diff options
Diffstat (limited to 'wqflask')
56 files changed, 1576 insertions, 1128 deletions
diff --git a/wqflask/.DS_Store b/wqflask/.DS_Store deleted file mode 100644 index d992942f..00000000 --- a/wqflask/.DS_Store +++ /dev/null Binary files differdiff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 6dc44829..8906ab69 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -277,7 +277,6 @@ class Markers: filtered_markers = [] for marker in self.markers: if marker['name'] in p_values: - # logger.debug("marker {} IS in p_values".format(i)) marker['p_value'] = p_values[marker['name']] if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 @@ -298,7 +297,6 @@ class HumanMarkers(Markers): self.markers = [] for line in marker_data_fh: splat = line.strip().split() - # logger.debug("splat:", splat) if len(specified_markers) > 0: if splat[1] in specified_markers: marker = {} @@ -398,6 +396,15 @@ class DatasetGroup: if maternal and paternal: self.parlist = [maternal, paternal] + def get_study_samplelists(self): + study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists') + try: + f = open(study_sample_file) + except: + return [] + study_samples = json.load(f) + return study_samples + def get_genofiles(self): jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) try: @@ -557,6 +564,7 @@ class DataSet: self.fullname = None self.type = None self.data_scale = None # ZS: For example log2 + self.accession_id = None self.setup() @@ -573,6 +581,17 @@ class DataSet: self.group.get_samplelist() self.species = species.TheSpecies(self) + def as_dict(self): + return { + 'name': self.name, + 'shortname': self.shortname, + 'fullname': self.fullname, + 'type': self.type, + 'data_scale': self.data_scale, + 'group': self.group.name, + 'accession_id': self.accession_id + } + def get_accession_id(self): if self.type == "Publish": results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where @@ -725,7 +744,6 @@ class DataSet: and Strain.SpeciesId=Species.Id and Species.name = '{}' """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) - logger.sql(query) results = dict(g.db.execute(query).fetchall()) sample_ids = [results[item] for item in self.samplelist] @@ -896,7 +914,6 @@ class PhenotypeDataSet(DataSet): Geno.Name = '%s' and Geno.SpeciesId = Species.Id """ % (species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -926,7 +943,6 @@ class PhenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -993,7 +1009,6 @@ class GenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() @@ -1114,8 +1129,6 @@ class MrnaAssayDataSet(DataSet): ProbeSet.Name = '%s' """ % (escape(str(this_trait.dataset.id)), escape(this_trait.name))) - - logger.sql(query) result = g.db.execute(query).fetchone() mean = result[0] if result else 0 @@ -1135,7 +1148,6 @@ class MrnaAssayDataSet(DataSet): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -1167,7 +1179,6 @@ class MrnaAssayDataSet(DataSet): Order BY Strain.Name """ % (escape(trait), escape(self.name)) - logger.sql(query) results = g.db.execute(query).fetchall() return results @@ -1178,7 +1189,6 @@ class MrnaAssayDataSet(DataSet): where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) - logger.sql(query) results = g.db.execute(query).fetchall() return dict(results) @@ -1212,7 +1222,6 @@ def geno_mrna_confidentiality(ob): query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name) - logger.sql(query) result = g.db.execute(query) (dataset_id, diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index d09cfd40..96a09302 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -27,11 +27,13 @@ def create_trait(**kw): assert bool(kw.get('name')), "Needs trait name" - if kw.get('dataset_name'): + if bool(kw.get('dataset')): + dataset = kw.get('dataset') + else: if kw.get('dataset_name') != "Temp": dataset = create_dataset(kw.get('dataset_name')) - else: - dataset = kw.get('dataset') + else: + dataset = create_dataset("Temp", group_name=kw.get('group_name')) if dataset.type == 'Publish': permissions = check_resource_availability( @@ -284,17 +286,19 @@ def get_sample_data(): return None -def jsonable(trait): +def jsonable(trait, dataset=None): """Return a dict suitable for using as json Actual turning into json doesn't happen here though""" - dataset = create_dataset(dataset_name=trait.dataset.name, - dataset_type=trait.dataset.type, - group_name=trait.dataset.group.name) + if not dataset: + dataset = create_dataset(dataset_name=trait.dataset.name, + dataset_type=trait.dataset.type, + group_name=trait.dataset.group.name) if dataset.type == "ProbeSet": return dict(name=trait.name, + view=trait.view, symbol=trait.symbol, dataset=dataset.name, dataset_name=dataset.shortname, @@ -308,37 +312,44 @@ def jsonable(trait): elif dataset.type == "Publish": if trait.pubmed_id: return dict(name=trait.name, + view=trait.view, dataset=dataset.name, dataset_name=dataset.shortname, description=trait.description_display, abbreviation=trait.abbreviation, authors=trait.authors, + pubmed_id=trait.pubmed_id, pubmed_text=trait.pubmed_text, pubmed_link=trait.pubmed_link, + mean=trait.mean, lrs_score=trait.LRS_score_repr, lrs_location=trait.LRS_location_repr, additive=trait.additive ) else: return dict(name=trait.name, + view=trait.view, dataset=dataset.name, dataset_name=dataset.shortname, description=trait.description_display, abbreviation=trait.abbreviation, authors=trait.authors, pubmed_text=trait.pubmed_text, + mean=trait.mean, lrs_score=trait.LRS_score_repr, lrs_location=trait.LRS_location_repr, additive=trait.additive ) elif dataset.type == "Geno": return dict(name=trait.name, + view=trait.view, dataset=dataset.name, dataset_name=dataset.shortname, location=trait.location_repr ) elif dataset.name == "Temp": return dict(name=trait.name, + view=trait.view, dataset="Temp", dataset_name="Temp") else: diff --git a/wqflask/runserver.py b/wqflask/runserver.py index df957bd9..8198b921 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -23,6 +23,9 @@ app_config() werkzeug_logger = logging.getLogger('werkzeug') if WEBSERVER_MODE == 'DEBUG': + from flask_debugtoolbar import DebugToolbarExtension + app.debug = True + toolbar = DebugToolbarExtension(app) app.run(host='0.0.0.0', port=SERVER_PORT, debug=True, diff --git a/wqflask/tests/integration/test_markdown_routes.py b/wqflask/tests/integration/test_markdown_routes.py deleted file mode 100644 index 5e3e5045..00000000 --- a/wqflask/tests/integration/test_markdown_routes.py +++ /dev/null @@ -1,21 +0,0 @@ -"Integration tests for markdown routes" -import unittest - -from bs4 import BeautifulSoup - -from wqflask import app - - -class TestGenMenu(unittest.TestCase): - """Tests for glossary""" - - def setUp(self): - self.app = app.test_client() - - def tearDown(self): - pass - - def test_glossary_page(self): - """Test that the glossary page is rendered properly""" - response = self.app.get('/glossary', follow_redirects=True) - pass diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py index 2bbeab1f..a8cf6006 100644 --- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py +++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py @@ -1,10 +1,30 @@ +"""module contains tests for correlation functions""" + import unittest from unittest import mock + from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss class TestCorrelationFunctions(unittest.TestCase): + """test for correlation helper functions""" + + @mock.patch("wqflask.correlation.correlation_functions.compute_corr_coeff_p_value") + def test_tissue_corr_computation(self, mock_tiss_corr_computation): + """test for cal_zero_order_corr_for_tiss""" + + primary_values = [9.288, 9.313, 8.988, 9.660, 8.21] + target_values = [9.586, 8.498, 9.362, 8.820, 8.786] + + mock_tiss_corr_computation.return_value = (0.51, 0.7) + + results = cal_zero_order_corr_for_tiss(primary_values, target_values) + mock_tiss_corr_computation.assert_called_once_with( + primary_values=primary_values, target_values=target_values, + corr_method="pearson") + + self.assertEqual(len(results), 3) @mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData") def test_get_trait_symbol_and_tissue_values(self, mock_class): diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 9b2c6735..d4256a46 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -139,7 +139,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab max_D = max(data) min_D = min(data) # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong - if max_D == float('inf') or max_D > webqtlConfig.MAXLRS: + if (max_D == float('inf') or max_D > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS: max_D = webqtlConfig.MAXLRS # maximum LRS value xLow, xTop, stepX = detScale(min_D, max_D) @@ -156,7 +156,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab j += step for i, item in enumerate(data): - if item == float('inf') or item > webqtlConfig.MAXLRS: + if (item == float('inf') or item > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS: item = webqtlConfig.MAXLRS # maximum LRS value j = int((item - xLow) / step) Count[j] += 1 diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 57dbf8ba..6802d689 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -11,7 +11,6 @@ from utility.redis_tools import (get_redis_conn, add_resource) Redis = get_redis_conn() - def check_resource_availability(dataset, trait_id=None): # At least for now assume temporary entered traits are accessible if type(dataset) == str or dataset.type == "Temp": @@ -133,12 +132,17 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None): else: resource_id = get_resource_id(dataset, trait_id) - if g.user_session.user_id in Redis.smembers("super_users"): + try: + user_id = g.user_session.user_id.encode('utf-8') + except: + user_id = g.user_session.user_id + + if user_id in Redis.smembers("super_users"): return "owner" resource_info = get_resource_info(resource_id) if resource_info: - if g.user_session.user_id == resource_info['owner_id']: + if user_id == resource_info['owner_id']: return "owner" else: return check_admin(resource_id) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index ff125bd2..de9dde46 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -127,22 +127,20 @@ def check_verification_code(code): def get_user_groups(user_id): - # ZS: Get the groups where a user is an admin or a member and + # Get the groups where a user is an admin or a member and # return lists corresponding to those two sets of groups - admin_group_ids = [] # ZS: Group IDs where user is an admin - user_group_ids = [] # ZS: Group IDs where user is a regular user + admin_group_ids = [] # Group IDs where user is an admin + user_group_ids = [] # Group IDs where user is a regular user groups_list = Redis.hgetall("groups") - for key in groups_list: + for group_id, group_details in groups_list.items(): try: - group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin.