Exception( + command_id + ' setting unknown or faulty (update default_settings.py?).') # print("Set "+command_id+"="+str(command)) return command @@ -113,7 +114,8 @@ def js_path(module=None): try_guix = get_setting("JS_GUIX_PATH") + "/" + module if valid_path(try_guix): return try_guix - raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)" + raise "No JS path found for " + module + \ + " (if not in Guix check JS_GN_PATH)" def reaper_command(guess=None): @@ -292,7 +294,8 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET: ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \ - ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" + ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \ + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') @@ -320,7 +323,8 @@ assert_dir(JS_GUIX_PATH + '/cytoscape-panzoom') CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS # assert_dir(JS_PATH) -JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher")) +JS_TWITTER_POST_FETCHER_PATH = get_setting( + "JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js") diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index f1dd148f..52026a82 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -25,13 +25,16 @@ def do_correlation(start_vars): assert('trait_id' in start_vars) this_dataset = data_set.create_dataset(dataset_name=start_vars['db']) - target_dataset = data_set.create_dataset(dataset_name=start_vars['target_db']) - this_trait = create_trait(dataset=this_dataset, name=start_vars['trait_id']) + target_dataset = data_set.create_dataset( + dataset_name=start_vars['target_db']) + this_trait = create_trait(dataset=this_dataset, + name=start_vars['trait_id']) this_trait = retrieve_sample_data(this_trait, this_dataset) corr_params = init_corr_params(start_vars) - corr_results = calculate_results(this_trait, this_dataset, target_dataset, corr_params) + corr_results = calculate_results( + this_trait, this_dataset, target_dataset, corr_params) #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) final_results = [] @@ -75,54 +78,66 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): if corr_params['type'] == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") - corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params) + corr_results = do_tissue_correlation_for_all_traits( + this_trait, trait_symbol_dict, corr_params) sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) - elif corr_params['type'] == "literature" or corr_params['type'] == "lit": # ZS: Just so a user can use either "lit" or "literature" + # ZS: Just so a user can use either "lit" or "literature" + elif corr_params['type'] == "literature" or corr_params['type'] == "lit": trait_geneid_dict = this_dataset.retrieve_genes("GeneId") - corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params) + corr_results = do_literature_correlation_for_all_traits( + this_trait, this_dataset, trait_geneid_dict, corr_params) sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) else: for target_trait, target_vals in list(target_dataset.trait_data.items()): - result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) + result = get_sample_r_and_p_values( + this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) if result is not None: corr_results[target_trait] = result - sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0]))) + sorted_results = collections.OrderedDict( + sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0]))) return sorted_results def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1): # Gets tissue expression values for the primary trait - primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol]) + primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( + symbol_list=[this_trait.symbol]) if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()] + primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower( + )] - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=list(trait_symbol_dict.values())) + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( + symbol_list=list(trait_symbol_dict.values())) tissue_corr_data = {} for trait, symbol in list(trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] + this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower( + )] result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, this_trait_tissue_values, corr_params['method']) - tissue_corr_data[trait] = [result[0], result[1], result[2], symbol] + tissue_corr_data[trait] = [ + result[0], result[1], result[2], symbol] return tissue_corr_data def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params): - input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid) + input_trait_mouse_gene_id = convert_to_mouse_gene_id( + target_dataset.group.species.lower(), this_trait.geneid) lit_corr_data = {} for trait, gene_id in list(trait_geneid_dict.items()): - mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id) + mouse_gene_id = convert_to_mouse_gene_id( + target_dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: result = g.db.execute( @@ -168,12 +183,15 @@ def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_data this_trait_vals.append(this_sample_value) shared_target_vals.append(target_sample_value) - this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, shared_target_vals) + this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values( + this_trait_vals, shared_target_vals) if type == 'pearson': - sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, shared_target_vals) + sample_r, sample_p = scipy.stats.pearsonr( + this_trait_vals, shared_target_vals) else: - sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, shared_target_vals) + sample_r, sample_p = scipy.stats.spearmanr( + this_trait_vals, shared_target_vals) if num_overlap > 5: if scipy.isnan(sample_r): diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 662090d5..c22b44a9 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -37,20 +37,25 @@ def do_mapping_for_api(start_vars): mapping_params = initialize_parameters(start_vars, dataset, this_trait) - covariates = "" # ZS: It seems to take an empty string as default. This should probably be changed. + # ZS: It seems to take an empty string as default. This should probably be changed. + covariates = "" if mapping_params['mapping_method'] == "gemma": header_row = ["name", "chr", "Mb", "lod_score", "p_value"] - if mapping_params['use_loco'] == "True": # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api - result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] + # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api + if mapping_params['use_loco'] == "True": + result_markers = gemma_mapping.run_gemma( + this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] else: - result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) + result_markers = gemma_mapping.run_gemma( + this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) elif mapping_params['mapping_method'] == "rqtl": header_row = ["name", "chr", "cM", "lod_score"] if mapping_params['num_perm'] > 0: _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], mapping_params['perm_check'], mapping_params['num_perm'], - mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['do_control'], mapping_params[ + 'control_marker'], mapping_params['manhattan_plot'], mapping_params['pair_scan']) else: result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 4f9cc6e5..e7dfa4e0 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -35,7 +35,8 @@ def hello_world(): @app.route("/api/v_{}/species".format(version)) def get_species_list(): - results = g.db.execute("SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;") + results = g.db.execute( + "SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;") the_species = results.fetchall() species_list = [] for species in the_species: @@ -313,7 +314,8 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"): @app.route("/api/v_{}/traits/".format(version), methods=("GET",)) @app.route("/api/v_{}/traits/.".format(version), methods=("GET",)) def fetch_traits(dataset_name, file_format="json"): - trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids( + dataset_name, request.args) if ("ids_only" in request.args) and (len(trait_ids) > 0): if file_format == "json": filename = dataset_name + "_trait_ids.json" @@ -361,7 +363,8 @@ def fetch_traits(dataset_name, file_format="json"): ProbeSet.Id """ - field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] + field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", + "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] elif data_type == "Geno": query = """ SELECT @@ -378,7 +381,8 @@ def fetch_traits(dataset_name, file_format="json"): Geno.Id """ - field_list = ["Id", "Name", "Marker_Name", "Chr", "Mb", "Sequence", "Source"] + field_list = ["Id", "Name", "Marker_Name", + "Chr", "Mb", "Sequence", "Source"] else: query = """ SELECT @@ -394,7 +398,8 @@ def fetch_traits(dataset_name, file_format="json"): PublishXRef.Id """ - field_list = ["Id", "PhenotypeId", "PublicationId", "Locus", "LRS", "Additive", "Sequence"] + field_list = ["Id", "PhenotypeId", "PublicationId", + "Locus", "LRS", "Additive", "Sequence"] if 'limit_to' in request.args: limit_number = request.args['limit_to'] @@ -442,7 +447,8 @@ def fetch_traits(dataset_name, file_format="json"): @app.route("/api/v_{}/sample_data/".format(version)) @app.route("/api/v_{}/sample_data/.".format(version)) def all_sample_data(dataset_name, file_format="csv"): - trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids( + dataset_name, request.args) if len(trait_ids) > 0: sample_list = get_samplelist(dataset_name) @@ -676,7 +682,8 @@ def get_trait_info(dataset_name, trait_name, file_format="json"): return flask.jsonify(trait_dict) else: - if "Publish" in dataset_name: # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish" + # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish" + if "Publish" in dataset_name: dataset_name = dataset_name.replace("Publish", "") group_id = get_group_id(dataset_name) @@ -711,7 +718,8 @@ def get_corr_results(): results = correlation.do_correlation(request.args) if len(results) > 0: - return flask.jsonify(results) # ZS: I think flask.jsonify expects a dict/list instead of JSON + # ZS: I think flask.jsonify expects a dict/list instead of JSON + return flask.jsonify(results) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @@ -768,7 +776,8 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): output_lines.append(line.split()) i += 1 - csv_writer = csv.writer(si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE) + csv_writer = csv.writer( + si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") elif file_format == "rqtl2": @@ -779,18 +788,23 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): filename = group_name if os.path.isfile("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name)): - yaml_file = json.load(open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name))) + yaml_file = json.load( + open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name))) yaml_file["geno"] = filename + "_geno.csv" yaml_file["gmap"] = filename + "_gmap.csv" yaml_file["pheno"] = filename + "_pheno.csv" config_file = [filename + ".json", json.dumps(yaml_file)] #config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))] - geno_file = [filename + "_geno.csv", open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))] - gmap_file = [filename + "_gmap.csv", open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))] + geno_file = [filename + "_geno.csv", + open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))] + gmap_file = [filename + "_gmap.csv", + open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))] if dataset_name: - phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name) + phenotypes = requests.get( + "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name) else: - phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish") + phenotypes = requests.get( + "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish") with ZipFile(memory_file, 'w', compression=ZIP_DEFLATED) as zf: zf.writestr(config_file[0], config_file[1]) @@ -813,7 +827,8 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): for line in genofile: if limit_num and i >= limit_num: break - output_lines.append([line.strip() for line in line.split(",")]) + output_lines.append([line.strip() + for line in line.split(",")]) i += 1 csv_writer = csv.writer(si, delimiter=",") @@ -898,7 +913,8 @@ def get_dataset_trait_ids(dataset_name, start_vars): results = g.db.execute(query).fetchall() trait_ids = [result[0] for result in results] - trait_names = [str(result[2]) + "_" + str(result[1]) for result in results] + trait_names = [str(result[2]) + "_" + str(result[1]) + for result in results] return trait_ids, trait_names, data_type, dataset_id diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 61f73106..1fcf15f0 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -158,7 +158,8 @@ def remove_traits(): traits_to_remove = params['trait_list'] traits_to_remove = process_traits(traits_to_remove) - members_now = g.user_session.remove_traits_from_collection(uc_id, traits_to_remove) + members_now = g.user_session.remove_traits_from_collection( + uc_id, traits_to_remove) return redirect(url_for("view_collection", uc_id=uc_id)) @@ -181,7 +182,8 @@ def delete_collection(): else: flash("We've deleted the selected collection.", "alert-info") else: - flash("We've deleted the collection: {}.".format(collection_name), "alert-info") + flash("We've deleted the collection: {}.".format( + collection_name), "alert-info") return redirect(url_for('list_collections')) @@ -191,7 +193,8 @@ def view_collection(): params = request.args uc_id = params['uc_id'] - uc = next((collection for collection in g.user_session.user_collections if collection["id"] == uc_id)) + uc = next( + (collection for collection in g.user_session.user_collections if collection["id"] == uc_id)) traits = uc["members"] trait_obs = [] @@ -203,12 +206,14 @@ def view_collection(): name, dataset_name = atrait.split(':') if dataset_name == "Temp": group = name.split("_")[2] - dataset = create_dataset(dataset_name, dataset_type="Temp", group_name=group) + dataset = create_dataset( + dataset_name, dataset_type="Temp", group_name=group) trait_ob = create_trait(name=name, dataset=dataset) else: dataset = create_dataset(dataset_name) trait_ob = create_trait(name=name, dataset=dataset) - trait_ob = retrieve_trait_info(trait_ob, dataset, get_qtl_info=True) + trait_ob = retrieve_trait_info( + trait_ob, dataset, get_qtl_info=True) trait_obs.append(trait_ob) json_version.append(jsonable(trait_ob)) diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index c135faa3..0fabb833 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -34,14 +34,16 @@ from flask import Flask, g class ComparisonBarChart: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.all_sample_list = [] self.traits = [] self.insufficient_shared_samples = False - this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop + # ZS: Getting initial group name before verifying all traits are in the same group in the following loop + this_group = self.trait_list[0][1].group.name for trait_db in self.trait_list: if trait_db[1].group.name != this_group: diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 6afea715..f9a0ea11 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -17,17 +17,21 @@ class CorrScatterPlot: def __init__(self, params): if "Temp" in params['dataset_1']: - self.dataset_1 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1]) + self.dataset_1 = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1]) else: self.dataset_1 = data_set.create_dataset(params['dataset_1']) if "Temp" in params['dataset_2']: - self.dataset_2 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1]) + self.dataset_2 = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1]) else: self.dataset_2 = data_set.create_dataset(params['dataset_2']) #self.dataset_3 = data_set.create_dataset(params['dataset_3']) - self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1) - self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2) + self.trait_1 = create_trait( + name=params['trait_1'], dataset=self.dataset_1) + self.trait_2 = create_trait( + name=params['trait_2'], dataset=self.dataset_2) #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.dataset_3) self.method = params['method'] @@ -38,10 +42,13 @@ class CorrScatterPlot: if self.dataset_1.group.f1list != None: primary_samples += self.dataset_1.group.f1list - self.trait_1 = retrieve_sample_data(self.trait_1, self.dataset_1, primary_samples) - self.trait_2 = retrieve_sample_data(self.trait_2, self.dataset_2, primary_samples) + self.trait_1 = retrieve_sample_data( + self.trait_1, self.dataset_1, primary_samples) + self.trait_2 = retrieve_sample_data( + self.trait_2, self.dataset_2, primary_samples) - samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data) + samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples( + self.trait_1.data, self.trait_2.data) self.data = [] self.indIDs = list(samples_1.keys()) @@ -54,7 +61,8 @@ class CorrScatterPlot: vals_2.append(samples_2[sample].value) self.data.append(vals_2) - slope, intercept, r_value, p_value, std_err = stats.linregress(vals_1, vals_2) + slope, intercept, r_value, p_value, std_err = stats.linregress( + vals_1, vals_2) if slope < 0.001: slope_string = '%.3E' % slope @@ -67,14 +75,16 @@ class CorrScatterPlot: x_range = [min(vals_1) - x_buffer, max(vals_1) + x_buffer] y_range = [min(vals_2) - y_buffer, max(vals_2) + y_buffer] - intercept_coords = get_intercept_coords(slope, intercept, x_range, y_range) + intercept_coords = get_intercept_coords( + slope, intercept, x_range, y_range) rx = stats.rankdata(vals_1) ry = stats.rankdata(vals_2) self.rdata = [] self.rdata.append(rx.tolist()) self.rdata.append(ry.tolist()) - srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(rx, ry) + srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress( + rx, ry) if srslope < 0.001: srslope_string = '%.3E' % srslope @@ -86,7 +96,8 @@ class CorrScatterPlot: sr_range = [min(rx) - x_buffer, max(rx) + x_buffer] - sr_intercept_coords = get_intercept_coords(srslope, srintercept, sr_range, sr_range) + sr_intercept_coords = get_intercept_coords( + srslope, srintercept, sr_range, sr_range) self.collections_exist = "False" if g.user_session.num_collections > 0: diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index e2fe1ff4..e75c4a85 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -78,7 +78,8 @@ class CorrelationResults: with Bench("Doing correlations"): if start_vars['dataset'] == "Temp": - self.dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group']) + self.dataset = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group']) self.trait_id = start_vars['trait_id'] self.this_trait = create_trait(dataset=self.dataset, name=self.trait_id, @@ -129,12 +130,15 @@ class CorrelationResults: if corr_samples_group == 'samples_other': primary_samples = [x for x in primary_samples if x not in ( self.dataset.group.parlist + self.dataset.group.f1list)] - self.process_samples(start_vars, list(self.this_trait.data.keys()), primary_samples) + self.process_samples(start_vars, list( + self.this_trait.data.keys()), primary_samples) - self.target_dataset = data_set.create_dataset(start_vars['corr_dataset']) + self.target_dataset = data_set.create_dataset( + start_vars['corr_dataset']) self.target_dataset.get_trait_data(list(self.sample_data.keys())) - self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method) + self.header_fields = get_header_fields( + self.target_dataset.type, self.corr_method) if self.target_dataset.type == "ProbeSet": self.filter_cols = [7, 6] @@ -153,7 +157,8 @@ class CorrelationResults: tissue_corr_data = self.do_tissue_correlation_for_all_traits() if tissue_corr_data != None: for trait in list(tissue_corr_data.keys())[:self.return_number]: - self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) + self.get_sample_r_and_p_values( + trait, self.target_dataset.trait_data[trait]) else: for trait, values in list(self.target_dataset.trait_data.items()): self.get_sample_r_and_p_values(trait, values) @@ -163,7 +168,8 @@ class CorrelationResults: lit_corr_data = self.do_lit_correlation_for_all_traits() for trait in list(lit_corr_data.keys())[:self.return_number]: - self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) + self.get_sample_r_and_p_values( + trait, self.target_dataset.trait_data[trait]) elif self.corr_type == "sample": for trait, values in list(self.target_dataset.trait_data.items()): @@ -180,7 +186,8 @@ class CorrelationResults: range_chr_as_int = order_id for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): - trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) + trait_object = create_trait( + dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) if not trait_object: continue @@ -235,7 +242,8 @@ class CorrelationResults: if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet": self.do_tissue_correlation_for_trait_list() - self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset) + self.json_results = generate_corr_json( + self.correlation_results, self.this_trait, self.dataset, self.target_dataset) ############################################################################################################################################ @@ -263,15 +271,18 @@ class CorrelationResults: symbol_list=[self.this_trait.symbol]) if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()] - gene_symbol_list = [trait.symbol for trait in self.correlation_results if trait.symbol] + primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower( + )] + gene_symbol_list = [ + trait.symbol for trait in self.correlation_results if trait.symbol] corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( symbol_list=gene_symbol_list) for trait in self.correlation_results: if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower()] + this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower( + )] result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, this_trait_tissue_values, @@ -286,7 +297,8 @@ class CorrelationResults: symbol_list=[self.this_trait.symbol]) if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()] + primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower( + )] #print("trait_gene_symbols: ", pf(trait_gene_symbols.values())) corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( @@ -299,7 +311,8 @@ class CorrelationResults: tissue_corr_data = {} for trait, symbol in list(self.trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] + this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower( + )] result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, this_trait_tissue_values, @@ -314,12 +327,14 @@ class CorrelationResults: def do_lit_correlation_for_trait_list(self): - input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) + input_trait_mouse_gene_id = self.convert_to_mouse_gene_id( + self.dataset.group.species.lower(), self.this_trait.geneid) for trait in self.correlation_results: if trait.geneid: - trait.mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), trait.geneid) + trait.mouse_gene_id = self.convert_to_mouse_gene_id( + self.dataset.group.species.lower(), trait.geneid) else: trait.mouse_gene_id = None @@ -348,11 +363,13 @@ class CorrelationResults: trait.lit_corr = 0 def do_lit_correlation_for_all_traits(self): - input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) + input_trait_mouse_gene_id = self.convert_to_mouse_gene_id( + self.dataset.group.species.lower(), self.this_trait.geneid) lit_corr_data = {} for trait, gene_id in list(self.trait_geneid_dict.items()): - mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id) + mouse_gene_id = self.convert_to_mouse_gene_id( + self.dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: #print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id) @@ -438,21 +455,26 @@ class CorrelationResults: self.this_trait_vals.append(sample_value) target_vals.append(target_sample_value) - self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) + self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values( + self.this_trait_vals, target_vals) if num_overlap > 5: # ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ if self.corr_method == 'bicor': - sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals) + sample_r, sample_p = do_bicor( + self.this_trait_vals, target_vals) elif self.corr_method == 'pearson': - sample_r, sample_p = scipy.stats.pearsonr(self.this_trait_vals, target_vals) + sample_r, sample_p = scipy.stats.pearsonr( + self.this_trait_vals, target_vals) else: - sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals) + sample_r, sample_p = scipy.stats.spearmanr( + self.this_trait_vals, target_vals) if numpy.isnan(sample_r): pass else: - self.correlation_data[trait] = [sample_r, sample_p, num_overlap] + self.correlation_data[trait] = [ + sample_r, sample_p, num_overlap] def process_samples(self, start_vars, sample_names, excluded_samples=None): if not excluded_samples: @@ -478,7 +500,8 @@ def do_bicor(this_trait_vals, target_trait_vals): this_vals = ro.Vector(this_trait_vals) target_vals = ro.Vector(target_trait_vals) - the_r, the_p, _fisher_transform, _the_t, _n_obs = [numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)] + the_r, the_p, _fisher_transform, _the_t, _n_obs = [ + numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)] return the_r, the_p @@ -492,7 +515,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_dict['index'] = i + 1 results_dict['trait_id'] = trait.name results_dict['dataset'] = trait.dataset.name - results_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) + results_dict['hmac'] = hmac.data_hmac( + '{}:{}'.format(trait.name, trait.dataset.name)) if target_dataset.type == "ProbeSet": results_dict['symbol'] = trait.symbol results_dict['description'] = "N/A" @@ -543,7 +567,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap if bool(trait.authors): authors_list = trait.authors.split(',') if len(authors_list) > 6: - results_dict['authors_display'] = ", ".join(authors_list[:6]) + ", et al." + results_dict['authors_display'] = ", ".join( + authors_list[:6]) + ", et al." else: results_dict['authors_display'] = trait.authors if bool(trait.pubmed_id): diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 331cb1dc..aefb4453 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -44,7 +44,8 @@ THIRTY_DAYS = 60 * 60 * 24 * 30 class CorrelationMatrix: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) @@ -52,7 +53,8 @@ class CorrelationMatrix: self.traits = [] self.insufficient_shared_samples = False self.do_PCA = True - this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop + # ZS: Getting initial group name before verifying all traits are in the same group in the following loop + this_group = self.trait_list[0][1].group.name for trait_db in self.trait_list: this_group = trait_db[1].group.name this_trait = trait_db[0] @@ -76,10 +78,12 @@ class CorrelationMatrix: this_trait_vals.append('') self.sample_data.append(this_trait_vals) - if len(this_trait_vals) < len(self.trait_list): # Shouldn't do PCA if there are more traits than observations/samples + # Shouldn't do PCA if there are more traits than observations/samples + if len(this_trait_vals) < len(self.trait_list): self.do_PCA = False - self.lowest_overlap = 8 # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning) + # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning) + self.lowest_overlap = 8 self.corr_results = [] self.pca_corr_results = [] @@ -112,7 +116,8 @@ class CorrelationMatrix: if sample in self.shared_samples_list: self.shared_samples_list.remove(sample) - this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals) + this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values( + this_trait_vals, target_vals) if num_overlap < self.lowest_overlap: self.lowest_overlap = num_overlap @@ -120,21 +125,25 @@ class CorrelationMatrix: corr_result_row.append([target_trait, 0, num_overlap]) pca_corr_result_row.append(0) else: - pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals) + pearson_r, pearson_p = scipy.stats.pearsonr( + this_trait_vals, target_vals) if is_spearman == False: sample_r, sample_p = pearson_r, pearson_p if sample_r == 1: is_spearman = True else: - sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals) + sample_r, sample_p = scipy.stats.spearmanr( + this_trait_vals, target_vals) - corr_result_row.append([target_trait, sample_r, num_overlap]) + corr_result_row.append( + [target_trait, sample_r, num_overlap]) pca_corr_result_row.append(pearson_r) self.corr_results.append(corr_result_row) self.pca_corr_results.append(pca_corr_result_row) - self.export_filename, self.export_filepath = export_corr_matrix(self.corr_results) + self.export_filename, self.export_filepath = export_corr_matrix( + self.corr_results) self.trait_data_array = [] for trait_db in self.trait_list: @@ -156,12 +165,14 @@ class CorrelationMatrix: try: corr_result_eigen = np.linalg.eig(np.array(self.pca_corr_results)) - corr_eigen_value, corr_eigen_vectors = sortEigenVectors(corr_result_eigen) + corr_eigen_value, corr_eigen_vectors = sortEigenVectors( + corr_result_eigen) if self.do_PCA == True: self.pca_works = "True" self.pca_trait_ids = [] - pca = self.calculate_pca(list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors) + pca = self.calculate_pca( + list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors) self.loadings_array = self.process_loadings() else: self.pca_works = "False" @@ -179,7 +190,8 @@ class CorrelationMatrix: base = importr('base') stats = importr('stats') - corr_results_to_list = robjects.FloatVector([item for sublist in self.pca_corr_results for item in sublist]) + corr_results_to_list = robjects.FloatVector( + [item for sublist in self.pca_corr_results for item in sublist]) m = robjects.r.matrix(corr_results_to_list, nrow=len(cols)) eigen = base.eigen(m) @@ -198,10 +210,12 @@ class CorrelationMatrix: pca_traits.append((vector * -1.0).tolist()) this_group_name = self.trait_list[0][1].group.name - temp_dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = this_group_name) + temp_dataset = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = this_group_name) temp_dataset.group.get_samplelist() for i, pca_trait in enumerate(pca_traits): - trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") + trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \ + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") this_vals_string = "" position = 0 for sample in temp_dataset.group.all_samples_ordered(): @@ -235,17 +249,23 @@ class CorrelationMatrix: def export_corr_matrix(corr_results): - corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) - matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename) + corr_matrix_filename = "corr_matrix_" + \ + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) + matrix_export_path = "{}{}.csv".format( + GENERATED_TEXT_DIR, corr_matrix_filename) with open(matrix_export_path, "w+") as output_file: - output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") + output_file.write( + "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") output_file.write("\n") output_file.write("Correlation ") for i, item in enumerate(corr_results[0]): - output_file.write("Trait" + str(i + 1) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") + output_file.write("Trait" + str(i + 1) + ": " + \ + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") output_file.write("\n") for i, row in enumerate(corr_results): - output_file.write("Trait" + str(i + 1) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") + output_file.write("Trait" + str(i + 1) + ": " + \ + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") for item in row: output_file.write(str(item[1]) + "\t") output_file.write("\n") @@ -254,10 +274,12 @@ def export_corr_matrix(corr_results): output_file.write("\n") output_file.write("N ") for i, item in enumerate(corr_results[0]): - output_file.write("Trait" + str(i) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") + output_file.write("Trait" + str(i) + ": " + \ + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") output_file.write("\n") for i, row in enumerate(corr_results): - output_file.write("Trait" + str(i) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") + output_file.write("Trait" + str(i) + ": " + \ + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") for item in row: output_file.write(str(item[2]) + "\t") output_file.write("\n") diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index ec66e59f..48a82435 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -46,13 +46,18 @@ class CTL: #log = r_file("/tmp/genenetwork_ctl.log", open = "wt") # r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file #r_sink(log, type = "message") - r_library("ctl") # Load CTL - Should only be done once, since it is quite expensive + # Load CTL - Should only be done once, since it is quite expensive + r_library("ctl") r_options(stringsAsFactors=False) logger.info("Initialization of CTL done, package loaded in R session") - self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function - self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function - self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function - self.r_plotCTLobject = ro.r["plot.CTLobject"] # Map the CTLsignificant function + # Map the CTLscan function + self.r_CTLscan = ro.r["CTLscan"] + # Map the CTLsignificant function + self.r_CTLsignificant = ro.r["CTLsignificant"] + # Map the ctl.lineplot function + self.r_lineplot = ro.r["ctl.lineplot"] + # Map the CTLsignificant function + self.r_plotCTLobject = ro.r["plot.CTLobject"] self.nodes_list = [] self.edges_list = [] logger.info("Obtained pointers to CTL functions") @@ -81,7 +86,8 @@ class CTL: def run_analysis(self, requestform): logger.info("Starting CTL analysis on dataset") - self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] + self.trait_db_list = [trait.strip() + for trait in requestform['trait_list'].split(',')] self.trait_db_list = [x for x in self.trait_db_list if x] logger.debug("strategy:", requestform.get("strategy")) @@ -113,9 +119,11 @@ class CTL: markers.append(marker["genotypes"]) genotypes = list(itertools.chain(*markers)) - logger.debug(len(genotypes) / len(individuals), "==", len(parser.markers)) + logger.debug(len(genotypes) / len(individuals), + "==", len(parser.markers)) - rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames=r_list(markernames, individuals), byrow=True)) + rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len( + individuals), dimnames=r_list(markernames, individuals), byrow=True)) # Create a phenotype matrix traits = [] @@ -131,7 +139,8 @@ class CTL: else: traits.append("-999") - rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True)) + rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len( + individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True)) logger.debug(rPheno) @@ -144,7 +153,8 @@ class CTL: #r_write_table(rPheno, "~/outputGN/pheno.csv") # Perform the CTL scan - res = self.r_CTLscan(rGeno, rPheno, strategy=strategy, nperm=nperm, parametric = parametric, nthreads=6) + res = self.r_CTLscan(rGeno, rPheno, strategy=strategy, + nperm=nperm, parametric = parametric, nthreads=6) # Get significant interactions significant = self.r_CTLsignificant(res, significance=significance) @@ -155,20 +165,27 @@ class CTL: self.results['imgloc1'] = GENERATED_IMAGE_DIR + self.results['imgurl1'] self.results['ctlresult'] = significant - self.results['requestform'] = requestform # Store the user specified parameters for the output page + # Store the user specified parameters for the output page + self.results['requestform'] = requestform # Create the lineplot - r_png(self.results['imgloc1'], width=1000, height=600, type='cairo-png') + r_png(self.results['imgloc1'], width=1000, + height=600, type='cairo-png') self.r_lineplot(res, significance=significance) r_dev_off() - n = 2 # We start from 2, since R starts from 1 :) + # We start from 2, since R starts from 1 :) + n = 2 for trait in self.trait_db_list: # Create the QTL like CTL plots - self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" - self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + self.results['imgurl' + str(n)] - r_png(self.results['imgloc' + str(n)], width=1000, height=600, type='cairo-png') - self.r_plotCTLobject(res, (n - 1), significance=significance, main='Phenotype ' + trait) + self.results['imgurl' + \ + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" + self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \ + self.results['imgurl' + str(n)] + r_png(self.results['imgloc' + str(n)], + width=1000, height=600, type='cairo-png') + self.r_plotCTLobject( + res, (n - 1), significance=significance, main='Phenotype ' + trait) r_dev_off() n = n + 1 @@ -178,17 +195,24 @@ class CTL: # Create the interactive graph for cytoscape visualization (Nodes and Edges) if not isinstance(significant, ri.RNULLType): for x in range(len(significant[0])): - logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console - tsS = significant[0][x].split(':') # Source - tsT = significant[2][x].split(':') # Target - gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) # Retrieve Source info from the DB - gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) # Retrieve Target info from the DB + logger.debug(significant[0][x], significant[1] + [x], significant[2][x]) # Debug to console + # Source + tsS = significant[0][x].split(':') + # Target + tsT = significant[2][x].split(':') + # Retrieve Source info from the DB + gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) + # Retrieve Target info from the DB + gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) self.addNode(gtS) self.addNode(gtT) self.addEdge(gtS, gtT, significant, x) - significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name) # Update the trait name for the displayed table - significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name) # Update the trait name for the displayed table + # Update the trait name for the displayed table + significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name) + # Update the trait name for the displayed table + significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name) self.elements = json.dumps(self.nodes_list + self.edges_list) diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 7442dc72..e50ff50b 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -26,14 +26,16 @@ class DoSearch: def __init__(self, search_term, search_operator=None, dataset=None, search_type=None): self.search_term = search_term # Make sure search_operator is something we expect - assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator" + assert search_operator in ( + None, "=", "<", ">", "<=", ">="), "Bad search operator" self.search_operator = search_operator self.dataset = dataset self.search_type = search_type if self.dataset: # Get group information for dataset and the species id - self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) + self.species_id = webqtlDatabaseFunction.retrieve_species_id( + self.dataset.group.name) def execute(self, query): """Executes query and returns results""" @@ -104,7 +106,8 @@ class MrnaAssaySearch(DoSearch): search_string = escape(self.search_term[0]) if self.search_term[0] != "*": - match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % (search_string) + match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % ( + search_string) else: match_clause = "" @@ -223,16 +226,19 @@ class PhenotypeSearch(DoSearch): # and comment here # if "'" not in self.search_term[0]: - search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]" + search_term = "[[:<:]]" + \ + self.handle_wildcard(self.search_term[0]) + "[[:>:]]" if "_" in self.search_term[0]: if len(self.search_term[0].split("_")[0]) == 3: - search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0].split("_")[1]) + "[[:>:]]" + search_term = "[[:<:]]" + self.handle_wildcard( + self.search_term[0].split("_")[1]) + "[[:>:]]" # This adds a clause to the query that matches the search term # against each field in the search_fields tuple where_clause_list = [] for field in self.search_fields: - where_clause_list.append('''%s REGEXP "%s"''' % (field, search_term)) + where_clause_list.append('''%s REGEXP "%s"''' % + (field, search_term)) where_clause = "(%s) " % ' OR '.join(where_clause_list) return where_clause @@ -364,7 +370,8 @@ class GenotypeSearch(DoSearch): if self.search_term[0] == "*": self.query = self.compile_final_query() else: - self.query = self.compile_final_query(where_clause=self.get_where_clause()) + self.query = self.compile_final_query( + where_clause=self.get_where_clause()) return self.execute(self.query) @@ -497,7 +504,8 @@ class LrsSearch(DoSearch): where_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s """ % self.mescape(self.dataset.type, - min(lrs_min, lrs_max), + min(lrs_min, + lrs_max), self.dataset.type, max(lrs_min, lrs_max)) @@ -537,7 +545,8 @@ class LrsSearch(DoSearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(self.from_clause, self.where_clause) + self.query = self.compile_final_query( + self.from_clause, self.where_clause) return self.execute(self.query) @@ -551,7 +560,8 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause) + self.query = self.compile_final_query( + from_clause=self.from_clause, where_clause=self.where_clause) return self.execute(self.query) @@ -566,7 +576,8 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause) + self.query = self.compile_final_query( + from_clause=self.from_clause, where_clause=self.where_clause) return self.execute(self.query) @@ -593,7 +604,8 @@ class CisTransLrsSearch(DoSearch): elif len(self.search_term) == 3: lrs_min, lrs_max, self.mb_buffer = self.search_term elif len(self.search_term) == 4: - lrs_min, lrs_max, self.mb_buffer = [float(value) for value in self.search_term[:3]] + lrs_min, lrs_max, self.mb_buffer = [ + float(value) for value in self.search_term[:3]] chromosome = self.search_term[3] if "Chr" in chromosome or "chr" in chromosome: chromosome = int(chromosome[3:]) @@ -636,14 +648,19 @@ class CisTransLrsSearch(DoSearch): if chromosome: location_clause = "(%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = '%s')" % (escape(self.dataset.type), chromosome, - escape(self.dataset.type), - escape(self.dataset.type), + escape( + self.dataset.type), + escape( + self.dataset.type), the_operator, - escape(str(self.mb_buffer)), - escape(self.dataset.type), + escape( + str(self.mb_buffer)), + escape( + self.dataset.type), chromosome) else: - location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type)) + location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape( + self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type)) where_clause = sub_clause + """ %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and @@ -683,7 +700,8 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(self.from_clause, self.where_clause) + self.query = self.compile_final_query( + self.from_clause, self.where_clause) return self.execute(self.query) @@ -714,7 +732,8 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(self.from_clause, self.where_clause) + self.query = self.compile_final_query( + self.from_clause, self.where_clause) return self.execute(self.query) @@ -733,7 +752,8 @@ class MeanSearch(MrnaAssaySearch): where_clause = """ %sXRef.mean > %s and %sXRef.mean < %s """ % self.mescape(self.dataset.type, - min(self.mean_min, self.mean_max), + min(self.mean_min, + self.mean_max), self.dataset.type, max(self.mean_min, self.mean_max)) else: @@ -796,7 +816,8 @@ class PositionSearch(DoSearch): DoSearch.search_types[search_key] = "PositionSearch" def get_where_clause(self): - self.search_term = [float(value) if is_number(value) else value for value in self.search_term] + self.search_term = [float(value) if is_number( + value) else value for value in self.search_term] chr, self.mb_min, self.mb_max = self.search_term[:3] self.chr = str(chr).lower() self.get_chr() @@ -806,7 +827,8 @@ class PositionSearch(DoSearch): %s.Mb < %s """ % self.mescape(self.dataset.type, self.chr, self.dataset.type, - min(self.mb_min, self.mb_max), + min(self.mb_min, + self.mb_max), self.dataset.type, max(self.mb_min, self.mb_max)) @@ -923,7 +945,8 @@ def get_aliases(symbol, species): return [] filtered_aliases = [] - response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) + response = requests.get( + GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) if response: alias_list = json.loads(response.content) diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 81424b9c..fc93248a 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -35,11 +35,13 @@ class Docs: def update_text(start_vars): content = start_vars['ckcontent'] - content = content.replace('%', '%%').replace('"', '\\"').replace("'", "\\'") + content = content.replace('%', '%%').replace( + '"', '\\"').replace("'", "\\'") try: if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com": - sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(content, start_vars['entry_type']) + sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format( + content, start_vars['entry_type']) g.db.execute(sql) except: pass diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index d0745ef7..5bd54f9d 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -35,9 +35,12 @@ def export_search_results_csv(targs): metadata.append(["Data Set: " + targs['database_name']]) if 'accession_id' in targs: if targs['accession_id'] != "None": - metadata.append(["Metadata Link: http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + targs['accession_id']]) - metadata.append(["Export Date: " + datetime.datetime.now().strftime("%B %d, %Y")]) - metadata.append(["Export Time: " + datetime.datetime.now().strftime("%H:%M GMT")]) + metadata.append( + ["Metadata Link: http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + targs['accession_id']]) + metadata.append( + ["Export Date: " + datetime.datetime.now().strftime("%B %d, %Y")]) + metadata.append( + ["Export Time: " + datetime.datetime.now().strftime("%H:%M GMT")]) if 'search_string' in targs: if targs['search_string'] != "None": metadata.append(["Search Query: " + targs['search_string']]) @@ -52,10 +55,12 @@ def export_search_results_csv(targs): for trait in table_rows: trait_name, dataset_name, _hash = trait.split(":") trait_ob = create_trait(name=trait_name, dataset_name=dataset_name) - trait_ob = retrieve_trait_info(trait_ob, trait_ob.dataset, get_qtl_info=True) + trait_ob = retrieve_trait_info( + trait_ob, trait_ob.dataset, get_qtl_info=True) trait_list.append(trait_ob) - table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] + table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', + 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] traits_by_group = sort_traits_by_group(trait_list) @@ -87,7 +92,8 @@ def export_search_results_csv(targs): trait_symbol = "N/A" row_contents = [ i + 1, - "https://genenetwork.org/show_trait?trait_id=" + str(trait.name) + "&dataset=" + str(trait.dataset.name), + "https://genenetwork.org/show_trait?trait_id=" + \ + str(trait.name) + "&dataset=" + str(trait.dataset.name), trait.dataset.group.species, trait.dataset.group.name, trait.dataset.name, @@ -117,13 +123,15 @@ def export_search_results_csv(targs): for sample in trait.dataset.group.samplelist: if sample in trait.data: - row_contents += [trait.data[sample].value, trait.data[sample].variance] + row_contents += [trait.data[sample].value, + trait.data[sample].variance] else: row_contents += ["x", "x"] csv_rows.append(row_contents) - csv_rows = list(map(list, itertools.zip_longest(*[row for row in csv_rows]))) + csv_rows = list( + map(list, itertools.zip_longest(*[row for row in csv_rows]))) writer.writerows(csv_rows) csv_data = buff.getvalue() buff.close() diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py index 1556c6a0..3c0f2ca7 100644 --- a/wqflask/wqflask/external_tools/send_to_bnw.py +++ b/wqflask/wqflask/external_tools/send_to_bnw.py @@ -27,7 +27,8 @@ logger = utility.logger.getLogger(__name__) class SendToBNW: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) trait_samples_list = [] @@ -39,7 +40,8 @@ class SendToBNW: trait1_samples = list(this_sample_data.keys()) trait_samples_list.append(trait1_samples) - shared_samples = list(set(trait_samples_list[0]).intersection(*trait_samples_list)) + shared_samples = list( + set(trait_samples_list[0]).intersection(*trait_samples_list)) self.form_value = "" # ZS: string that is passed to BNW through form values_list = [] diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index c55c43e6..8af9bee9 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -32,7 +32,8 @@ logger = utility.logger.getLogger(__name__) class SendToGeneWeaver: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.chip_name = test_chip(self.trait_list) diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index 