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