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']]) + _details = json.loads(group_details) + group_admins = set([this_admin if this_admin else None for this_admin in _details['admins']]) + group_members = set([this_member if this_member else None for this_member in _details['members']]) if user_id in group_admins: - admin_group_ids.append(group_ob['id']) + admin_group_ids.append(group_id) elif user_id in group_members: - user_group_ids.append(group_ob['id']) + user_group_ids.append(group_id) else: continue except: diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index 56d0af6f..778fb64d 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -20,8 +20,12 @@ def app_config(): import os app.config['SECRET_KEY'] = str(os.urandom(24)) mode = WEBSERVER_MODE - if mode == "DEV" or mode == "DEBUG": + if mode in ["DEV", "DEBUG"]: app.config['TEMPLATES_AUTO_RELOAD'] = True + if mode == "DEBUG": + from flask_debugtoolbar import DebugToolbarExtension + app.debug = True + toolbar = DebugToolbarExtension(app) print("==========================================") diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py index c8b9da0e..85b25d60 100644 --- a/wqflask/wqflask/correlation/correlation_functions.py +++ b/wqflask/wqflask/correlation/correlation_functions.py @@ -21,15 +21,10 @@ # This module is used by GeneNetwork project (www.genenetwork.org) # # Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by NL 2011/03/23 -import math -import string from base.mrna_assay_tissue_data import MrnaAssayTissueData - -from flask import Flask, g +from gn3.computations.correlations import compute_corr_coeff_p_value ##################################################################################### @@ -45,31 +40,14 @@ from flask import Flask, g # the same tissue order ##################################################################################### -def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearson'): - - N = len(primaryValue) - # R_primary = rpy2.robjects.FloatVector(list(range(len(primaryValue)))) - # for i in range(len(primaryValue)): - # R_primary[i] = primaryValue[i] - # R_target = rpy2.robjects.FloatVector(list(range(len(targetValue)))) - # for i in range(len(targetValue)): - # R_target[i] = targetValue[i] +def cal_zero_order_corr_for_tiss(primary_values, target_values, method="pearson"): + """function use calls gn3 to compute corr,p_val""" - # R_corr_test = rpy2.robjects.r['cor.test'] - # if method == 'spearman': - # R_result = R_corr_test(R_primary, R_target, method='spearman') - # else: - # R_result = R_corr_test(R_primary, R_target) - - # corr_result = [] - # corr_result.append(R_result[3][0]) - # corr_result.append(N) - # corr_result.append(R_result[2][0]) - - return [None, N, None] - # return corr_result + (corr_coeff, p_val) = compute_corr_coeff_p_value( + primary_values=primary_values, target_values=target_values, corr_method=method) + return (corr_coeff, len(primary_values), p_val) ######################################################################################################## # input: cursor, symbolList (list), dataIdDict(Dict): key is symbol @@ -80,8 +58,9 @@ def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearso # then call getSymbolValuePairDict function and merge the results. ######################################################################################################## + def get_trait_symbol_and_tissue_values(symbol_list=None): tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list) - if len(tissue_data.gene_symbols) >0: + if len(tissue_data.gene_symbols) > 0: results = tissue_data.get_symbol_values_pairs() - return results + return results diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index 30c05f03..a18bceaf 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -18,7 +18,10 @@ from gn3.db_utils import database_connector def create_target_this_trait(start_vars): """this function creates the required trait and target dataset for correlation""" - this_dataset = data_set.create_dataset(dataset_name=start_vars['dataset']) + if start_vars['dataset'] == "Temp": + this_dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group']) + else: + this_dataset = data_set.create_dataset(dataset_name=start_vars['dataset']) target_dataset = data_set.create_dataset( dataset_name=start_vars['corr_dataset']) this_trait = create_trait(dataset=this_dataset, @@ -145,15 +148,9 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait): def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset): sample_data = process_samples( - start_vars, this_dataset.group.samplelist) - - sample_data = test_process_data(this_trait, this_dataset, start_vars) - + start_vars, this_dataset.group.all_samples_ordered()) - if target_dataset.type == "ProbeSet": - target_dataset.get_probeset_data(list(sample_data.keys())) - else: - target_dataset.get_trait_data(list(sample_data.keys())) + target_dataset.get_trait_data(list(sample_data.keys())) this_trait = retrieve_sample_data(this_trait, this_dataset) this_trait_data = { "trait_sample_data": sample_data, @@ -165,8 +162,14 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset): return (this_trait_data, results) -def compute_correlation(start_vars, method="pearson"): - """compute correlation for to call gn3 api""" +def compute_correlation(start_vars, method="pearson", compute_all=False): + """Compute correlations using GN3 API + + Keyword arguments: + start_vars -- All input from form; includes things like the trait/dataset names + method -- Correlation method to be used (pearson, spearman, or bicor) + compute_all -- Include sample, tissue, and literature correlations (when applicable) + """ # pylint: disable-msg=too-many-locals corr_type = start_vars['corr_type'] @@ -196,17 +199,22 @@ def compute_correlation(start_vars, method="pearson"): if tissue_input is not None: (primary_tissue_data, target_tissue_data) = tissue_input - corr_input_data = { - "primary_tissue": primary_tissue_data, - "target_tissues_dict": target_tissue_data - } - correlation_results = compute_tissue_correlation( - primary_tissue_dict=corr_input_data["primary_tissue"], - target_tissues_data=corr_input_data[ - "target_tissues_dict"], - corr_method=method - - ) + corr_input_data = { + "primary_tissue": primary_tissue_data, + "target_tissues_dict": target_tissue_data + } + correlation_results = compute_tissue_correlation( + primary_tissue_dict=corr_input_data["primary_tissue"], + target_tissues_data=corr_input_data[ + "target_tissues_dict"], + corr_method=method + + ) + else: + return {"correlation_results": [], + "this_trait": this_trait.name, + "target_dataset": start_vars['corr_dataset'], + "return_results": corr_return_results} elif corr_type == "lit": (this_trait_geneid, geneid_dict, species) = do_lit_correlation( @@ -220,11 +228,9 @@ def compute_correlation(start_vars, method="pearson"): correlation_results = correlation_results[0:corr_return_results] - compute_all = True # later to be passed as argument - if (compute_all): - - correlation_results = compute_corr_for_top_results(correlation_results, + correlation_results = compute_corr_for_top_results(start_vars, + correlation_results, this_trait, this_dataset, target_dataset, @@ -238,7 +244,8 @@ def compute_correlation(start_vars, method="pearson"): return correlation_data -def compute_corr_for_top_results(correlation_results, +def compute_corr_for_top_results(start_vars, + correlation_results, this_trait, this_dataset, target_dataset, @@ -261,8 +268,12 @@ def compute_corr_for_top_results(correlation_results, correlation_results = merge_correlation_results( correlation_results, lit_result) - if corr_type != "sample": - pass + if corr_type != "sample" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet": + sample_result = sample_for_trait_lists( + correlation_results, target_dataset, this_trait, this_dataset, start_vars) + if sample_result: + correlation_results = merge_correlation_results( + correlation_results, sample_result) return correlation_results @@ -294,4 +305,3 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict): "symbol_tissue_vals_dict": corr_result_tissue_vals_dict } return (primary_tissue_data, target_tissue_data) - return None diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 2f3df67a..d73965da 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -18,491 +18,152 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -import collections import json -import scipy -import numpy -# import rpy2.robjects as ro # R Objects -import utility.logger -import utility.webqtlUtil -from base.trait import create_trait +from base.trait import create_trait, jsonable +from base.data_set import create_dataset -from base import data_set -from utility import helper_functions -from utility import corr_result_helpers from utility import hmac -from wqflask.correlation import correlation_functions -from utility.benchmark import Bench - -from utility.type_checking import is_str -from utility.type_checking import get_float -from utility.type_checking import get_int -from utility.type_checking import get_string -from utility.db_tools import escape - -from flask import g - -logger = utility.logger.getLogger(__name__) - -METHOD_LIT = "3" -METHOD_TISSUE_PEARSON = "4" -METHOD_TISSUE_RANK = "5" - -TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK] - -TISSUE_MOUSE_DB = 1 - - -class CorrelationResults: - def __init__(self, start_vars): - # get trait list from db (database name) - # calculate correlation with Base vector and targets - - # Check parameters - assert('corr_type' in start_vars) - assert(is_str(start_vars['corr_type'])) - assert('dataset' in start_vars) - # assert('group' in start_vars) permitted to be empty? - assert('corr_sample_method' in start_vars) - assert('corr_samples_group' in start_vars) - assert('corr_dataset' in start_vars) - assert('corr_return_results' in start_vars) - if 'loc_chr' in start_vars: - assert('min_loc_mb' in start_vars) - assert('max_loc_mb' in start_vars) - - with Bench("Doing correlations"): - if start_vars['dataset'] == "Temp": - self.dataset = data_set.create_dataset( - dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group']) - self.trait_id = start_vars['trait_id'] - self.this_trait = create_trait(dataset=self.dataset, - name=self.trait_id, - cellid=None) - else: - helper_functions.get_species_dataset_trait(self, start_vars) - - corr_samples_group = start_vars['corr_samples_group'] - - self.sample_data = {} - self.corr_type = start_vars['corr_type'] - self.corr_method = start_vars['corr_sample_method'] - self.min_expr = get_float(start_vars, 'min_expr') - self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0) - self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0) - - - if ('loc_chr' in start_vars - and 'min_loc_mb' in start_vars - and 'max_loc_mb' in start_vars): - self.location_type = get_string(start_vars, 'location_type') - self.location_chr = get_string(start_vars, 'loc_chr') - self.min_location_mb = get_int(start_vars, 'min_loc_mb') - self.max_location_mb = get_int(start_vars, 'max_loc_mb') - else: - self.location_type = self.location_chr = self.min_location_mb = self.max_location_mb = None - - self.get_formatted_corr_type() - self.return_number = int(start_vars['corr_return_results']) - - # The two if statements below append samples to the sample list based upon whether the user - # rselected Primary Samples Only, Other Samples Only, or All Samples - - primary_samples = self.dataset.group.samplelist - if self.dataset.group.parlist != None: - primary_samples += self.dataset.group.parlist - if self.dataset.group.f1list != None: - primary_samples += self.dataset.group.f1list - - # If either BXD/whatever Only or All Samples, append all of that group's samplelist - if corr_samples_group != 'samples_other': - self.process_samples(start_vars, primary_samples) - - # If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and - # exclude the primary samples (because they would have been added in the previous - # if statement if the user selected All Samples) - if corr_samples_group != 'samples_primary': - if corr_samples_group == 'samples_other': - primary_samples = [x for x in primary_samples if x not in ( - self.dataset.group.parlist + self.dataset.group.f1list)] - self.process_samples(start_vars, list( - self.this_trait.data.keys()), primary_samples) - - self.target_dataset = data_set.create_dataset( - start_vars['corr_dataset']) - self.target_dataset.get_trait_data(list(self.sample_data.keys())) - - self.header_fields = get_header_fields( - self.target_dataset.type, self.corr_method) - - if self.target_dataset.type == "ProbeSet": - self.filter_cols = [7, 6] - elif self.target_dataset.type == "Publish": - self.filter_cols = [6, 0] - else: - self.filter_cols = [4, 0] +def set_template_vars(start_vars, correlation_data): + corr_type = start_vars['corr_type'] + corr_method = start_vars['corr_sample_method'] - self.correlation_results = [] + if start_vars['dataset'] == "Temp": + this_dataset_ob = create_dataset(dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group']) + else: + this_dataset_ob = create_dataset(dataset_name=start_vars['dataset']) + this_trait = create_trait(dataset=this_dataset_ob, + name=start_vars['trait_id']) - self.correlation_data = {} + correlation_data['this_trait'] = jsonable(this_trait, this_dataset_ob) + correlation_data['this_dataset'] = this_dataset_ob.as_dict() - if self.corr_type == "tissue": - self.trait_symbol_dict = self.dataset.retrieve_genes("Symbol") + target_dataset_ob = create_dataset(correlation_data['target_dataset']) + correlation_data['target_dataset'] = target_dataset_ob.as_dict() - tissue_corr_data = self.do_tissue_correlation_for_all_traits() - if tissue_corr_data != None: - for trait in list(tissue_corr_data.keys())[:self.return_number]: - self.get_sample_r_and_p_values( - trait, self.target_dataset.trait_data[trait]) - else: - for trait, values in list(self.target_dataset.trait_data.items()): - self.get_sample_r_and_p_values(trait, values) - - elif self.corr_type == "lit": - self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId") - lit_corr_data = self.do_lit_correlation_for_all_traits() - - for trait in list(lit_corr_data.keys())[:self.return_number]: - self.get_sample_r_and_p_values( - trait, self.target_dataset.trait_data[trait]) - - elif self.corr_type == "sample": - for trait, values in list(self.target_dataset.trait_data.items()): - self.get_sample_r_and_p_values(trait, values) - - self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()), - key=lambda t: -abs(t[1][0]))) - - # ZS: Convert min/max chromosome to an int for the location range option - range_chr_as_int = None - for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): - if 'loc_chr' in start_vars: - if chr_info.name == self.location_chr: - range_chr_as_int = order_id - - for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): - trait_object = create_trait( - dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) - if not trait_object: - continue - - chr_as_int = 0 - for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): - if self.location_type == "highest_lod": - if chr_info.name == trait_object.locus_chr: - chr_as_int = order_id - else: - if chr_info.name == trait_object.chr: - chr_as_int = order_id - - - if (float(self.correlation_data[trait][0]) >= self.p_range_lower - and float(self.correlation_data[trait][0]) <= self.p_range_upper): - - if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean): - if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr): - continue - - if range_chr_as_int != None and (chr_as_int != range_chr_as_int): - continue - if self.location_type == "highest_lod": - if (self.min_location_mb != None) and (float(trait_object.locus_mb) < float(self.min_location_mb)): - continue - if (self.max_location_mb != None) and (float(trait_object.locus_mb) > float(self.max_location_mb)): - continue - else: - if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)): - continue - if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)): - continue - - (trait_object.sample_r, - trait_object.sample_p, - trait_object.num_overlap) = self.correlation_data[trait] - - # Set some sane defaults - trait_object.tissue_corr = 0 - trait_object.tissue_pvalue = 0 - trait_object.lit_corr = 0 - if self.corr_type == "tissue" and tissue_corr_data != None: - trait_object.tissue_corr = tissue_corr_data[trait][1] - 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) - - if self.corr_type != "lit" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet": - self.do_lit_correlation_for_trait_list() - - if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet": - self.do_tissue_correlation_for_trait_list() - - self.json_results = generate_corr_json( - self.correlation_results, self.this_trait, self.dataset, self.target_dataset) - -############################################################################################################################################ - - def get_formatted_corr_type(self): - self.formatted_corr_type = "" - if self.corr_type == "lit": - self.formatted_corr_type += "Literature Correlation " - elif self.corr_type == "tissue": - self.formatted_corr_type += "Tissue Correlation " - elif self.corr_type == "sample": - self.formatted_corr_type += "Genetic Correlation " - - if self.corr_method == "pearson": - self.formatted_corr_type += "(Pearson's r)" - elif self.corr_method == "spearman": - self.formatted_corr_type += "(Spearman's rho)" - elif self.corr_method == "bicor": - self.formatted_corr_type += "(Biweight r)" - - def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1): - """Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each""" - - # Gets tissue expression values for the primary trait - primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=[self.this_trait.symbol]) - - if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower( - )] - gene_symbol_list = [ - trait.symbol for trait in self.correlation_results if trait.symbol] - - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=gene_symbol_list) - - for trait in self.correlation_results: - if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower( - )] - - result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, - this_trait_tissue_values, - self.corr_method) - - trait.tissue_corr = result[0] - trait.tissue_pvalue = result[2] - - def do_tissue_correlation_for_all_traits(self, 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=[self.this_trait.symbol]) - - if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower( - )] - - #print("trait_gene_symbols: ", pf(trait_gene_symbols.values())) - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=list(self.trait_symbol_dict.values())) - - #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict)) - - #print("trait_gene_symbols: ", pf(trait_gene_symbols)) - - tissue_corr_data = {} - for trait, symbol in list(self.trait_symbol_dict.items()): - if symbol and symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower( - )] + table_json = correlation_json_for_table(correlation_data, + correlation_data['this_trait'], + correlation_data['this_dataset'], + target_dataset_ob) - result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, - this_trait_tissue_values, - self.corr_method) + correlation_data['table_json'] = table_json - tissue_corr_data[trait] = [symbol, result[0], result[2]] + if target_dataset_ob.type == "ProbeSet": + filter_cols = [7, 6] + elif target_dataset_ob.type == "Publish": + filter_cols = [6, 0] + else: + filter_cols = [4, 0] - tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()), - key=lambda t: -abs(t[1][1]))) + correlation_data['corr_method'] = corr_method + correlation_data['filter_cols'] = filter_cols + correlation_data['header_fields'] = get_header_fields( + target_dataset_ob.type, correlation_data['corr_method']) + correlation_data['formatted_corr_type'] = get_formatted_corr_type( + corr_type, corr_method) - return tissue_corr_data + return correlation_data - def do_lit_correlation_for_trait_list(self): - input_trait_mouse_gene_id = self.convert_to_mouse_gene_id( - self.dataset.group.species.lower(), self.this_trait.geneid) +def correlation_json_for_table(correlation_data, this_trait, this_dataset, target_dataset_ob): + """Return JSON data for use with the DataTable in the correlation result page - for trait in self.correlation_results: + Keyword arguments: + correlation_data -- Correlation results + this_trait -- Trait being correlated against