6b78725c..fd12562f 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -32,7 +32,8 @@ logger = utility.logger.getLogger(__name__) class SendToWebGestalt: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.chip_name = test_chip(self.trait_list) diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 69ce3e7a..55a7da0e 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -77,8 +77,10 @@ def remove_users(): admin_ids_to_remove = request.form['selected_admin_ids'] member_ids_to_remove = request.form['selected_member_ids'] - remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(":"), group_id, user_type="admins") - remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(":"), group_id, user_type="members") + remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split( + ":"), group_id, user_type="admins") + remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split( + ":"), group_id, user_type="members") return redirect(url_for('view_group', id=group_id)) @@ -88,10 +90,12 @@ def add_users(user_type='members'): group_id = request.form['group_id'] if user_type == "admins": user_emails = request.form['admin_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=True) + add_users_to_group(g.user_session.user_id, group_id, + user_emails, admins=True) elif user_type == "members": user_emails = request.form['member_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=False) + add_users_to_group(g.user_session.user_id, group_id, + user_emails, admins=False) return redirect(url_for('view_group', id=group_id)) @@ -111,7 +115,8 @@ def add_or_edit_group(): if "group_name" in params: member_user_ids = set() admin_user_ids = set() - admin_user_ids.add(g.user_session.user_id) # ZS: Always add the user creating the group as an admin + # ZS: Always add the user creating the group as an admin + admin_user_ids.add(g.user_session.user_id) if "admin_emails_to_add" in params: admin_emails = params['admin_emails_to_add'].split(",") for email in admin_emails: @@ -127,7 +132,8 @@ def add_or_edit_group(): member_user_ids.add(user_details['user_id']) #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") - create_group(list(admin_user_ids), list(member_user_ids), params['group_name']) + create_group(list(admin_user_ids), list( + member_user_ids), params['group_name']) return redirect(url_for('manage_groups')) else: return render_template("admin/create_group.html") @@ -149,9 +155,11 @@ def send_group_invites(group_id, user_email_list=[], user_type="members"): ((user_type == "members") and (user_details['user_id'] in group_info['members'])): continue else: - send_verification_email(user_details, template_name="email/group_verification.txt", key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group") + send_verification_email(user_details, template_name="email/group_verification.txt", + key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group") else: - temp_password = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + temp_password = ''.join(random.choice( + string.ascii_uppercase + string.digits) for _ in range(6)) user_details = { 'user_id': str(uuid.uuid4()), 'email_address': user_email, diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index a21dae84..9548d130 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -77,18 +77,21 @@ class GSearch: this_trait['name'] = line[5] this_trait['dataset'] = line[3] this_trait['dataset_fullname'] = line[4] - this_trait['hmac'] = hmac.data_hmac('{}:{}'.format(line[5], line[3])) + this_trait['hmac'] = hmac.data_hmac( + '{}:{}'.format(line[5], line[3])) this_trait['species'] = line[0] this_trait['group'] = line[1] this_trait['tissue'] = line[2] this_trait['symbol'] = line[6] if line[7]: - this_trait['description'] = line[7].decode('utf-8', 'replace') + this_trait['description'] = line[7].decode( + 'utf-8', 'replace') else: this_trait['description'] = "N/A" this_trait['location_repr'] = 'N/A' if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): - this_trait['location_repr'] = 'Chr%s: %.6f' % (line[8], float(line[9])) + this_trait['location_repr'] = 'Chr%s: %.6f' % ( + line[8], float(line[9])) try: this_trait['mean'] = '%.3f' % line[10] except: @@ -103,7 +106,8 @@ class GSearch: this_trait['locus_chr'] = line[16] this_trait['locus_mb'] = line[17] - dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"]) + dataset_ob = SimpleNamespace( + id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"]) if dataset_ob.id not in dataset_to_permissions: permissions = check_resource_availability(dataset_ob) dataset_to_permissions[dataset_ob.id] = permissions @@ -118,7 +122,9 @@ class GSearch: max_lrs_text = "N/A" if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None: - max_lrs_text = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb']) + max_lrs_text = "Chr" + \ + str(this_trait['locus_chr']) + \ + ": " + str(this_trait['locus_mb']) this_trait['max_lrs_text'] = max_lrs_text trait_list.append(this_trait) @@ -146,7 +152,8 @@ class GSearch: if "_" in self.terms: if len(self.terms.split("_")[0]) == 3: search_term = self.terms.split("_")[1] - group_clause = "AND InbredSet.`InbredSetCode` = '{}'".format(self.terms.split("_")[0]) + group_clause = "AND InbredSet.`InbredSetCode` = '{}'".format( + self.terms.split("_")[0]) sql = """ SELECT Species.`Name`, @@ -192,18 +199,22 @@ class GSearch: this_trait['index'] = i + 1 this_trait['name'] = str(line[4]) if len(str(line[12])) == 3: - this_trait['display_name'] = str(line[12]) + "_" + this_trait['name'] + this_trait['display_name'] = str( + line[12]) + "_" + this_trait['name'] else: this_trait['display_name'] = this_trait['name'] this_trait['dataset'] = line[2] this_trait['dataset_fullname'] = line[3] - this_trait['hmac'] = hmac.data_hmac('{}:{}'.format(line[4], line[2])) + this_trait['hmac'] = hmac.data_hmac( + '{}:{}'.format(line[4], line[2])) this_trait['species'] = line[0] this_trait['group'] = line[1] if line[9] != None and line[6] != None: - this_trait['description'] = line[6].decode('utf-8', 'replace') + this_trait['description'] = line[6].decode( + 'utf-8', 'replace') elif line[5] != None: - this_trait['description'] = line[5].decode('utf-8', 'replace') + this_trait['description'] = line[5].decode( + 'utf-8', 'replace') else: this_trait['description'] = "N/A" if line[13] != None and line[13] != "": @@ -221,7 +232,8 @@ class GSearch: else: this_trait['pubmed_link'] = "N/A" if line[12]: - this_trait['display_name'] = line[12] + "_" + str(this_trait['name']) + this_trait['display_name'] = line[12] + \ + "_" + str(this_trait['name']) this_trait['LRS_score_repr'] = "N/A" if line[10] != "" and line[10] != None: this_trait['LRS_score_repr'] = '%3.1f' % line[10] @@ -230,13 +242,16 @@ class GSearch: this_trait['additive'] = '%.3f' % line[11] this_trait['max_lrs_text'] = "N/A" - trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) + trait_ob = create_trait( + dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) if not trait_ob: continue if this_trait['dataset'] == this_trait['group'] + "Publish": try: if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": - this_trait['max_lrs_text'] = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb) + this_trait['max_lrs_text'] = "Chr" + \ + str(trait_ob.locus_chr) + \ + ": " + str(trait_ob.locus_mb) except: this_trait['max_lrs_text'] = "N/A" diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 0b477446..aa11caa8 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -18,7 +18,8 @@ logger = getLogger(__name__) class Heatmap: def __init__(self, start_vars, temp_uuid): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.temp_uuid = temp_uuid @@ -33,7 +34,8 @@ class Heatmap: chrnames = [] self.species = species.TheSpecies(dataset=self.trait_list[0][1]) for key in list(self.species.chromosomes.chromosomes.keys()): - chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) + chrnames.append([self.species.chromosomes.chromosomes[key].name, + self.species.chromosomes.chromosomes[key].mb_length]) for trait_db in self.trait_list: @@ -108,10 +110,13 @@ class Heatmap: trimmed_samples.append(str(samples[i])) trimmed_values.append(values[i]) - trait_filename = str(this_trait.name) + "_" + str(self.dataset.name) + "_pheno" + trait_filename = str(this_trait.name) + "_" + \ + str(self.dataset.name) + "_pheno" gen_pheno_txt_file(trimmed_samples, trimmed_values, trait_filename) - output_filename = self.dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + output_filename = self.dataset.group.name + "_GWA_" + \ + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt -n 1000 -o {4}{5}.txt'.format(flat_files('genotype'), genofile_name, @@ -129,9 +134,11 @@ class Heatmap: self.trait_results[this_trait.name] = [] for qtl in reaper_results: if qtl['additive'] > 0: - self.trait_results[this_trait.name].append(-float(qtl['lrs_value'])) + self.trait_results[this_trait.name].append( + -float(qtl['lrs_value'])) else: - self.trait_results[this_trait.name].append(float(qtl['lrs_value'])) + self.trait_results[this_trait.name].append( + float(qtl['lrs_value'])) def gen_pheno_txt_file(samples, vals, filename): diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 8dd1c7c0..cadff080 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -54,7 +54,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): Mb >= %2.6f AND Mb < %2.6f AND StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] - newdict["snpDensity"] = newdict["snpCount"] / (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 + newdict["snpDensity"] = newdict["snpCount"] / \ + (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 else: newdict["snpDensity"] = newdict["snpCount"] = 0 @@ -86,12 +87,14 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] - newdict2["snpDensity"] = newdict2["snpCount"] / (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 + newdict2["snpDensity"] = newdict2["snpCount"] / \ + (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 else: newdict2["snpDensity"] = newdict2["snpCount"] = 0 try: - newdict2['GeneLength'] = 1000.0 * (newdict2['TxEnd'] - newdict2['TxStart']) + newdict2['GeneLength'] = 1000.0 * \ + (newdict2['TxEnd'] - newdict2['TxStart']) except: pass diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 5c7b81dd..cde822e8 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -307,7 +307,8 @@ class DisplayMappingResults: if 'color_scheme' in start_vars: self.color_scheme = start_vars['color_scheme'] if self.color_scheme == "single": - self.manhattan_single_color = ImageColor.getrgb("#" + start_vars['manhattan_single_color']) + self.manhattan_single_color = ImageColor.getrgb( + "#" + start_vars['manhattan_single_color']) if 'permCheck' in list(start_vars.keys()): self.permChecked = start_vars['permCheck'] @@ -357,7 +358,8 @@ class DisplayMappingResults: if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper": self.reaper_version = start_vars['reaper_version'] if 'output_files' in start_vars: - self.output_files = ",".join([(the_file if the_file is not None else "") for the_file in start_vars['output_files']]) + self.output_files = ",".join( + [(the_file if the_file is not None else "") for the_file in start_vars['output_files']]) self.categorical_vars = "" self.perm_strata = "" @@ -386,16 +388,19 @@ class DisplayMappingResults: self.dataset.group.genofile = self.genofile_string.split(":")[0] if self.mapping_method == "reaper" and self.manhattan_plot != True: - self.genotype = self.dataset.group.read_genotype_file(use_reaper=True) + self.genotype = self.dataset.group.read_genotype_file( + use_reaper=True) else: self.genotype = self.dataset.group.read_genotype_file() # Darwing Options try: if self.selectedChr > -1: - self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) + self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( + self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) else: - self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) + self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( + self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) except: if self.selectedChr > -1: self.graphWidth = self.GRAPH_DEFAULT_WIDTH @@ -472,9 +477,11 @@ class DisplayMappingResults: """ % (self.dataset.group.name, ", ".join(["'%s'" % X[0] for X in self.ChrList[1:]]))) self.ChrLengthMbList = [x[0] / 1000000.0 for x in self.ChrLengthMbList] - self.ChrLengthMbSum = reduce(lambda x, y: x + y, self.ChrLengthMbList, 0.0) + self.ChrLengthMbSum = reduce( + lambda x, y: x + y, self.ChrLengthMbList, 0.0) if self.ChrLengthMbList: - self.MbGraphInterval = self.ChrLengthMbSum / (len(self.ChrLengthMbList) * 12) # Empirical Mb interval + self.MbGraphInterval = self.ChrLengthMbSum / \ + (len(self.ChrLengthMbList) * 12) # Empirical Mb interval else: self.MbGraphInterval = 1 @@ -482,7 +489,8 @@ class DisplayMappingResults: for i, _chr in enumerate(self.genotype): self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM) - self.ChrLengthCMSum = reduce(lambda x, y: x + y, self.ChrLengthCMList, 0.0) + self.ChrLengthCMSum = reduce( + lambda x, y: x + y, self.ChrLengthCMList, 0.0) if self.plotScale == 'physic': self.GraphInterval = self.MbGraphInterval # Mb @@ -496,7 +504,8 @@ class DisplayMappingResults: smd = [] for sample in self.sample_vals_dict.keys(): if self.sample_vals_dict[sample] != "x": - temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample])) + temp = GeneralObject(name=sample, value=float( + self.sample_vals_dict[sample])) smd.append(temp) else: continue @@ -506,7 +515,8 @@ class DisplayMappingResults: if item.name == samplelist[j]: self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1 # default: - self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT + self.graphHeight = self.graphHeight + 2 * \ + (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT # END HaplotypeAnalyst ######################### @@ -529,7 +539,8 @@ class DisplayMappingResults: self.diffCol = [] for i, strain in enumerate(self.diffCol): - self.diffCol[i] = g.db.execute("select Id from Strain where Symbol = %s", strain).fetchone()[0] + self.diffCol[i] = g.db.execute( + "select Id from Strain where Symbol = %s", strain).fetchone()[0] ################################################################ # GeneCollection goes here @@ -552,13 +563,15 @@ class DisplayMappingResults: chrName = "X" else: chrName = self.selectedChr - self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "mouse") + self.geneCol = GeneUtil.loadGenes( + chrName, self.diffCol, self.startMb, self.endMb, "mouse") elif self.dataset.group.species == "rat": if self.selectedChr == 21: chrName = "X" else: chrName = self.selectedChr - self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "rat") + self.geneCol = GeneUtil.loadGenes( + chrName, self.diffCol, self.startMb, self.endMb, "rat") if self.geneCol and self.intervalAnalystChecked: ####################################################################### @@ -577,7 +590,8 @@ class DisplayMappingResults: showLocusForm = "" intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight)) with Bench("Drawing Plot"): - gifmap = self.plotIntMapping(intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm) + gifmap = self.plotIntMapping( + intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm) self.gifmap = gifmap.__str__() @@ -593,8 +607,10 @@ class DisplayMappingResults: # Scales plot differently for high resolution if self.draw2X: - intCanvasX2 = Image.new("RGBA", size=(self.graphWidth * 2, self.graphHeight * 2)) - gifmapX2 = self.plotIntMapping(intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2) + intCanvasX2 = Image.new("RGBA", size=( + self.graphWidth * 2, self.graphHeight * 2)) + gifmapX2 = self.plotIntMapping( + intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2) intCanvasX2.save( "{}.png".format( os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, @@ -612,7 +628,8 @@ class DisplayMappingResults: name=showLocusForm, submit=HtmlGenWrapper.create_input_tag(type_='hidden')) - hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} + hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+ \ + "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} for key in hddn.keys(): showLocusForm.append(HtmlGenWrapper.create_input_tag( name=key, value=hddn[key], type_='hidden')) @@ -631,7 +648,8 @@ class DisplayMappingResults: if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno': btminfo.append(HtmlGenWrapper.create_br_tag()) - btminfo.append('Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') + btminfo.append( + 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb= None, endMb = None, showLocusForm = ""): im_drawer = ImageDraw.Draw(canvas) @@ -673,7 +691,8 @@ class DisplayMappingResults: else: drawAreaHeight -= 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom if self.geneChecked: - drawAreaHeight -= self.NUM_GENE_ROWS * self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom + drawAreaHeight -= self.NUM_GENE_ROWS * \ + self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom else: if self.selectedChr > -1: drawAreaHeight -= 20 @@ -682,7 +701,8 @@ class DisplayMappingResults: # BEGIN HaplotypeAnalyst if self.haplotypeAnalystChecked and self.selectedChr > -1: - drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS + 10) * 2 * zoom + drawAreaHeight -= self.EACH_GENE_HEIGHT * \ + (self.NR_INDIVIDUALS + 10) * 2 * zoom # END HaplotypeAnalyst if zoom == 2: @@ -693,38 +713,48 @@ class DisplayMappingResults: newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset) # Draw the alternating-color background first and get plotXScale - plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + plotXScale = self.drawGraphBackground( + canvas, gifmap, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # draw bootstap if self.bootChecked and not self.multipleInterval: - self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, + offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # Draw clickable region and gene band if selected if self.plotScale == 'physic' and self.selectedChr > -1: - self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, + zoom=zoom, startMb=startMb, endMb=endMb) if self.geneChecked and self.geneCol: - self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, + zoom=zoom, startMb=startMb, endMb=endMb) if self.SNPChecked: - self.drawSNPTrackNew(canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb) + self.drawSNPTrackNew( + canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb) # BEGIN HaplotypeAnalyst if self.haplotypeAnalystChecked: - self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawHaplotypeBand( + canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # END HaplotypeAnalyst # Draw X axis - self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, + offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # Draw QTL curve - self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, + offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # draw legend if self.multipleInterval: - self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset) + self.drawMultiTraitName( + fd, canvas, gifmap, showLocusForm, offset=newoffset) elif self.legendChecked: self.drawLegendPanel(canvas, offset=newoffset, zoom=zoom) else: pass # draw position, no need to use a separate function - self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom=zoom) + self.drawProbeSetPosition( + canvas, plotXScale, offset=newoffset, zoom=zoom) return gifmap @@ -756,19 +786,24 @@ class DisplayMappingResults: if previous_chr_as_int != 1: BootCoord.append(BootChrCoord) BootChrCoord = [] - startX += (self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale + startX += ( + self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale if self.plotScale == 'physic': Xc = startX + (result['Mb'] - self.startMb) * plotXScale else: - Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale + Xc = startX + \ + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale BootChrCoord.append([Xc, self.bootResult[i]]) else: for i, result in enumerate(self.qtlresults): if str(result['chr']) == str(self.ChrList[self.selectedChr][0]): if self.plotScale == 'physic': - Xc = startX + (result['Mb'] - self.startMb) * plotXScale + Xc = startX + (result['Mb'] - \ + self.startMb) * plotXScale else: - Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale + Xc = startX + \ + (result['cM'] - self.qtlresults[0] + ['cM']) * plotXScale BootChrCoord.append([Xc, self.bootResult[i]]) BootCoord = [BootChrCoord] @@ -793,14 +828,16 @@ class DisplayMappingResults: if maxBootCount < bootCount: maxBootCount = bootCount # end if - reducedBootCoord.append([bootStartPixX, BootChrCoord[i][0], bootCount]) + reducedBootCoord.append( + [bootStartPixX, BootChrCoord[i][0], bootCount]) bootStartPixX = BootChrCoord[i][0] bootCount = BootChrCoord[i][1] # end else # end for # add last piece if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap / 2.0: - reducedBootCoord.append([bootStartPixX, BootChrCoord[-1][0], bootCount]) + reducedBootCoord.append( + [bootStartPixX, BootChrCoord[-1][0], bootCount]) else: reducedBootCoord[-1][2] += bootCount reducedBootCoord[-1][1] = BootChrCoord[-1][0] @@ -827,11 +864,13 @@ class DisplayMappingResults: # draw boot scale highestPercent = (maxBootCount * 100.0) / nboot bootScale = Plot.detScale(0, highestPercent) - bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1] / bootScale[2]) + bootScale = Plot.frange( + bootScale[0], bootScale[1], bootScale[1] / bootScale[2]) bootScale = bootScale[:-1] + [highestPercent] bootOffset = 50 * fontZoom - bootScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=13 * fontZoom) + bootScaleFont = ImageFont.truetype( + font=VERDANA_FILE, size=13 * fontZoom) im_drawer.rectangle( xy=((canvas.size[0] - bootOffset, yZero - bootHeightThresh), (canvas.size[0] - bootOffset - 15*zoom, yZero)), @@ -860,10 +899,12 @@ class DisplayMappingResults: startPosY = 30 else: startPosY = 15 - smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom) + smallLabelFont = ImageFont.truetype( + font=TREBUC_FILE, size=12 * fontZoom) leftOffset = canvas.size[0] - xRightOffset - 190 im_drawer.rectangle( - xy=((leftOffset, startPosY - 6), (leftOffset + 12, startPosY + 6)), + xy=((leftOffset, startPosY - 6), + (leftOffset + 12, startPosY + 6)), fill=YELLOW, outline=BLACK) im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY + TEXT_Y_DISPLACEMENT), text='Frequency of the Peak LRS', @@ -905,7 +946,8 @@ class DisplayMappingResults: locPixel = xLeftOffset for i, _chr in enumerate(self.ChrList[1:]): if _chr[0] != Chr: - locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale + locPixel += (self.ChrLengthDistList[i] + \ + self.GraphInterval) * plotXScale else: locPixel += Mb * plotXScale break @@ -921,7 +963,8 @@ class DisplayMappingResults: # the trait's position is between two traits if i > 0 and self.qtlresults[i - 1]['Mb'] < Mb and qtlresult['Mb'] >= Mb: - locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * (Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb'])) + locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * ( + Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb'])) break # the trait's position is on the right of the last genotype @@ -932,12 +975,15 @@ class DisplayMappingResults: for i, _chr in enumerate(self.ChrList): if i < (len(self.ChrList) - 1): if _chr != Chr: - locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale + locPixel += (self.ChrLengthDistList[i] + \ + self.GraphInterval) * plotXScale else: - locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / self.ChrLengthCMList[i]) * plotXScale + locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / \ + self.ChrLengthCMList[i]) * plotXScale break if locPixel >= 0 and self.plotScale == 'physic': - traitPixel = ((locPixel, yZero), (locPixel - 7, yZero + 14), (locPixel + 7, yZero + 14)) + traitPixel = ((locPixel, yZero), (locPixel - 7, + yZero + 14), (locPixel + 7, yZero + 14)) draw_open_polygon(canvas, xy=traitPixel, outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR) @@ -979,7 +1025,8 @@ class DisplayMappingResults: maxCount = max(SNPCounts) if maxCount > 0: for i in range(xLeftOffset, xLeftOffset + plotWidth): - snpDensity = float(SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount) + snpDensity = float( + SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount) im_drawer.line( xy=((i, drawSNPLocationY + (snpDensity) * zoom), (i, drawSNPLocationY - (snpDensity) * zoom)), @@ -1015,12 +1062,16 @@ class DisplayMappingResults: (rectWidth + rightShift, yPaddingTop + 10+kstep*15)), fill=thisLRSColor, outline=BLACK) im_drawer.text( - text=name, xy=(rectWidth + 2 + rightShift, yPaddingTop + 10 + kstep * 15), + text=name, xy=(rectWidth + 2 + rightShift, + yPaddingTop + 10 + kstep * 15), font=colorFont, fill=BLACK) if thisTrait.db: - COORDS = "%d,%d,%d,%d" % (rectWidth + 2 + rightShift, yPaddingTop + kstep * 15, rectWidth + 2 + rightShift + nameWidth, yPaddingTop + 10 + kstep * 15,) - HREF = "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) - Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF) + COORDS = "%d,%d,%d,%d" % (rectWidth + 2 + rightShift, yPaddingTop + kstep * \ + 15, rectWidth + 2 + rightShift + nameWidth, yPaddingTop + 10 + kstep * 15,) + HREF = "javascript:showDatabase3('%s','%s','%s','');" % ( + showLocusForm, thisTrait.db.name, thisTrait.name) + Areas = HtmlGenWrapper.create_area_tag( + shape='rect', coords=COORDS, href=HREF) gifmap.append(Areas) # TODO def drawLegendPanel(self, canvas, offset=(40, 120, 80, 10), zoom=1): @@ -1042,7 +1093,8 @@ class DisplayMappingResults: if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'): startPosY = 15 nCol = 2 - smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom) + smallLabelFont = ImageFont.truetype( + font=TREBUC_FILE, size=12 * fontZoom) leftOffset = canvas.size[0] - xRightOffset - 190 draw_open_polygon( @@ -1064,7 +1116,8 @@ class DisplayMappingResults: xy=((startPosX, startPosY), (startPosX + 32, startPosY)), fill=self.LRS_COLOR, width=2) im_drawer.text( - text=self.LRS_LOD, xy=(startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT), + text=self.LRS_LOD, xy=( + startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) startPosY += stepPosY @@ -1118,10 +1171,12 @@ class DisplayMappingResults: xy=((thisStartX, startPosY), (startPosX + 32, startPosY)), fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH) im_drawer.line( - xy=((thisStartX, startPosY + stepPosY), (startPosX + 32, startPosY + stepPosY)), + xy=((thisStartX, startPosY + stepPosY), + (startPosX + 32, startPosY + stepPosY)), fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH) im_drawer.text( - text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant), + text='Significant %s = %2.2f' % ( + self.LRS_LOD, self.significant), xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) im_drawer.text( text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive), @@ -1134,7 +1189,8 @@ class DisplayMappingResults: if self.dataset.type == "Publish" or self.dataset.type == "Geno": dataset_label = self.dataset.fullname else: - dataset_label = "%s - %s" % (self.dataset.group.name, self.dataset.fullname) + dataset_label = "%s - %s" % (self.dataset.group.name, + self.dataset.fullname) string1 = 'Dataset: %s' % (dataset_label) @@ -1151,7 +1207,8 @@ class DisplayMappingResults: string3 = 'Using GEMMA mapping method with ' if self.covariates != "": string3 += 'the cofactors below:' - cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")]) + cofactor_names = ", ".join( + [covar.split(":")[0] for covar in self.covariates.split(",")]) string4 = cofactor_names else: string3 += 'no cofactors' @@ -1159,7 +1216,8 @@ class DisplayMappingResults: string3 = 'Using R/qtl mapping method with ' if self.covariates != "": string3 += 'the cofactors below:' - cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")]) + cofactor_names = ", ".join( + [covar.split(":")[0] for covar in self.covariates.split(",")]) string4 = cofactor_names elif self.controlLocus and self.doControl != "false": string3 += '%s as control' % self.controlLocus @@ -1177,15 +1235,19 @@ class DisplayMappingResults: if self.selectedChr == -1: identification = "Mapping on All Chromosomes for " else: - identification = "Mapping on Chromosome %s for " % (self.ChrList[self.selectedChr][0]) + identification = "Mapping on Chromosome %s for " % ( + self.ChrList[self.selectedChr][0]) if self.this_trait.symbol: - identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.symbol) + identification += "Trait: %s - %s" % ( + self.this_trait.name, self.this_trait.symbol) elif self.dataset.type == "Publish": if self.this_trait.post_publication_abbreviation: - identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.post_publication_abbreviation) + identification += "Trait: %s - %s" % ( + self.this_trait.name, self.this_trait.post_publication_abbreviation) elif self.this_trait.pre_publication_abbreviation: - identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.pre_publication_abbreviation) + identification += "Trait: %s - %s" % ( + self.this_trait.name, self.this_trait.pre_publication_abbreviation) else: identification += "Trait: %s" % (self.this_trait.name) else: @@ -1265,7 +1327,8 @@ class DisplayMappingResults: tenPercentLength = geneLength * 0.0001 SNPdensity = theGO["snpCount"] / geneLength - exonStarts = list(map(float, theGO['exonStarts'].split(",")[:-1])) + exonStarts = list( + map(float, theGO['exonStarts'].split(",")[:-1])) exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1])) cdsStart = theGO['cdsStart'] cdsEnd = theGO['cdsEnd'] @@ -1274,8 +1337,10 @@ class DisplayMappingResults: strand = theGO["Strand"] exonCount = theGO["exonCount"] - geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel + geneStartPix = xLeftOffset + \ + plotXScale * (float(txStart) - startMb) + geneEndPix = xLeftOffset + plotXScale * \ + (float(txEnd) - startMb) # at least one pixel if (geneEndPix < xLeftOffset): return; # this gene is not on the screen @@ -1290,7 +1355,8 @@ class DisplayMappingResults: # found earlier, needs to be recomputed as snps are added # always apply colors now, even if SNP Track not checked - Zach 11/24/2010 - densities = [1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] + densities = [1.0000000000000001e-05, 0.094094033555233408, + 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] if SNPdensity < densities[0]: myColor = BLACK elif SNPdensity < densities[1]: @@ -1309,7 +1375,8 @@ class DisplayMappingResults: outlineColor = myColor fillColor = myColor - TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount) + TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % ( + geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount) # NL: 06-02-2011 Rob required to change this link for gene related HREF = geneNCBILink % geneSymbol @@ -1324,8 +1391,10 @@ class DisplayMappingResults: strand = theGO["Strand"] exonCount = 0 - geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel + geneStartPix = xLeftOffset + \ + plotXScale * (float(txStart) - startMb) + geneEndPix = xLeftOffset + plotXScale * \ + (float(txEnd) - startMb) # at least one pixel if (geneEndPix < xLeftOffset): return; # this gene is not on the screen @@ -1338,7 +1407,8 @@ class DisplayMappingResults: outlineColor = DARKBLUE fillColor = DARKBLUE - TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand) + TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % ( + geneSymbol, float(txStart), float(txEnd), strand) # NL: 06-02-2011 Rob required to change this link for gene related HREF = geneNCBILink % geneSymbol else: @@ -1347,7 +1417,8 @@ class DisplayMappingResults: TITLE = "Gene: %s" % geneSymbol # Draw Genes - geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom + geneYLocation = yPaddingTop + \ + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING else: @@ -1361,7 +1432,8 @@ class DisplayMappingResults: # draw the line that runs the entire length of the gene im_drawer.line( xy=( - (geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 * zoom), + (geneStartPix, geneYLocation + \ + self.EACH_GENE_HEIGHT / 2 * zoom), (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 *zoom)), fill=outlineColor, width=1) @@ -1401,8 +1473,10 @@ class DisplayMappingResults: # draw the blocks for the exon regions for i in range(0, len(exonStarts)): - exonStartPix = (exonStarts[i] - startMb) * plotXScale + xLeftOffset - exonEndPix = (exonEnds[i] - startMb) * plotXScale + xLeftOffset + exonStartPix = ( + exonStarts[i] - startMb) * plotXScale + xLeftOffset + exonEndPix = (exonEnds[i] - startMb) * \ + plotXScale + xLeftOffset if (exonStartPix < xLeftOffset): exonStartPix = xLeftOffset if (exonEndPix < xLeftOffset): @@ -1418,7 +1492,8 @@ class DisplayMappingResults: # draw gray blocks for 3' and 5' UTR blocks if cdsStart and cdsEnd: - utrStartPix = (txStart - startMb) * plotXScale + xLeftOffset + utrStartPix = (txStart - startMb) * \ + plotXScale + xLeftOffset utrEndPix = (cdsStart - startMb) * plotXScale + xLeftOffset if (utrStartPix < xLeftOffset): utrStartPix = xLeftOffset @@ -1436,7 +1511,8 @@ class DisplayMappingResults: labelText = "5'" im_drawer.text( text=labelText, - xy=(utrStartPix - 9, geneYLocation + self.EACH_GENE_HEIGHT), + xy=(utrStartPix - 9, geneYLocation + \ + self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) # the second UTR region @@ -1459,7 +1535,8 @@ class DisplayMappingResults: labelText = "3'" im_drawer.text( text=labelText, - xy=(utrEndPix + 2, geneYLocation + self.EACH_GENE_HEIGHT), + xy=(utrEndPix + 2, geneYLocation + \ + self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) # draw the genes as rectangles @@ -1469,7 +1546,8 @@ class DisplayMappingResults: (geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))), outline=outlineColor, fill=fillColor) - COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) + COORDS = "%d, %d, %d, %d" % ( + geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) # NL: 06-02-2011 Rob required to display NCBI info in a new window gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1496,7 +1574,8 @@ class DisplayMappingResults: smd = [] for sample in self.sample_vals_dict.keys(): if self.sample_vals_dict[sample] != "x" and sample in samplelist: - temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample])) + temp = GeneralObject(name=sample, value=float( + self.sample_vals_dict[sample])) smd.append(temp) else: continue @@ -1517,8 +1596,10 @@ class DisplayMappingResults: txStart = _chr[i].Mb txEnd = _chr[i].Mb - geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0 - geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) - 0 + geneStartPix = xLeftOffset + plotXScale * \ + (float(txStart) - startMb) - 0 + geneEndPix = xLeftOffset + plotXScale * \ + (float(txEnd) - startMb) - 0 drawit = 1 if (geneStartPix < xLeftOffset): @@ -1546,8 +1627,10 @@ class DisplayMappingResults: txStart = _chr[j].Mb txEnd = _chr[j].Mb - geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0 - geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) + 0 + geneStartPix = xLeftOffset + plotXScale * \ + (float(txStart) - startMb) - 0 + geneEndPix = xLeftOffset + plotXScale * \ + (float(txEnd) - startMb) + 0 if oldgeneEndPix >= xLeftOffset: drawStart = oldgeneEndPix + 4 @@ -1585,7 +1668,8 @@ class DisplayMappingResults: # Draw Genes - geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT) * zoom + geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * \ + (self.EACH_GENE_HEIGHT) * zoom if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING else: @@ -1606,7 +1690,8 @@ class DisplayMappingResults: if (plotbxd == 1): ind = 0 if samplelist[k] in [item.name for item in smd]: - ind = [item.name for item in smd].index(samplelist[k]) + ind = [item.name for item in smd].index( + samplelist[k]) maxind = max(ind, maxind) @@ -1637,8 +1722,10 @@ class DisplayMappingResults: geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)), outline=outlineColor, fill=fillColor) - COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT)) - TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart)) + COORDS = "%d, %d, %d, %d" % ( + geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT)) + TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % ( + samplelist[k], _chr[j].name, float(txStart)) HREF = '' gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1683,7 +1770,8 @@ class DisplayMappingResults: plotbxd = 1 if (plotbxd == 1): - ind = [item.name for item in smd].index(samplelist[j]) - 1 + ind = [item.name for item in smd].index( + samplelist[j]) - 1 expr = smd[ind].value # Place where font is hardcoded @@ -1691,13 +1779,15 @@ class DisplayMappingResults: text="%s" % (samplelist[j]), xy=((xLeftOffset + plotWidth + 10), geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom), - font=ImageFont.truetype(font=VERDANA_FILE, size=12), + font=ImageFont.truetype( + font=VERDANA_FILE, size=12), fill=BLACK) im_drawer.text( text="%2.2f" % (expr), xy=((xLeftOffset + plotWidth + 60), geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom), - font=ImageFont.truetype(font=VERDANA_FILE, size=12), + font=ImageFont.truetype( + font=VERDANA_FILE, size=12), fill=BLACK) # END HaplotypeAnalyst @@ -1719,12 +1809,16 @@ class DisplayMappingResults: # but it makes the HTML huge, and takes forever to render the page in the first place) # Draw the bands that you can click on to go to UCSC / Ensembl MAX_CLICKABLE_REGION_DIVISIONS = 100 - clickableRegionLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=9) - pixelStep = max(5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS)) + clickableRegionLabelFont = ImageFont.truetype( + font=VERDANA_FILE, size=9) + pixelStep = max( + 5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS)) # pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome. - numBasesCurrentlyOnScreen = self.kONE_MILLION * abs(startMb - endMb) # Number of bases on screen now - flankingWidthInBases = int (min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION))) + numBasesCurrentlyOnScreen = self.kONE_MILLION * \ + abs(startMb - endMb) # Number of bases on screen now + flankingWidthInBases = int ( + min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION))) webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0 # Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing. @@ -1733,23 +1827,33 @@ class DisplayMappingResults: paddingTop = yTopOffset if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": - phenogenPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING) - ucscPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING) - ensemblPaddingTop = paddingTop + 3 * (self.BAND_HEIGHT + self.BAND_SPACING) + phenogenPaddingTop = paddingTop + \ + (self.BAND_HEIGHT + self.BAND_SPACING) + ucscPaddingTop = paddingTop + 2 * \ + (self.BAND_HEIGHT + self.BAND_SPACING) + ensemblPaddingTop = paddingTop + 3 * \ + (self.BAND_HEIGHT + self.BAND_SPACING) else: - ucscPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING) - ensemblPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING) + ucscPaddingTop = paddingTop + \ + (self.BAND_HEIGHT + self.BAND_SPACING) + ensemblPaddingTop = paddingTop + 2 * \ + (self.BAND_HEIGHT + self.BAND_SPACING) if zoom == 1: for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep): - calBase = self.kONE_MILLION * (startMb + (endMb - startMb) * (pixel - xLeftOffset - 0.0) / plotWidth) + calBase = self.kONE_MILLION * \ + (startMb + (endMb - startMb) * \ + (pixel - xLeftOffset - 0.0) / plotWidth) xBrowse1 = pixel - xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1)) + xBrowse2 = min(xLeftOffset + plotWidth, + (pixel + pixelStep - 1)) - WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT)) - WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0) + WEBQTL_COORDS = "%d, %d, %d, %d" % ( + xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT)) + WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max( + 0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" gifmap.append( @@ -1764,15 +1868,19 @@ class DisplayMappingResults: outline=self.CLICKABLE_WEBQTL_REGION_COLOR, fill=self.CLICKABLE_WEBQTL_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, paddingTop), (xBrowse1, (paddingTop + self.BAND_HEIGHT))), + xy=((xBrowse1, paddingTop), (xBrowse1, + (paddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": - PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT)) + PHENOGEN_COORDS = "%d, %d, %d, %d" % ( + xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % ( + self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) else: - PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % ( + self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1786,14 +1894,18 @@ class DisplayMappingResults: outline=self.CLICKABLE_PHENOGEN_REGION_COLOR, fill=self.CLICKABLE_PHENOGEN_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, (phenogenPaddingTop + self.BAND_HEIGHT))), + xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, + (phenogenPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR) - UCSC_COORDS = "%d, %d, %d, %d" % (xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT)) + UCSC_COORDS = "%d, %d, %d, %d" % ( + xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) + UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % ( + self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) else: - UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % ( + self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser" gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1811,11 +1923,14 @@ class DisplayMappingResults: (xBrowse1, (ucscPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR) - ENSEMBL_COORDS = "%d, %d, %d, %d" % (xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT)) + ENSEMBL_COORDS = "%d, %d, %d, %d" % ( + xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % ( + self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) else: - ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % ( + self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser" gifmap.append(HtmlGenWrapper.create_area_tag( shape='rect', @@ -1841,19 +1956,23 @@ class DisplayMappingResults: if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": im_drawer.text( text="Click to view the corresponding section of the genome in PhenoGen", - xy=((xLeftOffset + 10), phenogenPaddingTop), # + self.BAND_HEIGHT/2), + # + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), phenogenPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_PHENOGEN_TEXT_COLOR) im_drawer.text( text="Click to view the corresponding section of the genome in the UCSC Genome Browser", - xy=((xLeftOffset + 10), ucscPaddingTop), # + self.BAND_HEIGHT/2), + # + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), ucscPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_UCSC_TEXT_COLOR) im_drawer.text( text="Click to view the corresponding section of the genome in the Ensembl Genome Browser", - xy=((xLeftOffset + 10), ensemblPaddingTop), # + self.BAND_HEIGHT/2), + # + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), ensemblPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_ENSEMBL_TEXT_COLOR) # draw the gray text - chrFont = ImageFont.truetype(font=VERDANA_BOLD_FILE, size=26 * zoom) + chrFont = ImageFont.truetype( + font=VERDANA_BOLD_FILE, size=26 * zoom) chrX = xLeftOffset + plotWidth - 2 - im_drawer.textsize( "Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)[0] im_drawer.text( @@ -1922,8 +2041,10 @@ class DisplayMappingResults: (Xc, yZero + xMajorTickHeight)), fill=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark - labelStr = str(formatStr % _Mb) # What Mbase location to put on the label - strWidth, strHeight = im_drawer.textsize(labelStr, font=MBLabelFont) + # What Mbase location to put on the label + labelStr = str(formatStr % _Mb) + strWidth, strHeight = im_drawer.textsize( + labelStr, font=MBLabelFont) drawStringXc = (Xc - (strWidth / 2.0)) im_drawer.text(xy=(drawStringXc, strYLoc), text=labelStr, font=MBLabelFont, @@ -1956,9 +2077,11 @@ class DisplayMappingResults: canvas, text=str(tickdists), font=MBLabelFont, xy=(startPosX + tickdists * plotXScale, yZero + 10 * zoom), fill=BLACK, angle=270) - startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale + startPosX += (self.ChrLengthDistList[i] + \ + self.GraphInterval) * plotXScale - megabaseLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) + megabaseLabelFont = ImageFont.truetype( + font=VERDANA_FILE, size=int(18 * zoom * 1.5)) im_drawer.text( text="Megabases", xy=( @@ -1984,7 +2107,8 @@ class DisplayMappingResults: if _locus.cM != preLpos: distinctCount += 1 preLpos = _locus.cM - thisChr.append([_locus.name, _locus.cM - Locus0CM]) + thisChr.append( + [_locus.name, _locus.cM - Locus0CM]) else: for j in (0, nLoci / 4, nLoci / 2, nLoci*3/4, -1): while _chr[j].name == ' - ': @@ -1992,7 +2116,8 @@ class DisplayMappingResults: if _chr[j].cM != preLpos: distinctCount += 1 preLpos = _chr[j].cM - thisChr.append([_chr[j].name, _chr[j].cM - Locus0CM]) + thisChr.append( + [_chr[j].name, _chr[j].cM - Locus0CM]) ChrAInfo.append(thisChr) else: for i, _chr in enumerate(self.genotype): @@ -2004,7 +2129,8 @@ class DisplayMappingResults: if _locus.cM != preLpos: distinctCount += 1 preLpos = _locus.cM - thisChr.append([_locus.name, _locus.cM - Locus0CM]) + thisChr.append( + [_locus.name, _locus.cM - Locus0CM]) ChrAInfo.append(thisChr) stepA = (plotWidth + 0.0) / distinctCount @@ -2053,7 +2179,8 @@ class DisplayMappingResults: outline=rectColor, fill=rectColor, width=0) COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\ xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth) - HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name + "Geno") + HREF = "/show_trait?trait_id=%s&dataset=%s" % ( + Lname, self.dataset.group.name + "Geno") #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname) Areas = HtmlGenWrapper.create_area_tag( shape='rect', @@ -2067,9 +2194,11 @@ class DisplayMappingResults: im_drawer.line( xy=((startPosX, yZero), (startPosX, yZero + 40)), fill=lineColor) - startPosX += (self.ChrLengthDistList[j] + self.GraphInterval) * plotXScale + startPosX += (self.ChrLengthDistList[j] + \ + self.GraphInterval) * plotXScale - centimorganLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) + centimorganLabelFont = ImageFont.truetype( + font=VERDANA_FILE, size=int(18 * zoom * 1.5)) im_drawer.text( text="Centimorgans", xy=(xLeftOffset + (plotWidth - im_drawer.textsize( @@ -2100,29 +2229,39 @@ class DisplayMappingResults: # ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD if self.lrsMax <= 0: # sliding scale if "lrs_value" in self.qtlresults[0]: - LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults]) + LRS_LOD_Max = max([result['lrs_value'] + for result in self.qtlresults]) if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR if self.permChecked and self.nperm > 0 and not self.multipleInterval: - self.significant = min(self.significant / self.LODFACTOR, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS) + self.significant = min( + self.significant / self.LODFACTOR, webqtlConfig.MAXLRS) + self.suggestive = min( + self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS) else: if self.permChecked and self.nperm > 0 and not self.multipleInterval: - self.significant = min(self.significant, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) + self.significant = min( + self.significant, webqtlConfig.MAXLRS) + self.suggestive = min( + self.suggestive, webqtlConfig.MAXLRS) else: pass else: - LRS_LOD_Max = max([result['lod_score'] for result in self.qtlresults]) + LRS_LOD_Max = max([result['lod_score'] + for result in self.qtlresults]) if self.LRS_LOD == "LRS": LRS_LOD_Max = LRS_LOD_Max * self.LODFACTOR if self.permChecked and self.nperm > 0 and not self.multipleInterval: - self.significant = min(self.significant * self.LODFACTOR, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS) + self.significant = min( + self.significant * self.LODFACTOR, webqtlConfig.MAXLRS) + self.suggestive = min( + self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS) else: if self.permChecked and self.nperm > 0 and not self.multipleInterval: - self.significant = min(self.significant, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) + self.significant = min( + self.significant, webqtlConfig.MAXLRS) + self.suggestive = min( + self.suggestive, webqtlConfig.MAXLRS) else: pass @@ -2143,7 +2282,8 @@ class DisplayMappingResults: self.js_data = json.dumps(js_data) LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) - LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) + LRSLODFont = ImageFont.truetype( + font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight # LRSHeightThresh = drawAreaHeight @@ -2188,7 +2328,8 @@ class DisplayMappingResults: # draw the "LRS" or "LOD" string to the left of the axis LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) - LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) + LRSLODFont = ImageFont.truetype( + font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight # TEXT_X_DISPLACEMENT = -20 @@ -2239,7 +2380,8 @@ class DisplayMappingResults: # ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist): - rightEdge = int(start_pos_x + chr_length_dist * plotXScale - self.SUGGESTIVE_WIDTH / 1.5) + rightEdge = int(start_pos_x + chr_length_dist * \ + plotXScale - self.SUGGESTIVE_WIDTH / 1.5) im_drawer.line( xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY), (rightEdge, suggestiveY)), @@ -2253,15 +2395,19 @@ class DisplayMappingResults: width=self.SIGNIFICANT_WIDTH * zoom # , clipX=(xLeftOffset, xLeftOffset + plotWidth-2) ) - sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2) - sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2) + sugg_coords = "%d, %d, %d, %d" % ( + start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2) + sig_coords = "%d, %d, %d, %d" % ( + start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2) if self.LRS_LOD == 'LRS': sugg_title = "Suggestive LRS = %0.2f" % self.suggestive sig_title = "Significant LRS = %0.2f" % self.significant else: - sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive / 4.61) - sig_title = "Significant LOD = %0.2f" % (self.significant / 4.61) + sugg_title = "Suggestive LOD = %0.2f" % ( + self.suggestive / 4.61) + sig_title = "Significant LOD = %0.2f" % ( + self.significant / 4.61) Areas1 = HtmlGenWrapper.create_area_tag( shape='rect', coords=sugg_coords, @@ -2273,24 +2419,28 @@ class DisplayMappingResults: gifmap.append(Areas1) gifmap.append(Areas2) - start_pos_x += (chr_length_dist + self.GraphInterval) * plotXScale + start_pos_x += (chr_length_dist + \ + self.GraphInterval) * plotXScale return start_pos_x for i, _chr in enumerate(self.genotype): if self.selectedChr != -1: if _chr.name == self.ChrList[self.selectedChr][0]: - startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[0]) + startPosX = add_suggestive_significant_lines_and_legend( + startPosX, self.ChrLengthDistList[0]) break else: continue else: - startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[i]) + startPosX = add_suggestive_significant_lines_and_legend( + startPosX, self.ChrLengthDistList[i]) if self.multipleInterval: lrsEdgeWidth = 1 else: if self.additiveChecked: - additiveMax = max([abs(X['additive']) for X in self.qtlresults]) + additiveMax = max([abs(X['additive']) + for X in self.qtlresults]) lrsEdgeWidth = 3 if zoom == 2: @@ -2300,7 +2450,8 @@ class DisplayMappingResults: AdditiveCoordXY = [] DominanceCoordXY = [] - symbolFont = ImageFont.truetype(font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot + symbolFont = ImageFont.truetype( + font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot previous_chr = 1 previous_chr_as_int = 0 @@ -2332,7 +2483,8 @@ class DisplayMappingResults: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + Xcm = (yZero - Yc0) / \ + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2340,7 +2492,8 @@ class DisplayMappingResults: # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( - xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))), + xy=((Xcm, yZero), + (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) @@ -2391,7 +2544,8 @@ class DisplayMappingResults: AdditiveCoordXY = [] previous_chr = qtlresult['chr'] previous_chr_as_int += 1 - newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale + newStartPosX = ( + self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale if newStartPosX != oldStartPosX: startPosX += newStartPosX oldStartPosX = newStartPosX @@ -2408,10 +2562,12 @@ class DisplayMappingResults: if self.genotype.filler: if self.selectedChr != -1: start_cm = self.genotype[self.selectedChr - 1][0].cM - Xc = startPosX + (qtlresult['Mb'] - start_cm) * plotXScale + Xc = startPosX + \ + (qtlresult['Mb'] - start_cm) * plotXScale else: start_cm = self.genotype[previous_chr_as_int][0].cM - Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * (((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) + Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * ( + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) else: Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale @@ -2425,17 +2581,23 @@ class DisplayMappingResults: if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) - Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR) + Yc = yZero - webqtlConfig.MAXLRS * \ + LRSHeightThresh / \ + (LRS_LOD_Max * self.LODFACTOR) else: #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) - Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR) + Yc = yZero - \ + qtlresult['lrs_value'] * LRSHeightThresh / \ + (LRS_LOD_Max * self.LODFACTOR) else: if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max else: #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / LRS_LOD_Max + Yc = yZero - \ + qtlresult['lrs_value'] * \ + LRSHeightThresh / LRS_LOD_Max else: if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] @@ -2443,10 +2605,14 @@ class DisplayMappingResults: else: if self.LRS_LOD == "LRS": #Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lod_score'] * self.LODFACTOR * LRSHeightThresh / LRS_LOD_Max + Yc = yZero - \ + qtlresult['lod_score'] * self.LODFACTOR * \ + LRSHeightThresh / LRS_LOD_Max else: #Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lod_score'] * LRSHeightThresh / LRS_LOD_Max + Yc = yZero - \ + qtlresult['lod_score'] * \ + LRSHeightThresh / LRS_LOD_Max if self.manhattan_plot == True: if self.color_scheme == "single": @@ -2462,7 +2628,8 @@ class DisplayMappingResults: im_drawer.text( text="5", xy=( - Xc - im_drawer.textsize("5", font=symbolFont)[0] / 2 + 1, + Xc - im_drawer.textsize("5", + font=symbolFont)[0] / 2 + 1, Yc - 4), fill=point_color, font=symbolFont) else: @@ -2471,7 +2638,8 @@ class DisplayMappingResults: if not self.multipleInterval and self.additiveChecked: if additiveMax == 0.0: additiveMax = 0.000001 - Yc = yZero - qtlresult['additive'] * AdditiveHeightThresh / additiveMax + Yc = yZero - qtlresult['additive'] * \ + AdditiveHeightThresh / additiveMax AdditiveCoordXY.append((Xc, Yc)) m += 1 @@ -2496,7 +2664,8 @@ class DisplayMappingResults: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + Xcm = (yZero - Yc0) / \ + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2561,7 +2730,8 @@ class DisplayMappingResults: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + Xcm = (yZero - Yc0) / \ + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2616,9 +2786,11 @@ class DisplayMappingResults: # draw additive scale if not self.multipleInterval and self.additiveChecked: - additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) + additiveScaleFont = ImageFont.truetype( + font=VERDANA_FILE, size=16 * zoom) additiveScale = Plot.detScaleOld(0, additiveMax) - additiveStep = (additiveScale[1] - additiveScale[0]) / additiveScale[2] + additiveStep = (additiveScale[1] - \ + additiveScale[0]) / additiveScale[2] additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) addPlotScale = AdditiveHeightThresh / additiveMax TEXT_Y_DISPLACEMENT = -8 @@ -2633,7 +2805,8 @@ class DisplayMappingResults: scaleStr = "%2.3f" % item im_drawer.text( text=scaleStr, - xy= (xLeftOffset + plotWidth + 6, additiveY + TEXT_Y_DISPLACEMENT), + xy= (xLeftOffset + plotWidth + 6, + additiveY + TEXT_Y_DISPLACEMENT), font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE) im_drawer.line( @@ -2690,14 +2863,16 @@ class DisplayMappingResults: plotXScale = plotWidth / drawRegionDistance else: # multiple chromosome view - plotXScale = plotWidth / ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance) + plotXScale = plotWidth / \ + ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance) startPosX = xLeftOffset if fontZoom == 1.5: chrFontZoom = 2 else: chrFontZoom = 1 - chrLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=24 * chrFontZoom) + chrLabelFont = ImageFont.truetype( + font=VERDANA_FILE, size=24 * chrFontZoom) for i, _chr in enumerate(self.genotype): if (i % 2 == 0): @@ -2712,14 +2887,18 @@ class DisplayMappingResults: outline=GAINSBORO, fill=theBackColor) - chrNameWidth, chrNameHeight = im_drawer.textsize(_chr.name, font=chrLabelFont) - chrStartPix = startPosX + (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2 - chrEndPix = startPosX + (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2 + chrNameWidth, chrNameHeight = im_drawer.textsize( + _chr.name, font=chrLabelFont) + chrStartPix = startPosX + \ + (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2 + chrEndPix = startPosX + \ + (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2 TEXT_Y_DISPLACEMENT = 0 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT), text=_chr.name, font=chrLabelFont, fill=BLACK) - COORDS = "%d,%d,%d,%d" % (chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20) + COORDS = "%d,%d,%d,%d" % ( + chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20) # add by NL 09-03-2010 HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList) @@ -2729,7 +2908,8 @@ class DisplayMappingResults: coords=COORDS, href=HREF) gifmap.append(Areas) - startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale + startPosX += (self.ChrLengthDistList[i] + \ + self.GraphInterval) * plotXScale return plotXScale @@ -2746,7 +2926,8 @@ class DisplayMappingResults: perm_output = self.perm_output filename = webqtlUtil.genRandStr("Reg_") - Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test') + Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, + YLabel='Frequency', title=' Histogram of Permutation Test') myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR + filename), format='gif') @@ -2825,7 +3006,8 @@ class DisplayMappingResults: txEnd = theGO["TxEnd"] theGO["snpDensity"] = theGO["snpCount"] / geneLength if self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST: - geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"] + geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO[ + "GeneID"] if theGO["snpCount"]: snpString = HT.Link( @@ -2842,7 +3024,9 @@ class DisplayMappingResults: else: snpString = 0 - mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit" + mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + \ + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str( + int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit" # the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: @@ -2854,7 +3038,8 @@ class DisplayMappingResults: humanChr = theGO['humanGene']["Chromosome"] humanTxStart = theGO['humanGene']["TxStart"] - humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"])) + humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % ( + humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"])) else: humanStartString = humanChr = humanStartDisplay = "--" @@ -2879,7 +3064,8 @@ class DisplayMappingResults: else: chr_as_int = int(theGO["Chromosome"]) - 1 if refGene: - literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A") + literatureCorrelationString = str(self.getLiteratureCorrelation( + self.cursor, refGene, theGO['GeneID']) or "N/A") this_row = [selectCheck.__str__(), str(tableIterationsCnt), @@ -2947,7 +3133,8 @@ class DisplayMappingResults: if theGO["GeneID"] != "": geneSymbolNCBI = str(HtmlGenWrapper.create_link_tag( - "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format(theGO["GeneID"]), + "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format( + theGO["GeneID"]), theGO["GeneSymbol"], Class="normalsize", target="_blank")) @@ -2960,7 +3147,8 @@ class DisplayMappingResults: chr_as_int = int(theGO["Chromosome"]) - 1 geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"])) - geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1)) + geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float( + theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1)) avgExprVal = [] if avgExprVal != "" and avgExprVal: diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 68689104..289f1d5c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -149,7 +149,8 @@ def gen_covariates_file(this_dataset, covariates, samples): dataset_name = covariate.split(":")[1] if dataset_name == "Temp": temp_group = trait_name.split("_")[2] - dataset_ob = create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = temp_group) + dataset_ob = create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = temp_group) else: dataset_ob = create_dataset(covariate.split(":")[1]) trait_ob = create_trait(dataset=dataset_ob, diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 22a50bb8..2fa80841 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -10,7 +10,8 @@ logger = utility.logger.getLogger(__name__) def run_plink(this_trait, dataset, species, vals, maf): - plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_") + plink_output_filename = webqtlUtil.genRandStr( + f"{dataset.group.name}_{this_trait.name}_") gen_pheno_txt_file(dataset, vals) plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc " @@ -41,7 +42,8 @@ def gen_pheno_txt_file(this_dataset, vals): this_val = -9 else: this_val = vals[i] - outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") + outfile.write("0 " + line[1] + " " + line[2] + " " + \ + line[3] + " " + line[4] + " " + str(this_val) + "\n") def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''): @@ -162,7 +164,8 @@ def parse_plink_output(output_filename, species): def build_line_list(line=""): - line_list = line.strip().split(' ') # irregular number of whitespaces between columns + # irregular number of whitespaces between columns + line_list = line.strip().split(' ') line_list = [item for item in line_list if item != ''] line_list = [item.strip() for item in line_list] diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index b8fe2c37..f932498f 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -26,7 +26,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo gen_pheno_txt_file(samples, vals, trait_filename) output_filename = (f"{this_dataset.group.name}_GWA_" + - ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) ) bootstrap_filename = None permu_filename = None @@ -34,19 +35,22 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo opt_list = [] if boot_check and num_bootstrap > 0: bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" + - ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) ) opt_list.append("-b") opt_list.append(f"--n_bootstrap {str(num_bootstrap)}") - opt_list.append(f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") + opt_list.append( + f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") if num_perm > 0: permu_filename = ("{this_dataset.group.name}_PERM_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) ) opt_list.append("-n " + str(num_perm)) - opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") + opt_list.append( + "--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") if control_marker != "" and do_control == "true": opt_list.append("-c " + control_marker) if manhattan_plot != True: @@ -58,7 +62,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo genofile_name, TEMPDIR, trait_filename, - " ".join(opt_list), + " ".join( + opt_list), webqtlConfig.GENERATED_IMAGE_DIR, output_filename)) @@ -67,7 +72,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo else: output_filename, permu_filename, bootstrap_filename = output_files - marker_obs, permu_vals, bootstrap_vals = parse_reaper_output(output_filename, permu_filename, bootstrap_filename) + marker_obs, permu_vals, bootstrap_vals = parse_reaper_output( + output_filename, permu_filename, bootstrap_filename) suggestive = 0 significant = 0 @@ -193,7 +199,8 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da suggestive = 0 significant = 0 else: - perm_output = genotype.permutation(strains=trimmed_samples, trait=trimmed_values, nperm=num_perm) + perm_output = genotype.permutation( + strains=trimmed_samples, trait=trimmed_values, nperm=num_perm) suggestive = perm_output[int(num_perm * 0.37 - 1)] significant = perm_output[int(num_perm * 0.95 - 1)] # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case @@ -257,7 +264,8 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da json_data['markernames'].append(reaper_locus.name) # if self.additive: # self.json_data['additive'].append(qtl.additive) - locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} + locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, + "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb, "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance} qtl_results.append(qtl) @@ -270,5 +278,6 @@ def natural_sort(marker_list): Changed to return indices instead of values, though, since the same reordering needs to be applied to bootstrap results """ convert = lambda text: int(text) if text.isdigit() else text.lower() - alphanum_key = lambda key: [convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr']))] + alphanum_key = lambda key: [convert(c) for c in re.split( + '([0-9]+)', str(marker_list[key]['chr']))] return sorted(list(range(len(marker_list))), key=alphanum_key) diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 588600f5..c2b165a4 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -51,7 +51,8 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec # Get pointers to some R/qtl functions scanone = ro.r["scanone"] # Map the scanone function scantwo = ro.r["scantwo"] # Map the scantwo function - calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function + # Map the calc.genoprob function + calc_genoprob = ro.r["calc.genoprob"] crossname = dataset.group.name # try: @@ -67,14 +68,16 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec scale_units = "Mb" generate_cross_from_geno(dataset, scale_units) - GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function + # Map the local GENOtoCSVR function + GENOtoCSVR = ro.r["GENOtoCSVR"] crossfilelocation = TMPDIR + crossname + ".cross" if dataset.group.genofile: genofilelocation = locate(dataset.group.genofile, "genotype") else: genofilelocation = locate(dataset.group.name + ".geno", "genotype") logger.info("Going to create a cross from geno"); - cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available + # TODO: Add the SEX if that is available + cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) logger.info("before calc_genoprob"); if manhattan_plot: cross_object = calc_genoprob(cross_object) @@ -85,14 +88,19 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec logger.info("phenostring done"); names_string = sanitize_rqtl_names(samples) logger.info("sanitized pheno and names"); - cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype - cross_object = add_names(cross_object, names_string, "the_names") # Add the phenotype + # Add the phenotype + cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") + # Add the phenotype + cross_object = add_names(cross_object, names_string, "the_names") logger.info("Added pheno and names"); - marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers + # Create the additive covariate markers + marker_covars = create_marker_covariates(control_marker, cross_object) logger.info("Marker covars done"); if cofactors != "": logger.info("Cofactors: " + cofactors); - cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits + # Create the covariates from selected traits + cross_object, trait_covars = add_cofactors( + cross_object, dataset, cofactors, samples) ro.r('all_covars <- cbind(marker_covars, trait_covars)') else: ro.r('all_covars <- marker_covars') @@ -100,9 +108,11 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec # DEBUG to save the session object to file if pair_scan: if do_control == "true": - logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16) + logger.info("Using covariate"); result_data_frame = scantwo( + cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16) else: - logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16) + logger.info("No covariates"); result_data_frame = scantwo( + cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16) pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png" png(file=TEMPDIR + pair_scan_filename) @@ -112,25 +122,36 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec return process_pair_scan_results(result_data_frame) else: if do_control == "true" or cofactors != "": - logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method) + logger.info("Using covariate"); result_data_frame = scanone( + cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method) ro.r('save.image(file = "/home/zas1024/gn2-zach/itp_cofactor_test.RData")') else: - logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno="the_pheno", model=model, method=method) - - if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user) - if len(perm_strata_list) > 0: # ZS: The strata list would only be populated if "Stratified" was checked on before mapping - cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list) + logger.info("No covariates"); result_data_frame = scanone( + cross_object, pheno="the_pheno", model=model, method=method) + + # Do permutation (if requested by user) + if num_perm > 0 and permCheck == "ON": + # ZS: The strata list would only be populated if "Stratified" was checked on before mapping + if len(perm_strata_list) > 0: + cross_object, strata_ob = add_perm_strata( + cross_object, perm_strata_list) if do_control == "true" or cofactors != "": - perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method) + perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int( + num_perm), perm_strata = strata_ob, model=model, method=method) else: - perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method) + perm_data_frame = scanone( + cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method) else: if do_control == "true" or cofactors != "": - perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), model=model, method=method) + perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int( + num_perm), model=model, method=method) else: - perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, model=model, method=method) + perm_data_frame = scanone( + cross_object, pheno_col="the_pheno", n_perm=num_perm, model=model, method=method) - perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface + # Functions that sets the thresholds for the webinterface + perm_output, suggestive, significant = process_rqtl_perm_results( + num_perm, perm_data_frame) return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species) else: return process_rqtl_results(result_data_frame, dataset.group.species) @@ -147,7 +168,8 @@ def generate_cross_from_rdata(dataset): """ % (rdata_location)) -def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly +# TODO: Need to figure out why some genofiles have the wrong format and don't convert properly +def generate_cross_from_geno(dataset, scale_units): ro.r(""" trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) } @@ -246,7 +268,8 @@ def sanitize_rqtl_names(vals): def add_phenotype(cross, pheno_as_string, col_name): ro.globalenv["the_cross"] = cross ro.r('pheno <- data.frame(pull.pheno(the_cross))') - ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))') + ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + \ + ' = as.numeric(' + pheno_as_string + '))') return ro.r["the_cross"] @@ -270,7 +293,8 @@ def add_categorical_covar(cross, covar_as_string, i): #logger.info("loop" + str(x)); col_name = "covar_" + str(i) + "_" + str(x) #logger.info("col_name" + col_name); - ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = newcovar[,' + str(x) + '])') + ro.r('the_cross$pheno <- cbind(pheno, ' + \ + col_name + ' = newcovar[,' + str(x) + '])') col_names.append(col_name) #logger.info("loop" + str(x) + "done"); @@ -281,7 +305,8 @@ def add_categorical_covar(cross, covar_as_string, i): def add_names(cross, names_as_string, col_name): ro.globalenv["the_cross"] = cross ro.r('pheno <- data.frame(pull.pheno(the_cross))') - ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')') + ro.r('the_cross$pheno <- cbind(pheno, ' + \ + col_name + ' = ' + names_as_string + ')') return ro.r["the_cross"] @@ -330,9 +355,11 @@ def add_cofactors(cross, this_dataset, covariates, samples): logger.info("Covariate: " + covariate + " is of type: " + datatype); if(datatype == "categorical"): # Cat variable logger.info("call of add_categorical_covar"); - cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross + cross, col_names = add_categorical_covar( + cross, covar_as_string, i) # Expand and add it to the cross logger.info("add_categorical_covar returned"); - for z, col_name in enumerate(col_names): # Go through the additional covar names + # Go through the additional covar names + for z, col_name in enumerate(col_names): if i < (len(covariate_list) - 1): covar_name_string += '"' + col_name + '", ' else: @@ -355,18 +382,22 @@ def