a dataset, as a dict + this_dataset -- Dataset of this_trait, as a dict + target_dataset_ob - Target dataset, as a Dataset ob + """ + this_trait = correlation_data['this_trait'] + this_dataset = correlation_data['this_dataset'] + target_dataset = target_dataset_ob.as_dict() - if trait.geneid: - trait.mouse_gene_id = self.convert_to_mouse_gene_id( - self.dataset.group.species.lower(), trait.geneid) - else: - trait.mouse_gene_id = None - - if trait.mouse_gene_id and str(trait.mouse_gene_id).find(";") == -1: - result = g.db.execute( - """SELECT value - FROM LCorrRamin3 - WHERE GeneId1='%s' and - GeneId2='%s' - """ % (escape(str(trait.mouse_gene_id)), escape(str(input_trait_mouse_gene_id))) - ).fetchone() - if not result: - result = g.db.execute("""SELECT value - FROM LCorrRamin3 - WHERE GeneId2='%s' and - GeneId1='%s' - """ % (escape(str(trait.mouse_gene_id)), escape(str(input_trait_mouse_gene_id))) - ).fetchone() - - if result: - lit_corr = result.value - trait.lit_corr = lit_corr - else: - trait.lit_corr = 0 - else: - trait.lit_corr = 0 - - def do_lit_correlation_for_all_traits(self): - input_trait_mouse_gene_id = self.convert_to_mouse_gene_id( - self.dataset.group.species.lower(), self.this_trait.geneid) - - lit_corr_data = {} - for trait, gene_id in list(self.trait_geneid_dict.items()): - mouse_gene_id = self.convert_to_mouse_gene_id( - self.dataset.group.species.lower(), gene_id) - - if mouse_gene_id and str(mouse_gene_id).find(";") == -1: - #print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id) - 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: - #print("result:", result) - lit_corr = result.value - lit_corr_data[trait] = [gene_id, lit_corr] + corr_results = correlation_data['correlation_results'] + results_list = [] + for i, trait_dict in enumerate(corr_results): + trait_name = list(trait_dict.keys())[0] + trait = trait_dict[trait_name] + target_trait_ob = create_trait(dataset=target_dataset_ob, + name=trait_name, + get_qtl_info=True) + target_trait = jsonable(target_trait_ob, target_dataset_ob) + if target_trait['view'] == False: + continue + results_dict = {} + results_dict['index'] = i + 1 + results_dict['trait_id'] = target_trait['name'] + results_dict['dataset'] = target_dataset['name'] + results_dict['hmac'] = hmac.data_hmac( + '{}:{}'.format(target_trait['name'], target_dataset['name'])) + results_dict['sample_r'] = f"{float(trait['corr_coefficient']):.3f}" + results_dict['num_overlap'] = trait['num_overlap'] + results_dict['sample_p'] = f"{float(trait['p_value']):.3e}" + if target_dataset['type'] == "ProbeSet": + results_dict['symbol'] = target_trait['symbol'] + results_dict['description'] = "N/A" + results_dict['location'] = target_trait['location'] + results_dict['mean'] = "N/A" + results_dict['additive'] = "N/A" + if bool(target_trait['description']): + results_dict['description'] = target_trait['description'] + if bool(target_trait['mean']): + results_dict['mean'] = f"{float(target_trait['mean']):.3f}" + try: + results_dict['lod_score'] = f"{float(target_trait['lrs_score']) / 4.61:.1f}" + except: + results_dict['lod_score'] = "N/A" + results_dict['lrs_location'] = target_trait['lrs_location'] + if bool(target_trait['additive']): + results_dict['additive'] = f"{float(target_trait['additive']):.3f}" + results_dict['lit_corr'] = "--" + results_dict['tissue_corr'] = "--" + results_dict['tissue_pvalue'] = "--" + if this_dataset['type'] == "ProbeSet": + if 'lit_corr' in trait: + results_dict['lit_corr'] = f"{float(trait['lit_corr']):.3f}" + if 'tissue_corr' in trait: + results_dict['tissue_corr'] = f"{float(trait['tissue_corr']):.3f}" + results_dict['tissue_pvalue'] = f"{float(trait['tissue_p_val']):.3e}" + elif target_dataset['type'] == "Publish": + results_dict['abbreviation_display'] = "N/A" + results_dict['description'] = "N/A" + results_dict['mean'] = "N/A" + results_dict['authors_display'] = "N/A" + results_dict['additive'] = "N/A" + results_dict['pubmed_link'] = "N/A" + results_dict['pubmed_text'] = "N/A" + + if bool(target_trait['abbreviation']): + results_dict['abbreviation_display'] = target_trait['abbreviation'] + if bool(target_trait['description']): + results_dict['description'] = target_trait['description'] + if bool(target_trait['mean']): + results_dict['mean'] = f"{float(target_trait['mean']):.3f}" + if bool(target_trait['authors']): + authors_list = target_trait['authors'].split(',') + if len(authors_list) > 6: + results_dict['authors_display'] = ", ".join( + authors_list[:6]) + ", et al." else: - lit_corr_data[trait] = [gene_id, 0] - else: - lit_corr_data[trait] = [gene_id, 0] - - lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()), - key=lambda t: -abs(t[1][1]))) - - return lit_corr_data - - def convert_to_mouse_gene_id(self, 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 get_sample_r_and_p_values(self, trait, target_samples): - """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. - - """ - - self.this_trait_vals = [] - target_vals = [] - for index, sample in enumerate(self.target_dataset.samplelist): - if sample in self.sample_data: - sample_value = self.sample_data[sample] - target_sample_value = target_samples[index] - self.this_trait_vals.append(sample_value) - target_vals.append(target_sample_value) - - self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values( - self.this_trait_vals, target_vals) - - if num_overlap > 5: - # ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ - # if self.corr_method == 'bicor': - # sample_r, sample_p = do_bicor( - # self.this_trait_vals, target_vals) - if self.corr_method == 'pearson': - sample_r, sample_p = scipy.stats.pearsonr( - self.this_trait_vals, target_vals) - else: - sample_r, sample_p = scipy.stats.spearmanr( - self.this_trait_vals, target_vals) - - if numpy.isnan(sample_r): - pass - else: - self.correlation_data[trait] = [ - sample_r, sample_p, num_overlap] - - def process_samples(self, start_vars, sample_names, excluded_samples=None): - if not excluded_samples: - excluded_samples = () - - sample_val_dict = json.loads(start_vars['sample_vals']) - for sample in sample_names: - if sample not in excluded_samples: - value = sample_val_dict[sample] - if not value.strip().lower() == 'x': - self.sample_data[str(sample)] = float(value) - - -# def do_bicor(this_trait_vals, target_trait_vals): -# r_library = ro.r["library"] # Map the library function -# r_options = ro.r["options"] # Map the options function - -# r_library("WGCNA") -# r_bicor = ro.r["bicorAndPvalue"] # Map the bicorAndPvalue function - -# r_options(stringsAsFactors=False) - -# this_vals = ro.Vector(this_trait_vals) -# target_vals = ro.Vector(target_trait_vals) + results_dict['authors_display'] = target_trait['authors'] + if 'pubmed_id' in target_trait: + results_dict['pubmed_link'] = target_trait['pubmed_link'] + results_dict['pubmed_text'] = target_trait['pubmed_text'] + try: + results_dict['lod_score'] = f"{float(target_trait['lrs_score']) / 4.61:.1f}" + except: + results_dict['lod_score'] = "N/A" + results_dict['lrs_location'] = target_trait['lrs_location'] + if bool(target_trait['additive']): + results_dict['additive'] = f"{float(target_trait['additive']):.3f}" + else: + results_dict['location'] = target_trait['location'] -# the_r, the_p, _fisher_transform, _the_t, _n_obs = [ -# numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)] + results_list.append(results_dict) -# return the_r, the_p + return json.dumps(results_list) def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False): @@ -598,6 +259,25 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap return json.dumps(results_list) +def get_formatted_corr_type(corr_type, corr_method): + formatted_corr_type = "" + if corr_type == "lit": + formatted_corr_type += "Literature Correlation " + elif corr_type == "tissue": + formatted_corr_type += "Tissue Correlation " + elif corr_type == "sample": + formatted_corr_type += "Genetic Correlation " + + if corr_method == "pearson": + formatted_corr_type += "(Pearson's r)" + elif corr_method == "spearman": + formatted_corr_type += "(Spearman's rho)" + elif corr_method == "bicor": + formatted_corr_type += "(Biweight r)" + + return formatted_corr_type + + def get_header_fields(data_type, corr_method): if data_type == "ProbeSet": if corr_method == "spearman": diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 9ac02ac5..e7b16e77 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -23,6 +23,9 @@ import math import random import string +import rpy2.robjects as ro +from rpy2.robjects.packages import importr + import numpy as np import scipy @@ -160,23 +163,22 @@ class CorrelationMatrix: for sample in self.all_sample_list: groups.append(1) - # Not doing PCA until rpy2 is excised self.pca_works = "False" - # try: - # corr_result_eigen = np.linalg.eig(np.array(self.pca_corr_results)) - # corr_eigen_value, corr_eigen_vectors = sortEigenVectors( - # corr_result_eigen) - - # if self.do_PCA == True: - # self.pca_works = "True" - # self.pca_trait_ids = [] - # pca = self.calculate_pca( - # list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors) - # self.loadings_array = self.process_loadings() - # else: - # self.pca_works = "False" - # except: - # self.pca_works = "False" + try: + corr_result_eigen = np.linalg.eig(np.array(self.pca_corr_results)) + corr_eigen_value, corr_eigen_vectors = sortEigenVectors( + corr_result_eigen) + + if self.do_PCA == True: + self.pca_works = "True" + self.pca_trait_ids = [] + pca = self.calculate_pca( + list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors) + self.loadings_array = self.process_loadings() + else: + self.pca_works = "False" + except: + self.pca_works = "False" self.js_data = dict(traits=[trait.name for trait in self.traits], groups=groups, @@ -185,51 +187,51 @@ class CorrelationMatrix: samples=self.all_sample_list, sample_data=self.sample_data,) - # def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors): - # base = importr('base') - # stats = importr('stats') - - # corr_results_to_list = robjects.FloatVector( - # [item for sublist in self.pca_corr_results for item in sublist]) - - # m = robjects.r.matrix(corr_results_to_list, nrow=len(cols)) - # eigen = base.eigen(m) - # pca = stats.princomp(m, cor="TRUE") - # self.loadings = pca.rx('loadings') - # self.scores = pca.rx('scores') - # self.scale = pca.rx('scale') - - # trait_array = zScore(self.trait_data_array) - # trait_array_vectors = np.dot(corr_eigen_vectors, trait_array) - - # pca_traits = [] - # for i, vector in enumerate(trait_array_vectors): - # # ZS: Check if below check is necessary - # # if corr_eigen_value[i-1] > 100.0/len(self.trait_list): - # pca_traits.append((vector * -1.0).tolist()) - - # this_group_name = self.trait_list[0][1].group.name - # temp_dataset = data_set.create_dataset( - # dataset_name="Temp", dataset_type="Temp", group_name=this_group_name) - # temp_dataset.group.get_samplelist() - # for i, pca_trait in enumerate(pca_traits): - # trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \ - # this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") - # this_vals_string = "" - # position = 0 - # for sample in temp_dataset.group.all_samples_ordered(): - # if sample in self.shared_samples_list: - # this_vals_string += str(pca_trait[position]) - # this_vals_string += " " - # position += 1 - # else: - # this_vals_string += "x " - # this_vals_string = this_vals_string[:-1] - - # Redis.set(trait_id, this_vals_string, ex=THIRTY_DAYS) - # self.pca_trait_ids.append(trait_id) - - # return pca + def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors): + base = importr('base') + stats = importr('stats') + + corr_results_to_list = ro.FloatVector( + [item for sublist in self.pca_corr_results for item in sublist]) + + m = ro.r.matrix(corr_results_to_list, nrow=len(cols)) + eigen = base.eigen(m) + pca = stats.princomp(m, cor="TRUE") + self.loadings = pca.rx('loadings') + self.scores = pca.rx('scores') + self.scale = pca.rx('scale') + + trait_array = zScore(self.trait_data_array) + trait_array_vectors = np.dot(corr_eigen_vectors, trait_array) + + pca_traits = [] + for i, vector in enumerate(trait_array_vectors): + # ZS: Check if below check is necessary + # if corr_eigen_value[i-1] > 100.0/len(self.trait_list): + pca_traits.append((vector * -1.0).tolist()) + + this_group_name = self.trait_list[0][1].group.name + temp_dataset = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name=this_group_name) + temp_dataset.group.get_samplelist() + for i, pca_trait in enumerate(pca_traits): + trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \ + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") + this_vals_string = "" + position = 0 + for sample in temp_dataset.group.all_samples_ordered(): + if sample in self.shared_samples_list: + this_vals_string += str(pca_trait[position]) + this_vals_string += " " + position += 1 + else: + this_vals_string += "x " + this_vals_string = this_vals_string[:-1] + + Redis.set(trait_id, this_vals_string, ex=THIRTY_DAYS) + self.pca_trait_ids.append(trait_id) + + return pca def process_loadings(self): loadings_array = [] diff --git a/wqflask/wqflask/decorators.py b/wqflask/wqflask/decorators.py index f0978fd3..54aa6795 100644 --- a/wqflask/wqflask/decorators.py +++ b/wqflask/wqflask/decorators.py @@ -1,14 +1,36 @@ """This module contains gn2 decorators""" from flask import g +from typing import Dict from functools import wraps +from utility.hmac import hmac_creation +import json +import requests -def admin_login_required(f): + +def edit_access_required(f): """Use this for endpoints where admins are required""" @wraps(f) def wrap(*args, **kwargs): - if g.user_session.record.get(b"user_email_address") not in [ - b"labwilliams@gmail.com"]: + resource_id: str = "" + if kwargs.get("inbredset_id"): # data type: dataset-publish + resource_id = hmac_creation("dataset-publish:" + f"{kwargs.get('inbredset_id')}:" + f"{kwargs.get('name')}") + if kwargs.get("dataset_name"): # data type: dataset-probe + resource_id = hmac_creation("dataset-probeset:" + f"{kwargs.get('dataset_name')}") + response: Dict = {} + try: + _user_id = g.user_session.record.get(b"user_id", + "").decode("utf-8") + response = json.loads( + requests.get("http://localhost:8080/" + "available?resource=" + f"{resource_id}&user={_user_id}").content) + except: + response = {} + if "edit" not in response.get("data", []): return "You need to be admin", 401 return f(*args, **kwargs) return wrap diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index ec17d3b0..6254b9b9 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -24,6 +24,7 @@ # # Last updated by Zach 12/14/2010 +import datetime import string from math import * from PIL import Image @@ -271,6 +272,7 @@ class DisplayMappingResults: # Needing for form submission when doing single chr # mapping or remapping after changing options self.sample_vals = start_vars['sample_vals'] + self.vals_hash= start_vars['vals_hash'] self.sample_vals_dict = json.loads(self.sample_vals) self.transform = start_vars['transform'] @@ -355,8 +357,7 @@ class DisplayMappingResults: if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] - if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper": - self.reaper_version = start_vars['reaper_version'] + if self.mapping_method == "reaper": if 'output_files' in start_vars: self.output_files = ",".join( [(the_file if the_file is not None else "") for the_file in start_vars['output_files']]) @@ -651,7 +652,7 @@ class DisplayMappingResults: btminfo.append( 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') - def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""): + def plotIntMapping(self, canvas, offset=(80, 120, 110, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""): im_drawer = ImageDraw.Draw(canvas) # calculating margins xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset @@ -661,7 +662,7 @@ class DisplayMappingResults: if self.legendChecked: yTopOffset += 10 if self.covariates != "" and self.controlLocus and self.doControl != "false": - yTopOffset += 20 + yTopOffset += 25 if len(self.transform) > 0: yTopOffset += 5 else: @@ -861,6 +862,9 @@ class DisplayMappingResults: (item[1], yZero - item[2] * bootHeightThresh / maxBootCount)), fill=self.BOOTSTRAP_BOX_COLOR, outline=BLACK) + if maxBootCount == 0: + return + # draw boot scale highestPercent = (maxBootCount * 100.0) / nboot bootScale = Plot.detScale(0, highestPercent) @@ -1192,43 +1196,47 @@ class DisplayMappingResults: dataset_label = "%s - %s" % (self.dataset.group.name, self.dataset.fullname) - string1 = 'Dataset: %s' % (dataset_label) + + self.current_datetime = datetime.datetime.now().strftime("%b %d %Y %H:%M:%S") + string1 = 'UTC Timestamp: %s' % (self.current_datetime) + string2 = 'Dataset: %s' % (dataset_label) + string3 = 'Trait Hash: %s' % (self.vals_hash) if self.genofile_string == "": - string2 = 'Genotype File: %s.geno' % self.dataset.group.name + string4 = 'Genotype File: %s.geno' % self.dataset.group.name else: - string2 = 'Genotype File: %s' % self.genofile_string + string4 = 'Genotype File: %s' % self.genofile_string.split(":")[1] - string4 = '' + string6 = '' if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": if self.use_loco == "True": - string3 = 'Using GEMMA mapping method with LOCO and ' + string5 = 'Using GEMMA mapping method with LOCO and ' else: - string3 = 'Using GEMMA mapping method with ' + string5 = 'Using GEMMA mapping method with ' if self.covariates != "": - string3 += 'the cofactors below:' + string5 += 'the cofactors below:' cofactor_names = ", ".join( [covar.split(":")[0] for covar in self.covariates.split(",")]) - string4 = cofactor_names + string6 = cofactor_names else: - string3 += 'no cofactors' + string5 += 'no cofactors' elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": - string3 = 'Using R/qtl mapping method with ' + string5 = 'Using R/qtl mapping method with ' if self.covariates != "": - string3 += 'the cofactors below:' + string5 += 'the cofactors below:' cofactor_names = ", ".join( [covar.split(":")[0] for covar in self.covariates.split(",")]) - string4 = cofactor_names + string6 = cofactor_names elif self.controlLocus and self.doControl != "false": - string3 += '%s as control' % self.controlLocus + string5 += '%s as control' % self.controlLocus else: - string3 += 'no cofactors' + string5 += 'no cofactors' else: - string3 = 'Using Haldane mapping function with ' + string5 = 'Using Haldane mapping function with ' if self.controlLocus and self.doControl != "false": - string3 += '%s as control' % self.controlLocus + string5 += '%s as control' % self.controlLocus else: - string3 += 'no control for other QTLs' + string5 += 'no control for other QTLs' y_constant = 10 if self.this_trait.name: @@ -1240,24 +1248,26 @@ class DisplayMappingResults: if self.this_trait.symbol: identification += "Trait: %s - %s" % ( - self.this_trait.name, self.this_trait.symbol) + self.this_trait.display_name, self.this_trait.symbol) elif self.dataset.type == "Publish": if self.this_trait.post_publication_abbreviation: identification += "Trait: %s - %s" % ( - self.this_trait.name, self.this_trait.post_publication_abbreviation) + self.this_trait.display_name, self.this_trait.post_publication_abbreviation) elif self.this_trait.pre_publication_abbreviation: identification += "Trait: %s - %s" % ( - self.this_trait.name, self.this_trait.pre_publication_abbreviation) + self.this_trait.display_name, self.this_trait.pre_publication_abbreviation) else: - identification += "Trait: %s" % (self.this_trait.name) + identification += "Trait: %s" % (self.this_trait.display_name) else: - identification += "Trait: %s" % (self.this_trait.name) + identification += "Trait: %s" % (self.this_trait.display_name) identification += " with %s samples" % (self.n_samples) d = 4 + max( im_drawer.textsize(identification, font=labelFont)[0], im_drawer.textsize(string1, font=labelFont)[0], - im_drawer.textsize(string2, font=labelFont)[0]) + im_drawer.textsize(string2, font=labelFont)[0], + im_drawer.textsize(string3, font=labelFont)[0], + im_drawer.textsize(string4, font=labelFont)[0]) im_drawer.text( text=identification, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, @@ -1266,7 +1276,9 @@ class DisplayMappingResults: else: d = 4 + max( im_drawer.textsize(string1, font=labelFont)[0], - im_drawer.textsize(string2, font=labelFont)[0]) + im_drawer.textsize(string2, font=labelFont)[0], + im_drawer.textsize(string3, font=labelFont)[0], + im_drawer.textsize(string4, font=labelFont)[0]) if len(self.transform) > 0: transform_text = "Transform - " @@ -1293,14 +1305,22 @@ class DisplayMappingResults: text=string2, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 - if string3 != '': + im_drawer.text( + text=string3, xy=(xLeftOffset, y_constant * fontZoom), + font=labelFont, fill=labelColor) + y_constant += 15 + im_drawer.text( + text=string4, xy=(xLeftOffset, y_constant * fontZoom), + font=labelFont, fill=labelColor) + y_constant += 15 + if string4 != '': im_drawer.text( - text=string3, xy=(xLeftOffset, y_constant * fontZoom), + text=string5, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 - if string4 != '': + if string5 != '': im_drawer.text( - text=string4, xy=(xLeftOffset, y_constant * fontZoom), + text=string6, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None): @@ -2110,7 +2130,7 @@ class DisplayMappingResults: thisChr.append( [_locus.name, _locus.cM - Locus0CM]) else: - for j in (0, nLoci / 4, nLoci / 2, nLoci * 3 / 4, -1): + for j in (0, round(nLoci / 4), round(nLoci / 2), round(nLoci * 3 / 4), -1): while _chr[j].name == ' - ': j += 1 if _chr[j].cM != preLpos: @@ -2286,20 +2306,9 @@ class DisplayMappingResults: font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight - # LRSHeightThresh = drawAreaHeight - # AdditiveHeightThresh = drawAreaHeight/2 - # DominanceHeightThresh = drawAreaHeight/2 - if self.selectedChr == 1: - LRSHeightThresh = drawAreaHeight - yTopOffset + 30 * (zoom - 1) - AdditiveHeightThresh = LRSHeightThresh / 2 - DominanceHeightThresh = LRSHeightThresh / 2 - else: - LRSHeightThresh = drawAreaHeight - AdditiveHeightThresh = drawAreaHeight / 2 - DominanceHeightThresh = drawAreaHeight / 2 - # LRSHeightThresh = (yZero - yTopOffset + 30*(zoom - 1)) - # AdditiveHeightThresh = LRSHeightThresh/2 - # DominanceHeightThresh = LRSHeightThresh/2 + LRSHeightThresh = drawAreaHeight + AdditiveHeightThresh = drawAreaHeight / 2 + DominanceHeightThresh = drawAreaHeight / 2 if LRS_LOD_Max > 100: LRSScale = 20.0 @@ -2380,8 +2389,7 @@ class DisplayMappingResults: # ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist): - rightEdge = int(start_pos_x + chr_length_dist * \ - plotXScale - self.SUGGESTIVE_WIDTH / 1.5) + rightEdge = xLeftOffset + plotWidth im_drawer.line( xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY), (rightEdge, suggestiveY)), @@ -2569,7 +2577,10 @@ class DisplayMappingResults: Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * ( ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) else: - Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale + if self.selectedChr != -1 and qtlresult['Mb'] > endMb: + Xc = startPosX + endMb * plotXScale + else: + Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale # updated by NL 06-18-2011: # fix the over limit LRS graph issue since genotype trait may give infinite LRS; @@ -2580,36 +2591,29 @@ class DisplayMappingResults: if 'lrs_value' in qtlresult: if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': - #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) Yc = yZero - webqtlConfig.MAXLRS * \ LRSHeightThresh / \ (LRS_LOD_Max * self.LODFACTOR) else: - #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) Yc = yZero - \ qtlresult['lrs_value'] * LRSHeightThresh / \ (LRS_LOD_Max * self.LODFACTOR) else: if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': - #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max else: - #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lrs_value'] * \ LRSHeightThresh / LRS_LOD_Max else: if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf': - #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max else: if self.LRS_LOD == "LRS": - #Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lod_score'] * self.LODFACTOR * \ LRSHeightThresh / LRS_LOD_Max else: - #Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lod_score'] * \ LRSHeightThresh / LRS_LOD_Max @@ -2642,14 +2646,12 @@ class DisplayMappingResults: AdditiveHeightThresh / additiveMax AdditiveCoordXY.append((Xc, Yc)) + if self.selectedChr != -1 and qtlresult['Mb'] > endMb: + break + m += 1 if self.manhattan_plot != True: - # im_drawer.polygon( - # xy=LRSCoordXY, - # outline=thisLRSColor - # #, closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth) - # ) draw_open_polygon(canvas, xy=LRSCoordXY, outline=thisLRSColor, width=lrsEdgeWidth) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index f88c5ac8..623ab87f 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -11,6 +11,7 @@ from utility.tools import flat_files from utility.tools import GEMMA_WRAPPER_COMMAND from utility.tools import TEMPDIR from utility.tools import WEBSERVER_MODE +from gn3.computations.gemma import generate_hash_of_string import utility.logger logger = utility.logger.getLogger(__name__) @@ -34,10 +35,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, genofile_name = this_dataset.group.name if first_run: - trait_filename = (f"{str(this_dataset.group.name)}_" - f"{str(this_trait.name)}_" - f"{generate_random_n_string(6)}") - gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename) + pheno_filename = gen_pheno_txt_file(this_dataset, genofile_name, vals) if not os.path.isfile(f"{webqtlConfig.GENERATED_IMAGE_DIR}" f"{genofile_name}_output.assoc.txt"): @@ -56,13 +54,13 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, chr_list_string = ",".join(this_chromosomes_name) if covariates != "": - gen_covariates_file(this_dataset, covariates, samples) + covar_filename = gen_covariates_file(this_dataset, covariates, samples) if use_loco == "True": generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco " f"{chr_list_string} -- {GEMMAOPTS} " f"-g {flat_files('genotype/bimbam')}/" f"{genofile_name}_geno.txt -p " - f"{TEMPDIR}/gn2/{trait_filename}.txt -a " + f"{TEMPDIR}/gn2/{pheno_filename}.txt -a " f"{flat_files('genotype/bimbam')}/" f"{genofile_name}_snps.txt -gk > " f"{TEMPDIR}/gn2/{k_output_filename}.json") @@ -73,10 +71,10 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, f"-- {GEMMAOPTS} " f"-g {flat_files('genotype/bimbam')}/" f"{genofile_name}_geno.txt " - f"-p {TEMPDIR}/gn2/{trait_filename}.txt ") + f"-p {TEMPDIR}/gn2/{pheno_filename}.txt ") if covariates != "": gemma_command += (f"-c {flat_files('mapping')}/" - f"{this_dataset.group.name}_covariates.txt " + f"{covar_filename}.txt " f"-a {flat_files('genotype/bimbam')}/" f"{genofile_name}_snps.txt " f"-lmm 9 -maf {maf} > {TEMPDIR}/gn2/" @@ -92,7 +90,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, f"{GEMMAOPTS} " f" -g {flat_files('genotype/bimbam')}/" f"{genofile_name}_geno.txt -p " - f"{TEMPDIR}/gn2/{trait_filename}.txt -a " + f"{TEMPDIR}/gn2/{pheno_filename}.txt -a " f"{flat_files('genotype/bimbam')}/" f"{genofile_name}_snps.txt -gk > " f"{TEMPDIR}/gn2/{k_output_filename}.json") @@ -106,12 +104,11 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, f"{genofile_name}_snps.txt " f"-lmm 9 -g {flat_files('genotype/bimbam')}/" f"{genofile_name}_geno.txt -p " - f"{TEMPDIR}/gn2/{trait_filename}.txt ") + f"{TEMPDIR}/gn2/{pheno_filename}.txt ") if covariates != "": gemma_command += (f" -c {flat_files('mapping')}/" - f"{this_dataset.group.name}" - f"_covariates.txt > " + f"{covar_filename}.txt > " f"{TEMPDIR}/gn2/{gwa_output_filename}.json") else: gemma_command += f" > {TEMPDIR}/gn2/{gwa_output_filename}.json" @@ -129,16 +126,20 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, return marker_obs, gwa_output_filename -def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename): +def gen_pheno_txt_file(this_dataset, genofile_name, vals): """Generates phenotype file for GEMMA""" - with open(f"{TEMPDIR}/gn2/{trait_filename}.txt", "w") as outfile: + filename = "PHENO_" + generate_hash_of_string(this_dataset.name + str(vals)).replace("/", "_") + + with open(f"{TEMPDIR}/gn2/{filename}.txt", "w") as outfile: for value in vals: if value == "x": outfile.write("NA\n") else: outfile.write(value + "\n") + return filename + def gen_covariates_file(this_dataset, covariates, samples): covariate_list = covariates.split(",") @@ -168,14 +169,18 @@ def gen_covariates_file(this_dataset, covariates, samples): this_covariate_data.append("-9") covariate_data_object.append(this_covariate_data) + filename = "COVAR_" + generate_hash_of_string(this_dataset.name + str(covariate_data_object)).replace("/", "_") + with open((f"{flat_files('mapping')}/" - f"{this_dataset.group.name}_covariates.txt"), + f"{filename}.txt"), "w") as outfile: for i in range(len(covariate_data_object[0])): for this_covariate in covariate_data_object: outfile.write(str(this_covariate[i]) + "\t") outfile.write("\n") + return filename + def parse_loco_output(this_dataset, gwa_output_filename, loco="True"): diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 4d6715ba..801674e1 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -178,101 +178,6 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): return marker_obs, permu_vals, bootstrap_vals -def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): - genotype = dataset.group.read_genotype_file(use_reaper=True) - - if manhattan_plot != True: - genotype = genotype.addinterval() - - trimmed_samples = [] - trimmed_values = [] - for i in range(0, len(samples_before)): - try: - trimmed_values.append(float(trait_vals[i])) - trimmed_samples.append(str(samples_before[i])) - except: - pass - - perm_output = [] - bootstrap_results = [] - - if num_perm < 100: - suggestive = 0 - significant = 0 - else: - perm_output = genotype.permutation( - strains=trimmed_samples, trait=trimmed_values, nperm=num_perm) - suggestive = perm_output[int(num_perm * 0.37 - 1)] - significant = perm_output[int(num_perm * 0.95 - 1)] - # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case - - json_data['suggestive'] = suggestive - json_data['significant'] = significant - - if control_marker != "" and do_control == "true": - reaper_results = genotype.regression(strains=trimmed_samples, - trait=trimmed_values, - control=str(control_marker)) - if bootCheck: - control_geno = [] - control_geno2 = [] - _FIND = 0 - for _chr in genotype: - for _locus in _chr: - if _locus.name == control_marker: - control_geno2 = _locus.genotype - _FIND = 1 - break - if _FIND: - break - if control_geno2: - _prgy = list(genotype.prgy) - for _strain in trimmed_samples: - _idx = _prgy.index(_strain) - control_geno.append(control_geno2[_idx]) - - bootstrap_results = genotype.bootstrap(strains=trimmed_samples, - trait=trimmed_values, - control=control_geno, - nboot=num_bootstrap) - else: - reaper_results = genotype.regression(strains=trimmed_samples, - trait=trimmed_values) - - if bootCheck: - bootstrap_results = genotype.bootstrap(strains=trimmed_samples, - trait=trimmed_values, - nboot=num_bootstrap) - - json_data['chr'] = [] - json_data['pos'] = [] - json_data['lod.hk'] = [] - json_data['markernames'] = [] - # if