add_cofactors(cross, this_dataset, covariates, samples): def create_marker_covariates(control_marker, cross): ro.globalenv["the_cross"] = cross - ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix - userinput_sanitized = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user + # Get the genotype matrix + ro.r('genotypes <- pull.geno(the_cross)') + # TODO: sanitize user input, Never Ever trust a user + userinput_sanitized = control_marker.replace(" ", "").split(",") logger.debug(userinput_sanitized) if len(userinput_sanitized) > 0: - covariate_names = ', '.join('"{0}"'.format(w) for w in userinput_sanitized) + covariate_names = ', '.join('"{0}"'.format(w) + for w in userinput_sanitized) ro.r('covnames <- c(' + covariate_names + ')') else: ro.r('covnames <- c()') ro.r('covInGeno <- which(covnames %in% colnames(genotypes))') ro.r('covnames <- covnames[covInGeno]') ro.r("cat('covnames (purged): ', covnames,'\n')") - ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file + # Get the covariate matrix by using the marker name as index to the genotype file + ro.r('marker_covars <- genotypes[,covnames]') # TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc return ro.r["marker_covars"] @@ -375,7 +406,8 @@ def process_pair_scan_results(result): pair_scan_results = [] result = result[1] - output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)] + output = [tuple([result[j][i] for j in range(result.ncol)]) + for i in range(result.nrow)] for i, line in enumerate(result.iter_row()): marker = {} @@ -401,14 +433,17 @@ def process_rqtl_perm_results(num_perm, results): return perm_output, suggestive, significant -def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop +# TODO: how to make this a one liner and not copy the stuff in a loop +def process_rqtl_results(result, species_name): qtl_results = [] - output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)] + output = [tuple([result[j][i] for j in range(result.ncol)]) + for i in range(result.nrow)] for i, line in enumerate(result.iter_row()): marker = {} marker['name'] = result.rownames[i] - if species_name == "mouse" and output[i][0] == 20: # ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file + # ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file + if species_name == "mouse" and output[i][0] == 20: marker['chr'] = "X" else: marker['chr'] = output[i][0] diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 31c58083..d9b28fba 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -51,7 +51,8 @@ class RunMapping: def __init__(self, start_vars, temp_uuid): helper_functions.get_species_dataset_trait(self, start_vars) - self.temp_uuid = temp_uuid # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py) + # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py) + self.temp_uuid = temp_uuid # ZS: Needed to zoom in or remap temp traits like PCA traits if "temp_trait" in start_vars and start_vars['temp_trait'] != "False": @@ -102,8 +103,11 @@ class RunMapping: if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] else: - mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) - self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) + mapping_results_filename = self.dataset.group.name + "_" + \ + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) + self.mapping_results_path = "{}{}.csv".format( + webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) self.manhattan_plot = False if 'manhattan_plot' in start_vars: @@ -122,7 +126,8 @@ class RunMapping: self.use_loco = None self.suggestive = "" self.significant = "" - self.pair_scan = False # Initializing this since it is checked in views to determine which template to use + # Initializing this since it is checked in views to determine which template to use + self.pair_scan = False if 'transform' in start_vars: self.transform = start_vars['transform'] else: @@ -140,7 +145,8 @@ class RunMapping: # ZS: This is passed to GN1 code for single chr mapping self.selected_chr = -1 if "selected_chr" in start_vars: - if int(start_vars['selected_chr']) != -1: # ZS: Needs to be -1 if showing full map; there's probably a better way to fix this + # ZS: Needs to be -1 if showing full map; there's probably a better way to fix this + if int(start_vars['selected_chr']) != -1: self.selected_chr = int(start_vars['selected_chr']) + 1 else: self.selected_chr = int(start_vars['selected_chr']) @@ -198,28 +204,33 @@ class RunMapping: self.output_files = None if 'output_files' in start_vars: self.output_files = start_vars['output_files'] - if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + if 'first_run' in start_vars: self.first_run = False self.score_type = "-logP" self.manhattan_plot = True with Bench("Running GEMMA"): if self.use_loco == "True": - marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) + marker_obs, self.output_files = gemma_mapping.run_gemma( + self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) else: - marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) + marker_obs, self.output_files = gemma_mapping.run_gemma( + self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) results = marker_obs elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() elif self.mapping_method == "rqtl_geno": perm_strata = [] if "perm_strata" in start_vars and "categorical_vars" in start_vars: - self.categorical_vars = start_vars["categorical_vars"].split(",") + self.categorical_vars = start_vars["categorical_vars"].split( + ",") if len(self.categorical_vars) and start_vars["perm_strata"] == "True": primary_samples = SampleList(dataset=self.dataset, sample_names=self.samples, this_trait=self.this_trait) - perm_strata = get_perm_strata(self.this_trait, primary_samples, self.categorical_vars, self.samples) + perm_strata = get_perm_strata( + self.this_trait, primary_samples, self.categorical_vars, self.samples) self.score_type = "LOD" self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] @@ -231,9 +242,11 @@ class RunMapping: # if start_vars['pair_scan'] == "true": # self.pair_scan = True if self.permCheck and self.num_perm > 0: - self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) + self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno( + self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) else: - results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) + results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, + self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) elif self.mapping_method == "reaper": if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON if "additiveCheck" in start_vars: @@ -268,10 +281,12 @@ class RunMapping: if self.reaper_version == "new": self.first_run = True self.output_files = None - if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + if 'first_run' in start_vars: self.first_run = False if 'output_files' in start_vars: - self.output_files = start_vars['output_files'].split(",") + self.output_files = start_vars['output_files'].split( + ",") results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait, self.dataset, @@ -301,7 +316,8 @@ class RunMapping: elif self.mapping_method == "plink": self.score_type = "-logP" self.manhattan_plot = True - results = plink_mapping.run_plink(self.this_trait, self.dataset, self.species, self.vals, self.maf) + results = plink_mapping.run_plink( + self.this_trait, self.dataset, self.species, self.vals, self.maf) #results = self.run_plink() else: logger.debug("RUNNING NOTHING") @@ -353,7 +369,9 @@ class RunMapping: chr=str(marker['chr']), rs=marker['name'], ps=this_ps, - url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + url="/show_trait?trait_id=" + \ + marker['name'] + "&dataset=" + \ + self.dataset.group.name + "Geno" ) if self.geno_db_exists == "True": @@ -362,7 +380,9 @@ class RunMapping: chr=str(marker['chr']), rs=marker['name'], pos=this_ps, - url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + url="/show_trait?trait_id=" + \ + marker['name'] + "&dataset=" + \ + self.dataset.group.name + "Geno" ) else: annot_marker = dict( @@ -373,7 +393,8 @@ class RunMapping: ) if 'lrs_value' in marker and marker['lrs_value'] > 0: - browser_marker['p_wald'] = 10**-(marker['lrs_value'] / 4.61) + browser_marker['p_wald'] = 10**- \ + (marker['lrs_value'] / 4.61) elif 'lod_score' in marker and marker['lod_score'] > 0: browser_marker['p_wald'] = 10**-(marker['lod_score']) else: @@ -386,9 +407,13 @@ class RunMapping: highest_chr = marker['chr'] if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): if 'Mb' in marker.keys(): - marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.6f}".format(marker['Mb']) + marker['display_pos'] = "Chr" + \ + str(marker['chr']) + ": " + \ + "{:.6f}".format(marker['Mb']) elif 'cM' in marker.keys(): - marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM']) + marker['display_pos'] = "Chr" + \ + str(marker['chr']) + ": " + \ + "{:.3f}".format(marker['cM']) else: marker['display_pos'] = "N/A" self.qtl_results.append(marker) @@ -396,12 +421,15 @@ class RunMapping: total_markers = len(self.qtl_results) with Bench("Exporting Results"): - export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) + export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, + self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) with Bench("Trimming Markers for Figure"): if len(self.qtl_results) > 30000: - self.qtl_results = trim_markers_for_figure(self.qtl_results) - self.results_for_browser = trim_markers_for_figure(self.results_for_browser) + self.qtl_results = trim_markers_for_figure( + self.qtl_results) + self.results_for_browser = trim_markers_for_figure( + self.results_for_browser) filtered_annotations = [] for marker in self.results_for_browser: for annot_marker in self.annotations_for_browser: @@ -409,14 +437,17 @@ class RunMapping: filtered_annotations.append(annot_marker) break self.annotations_for_browser = filtered_annotations - browser_files = write_input_for_browser(self.dataset, self.results_for_browser, self.annotations_for_browser) + browser_files = write_input_for_browser( + self.dataset, self.results_for_browser, self.annotations_for_browser) else: - browser_files = write_input_for_browser(self.dataset, self.results_for_browser, self.annotations_for_browser) + browser_files = write_input_for_browser( + self.dataset, self.results_for_browser, self.annotations_for_browser) with Bench("Trimming Markers for Table"): self.trimmed_markers = trim_markers_for_table(results) - chr_lengths = get_chr_lengths(self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results) + chr_lengths = get_chr_lengths( + self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results) # ZS: For zooming into genome browser, need to pass chromosome name instead of number if self.dataset.group.species == "mouse": @@ -472,11 +503,14 @@ class RunMapping: def run_rqtl_plink(self): # os.chdir("") never do this inside a webserver!! - output_filename = webqtlUtil.genRandStr("%s_%s_" % (self.dataset.group.name, self.this_trait.name)) + output_filename = webqtlUtil.genRandStr("%s_%s_" % ( + self.dataset.group.name, self.this_trait.name)) - plink_mapping.gen_pheno_txt_file_plink(self.this_trait, self.dataset, self.vals, pheno_filename=output_filename) + plink_mapping.gen_pheno_txt_file_plink( + self.this_trait, self.dataset, self.vals, pheno_filename=output_filename) - rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename) + rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % ( + self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename) os.system(rqtl_command) @@ -508,8 +542,10 @@ class RunMapping: def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples): with open(results_path, "w+") as output_file: - output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") - output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") + output_file.write( + "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") + output_file.write( + "Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") output_file.write("Data Set: " + dataset.fullname + "\n") output_file.write("N Samples: " + str(n_samples) + "\n") if len(transform) > 0: @@ -529,7 +565,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write(transform_text + "\n") if dataset.type == "ProbeSet": output_file.write("Gene Symbol: " + trait.symbol + "\n") - output_file.write("Location: " + str(trait.chr) + " @ " + str(trait.mb) + " Mb\n") + output_file.write("Location: " + str(trait.chr) + \ + " @ " + str(trait.mb) + " Mb\n") if len(covariates) > 0: output_file.write("Cofactors (dataset - trait):\n") for covariate in covariates.split(","): @@ -630,9 +667,11 @@ def trim_markers_for_figure(markers): def trim_markers_for_table(markers): if 'lod_score' in list(markers[0].keys()): - sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True) + sorted_markers = sorted( + markers, key=lambda k: k['lod_score'], reverse=True) else: - sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True) + sorted_markers = sorted( + markers, key=lambda k: k['lrs_value'], reverse=True) # ZS: So we end up with a list of just 2000 markers if len(sorted_markers) >= 2000: @@ -643,7 +682,9 @@ def trim_markers_for_table(markers): def write_input_for_browser(this_dataset, gwas_results, annotations): - file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + file_base = this_dataset.group.name + "_" + \ + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) gwas_filename = file_base + "_GWAS" annot_filename = file_base + "_ANNOT" gwas_path = "{}/gn2/".format(TEMPDIR) + gwas_filename @@ -659,7 +700,8 @@ def write_input_for_browser(this_dataset, gwas_results, annotations): def geno_db_exists(this_dataset): geno_db_name = this_dataset.group.name + "Geno" try: - geno_db = data_set.create_dataset(dataset_name=geno_db_name, get_samplelist=False) + geno_db = data_set.create_dataset( + dataset_name=geno_db_name, get_samplelist=False) return "True" except: return "False" @@ -689,9 +731,11 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results): highest_pos = float(result['cM']) * 1000000 else: highest_pos = float(result['Mb']) * 1000000 - chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)}) + chr_lengths.append( + {"chr": str(this_chr), "size": str(highest_pos)}) else: - chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)}) + chr_lengths.append( + {"chr": str(this_chr), "size": str(highest_pos)}) this_chr = chr_as_num else: if mapping_method == "reaper": @@ -722,7 +766,8 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): combined_string = "" for var in categorical_vars: if var in list(sample_list.sample_attribute_values[sample].keys()): - combined_string += str(sample_list.sample_attribute_values[sample][var]) + combined_string += str( + sample_list.sample_attribute_values[sample][var]) else: combined_string += "NA" else: @@ -730,7 +775,8 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings.append(combined_string) - d = dict([(y, x + 1) for x, y in enumerate(sorted(set(perm_strata_strings)))]) + d = dict([(y, x + 1) + for x, y in enumerate(sorted(set(perm_strata_strings)))]) list_to_numbers = [d[x] for x in perm_strata_strings] perm_strata = list_to_numbers diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index d7c9ef95..7b9ff8fe 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -17,7 +17,8 @@ from wqflask.database import Base, init_db class User(Base): __tablename__ = "user" - id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, + default=lambda: str(uuid.uuid4())) email_address = Column(Unicode(50), unique=True, nullable=False) # Todo: Turn on strict mode for Mysql @@ -28,11 +29,13 @@ class User(Base): active = Column(Boolean(), nullable=False, default=True) - registration_info = Column(Text) # json detailing when they were registered, etc. + # json detailing when they were registered, etc. + registration_info = Column(Text) confirmed = Column(Text) # json detailing when they confirmed, etc. - superuser = Column(Text) # json detailing when they became a superuser, otherwise empty + # json detailing when they became a superuser, otherwise empty + superuser = Column(Text) # if not superuser logins = relationship("Login", @@ -66,7 +69,8 @@ class User(Base): def get_collection_by_name(self, collection_name): try: - collect = self.user_collections.filter_by(name=collection_name).first() + collect = self.user_collections.filter_by( + name=collection_name).first() except sqlalchemy.orm.exc.NoResultFound: collect = None return collect @@ -118,12 +122,15 @@ class User(Base): class Login(Base): __tablename__ = "login" - id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, + default=lambda: str(uuid.uuid4())) user = Column(Unicode(36), ForeignKey('user.id')) timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow()) ip_address = Column(Unicode(39)) - successful = Column(Boolean(), nullable=False) # False if wrong password was entered - session_id = Column(Text) # Set only if successfully logged in, otherwise should be blank + # False if wrong password was entered + successful = Column(Boolean(), nullable=False) + # Set only if successfully logged in, otherwise should be blank + session_id = Column(Text) # Set to user who assumes identity if this was a login for debugging purposes by a superuser assumed_by = Column(Unicode(36), ForeignKey('user.id')) @@ -137,13 +144,16 @@ class Login(Base): class UserCollection(Base): __tablename__ = "user_collection" - id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, + default=lambda: str(uuid.uuid4())) user = Column(Unicode(36), ForeignKey('user.id')) # I'd prefer this to not have a length, but for the index below it needs one name = Column(Unicode(50)) - created_timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow()) - changed_timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow()) + created_timestamp = Column( + DateTime(), default=lambda: datetime.datetime.utcnow()) + changed_timestamp = Column( + DateTime(), default=lambda: datetime.datetime.utcnow()) members = Column(Text) # We're going to store them as a json list # This index ensures a user doesn't have more than one collection with the same name diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 4591710c..36d4cd61 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -47,7 +47,8 @@ def search_for_user(): params = request.form user_list = [] user_list += get_users_like_unique_column("full_name", params['user_name']) - user_list += get_users_like_unique_column("email_address", params['user_email']) + user_list += get_users_like_unique_column( + "email_address", params['user_email']) return json.dumps(user_list) @@ -61,7 +62,8 @@ def search_for_groups(): user_list = [] user_list += get_users_like_unique_column("full_name", params['user_name']) - user_list += get_users_like_unique_column("email_address", params['user_email']) + user_list += get_users_like_unique_column( + "email_address", params['user_email']) for user in user_list: group_list += get_groups_like_unique_column("admins", user['user_id']) group_list += get_groups_like_unique_column("members", user['user_id']) @@ -124,7 +126,8 @@ def add_group_to_resource(): 'admin': request.form['admin_privilege'] } add_access_mask(resource_id, group_id, access_mask) - flash("Privileges have been added for group {}.".format(group_name), "alert-info") + flash("Privileges have been added for group {}.".format( + group_name), "alert-info") return redirect(url_for("manage_resource", resource_id=resource_id)) else: return render_template("admin/search_for_groups.html", resource_id=resource_id) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index ed5f9bad..273a97a4 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -52,7 +52,8 @@ class SearchResultPage: search = self.search_terms self.original_search_string = self.search_terms # check for dodgy search terms - rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE) + rx = re.compile( + r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE) if rx.match(search): logger.info("Regex failed search") self.search_term_exists = False @@ -96,7 +97,8 @@ class SearchResultPage: trait_list = [] json_trait_list = [] - species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name) + species = webqtlDatabaseFunction.retrieve_species( + self.dataset.group.name) # result_set represents the results for each search term; a search of # "shh grin2b" would have two sets of results, one for each term logger.debug("self.results is:", pf(self.results)) @@ -109,7 +111,8 @@ class SearchResultPage: trait_dict = {} trait_id = result[0] - this_trait = create_trait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) + this_trait = create_trait( + dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) if this_trait: trait_dict['index'] = index + 1 trait_dict['name'] = this_trait.name @@ -118,7 +121,8 @@ class SearchResultPage: else: trait_dict['display_name'] = this_trait.name trait_dict['dataset'] = this_trait.dataset.name - trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) + trait_dict['hmac'] = hmac.data_hmac( + '{}:{}'.format(this_trait.name, this_trait.dataset.name)) if this_trait.dataset.type == "ProbeSet": trait_dict['symbol'] = this_trait.symbol if this_trait.symbol else "N/A" trait_dict['description'] = "N/A" @@ -168,9 +172,11 @@ class SearchResultPage: self.trait_list = trait_list if self.dataset.type == "ProbeSet": - self.header_data_names = ['index', 'display_name', 'symbol', 'description', 'location', 'mean', 'lrs_score', 'lrs_location', 'additive'] + self.header_data_names = ['index', 'display_name', 'symbol', 'description', + 'location', 'mean', 'lrs_score', 'lrs_location', 'additive'] elif self.dataset.type == "Publish": - self.header_data_names = ['index', 'display_name', 'description', 'mean', 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive'] + self.header_data_names = ['index', 'display_name', 'description', 'mean', + 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive'] elif self.dataset.type == "Geno": self.header_data_names = ['index', 'display_name', 'location'] @@ -184,7 +190,8 @@ class SearchResultPage: combined_from_clause = "" combined_where_clause = "" - previous_from_clauses = [] # The same table can't be referenced twice in the from clause + # The same table can't be referenced twice in the from clause + previous_from_clauses = [] logger.debug("len(search_terms)>1") symbol_list = [] @@ -198,7 +205,8 @@ class SearchResultPage: for i, a_search in enumerate(alias_terms): the_search = self.get_search_ob(a_search) if the_search != None: - get_from_clause = getattr(the_search, "get_from_clause", None) + get_from_clause = getattr( + the_search, "get_from_clause", None) if callable(get_from_clause): from_clause = the_search.get_from_clause() if from_clause in previous_from_clauses: @@ -222,7 +230,8 @@ class SearchResultPage: else: the_search = self.get_search_ob(a_search) if the_search != None: - get_from_clause = getattr(the_search, "get_from_clause", None) + get_from_clause = getattr( + the_search, "get_from_clause", None) if callable(get_from_clause): from_clause = the_search.get_from_clause() if from_clause in previous_from_clauses: @@ -241,7 +250,8 @@ class SearchResultPage: self.search_term_exists = False if self.search_term_exists: combined_where_clause = "(" + combined_where_clause + ")" - final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause) + final_query = the_search.compile_final_query( + combined_from_clause, combined_where_clause) results = the_search.execute(final_query) self.results.extend(results) @@ -312,7 +322,8 @@ def get_aliases(symbol_list, species): symbols_string = ",".join(updated_symbols) filtered_aliases = [] - response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string) + response = requests.get( + GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string) if response: alias_lists = json.loads(response.content) seen = set() diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 496dee57..6419335e 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -74,14 +74,20 @@ class SampleList: if 'rrid' in sample.extra_attributes: if self.dataset.group.species == "mouse": if len(sample.extra_attributes['rrid'].split(":")) > 1: - the_rrid = sample.extra_attributes['rrid'].split(":")[1] - sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append(webqtlConfig.RRID_MOUSE_URL % the_rrid) + the_rrid = sample.extra_attributes['rrid'].split(":")[ + 1] + sample.extra_attributes['rrid'] = [ + sample.extra_attributes['rrid']] + sample.extra_attributes['rrid'].append( + webqtlConfig.RRID_MOUSE_URL % the_rrid) elif self.dataset.group.species == "rat": if len(str(sample.extra_attributes['rrid'])): - the_rrid = sample.extra_attributes['rrid'].split("_")[1] - sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append(webqtlConfig.RRID_RAT_URL % the_rrid) + the_rrid = sample.extra_attributes['rrid'].split("_")[ + 1] + sample.extra_attributes['rrid'] = [ + sample.extra_attributes['rrid']] + sample.extra_attributes['rrid'].append( + webqtlConfig.RRID_RAT_URL % the_rrid) self.sample_list.append(sample) @@ -130,7 +136,8 @@ class SampleList: self.attributes[key].name = name self.attributes[key].distinct_values = [ item.Value for item in values] - self.attributes[key].distinct_values = natural_sort(self.attributes[key].distinct_values) + self.attributes[key].distinct_values = natural_sort( + self.attributes[key].distinct_values) all_numbers = True for value in self.attributes[key].distinct_values: try: @@ -170,7 +177,8 @@ class SampleList: except ValueError: pass - attribute_values[self.attributes[item.Id].name.lower()] = attribute_value + attribute_values[self.attributes[item.Id].name.lower( + )] = attribute_value self.sample_attribute_values[sample_name] = attribute_values def get_first_attr_col(self): diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index f0fcd27d..81e7903b 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -40,16 +40,23 @@ def get_export_metadata(trait_id, dataset_name): metadata = [] if dataset.type == "Publish": metadata.append(["Phenotype ID: " + trait_id]) - metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name]) + metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + \ + trait_id + "&dataset=" + dataset_name]) metadata.append(["Group: " + dataset.group.name]) - metadata.append(["Phenotype: " + this_trait.description_display.replace(",", "\",\"")]) - metadata.append(["Authors: " + (this_trait.authors if this_trait.authors else "N/A")]) - metadata.append(["Title: " + (this_trait.title if this_trait.title else "N/A")]) - metadata.append(["Journal: " + (this_trait.journal if this_trait.journal else "N/A")]) - metadata.append(["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name]) + metadata.append( + ["Phenotype: " + this_trait.description_display.replace(",", "\",\"")]) + metadata.append( + ["Authors: " + (this_trait.authors if this_trait.authors else "N/A")]) + metadata.append( + ["Title: " + (this_trait.title if this_trait.title else "N/A")]) + metadata.append( + ["Journal: " + (this_trait.journal if this_trait.journal else "N/A")]) + metadata.append( + ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name]) else: metadata.append(["Record ID: " + trait_id]) - metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name]) + metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + \ + trait_id + "&dataset=" + dataset_name]) if this_trait.symbol: metadata.append(["Symbol: " + this_trait.symbol]) metadata.append(["Dataset: " + dataset.name]) diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index e5c67165..7fcbe984 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -27,9 +27,11 @@ class SnpBrowser: self.table_rows = [] if self.limit_strains == "true": - self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns) + self.header_fields, self.empty_field_count, self.header_data_names = get_header_list( + variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns) else: - self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns) + self.header_fields, self.empty_field_count, self.header_data_names = get_header_list( + variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns) def initialize_parameters(self, start_vars): if 'first_run' in start_vars: @@ -53,10 +55,12 @@ class SnpBrowser: self.rat_chr_list = [] mouse_species_ob = species.TheSpecies(species_name="Mouse") for key in mouse_species_ob.chromosomes.chromosomes: - self.mouse_chr_list.append(mouse_species_ob.chromosomes.chromosomes[key].name) + self.mouse_chr_list.append( + mouse_species_ob.chromosomes.chromosomes[key].name) rat_species_ob = species.TheSpecies(species_name="Rat") for key in rat_species_ob.chromosomes.chromosomes: - self.rat_chr_list.append(rat_species_ob.chromosomes.chromosomes[key].name) + self.rat_chr_list.append( + rat_species_ob.chromosomes.chromosomes[key].name) if self.species_id == 1: self.this_chr_list = self.mouse_chr_list @@ -109,9 +113,11 @@ class SnpBrowser: "CAST/EiJ"] self.chosen_strains_rat = ["BN", "F344", "WLI", "WMI"] if 'chosen_strains_mouse' in start_vars: - self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split(",") + self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split( + ",") if 'chosen_strains_rat' in start_vars: - self.chosen_strains_rat = start_vars['chosen_strains_rat'].split(",") + self.chosen_strains_rat = start_vars['chosen_strains_rat'].split( + ",") if self.species_id == 1: self.chosen_strains = self.chosen_strains_mouse @@ -150,9 +156,11 @@ class SnpBrowser: if self.gene_name != "": if self.species_id != 0: - query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = '%s'" % (self.species_id, self.gene_name) + query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = '%s'" % ( + self.species_id, self.gene_name) else: - query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE geneSymbol = '%s'" % (self.gene_name) + query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE geneSymbol = '%s'" % ( + self.gene_name) result = g.db.execute(query).fetchone() if result: self.gene_name, self.chr, self.start_mb, self.end_mb = result @@ -163,9 +171,11 @@ class SnpBrowser: query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll WHERE Rs = '%s'" % self.gene_name else: if self.species_id != 0: - query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SpeciesId = %s AND SnpName = '%s'" % (self.species_id, self.gene_name) + query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SpeciesId = %s AND SnpName = '%s'" % ( + self.species_id, self.gene_name) else: - query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SnpName = '%s'" % (self.gene_name) + query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SnpName = '%s'" % ( + self.gene_name) result_snp = g.db.execute(query).fetchall() if result_snp: self.snp_list = [item[0] for item in result_snp] @@ -177,9 +187,11 @@ class SnpBrowser: elif self.variant_type == "InDel": if self.gene_name[0] == "I": if self.species_id != 0: - query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = '%s'" % (self.species_id, self.gene_name) + query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = '%s'" % ( + self.species_id, self.gene_name) else: - query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE Name = '%s'" % (self.gene_name) + query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE Name = '%s'" % ( + self.gene_name) result_snp = g.db.execute(query).fetchall() if result_snp: self.snp_list = [item[0] for item in result_snp] @@ -255,7 +267,8 @@ class SnpBrowser: if self.limit_strains == "true" and len(self.chosen_strains) > 0: for item in self.chosen_strains: - index = self.strain_lists[self.species_name.lower()].index(item) + index = self.strain_lists[self.species_name.lower()].index( + item) strain_index_list.append(index) for seq, result in enumerate(results): @@ -263,7 +276,8 @@ class SnpBrowser: if self.variant_type == "SNP": display_strains = [] - snp_id, species_id, snp_name, rs, chr, mb, mb_2016, alleles, snp_source, conservation_score = result[:10] + snp_id, species_id, snp_name, rs, chr, mb, mb_2016, alleles, snp_source, conservation_score = result[ + :10] effect_list = result[10:28] if self.species_id == 1: self.allele_list = result[30:] @@ -279,7 +293,8 @@ class SnpBrowser: self.allele_list = display_strains effect_info_dict = get_effect_info(effect_list) - coding_domain_list = ['Start Gained', 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] + coding_domain_list = ['Start Gained', 'Start Lost', + 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] intron_domain_list = ['Splice Site', 'Nonsplice Site'] for key in effect_info_dict: @@ -296,19 +311,22 @@ class SnpBrowser: if 'Intergenic' in domain: if self.gene_name != "": - gene_id = get_gene_id(self.species_id, self.gene_name) + gene_id = get_gene_id( + self.species_id, self.gene_name) gene = [gene_id, self.gene_name] else: gene = check_if_in_gene(species_id, chr, mb) transcript = exon = function = function_details = '' if self.redundant == "false" or last_mb != mb: # filter redundant if self.include_record(domain, function, snp_source, conservation_score): - info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id] + info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, + function, function_details, snp_source, conservation_score, snp_id] info_list.extend(self.allele_list) filtered_results.append(info_list) last_mb = mb else: - gene_list, transcript_list, exon_list, function_list, function_details_list = effect_info_dict[key] + gene_list, transcript_list, exon_list, function_list, function_details_list = effect_info_dict[ + key] for index, item in enumerate(gene_list): gene = item transcript = transcript_list[index] @@ -325,13 +343,15 @@ class SnpBrowser: function = "" if function_details_list: - function_details = "Biotype: " + function_details_list[index] + function_details = "Biotype: " + \ + function_details_list[index] else: function_details = "" if self.redundant == "false" or last_mb != mb: if self.include_record(domain, function, snp_source, conservation_score): - info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id] + info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, + function, function_details, snp_source, conservation_score, snp_id] info_list.extend(self.allele_list) filtered_results.append(info_list) last_mb = mb @@ -345,7 +365,8 @@ class SnpBrowser: gene = "No Gene" domain = conservation_score = snp_id = snp_name = rs = flank_3 = flank_5 = ncbi = function = "" if self.include_record(domain, function, source_name, conservation_score): - filtered_results.append([indel_name, indel_chr, indel_mb_start, indel_mb_end, indel_strand, indel_type, indel_size, indel_sequence, source_name]) + filtered_results.append([indel_name, indel_chr, indel_mb_start, indel_mb_end, + indel_strand, indel_type, indel_size, indel_sequence, source_name]) last_mb = indel_mb_start else: @@ -365,7 +386,8 @@ class SnpBrowser: if gene_name and (gene_name not in gene_name_list): gene_name_list.append(gene_name) if len(gene_name_list) > 0: - gene_id_name_dict = get_gene_id_name_dict(self.species_id, gene_name_list) + gene_id_name_dict = get_gene_id_name_dict( + self.species_id, gene_name_list) # ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc) self.empty_columns = { @@ -383,7 +405,8 @@ class SnpBrowser: for i, result in enumerate(self.filtered_results): this_row = {} if self.variant_type == "SNP": - snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14] + snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[ + :14] allele_value_list = result[14:] if rs: snp_url = webqtlConfig.DBSNP % (rs) @@ -394,9 +417,11 @@ class SnpBrowser: end_bp = int(mb * 1000000 + 100) position_info = "chr%s:%d-%d" % (chr, start_bp, end_bp) if self.species_id == 2: - snp_url = webqtlConfig.GENOMEBROWSER_URL % ("rn6", position_info) + snp_url = webqtlConfig.GENOMEBROWSER_URL % ( + "rn6", position_info) else: - snp_url = webqtlConfig.GENOMEBROWSER_URL % ("mm10", position_info) + snp_url = webqtlConfig.GENOMEBROWSER_URL % ( + "mm10", position_info) mb = float(mb) mb_formatted = "%2.6f" % mb @@ -429,7 +454,8 @@ class SnpBrowser: gene_link = "" if transcript: - transcript_link = webqtlConfig.ENSEMBLETRANSCRIPT_URL % (transcript) + transcript_link = webqtlConfig.ENSEMBLETRANSCRIPT_URL % ( + transcript) self.empty_columns['transcript'] = "true" else: transcript_link = "" @@ -460,7 +486,8 @@ class SnpBrowser: function_list = function_details.strip().split(",") function_list = [item.strip() for item in function_list] function_list[0] = function_list[0].title() - function_details = ", ".join(item for item in function_list) + function_details = ", ".join( + item for item in function_list) function_details = function_details.replace("_", " ") function_details = function_details.replace("/", " -> ") if function_details == "Biotype: Protein Coding": @@ -675,8 +702,10 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None): header_fields = [] header_data_names = [] if variant_type == "SNP": - header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details']) - header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details'] + header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', + 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details']) + header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', + 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details'] header_fields.append(strain_list) header_data_names += strain_list @@ -712,8 +741,10 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None): header_data_names.remove(col) elif variant_type == "InDel": - header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'] - header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'] + header_fields = ['Index', 'ID', 'Type', 'InDel Chr', + 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'] + header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', + 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'] return header_fields, empty_field_count, header_data_names @@ -726,10 +757,13 @@ def get_effect_details_by_category(effect_name=None, effect_value=None): function_detail_list = [] tmp_list = [] - gene_group_list = ['Upstream', 'Downstream', 'Splice Site', 'Nonsplice Site', '3\' UTR'] - biotype_group_list = ['Unknown Effect In Exon', 'Start Gained', 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] + gene_group_list = ['Upstream', 'Downstream', + 'Splice Site', 'Nonsplice Site', '3\' UTR'] + biotype_group_list = ['Unknown Effect In Exon', 'Start Gained', + 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] new_codon_group_list = ['Start Gained'] - codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] + codon_effect_group_list = [ + 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] effect_detail_list = effect_value.strip().split('|') effect_detail_list = [item.strip() for item in effect_detail_list] @@ -773,8 +807,10 @@ def get_effect_info(effect_list): effect_detail_list = [] effect_info_dict = {} - prime3_utr, prime5_utr, upstream, downstream, intron, nonsplice_site, splice_site, intergenic = effect_list[:8] - exon, non_synonymous_coding, synonymous_coding, start_gained, start_lost, stop_gained, stop_lost, unknown_effect_in_exon = effect_list[8:16] + prime3_utr, prime5_utr, upstream, downstream, intron, nonsplice_site, splice_site, intergenic = effect_list[ + :8] + exon, non_synonymous_coding, synonymous_coding, start_gained, start_lost, stop_gained, stop_lost, unknown_effect_in_exon = effect_list[ + 8:16] if intergenic: domain = "Intergenic" @@ -783,59 +819,72 @@ def get_effect_info(effect_list): # if not exon, get gene list/transcript list info if upstream: domain = "Upstream" - effect_detail_list = get_effect_details_by_category(effect_name='Upstream', effect_value=upstream) + effect_detail_list = get_effect_details_by_category( + effect_name='Upstream', effect_value=upstream) effect_info_dict[domain] = effect_detail_list if downstream: domain = "Downstream" - effect_detail_list = get_effect_details_by_category(effect_name='Downstream', effect_value=downstream) + effect_detail_list = get_effect_details_by_category( + effect_name='Downstream', effect_value=downstream) effect_info_dict[domain] = effect_detail_list if intron: if splice_site: domain = "Splice Site" - effect_detail_list = get_effect_details_by_category(effect_name='Splice Site', effect_value=splice_site) + effect_detail_list = get_effect_details_by_category( + effect_name='Splice Site', effect_value=splice_site) effect_info_dict[domain] = effect_detail_list if nonsplice_site: domain = "Nonsplice Site" - effect_detail_list = get_effect_details_by_category(effect_name='Nonsplice Site', effect_value=nonsplice_site) + effect_detail_list = get_effect_details_by_category( + effect_name='Nonsplice Site', effect_value=nonsplice_site) effect_info_dict[domain] = effect_detail_list # get gene, transcript_list, and exon info if prime3_utr: domain = "3\' UTR" - effect_detail_list = get_effect_details_by_category(effect_name='3\' UTR', effect_value=prime3_utr) + effect_detail_list = get_effect_details_by_category( + effect_name='3\' UTR', effect_value=prime3_utr) effect_info_dict[domain] = effect_detail_list if prime5_utr: domain = "5\' UTR" - effect_detail_list = get_effect_details_by_category(effect_name='5\' UTR', effect_value=prime5_utr) + effect_detail_list = get_effect_details_by_category( + effect_name='5\' UTR', effect_value=prime5_utr) effect_info_dict[domain] = effect_detail_list if start_gained: domain = "Start Gained" - effect_detail_list = get_effect_details_by_category(effect_name='Start Gained', effect_value=start_gained) + effect_detail_list = get_effect_details_by_category( + effect_name='Start Gained', effect_value=start_gained) effect_info_dict[domain] = effect_detail_list if unknown_effect_in_exon: domain = "Unknown Effect In Exon" - effect_detail_list = get_effect_details_by_category(effect_name='Unknown Effect In Exon', effect_value=unknown_effect_in_exon) + effect_detail_list = get_effect_details_by_category( + effect_name='Unknown Effect In Exon', effect_value=unknown_effect_in_exon) effect_info_dict[domain] = effect_detail_list if start_lost: domain = "Start Lost" - effect_detail_list = get_effect_details_by_category(effect_name='Start Lost', effect_value=start_lost) + effect_detail_list = get_effect_details_by_category( + effect_name='Start Lost', effect_value=start_lost) effect_info_dict[domain] = effect_detail_list if stop_gained: domain = "Stop Gained" - effect_detail_list = get_effect_details_by_category(effect_name='Stop Gained', effect_value=stop_gained) + effect_detail_list = get_effect_details_by_category( + effect_name='Stop Gained', effect_value=stop_gained) effect_info_dict[domain] = effect_detail_list if stop_lost: domain = "Stop Lost" - effect_detail_list = get_effect_details_by_category(effect_name='Stop Lost', effect_value=stop_lost) + effect_detail_list = get_effect_details_by_category( + effect_name='Stop Lost', effect_value=stop_lost) effect_info_dict[domain] = effect_detail_list if non_synonymous_coding: domain = "Nonsynonymous" - effect_detail_list = get_effect_details_by_category(effect_name='Nonsynonymous', effect_value=non_synonymous_coding) + effect_detail_list = get_effect_details_by_category( + effect_name='Nonsynonymous', effect_value=non_synonymous_coding) effect_info_dict[domain] = effect_detail_list if synonymous_coding: domain = "Synonymous" - effect_detail_list = get_effect_details_by_category(effect_name='Synonymous', effect_value=synonymous_coding) + effect_detail_list = get_effect_details_by_category( + effect_name='Synonymous', effect_value=synonymous_coding) effect_info_dict[domain] = effect_detail_list return effect_info_dict @@ -863,7 +912,8 @@ def get_gene_id_name_dict(species_id, gene_name_list): gene_id_name_dict = {} if len(gene_name_list) == 0: return "" - gene_name_str_list = ["'" + gene_name + "'" for gene_name in gene_name_list] + gene_name_str_list = ["'" + gene_name + \ + "'" for gene_name in gene_name_list] gene_name_str = ",".join(gene_name_str_list) query = """ diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py index 07073d6a..2e467dc8 100644 --- a/wqflask/wqflask/update_search_results.py +++ b/wqflask/wqflask/update_search_results.py @@ -52,10 +52,12 @@ class GSearch: self.trait_list = [] with Bench("Creating trait objects"): for line in re: - dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False) + dataset = create_dataset( + line[3], "ProbeSet", get_samplelist=False) trait_id = line[4] # with Bench("Building trait object"): - this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) + this_trait = GeneralTrait( + dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) elif self.type == "phenotype": @@ -97,7 +99,8 @@ class GSearch: for line in re: dataset = create_dataset(line[2], "Publish") trait_id = line[3] - this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) + this_trait = GeneralTrait( + dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) self.results = self.convert_to_json() diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index 2a2f8484..708d43d2 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -70,7 +70,8 @@ def set_password(password): assert len(password) >= 6, "Password shouldn't be shorter than 6 characters" - encoded_password = encode_password(pass_gen_fields, pass_gen_fields['unencrypted_password']) + encoded_password = encode_password( + pass_gen_fields, pass_gen_fields['unencrypted_password']) return encoded_password @@ -161,12 +162,16 @@ def verify_email(): # As long as they have access to the email account # We might as well log them in session_id_signed = get_signed_session_id(user_details) - flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success") - response = make_response(redirect(url_for('index_page', import_collections=import_col, anon_id=anon_id))) - response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) + flash("Thank you for logging in {}.".format( + user_details['full_name']), "alert-success") + response = make_response(redirect( + url_for('index_page', import_collections=import_col, anon_id=anon_id))) + response.set_cookie(UserSession.user_cookie_name, + session_id_signed, max_age=None) return response else: - flash("Invalid code: Password reset code does not exist or might have expired!", "error") + flash( + "Invalid code: Password reset code does not exist or might have expired!", "error") @app.route("/n/login", methods=('GET', 'POST')) @@ -195,23 +200,28 @@ def login(): display_id = user_details['orcid'] else: display_id = "" - flash("Thank you for logging in {}.".format(display_id), "alert-success") + flash("Thank you for logging in {}.".format( + display_id), "alert-success") response = make_response(redirect(url_for('index_page'))) - response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) + response.set_cookie( + UserSession.user_cookie_name, session_id_signed, max_age=None) else: flash("Something went unexpectedly wrong.", "alert-danger") response = make_response(redirect(url_for('index_page'))) return response else: - user_details = get_user_by_unique_column("email_address", params['email_address']) + user_details = get_user_by_unique_column( + "email_address", params['email_address']) password_match = False if user_details: submitted_password = params['password'] pwfields = user_details['password'] if isinstance(pwfields, str): pwfields = json.loads(pwfields) - encrypted_pass_fields = encode_password(pwfields, submitted_password) - password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password']) + encrypted_pass_fields = encode_password( + pwfields, submitted_password) + password_match = pbkdf2.safe_str_cmp( + encrypted_pass_fields['password'], pwfields['password']) else: # Invalid e-mail flash("Invalid e-mail address. Please try again.", "alert-danger") @@ -227,12 +237,16 @@ def login(): anon_id = params['anon_id'] session_id_signed = get_signed_session_id(user_details) - flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success") - response = make_response(redirect(url_for('index_page', import_collections=import_col, anon_id=anon_id))) - response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) + flash("Thank you for logging in {}.".format( + user_details['full_name']), "alert-success") + response = make_response(redirect( + url_for('index_page', import_collections=import_col, anon_id=anon_id))) + response.set_cookie( + UserSession.user_cookie_name, session_id_signed, max_age=None) return response else: - email_ob = send_verification_email(user_details, template_name="email/user_verification.txt") + email_ob = send_verification_email( + user_details, template_name="email/user_verification.txt") return render_template("newsecurity/verification_still_needed.html", subject=email_ob['subject']) else: # Incorrect password # ZS: It previously seemed to store that there was an incorrect log-in attempt here, but it did so in the MySQL DB so this might need to be reproduced with Redis @@ -252,8 +266,10 @@ def github_oauth2(): "code": code } - result = requests.post("https://github.com/login/oauth/access_token", json=data) - result_dict = {arr[0]: arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]} + result = requests.post( + "https://github.com/login/oauth/access_token", json=data) + result_dict = {arr[0]: arr[1] + for arr in [tok.split("=") for tok in result.text.split("&")]} github_user = get_github_user_details(result_dict["access_token"]) @@ -277,7 +293,8 @@ def github_oauth2(): def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content + result = requests.get(GITHUB_API_URL, headers={ + 'Authorization': 'token ' + access_token}).content return json.loads(result) @@ -323,7 +340,8 @@ def orcid_oauth2(): def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content + result = requests.get(GITHUB_API_URL, headers={ + 'Authorization': 'token ' + access_token}).content return json.loads(result) @@ -389,13 +407,16 @@ def forgot_password_submit(): next_page = None if email_address != "": logger.debug("Wants to send password E-mail to ", email_address) - user_details = get_user_by_unique_column("email_address", email_address) + user_details = get_user_by_unique_column( + "email_address", email_address) if user_details: - email_subject = send_forgot_password_email(user_details["email_address"]) + email_subject = send_forgot_password_email( + user_details["email_address"]) return render_template("new_security/forgot_password_step2.html", subject=email_subject) else: - flash("The e-mail entered is not associated with an account.", "alert-danger") + flash("The e-mail entered is not associated with an account.", + "alert-danger") return redirect(url_for("forgot_password")) else: @@ -417,7 +438,8 @@ def password_reset(): return render_template( "new_security/password_reset.html", user_encode=user_details["email_address"]) else: - flash("Invalid code: Password reset code does not exist or might have expired!", "error") + flash( + "Invalid code: Password reset code does not exist or might have expired!", "error") return redirect(url_for("login")) else: return redirect(url_for("login")) @@ -446,21 +468,27 @@ def register_user(params): errors = [] user_details = {} - user_details['email_address'] = params.get('email_address', '').encode("utf-8").strip() + user_details['email_address'] = params.get( + 'email_address', '').encode("utf-8").strip() if not (5 <= len(user_details['email_address']) <= 50): - errors.append('Email Address needs to be between 5 and 50 characters.') + errors.append( + 'Email Address needs to be between 5 and 50 characters.') else: - email_exists = get_user_by_unique_column("email_address", user_details['email_address']) + email_exists = get_user_by_unique_column( + "email_address", user_details['email_address']) if email_exists: errors.append('User already exists with that email') - user_details['full_name'] = params.get('full_name', '').encode("utf-8").strip() + user_details['full_name'] = params.get( + 'full_name', '').encode("utf-8").strip() if not (5 <= len(user_details['full_name']) <= 50): errors.append('Full Name needs to be between 5 and 50 characters.') - user_details['organization'] = params.get('organization', '').encode("utf-8").strip() + user_details['organization'] = params.get( + 'organization', '').encode("utf-8").strip() if user_details['organization'] and not (5 <= len(user_details['organization']) <= 50): - errors.append('Organization needs to be empty or between 5 and 50 characters.') + errors.append( + 'Organization needs to be empty or between 5 and 50 characters.') password = str(params.get('password', '')) if not (6 <= len(password)): @@ -493,7 +521,8 @@ def register(): errors = register_user(params) if len(errors) == 0: - flash("Registration successful. You may login with your new account", "alert-info") + flash( + "Registration successful. You may login with your new account", "alert-info") return redirect(url_for("login")) return render_template("new_security/register_user.html", values=params, errors=errors) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index a9bd65e6..5610833b 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -93,8 +93,10 @@ class AnonUser: this_collection = {} this_collection['id'] = collection['id'] this_collection['name'] = collection['name'] - this_collection['created_timestamp'] = collection['created_timestamp'].strftime('%b %d %Y %I:%M%p') - this_collection['changed_timestamp'] = collection['changed_timestamp'].strftime('%b %d %Y %I:%M%p') + this_collection['created_timestamp'] = collection['created_timestamp'].strftime( + '%b %d %Y %I:%M%p') + this_collection['changed_timestamp'] = collection['changed_timestamp'].strftime( + '%b %d %Y %I:%M%p') this_collection['num_members'] = collection['num_members'] this_collection['members'] = collection['members'] updated_collections.append(this_collection) @@ -108,21 +110,26 @@ class AnonUser: else: collections = json.loads(json_collections) for collection in collections: - collection['created_timestamp'] = datetime.datetime.strptime(collection['created_timestamp'], '%b %d %Y %I:%M%p') - collection['changed_timestamp'] = datetime.datetime.strptime(collection['changed_timestamp'], '%b %d %Y %I:%M%p') + collection['created_timestamp'] = datetime.datetime.strptime( + collection['created_timestamp'], '%b %d %Y %I:%M%p') + collection['changed_timestamp'] = datetime.datetime.strptime( + collection['changed_timestamp'], '%b %d %Y %I:%M%p') - collections = sorted(collections, key=lambda i: i['changed_timestamp'], reverse=True) + collections = sorted( + collections, key=lambda i: i['changed_timestamp'], reverse=True) return collections def import_traits_to_user(self): result = Redis.get(self.key) collections_list = json.loads(result if result else "[]") for collection in collections_list: - collection_exists = g.user_session.get_collection_by_name(collection['name']) + collection_exists = g.user_session.get_collection_by_name( + collection['name']) if collection_exists: continue else: - g.user_session.add_collection(collection['name'], collection['members']) + g.user_session.add_collection( + collection['name'], collection['members']) def display_num_collections(self): """ @@ -148,7 +155,8 @@ def verify_cookie(cookie): the_uuid, separator, the_signature = cookie.partition(':') assert len(the_uuid) == 36, "Is session_id a uuid?" assert separator == ":", "Expected a : here" - assert the_signature == actual_hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?" + assert the_signature == actual_hmac_creation( + the_uuid), "Uh-oh, someone tampering with the cookie?" return the_uuid @@ -282,7 +290,8 @@ class UserSession: updated_collection['members'] = updated_traits updated_collection['num_members'] = len(updated_traits) - updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') updated_collections = [] for collection in self.user_collections: @@ -308,7 +317,8 @@ class UserSession: updated_collection['members'] = updated_traits updated_collection['num_members'] = len(updated_traits) - updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') updated_collections = [] for collection in self.user_collections: @@ -355,7 +365,8 @@ def get_cookie(): def set_cookie(response): if not request.cookies.get(g.cookie_session.cookie_name): - response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie) + response.set_cookie(g.cookie_session.cookie_name, + g.cookie_session.cookie) return response @@ -390,22 +401,28 @@ class RegisterUser: self.errors = [] self.user = Bunch() - self.user.email_address = kw.get('email_address', '').encode("utf-8").strip() + self.user.email_address = kw.get( + 'email_address', '').encode("utf-8").strip() if not (5 <= len(self.user.email_address) <= 50): - self.errors.append('Email Address needs to be between 5 and 50 characters.') + self.errors.append( + 'Email Address needs to be between 5 and 50 characters.') else: - email_exists = get_user_by_unique_column("email_address", self.user.email_address) + email_exists = get_user_by_unique_column( + "email_address", self.user.email_address) #email_exists = get_user_by_unique_column(es, "email_address", self.user.email_address) if email_exists: self.errors.append('User already exists with that email') self.user.full_name = kw.get('full_name', '').encode("utf-8").strip() if not (5 <= len(self.user.full_name) <= 50): - self.errors.append('Full Name needs to be between 5 and 50 characters.') + self.errors.append( + 'Full Name needs to be between 5 and 50 characters.') - self.user.organization = kw.get('organization', '').encode("utf-8").strip() + self.user.organization = kw.get( + 'organization', '').encode("utf-8").strip() if self.user.organization and not (5 <= len(self.user.organization) <= 50): - self.errors.append('Organization needs to be empty or between 5 and 50 characters.') + self.errors.append( + 'Organization needs to be empty or between 5 and 50 characters.') password = str(kw.get('password', '')) if not (6 <= len(password)): @@ -568,14 +585,16 @@ def password_reset(): if verification_code: user_email = check_verification_code(verification_code) if user_email: - user_details = get_user_by_unique_column('email_address', user_email) + user_details = get_user_by_unique_column( + 'email_address', user_email) if user_details: return render_template( "new_security/password_reset.html", user_encode=user_details["user_id"]) else: flash("Invalid code: User no longer exists!", "error") else: - flash("Invalid code: Password reset code does not exist or might have expired!", "error") + flash( + "Invalid code: Password reset code does not exist or might have expired!", "error") else: return redirect(url_for("login")) @@ -648,8 +667,10 @@ def github_oauth2(): "client_secret": GITHUB_CLIENT_SECRET, "code": code } - result = requests.post("https://github.com/login/oauth/access_token", json=data) - result_dict = {arr[0]: arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]} + result = requests.post( + "https://github.com/login/oauth/access_token", json=data) + result_dict = {arr[0]: arr[1] for arr in [tok.split( + "=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]} github_user = get_github_user_details(result_dict["access_token"]) @@ -696,7 +717,8 @@ def orcid_oauth2(): def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, params={"access_token": access_token}) + result = requests.get(GITHUB_API_URL, params={ + "access_token": access_token}) return result.json() @@ -737,7 +759,8 @@ class LoginUser: return render_template( "new_security/login_user.html", external_login=external_login, redis_is_available=is_redis_available()) else: - user_details = get_user_by_unique_column("email_address", params["email_address"]) + user_details = get_user_by_unique_column( + "email_address", params["email_address"]) #user_details = get_user_by_unique_column(es, "email_address", params["email_address"]) user = None valid = None @@ -755,8 +778,10 @@ class LoginUser: pwfields.iterations, pwfields.keylength, pwfields.hashfunc) - logger.debug("\n\nComparing:\n{}\n{}\n".format(encrypted.password, pwfields.password)) - valid = pbkdf2.safe_str_cmp(encrypted.password, pwfields.password) + logger.debug("\n\nComparing:\n{}\n{}\n".format( + encrypted.password, pwfields.password)) + valid = pbkdf2.safe_str_cmp( + encrypted.password, pwfields.password) logger.debug("valid is:", valid) if valid and not user.confirmed: @@ -782,7 +807,8 @@ class LoginUser: else: if user: self.unsuccessful_login(user) - flash("Invalid email-address or password. Please try again.", "alert-danger") + flash("Invalid email-address or password. Please try again.", + "alert-danger") response = make_response(redirect(url_for('login'))) return response @@ -790,14 +816,17 @@ class LoginUser: def actual_login(self, user, assumed_by=None, import_collections=None): """The meat of the logging in process""" session_id_signed = self.successful_login(user, assumed_by) - flash("Thank you for logging in {}.".format(user.full_name), "alert-success") - response = make_response(redirect(url_for('index_page', import_collections=import_collections))) + flash("Thank you for logging in {}.".format( + user.full_name), "alert-success") + response = make_response( + redirect(url_for('index_page', import_collections=import_collections))) if self.remember_me: max_age = self.remember_time else: max_age = None - response.set_cookie(UserSession.cookie_name, session_id_signed, max_age=max_age) + response.set_cookie(UserSession.cookie_name, + session_id_signed, max_age=max_age) return response def successful_login(self, user, assumed_by=None): @@ -866,13 +895,15 @@ def forgot_password_submit(): next_page = None if email_address != "": logger.debug("Wants to send password E-mail to ", email_address) - user_details = get_user_by_unique_column("email_address", email_address) + user_details = get_user_by_unique_column( + "email_address", email_address) if user_details: ForgotPasswordEmail(user_details["email_address"]) return render_template("new_security/forgot_password_step2.html", subject=ForgotPasswordEmail.subject) else: - flash("The e-mail entered is not associated with an account.", "alert-danger") + flash("The e-mail entered is not associated with an account.", + "alert-danger") return redirect(url_for("forgot_password")) else: @@ -959,7 +990,8 @@ def register(): errors = result.errors if len(errors) == 0: - flash("Registration successful. You may login with your new account", "alert-info") + flash( + "Registration successful. You may login with your new account", "alert-info") return redirect(url_for("login")) return render_template("new_security/register_user.html", values=params, errors=errors) diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index f0f0d60c..6ccb2e80 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -36,7 +36,8 @@ def get_user_session(): def set_user_session(response): if hasattr(g, 'user_session'): if not request.cookies.get(g.user_session.cookie_name): - response.set_cookie(g.user_session.cookie_name, g.user_session.cookie) + response.set_cookie(g.user_session.cookie_name, + g.user_session.cookie) return response @@ -44,7 +45,8 @@ def verify_cookie(cookie): the_uuid, separator, the_signature = cookie.partition(':') assert len(the_uuid) == 36, "Is session_id a uuid?" assert separator == ":", "Expected a : here" - assert the_signature == hmac.hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?" + assert the_signature == hmac.hmac_creation( + the_uuid), "Uh-oh, someone tampering with the cookie?" return the_uuid @@ -60,9 +62,11 @@ def create_signed_cookie(): def manage_user(): params = request.form if request.form else request.args if 'new_full_name' in params: - set_user_attribute(g.user_session.user_id, 'full_name', params['new_full_name']) + set_user_attribute(g.user_session.user_id, + 'full_name', params['new_full_name']) if 'new_organization' in params: - set_user_attribute(g.user_session.user_id, 'organization', params['new_organization']) + set_user_attribute(g.user_session.user_id, + 'organization', params['new_organization']) user_details = get_user_by_unique_column("user_id", g.user_session.user_id) @@ -108,7 +112,8 @@ class UserSession: # Grrr...this won't work because of the way flask handles cookies # Delete the cookie - flash("Due to inactivity your session has expired. If you'd like please login again.") + flash( + "Due to inactivity your session has expired. If you'd like please login again.") return None else: self.record = dict(login_time=time.time(), @@ -178,7 +183,9 @@ class UserSession: # ZS: Get user's collections if they exist collections = get_user_collections(self.user_id) - collections = [item for item in collections if item['name'] != "Your Default Collection"] + [item for item in collections if item['name'] == "Your Default Collection"] # ZS: Ensure Default Collection is last in list + collections = [item for item in collections if item['name'] != "Your Default Collection"] + \ + [item for item in collections if item['name'] == + "Your Default Collection"] # ZS: Ensure Default Collection is last in list return collections @property @@ -234,12 +241,14 @@ class UserSession: this_collection = self.get_collection_by_id(collection_id) updated_collection = this_collection - current_members_minus_new = [member for member in this_collection['members'] if member not in traits_to_add] + current_members_minus_new = [ + member for member in this_collection['members'] if member not in traits_to_add] updated_traits = traits_to_add + current_members_minus_new updated_collection['members'] = updated_traits updated_collection['num_members'] = len(updated_traits) - updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') updated_collections = [] for collection in self.user_collections: @@ -265,7 +274,8 @@ class UserSession: updated_collection['members'] = updated_traits updated_collection['num_members'] = len(updated_traits) - updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') updated_collections = [] for collection in self.user_collections: -- cgit v1.2.3 From f4ad7bc3ebfa9be6ff98c9f935a9e8576974ddd6 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 15 Jun 2021 17:51:15 +0000 Subject: Fix issue where column values were used as str instead of bytes; pretty sure this was introduced by Python3 --- wqflask/utility/redis_tools.py | 2 ++ 1 file changed, 2 insertions(+) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 96a4be12..ff125bd2 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -26,6 +26,8 @@ def is_redis_available(): def load_json_from_redis(item_list, column_value): + if type(column_value) == str: + column_value = str.encode(column_value) return json.loads(item_list[column_value]) -- cgit v1.2.3 From f51569c80a4e00ad7dcd99ed9bf3ed6d9aaf4051 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 10 Sep 2021 18:54:44 +0000 Subject: Removed encoding, since it's apparently not needed since the Python 3 switchover (and was causing there to be no matches between user IDs and groups) --- wqflask/utility/redis_tools.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index ff125bd2..99295c67 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -135,10 +135,8 @@ def get_user_groups(user_id): for key in groups_list: try: group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin.encode( - 'utf-8') if this_admin else None for this_admin in group_ob['admins']]) - group_members = set([this_member.encode( - 'utf-8') if this_member else None for this_member in group_ob['members']]) + group_admins = set([this_admin if this_admin else None for this_admin in group_ob['admins']]) + group_members = set([this_member if this_member else None for this_member in group_ob['members']]) if user_id in group_admins: admin_group_ids.append(group_ob['id']) elif user_id in group_members: -- cgit v1.2.3 From 5b116de4aaf796be138ee0ad06c2242b3f3c33c7 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 4 Oct 2021 21:02:37 +0000 Subject: Changed get_user_groups to pull both the ID and details in the for loop from group_list by using group_list.items() --- wqflask/utility/redis_tools.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 99295c67..de9dde46 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -127,20 +127,20 @@ def check_verification_code(code): def get_user_groups(user_id): - # ZS: Get the groups where a user is an admin or a member and + # Get the groups where a user is an admin or a member and # return lists corresponding to those two sets of groups - admin_group_ids = [] # ZS: Group IDs where user is an admin - user_group_ids = [] # ZS: Group IDs where user is a regular user + admin_group_ids = [] # Group IDs where user is an admin + user_group_ids = [] # Group IDs where user is a regular user groups_list = Redis.hgetall("groups") - for key in groups_list: + for group_id, group_details in groups_list.items(): try: - group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin if this_admin else None for this_admin in group_ob['admins']]) - group_members = set([this_member if this_member else None for this_member in group_ob['members']]) + _details = json.loads(group_details) + group_admins = set([this_admin if this_admin else None for this_admin in _details['admins']]) + group_members = set([this_member if this_member else None for this_member in _details['members']]) if user_id in group_admins: - admin_group_ids.append(group_ob['id']) + admin_group_ids.append(group_id) elif user_id in group_members: - user_group_ids.append(group_ob['id']) + user_group_ids.append(group_id) else: continue except: -- cgit v1.2.3 From eb2e43434c137a070db5943db21d3b92afdd9a91 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 12 Oct 2021 14:19:26 +0300 Subject: Mark `get_resource_info` as deprecated --- wqflask/utility/redis_tools.py | 2 ++ 1 file changed, 2 insertions(+) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index de9dde46..e68397ab 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -4,6 +4,7 @@ import datetime import redis # used for collections +from deprecated import deprecated from utility.hmac import hmac_creation from utility.logger import getLogger logger = getLogger(__name__) @@ -321,6 +322,7 @@ def get_resource_id(dataset, trait_id=None): return resource_id +@deprecated def get_resource_info(resource_id): resource_info = Redis.hget("resources", resource_id) if resource_info: -- cgit v1.2.3 From 935270b1cc1e265b785958cf5805bf155d8ae859 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 20 Oct 2021 14:38:11 +0300 Subject: utility: redis_tools: Remove dead functions --- wqflask/utility/redis_tools.py | 78 ------------------------------------------ 1 file changed, 78 deletions(-) (limited to 'wqflask/utility/redis_tools.py') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index e68397ab..c2a3b057 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -58,30 +58,6 @@ def get_user_by_unique_column(column_name, column_value): return item_details -def get_users_like_unique_column(column_name, column_value): - """Like previous function, but this only checks if the input is a - subset of a field and can return multiple results - - """ - matched_users = [] - - if column_value != "": - user_list = Redis.hgetall("users") - if column_name != "user_id": - for key in user_list: - user_ob = json.loads(user_list[key]) - if "user_id" not in user_ob: - set_user_attribute(key, "user_id", key) - user_ob["user_id"] = key - if column_name in user_ob: - if column_value in user_ob[column_name]: - matched_users.append(user_ob) - else: - matched_users.append(load_json_from_redis(user_list, column_value)) - - return matched_users - - def set_user_attribute(user_id, column_name, column_value): user_info = json.loads(Redis.hget("users", user_id)) user_info[column_name] = column_value @@ -166,52 +142,6 @@ def get_group_info(group_id): return group_info -def get_group_by_unique_column(column_name, column_value): - """ Get group by column; not sure if there's a faster way to do this """ - - matched_groups = [] - - all_group_list = Redis.hgetall("groups") - for key in all_group_list: - group_info = json.loads(all_group_list[key]) - # ZS: Since these fields are lists, search in the list - if column_name == "admins" or column_name == "members": - if column_value in group_info[column_name]: - matched_groups.append(group_info) - else: - if group_info[column_name] == column_value: - matched_groups.append(group_info) - - return matched_groups - - -def get_groups_like_unique_column(column_name, column_value): - """Like previous function, but this only checks if the input is a - subset of a field and can return multiple results - - """ - matched_groups = [] - - if column_value != "": - group_list = Redis.hgetall("groups") - if column_name != "group_id": - for key in group_list: - group_info = json.loads(group_list[key]) - # ZS: Since these fields are lists, search in the list - if column_name == "admins" or column_name == "members": - if column_value in group_info[column_name]: - matched_groups.append(group_info) - else: - if column_name in group_info: - if column_value in group_info[column_name]: - matched_groups.append(group_info) - else: - matched_groups.append( - load_json_from_redis(group_list, column_value)) - - return matched_groups - - def create_group(admin_user_ids, member_user_ids=[], group_name="Default Group Name"): group_id = str(uuid.uuid4()) @@ -354,11 +284,3 @@ def add_access_mask(resource_id, group_id, access_mask): Redis.hset("resources", resource_id, json.dumps(the_resource)) return the_resource - - -def change_resource_owner(resource_id, new_owner_id): - the_resource = get_resource_info(resource_id) - the_resource['owner_id'] = new_owner_id - - Redis.delete("resource") - Redis.hset("resources", resource_id, json.dumps(the_resource)) -- cgit v1.2.3