self.additive: - # self.json_data['additive'] = [] - - # Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary - qtl_results = [] - for qtl in reaper_results: - reaper_locus = qtl.locus - # ZS: Convert chr to int - converted_chr = reaper_locus.chr - if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y": - converted_chr = int(reaper_locus.chr) - json_data['chr'].append(converted_chr) - json_data['pos'].append(reaper_locus.Mb) - json_data['lod.hk'].append(qtl.lrs) - json_data['markernames'].append(reaper_locus.name) - # if self.additive: - # self.json_data['additive'].append(qtl.additive) - locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, - "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} - qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb, - "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance} - qtl_results.append(qtl) - return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results - - def natural_sort(marker_list): """ Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 09afb8d1..1dca1b1b 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -39,7 +39,7 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n } if do_control == "true" and control_marker: - post_data["control_marker"] = control_marker + post_data["control"] = control_marker if not manhattan_plot: post_data["interval"] = True @@ -61,6 +61,7 @@ def get_hash_of_textio(the_file: TextIO) -> str: the_file.seek(0) hash_of_file = hashlib.md5(the_file.read().encode()).hexdigest() + hash_of_file = hash_of_file.replace("/", "_") # Replace / with _ to prevent issue with filenames being translated to directories return hash_of_file @@ -89,7 +90,7 @@ def write_phenotype_file(trait_name: str, for i, sample in enumerate(samples): this_row = [sample] if vals[i] != "x": - this_row.append(vals[i]) + this_row.append(str(round(float(vals[i]), 3))) else: this_row.append("NA") for cofactor in cofactor_data: @@ -126,7 +127,7 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict: sample_data = trait_ob.data for index, sample in enumerate(samples): if sample in sample_data: - sample_value = sample_data[sample].value + sample_value = str(round(float(sample_data[sample].value), 3)) cofactor_dict[cofactor_name].append(sample_value) else: cofactor_dict[cofactor_name].append("NA") diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index c5b980a7..290c4a14 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -75,6 +75,7 @@ class RunMapping: self.vals = [] self.samples = [] self.sample_vals = start_vars['sample_vals'] + self.vals_hash = start_vars['vals_hash'] sample_val_dict = json.loads(self.sample_vals) samples = sample_val_dict.keys() if (len(genofile_samplelist) != 0): @@ -103,9 +104,7 @@ class RunMapping: if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] else: - mapping_results_filename = self.dataset.group.name + "_" + \ - ''.join(random.choice(string.ascii_uppercase + string.digits) - for _ in range(6)) + mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash]).replace("/", "_") self.mapping_results_path = "{}{}.csv".format( webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) @@ -220,7 +219,7 @@ class RunMapping: elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() elif self.mapping_method == "rqtl_geno": - perm_strata = [] + self.perm_strata = [] if "perm_strata" in start_vars and "categorical_vars" in start_vars: self.categorical_vars = start_vars["categorical_vars"].split( ",") @@ -229,7 +228,7 @@ class RunMapping: sample_names=self.samples, this_trait=self.this_trait) - perm_strata = get_perm_strata( + self.perm_strata = get_perm_strata( self.this_trait, primary_samples, self.categorical_vars, self.samples) self.score_type = "LOD" self.control_marker = start_vars['control_marker'] @@ -243,10 +242,10 @@ class RunMapping: # self.pair_scan = True if self.permCheck and self.num_perm > 0: self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl( - self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) + self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) else: results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, - self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) + self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) elif self.mapping_method == "reaper": if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON if "additiveCheck" in start_vars: @@ -272,47 +271,32 @@ class RunMapping: self.bootCheck = False self.num_bootstrap = 0 - self.reaper_version = start_vars['reaper_version'] - self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] logger.info("Running qtlreaper") - if self.reaper_version == "new": - self.first_run = True - self.output_files = None - # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) - if 'first_run' in start_vars: - self.first_run = False - if 'output_files' in start_vars: - self.output_files = start_vars['output_files'].split( - ",") - - results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait, - self.dataset, - self.samples, - self.vals, - self.json_data, - self.num_perm, - self.bootCheck, - self.num_bootstrap, - self.do_control, - self.control_marker, - self.manhattan_plot, - self.first_run, - self.output_files) - else: - results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.run_original_reaper(self.this_trait, - self.dataset, - self.samples, - self.vals, - self.json_data, - self.num_perm, - self.bootCheck, - self.num_bootstrap, - self.do_control, - self.control_marker, - self.manhattan_plot) + self.first_run = True + self.output_files = None + # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + if 'first_run' in start_vars: + self.first_run = False + if 'output_files' in start_vars: + self.output_files = start_vars['output_files'].split( + ",") + + results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait, + self.dataset, + self.samples, + self.vals, + self.json_data, + self.num_perm, + self.bootCheck, + self.num_bootstrap, + self.do_control, + self.control_marker, + self.manhattan_plot, + self.first_run, + self.output_files) elif self.mapping_method == "plink": self.score_type = "-logP" self.manhattan_plot = True @@ -421,8 +405,9 @@ class RunMapping: total_markers = len(self.qtl_results) with Bench("Exporting Results"): - export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, - self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) + export_mapping_results(self.dataset, self.this_trait, self.qtl_results, + self.mapping_results_path, self.mapping_scale, self.score_type, + self.transform, self.covariates, self.n_samples, self.vals_hash) with Bench("Trimming Markers for Figure"): if len(self.qtl_results) > 30000: @@ -540,13 +525,15 @@ class RunMapping: return trimmed_genotype_data -def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples): +def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples, vals_hash): with open(results_path, "w+") as output_file: output_file.write( "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") output_file.write( "Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") output_file.write("Data Set: " + dataset.fullname + "\n") + output_file.write("Trait: " + trait.display_name + "\n") + output_file.write("Trait Hash: " + vals_hash + "\n") output_file.write("N Samples: " + str(n_samples) + "\n") if len(transform) > 0: transform_text = "Transform - " @@ -673,9 +660,9 @@ def trim_markers_for_table(markers): sorted_markers = sorted( markers, key=lambda k: k['lrs_value'], reverse=True) - # ZS: So we end up with a list of just 2000 markers - if len(sorted_markers) >= 2000: - trimmed_sorted_markers = sorted_markers[:2000] + #ZS: So we end up with a list of just 2000 markers + if len(sorted_markers) >= 10000: + trimmed_sorted_markers = sorted_markers[:10000] return trimmed_sorted_markers else: return sorted_markers @@ -765,9 +752,9 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): if sample in list(sample_list.sample_attribute_values.keys()): combined_string = "" for var in categorical_vars: - if var.lower() in sample_list.sample_attribute_values[sample]: + if var in sample_list.sample_attribute_values[sample]: combined_string += str( - sample_list.sample_attribute_values[sample][var.lower()]) + sample_list.sample_attribute_values[sample][var]) else: combined_string += "NA" else: diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index b28c1b04..c54dd0b3 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -8,8 +8,6 @@ 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')) diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 92cea550..ae30aa59 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -32,7 +32,7 @@ class SampleList: for counter, sample_name in enumerate(sample_names, 1): sample_name = sample_name.replace("_2nd_", "") - # ZS: self.this_trait will be a list if it is a Temp trait + # self.this_trait will be a list if it is a Temp trait if isinstance(self.this_trait, list): sample = webqtlCaseData.webqtlCaseData(name=sample_name) if counter <= len(self.this_trait): @@ -47,7 +47,7 @@ class SampleList: name=sample_name, value=float(self.this_trait[counter - 1])) else: - # ZS - If there's no value for the sample/strain, + # If there's no value for the sample/strain, # create the sample object (so samples with no value # are still displayed in the table) try: @@ -63,29 +63,29 @@ class SampleList: sample.this_id = str(counter) - # ZS: For extra attribute columns; currently only used by + # For extra attribute columns; currently only used by # several datasets if self.sample_attribute_values: sample.extra_attributes = self.sample_attribute_values.get( sample_name, {}) - # ZS: Add a url so RRID case attributes can be displayed as links - if 'rrid' in sample.extra_attributes: + # Add a url so RRID case attributes can be displayed as links + if '36' in sample.extra_attributes: if self.dataset.group.species == "mouse": - if len(sample.extra_attributes['rrid'].split(":")) > 1: - the_rrid = sample.extra_attributes['rrid'].split(":")[ + if len(sample.extra_attributes['36'].split(":")) > 1: + the_rrid = sample.extra_attributes['36'].split(":")[ 1] - sample.extra_attributes['rrid'] = [ - sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append( + sample.extra_attributes['36'] = [ + sample.extra_attributes['36']] + sample.extra_attributes['36'].append( webqtlConfig.RRID_MOUSE_URL % the_rrid) elif self.dataset.group.species == "rat": - if len(str(sample.extra_attributes['rrid'])): - the_rrid = sample.extra_attributes['rrid'].split("_")[ + if len(str(sample.extra_attributes['36'])): + the_rrid = sample.extra_attributes['36'].split("_")[ 1] - sample.extra_attributes['rrid'] = [ - sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append( + sample.extra_attributes['36'] = [ + sample.extra_attributes['36']] + sample.extra_attributes['36'].append( webqtlConfig.RRID_RAT_URL % the_rrid) self.sample_list.append(sample) @@ -124,17 +124,19 @@ class SampleList: # Get attribute names and distinct values for each attribute results = g.db.execute(''' - SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttributeXRefNew.Value + SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttribute.Description, CaseAttributeXRefNew.Value FROM CaseAttribute, CaseAttributeXRefNew WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id AND CaseAttributeXRefNew.InbredSetId = %s - ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),)) + ORDER BY CaseAttribute.Id''', (str(self.dataset.group.id),)) self.attributes = {} - for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)): - key, name = attr + for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name, row.Description)): + key, name, description = attr self.attributes[key] = Bunch() + self.attributes[key].id = key self.attributes[key].name = name + self.attributes[key].description = description self.attributes[key].distinct_values = [ item.Value for item in values] self.attributes[key].distinct_values = natural_sort( @@ -168,10 +170,13 @@ class SampleList: for sample_name, items in itertools.groupby(results.fetchall(), lambda row: row.SampleName): attribute_values = {} + # Make a list of attr IDs without values (that have values for other samples) + valueless_attr_ids = [self.attributes[key].id for key in self.attributes.keys()] for item in items: + valueless_attr_ids.remove(item.Id) attribute_value = item.Value - # ZS: If it's an int, turn it into one for sorting + # If it's an int, turn it into one for sorting # (for example, 101 would be lower than 80 if # they're strings instead of ints) try: @@ -179,8 +184,10 @@ class SampleList: except ValueError: pass - attribute_values[self.attributes[item.Id].name.lower( - )] = attribute_value + attribute_values[str(item.Id)] = attribute_value + for attr_id in valueless_attr_ids: + attribute_values[str(attr_id)] = "" + self.sample_attribute_values[sample_name] = attribute_values def get_first_attr_col(self): diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index c07430dd..c4d1ae1c 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -1,3 +1,5 @@ +from typing import Dict + import string import datetime import uuid @@ -176,11 +178,11 @@ class ShowTrait: self.sample_group_types['samples_primary'] = self.dataset.group.name sample_lists = [group.sample_list for group in self.sample_groups] - categorical_var_list = [] + self.categorical_var_list = [] self.numerical_var_list = [] if not self.temp_trait: # ZS: Only using first samplelist, since I think mapping only uses those samples - categorical_var_list = get_categorical_variables( + self.categorical_var_list = get_categorical_variables( self.this_trait, self.sample_groups[0]) self.numerical_var_list = get_numerical_variables( self.this_trait, self.sample_groups[0]) @@ -192,6 +194,8 @@ class ShowTrait: [self.dataset.species.chromosomes.chromosomes[this_chr].name, i]) self.genofiles = self.dataset.group.get_genofiles() + study_samplelist_json = self.dataset.group.get_study_samplelists() + self.study_samplelists = [study["title"] for study in study_samplelist_json] # ZS: No need to grab scales from .geno file unless it's using # a mapping method that reads .geno files @@ -280,10 +284,11 @@ class ShowTrait: hddn['selected_chr'] = -1 hddn['mapping_display_all'] = True hddn['suggestive'] = 0 + hddn['study_samplelists'] = json.dumps(study_samplelist_json) hddn['num_perm'] = 0 hddn['categorical_vars'] = "" - if categorical_var_list: - hddn['categorical_vars'] = ",".join(categorical_var_list) + if self.categorical_var_list: + hddn['categorical_vars'] = ",".join(self.categorical_var_list) hddn['manhattan_plot'] = "" hddn['control_marker'] = "" if not self.temp_trait: @@ -295,7 +300,7 @@ class ShowTrait: hddn['compare_traits'] = [] hddn['export_data'] = "" hddn['export_format'] = "excel" - if len(self.scales_in_geno) < 2: + if len(self.scales_in_geno) < 2 and bool(self.scales_in_geno): hddn['mapping_scale'] = self.scales_in_geno[list( self.scales_in_geno.keys())[0]][0][0] @@ -318,7 +323,7 @@ class ShowTrait: has_num_cases=self.has_num_cases, attributes=self.sample_groups[0].attributes, categorical_attr_exists=self.categorical_attr_exists, - categorical_vars=",".join(categorical_var_list), + categorical_vars=",".join(self.categorical_var_list), num_values=self.num_values, qnorm_values=self.qnorm_vals, zscore_values=self.z_scores, @@ -520,6 +525,9 @@ class ShowTrait: sample_group_type='primary', header="%s Only" % (self.dataset.group.name)) self.sample_groups = (primary_samples,) + print("\nttttttttttttttttttttttttttttttttttttttttttttt\n") + print(self.sample_groups) + print("\nttttttttttttttttttttttttttttttttttttttttttttt\n") self.primary_sample_names = primary_sample_names self.dataset.group.allsamples = all_samples_ordered @@ -693,7 +701,7 @@ def get_categorical_variables(this_trait, sample_list) -> list: if len(sample_list.attributes) > 0: for attribute in sample_list.attributes: if len(sample_list.attributes[attribute].distinct_values) < 10: - categorical_var_list.append(sample_list.attributes[attribute].name) + categorical_var_list.append(str(sample_list.attributes[attribute].id)) return categorical_var_list @@ -799,3 +807,41 @@ def get_scales_from_genofile(file_location): return [["physic", "Mb"], ["morgan", "cM"]] else: return [["physic", "Mb"]] + + + +def get_diff_of_vals(new_vals: Dict, trait_id: str) -> Dict: + """ Get the diff between current sample values and the values in the DB + + Given a dict of the changed values and the trait/dataset ID, return a Dict + with keys corresponding to each sample with a changed value and a value + that is a dict with keys for the old_value and new_value + + """ + + trait_name = trait_id.split(":")[0] + dataset_name = trait_id.split(":")[1] + trait_ob = create_trait(name=trait_name, dataset_name=dataset_name) + + old_vals = {sample : trait_ob.data[sample].value for sample in trait_ob.data} + + shared_samples = set.union(set(new_vals.keys()), set(old_vals.keys())) + + diff_dict = {} + for sample in shared_samples: + try: + new_val = round(float(new_vals[sample]), 3) + except: + new_val = "x" + try: + old_val = round(float(old_vals[sample]), 3) + except: + old_val = "x" + + if new_val != old_val: + diff_dict[sample] = { + "new_val": new_val, + "old_val": old_val + } + + return diff_dict diff --git a/wqflask/wqflask/static/new/css/bootstrap-custom.css b/wqflask/wqflask/static/new/css/bootstrap-custom.css index 7c8549e1..a0d3ff6a 100644 --- a/wqflask/wqflask/static/new/css/bootstrap-custom.css +++ b/wqflask/wqflask/static/new/css/bootstrap-custom.css @@ -327,7 +327,7 @@ th { font-family: 'Glyphicons Halflings'; src: url('../fonts/glyphicons-halflings-regular.eot'); - src: url('../fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('../fonts/glyphicons-halflings-regular.woff') format('woff'), url('../fonts/glyphicons-halflings-regular.ttf') format('truetype'), url('../fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg'); + src: url('../fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('../fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg'); } .glyphicon { @@ -7554,5 +7554,3 @@ button.close { display: none !important; } } - -/*# sourceMappingURL=bootstrap.css.map */ \ No newline at end of file diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 0486da4d..f5e8c22a 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -159,10 +159,10 @@ div.normalize-div { } div.mapping-main { - min-width: 1200px; + min-width: 1400px; } div.mapping-options { - min-width: 500px; + min-width: 700px; } div.covar-options { @@ -194,7 +194,7 @@ div.select-covar-div { .selected-covariates { overflow-y: scroll; resize: none; - width: 200px; + width: 400px; } .cofactor-input { @@ -259,3 +259,33 @@ input.trait-value-input { div.inline-div { display: inline; } + +/* div.colorbox_border { + border: 1px solid grey; +} */ +div#cboxContent { + /* box-shadow: + 0 2.8px 2.2px rgba(0, 0, 0, 0.034), + 0 6.7px 5.3px rgba(0, 0, 0, 0.048), + 0 12.5px 10px rgba(0, 0, 0, 0.06), + 0 22.3px 17.9px rgba(0, 0, 0, 0.072), + 0 41.8px 33.4px rgba(0, 0, 0, 0.086), + 0 100px 80px rgba(0, 0, 0, 0.12) */ + + padding: 10px 10px 5px 10px; + + -moz-box-shadow: 3px 3px 5px #535353; + -webkit-box-shadow: 3px 3px 5px #535353; + box-shadow: 3px 3px 5px #535353; + + -moz-border-radius: 6px 6px 6px 6px; + -webkit-border-radius: 6px; + border-radius: 6px 6px 6px 6px; + + /* border: 2px solid grey; */ +} + +#cboxClose { + margin-right: 5px; + margin-bottom: 2px; +} diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js index 3e414034..00025a32 100644 --- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js +++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js @@ -65,10 +65,8 @@ if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) { collection_click = function() { var this_collection_url; - console.log("Clicking on:", $(this)); this_collection_url = $(this).find('.collection_name').prop("href"); this_collection_url += "&json"; - console.log("this_collection_url", this_collection_url); collection_list = $("#collections_holder").html(); return $.ajax({ dataType: "json", @@ -79,32 +77,57 @@ collection_click = function() { submit_click = function() { var covariates_string = ""; - var covariates_display_string = ""; + var covariates_as_set = new Set(); + $(".selected-covariates:first option").each(function() { + if ($(this).val() != ""){ + covariates_as_set.add($(this).val() + "," + $(this).text()); + } + }); $('#collections_holder').find('input[type=checkbox]:checked').each(function() { var this_dataset, this_trait; this_trait = $(this).parents('tr').find('.trait').text(); this_trait_display = $(this).parents('tr').find('.trait').data("display_name"); this_description = $(this).parents('tr').find('.description').text(); - console.log("this_trait is:", this_trait_display); this_dataset = $(this).parents('tr').find('.dataset').data("dataset"); - console.log("this_dataset is:", this_dataset); - covariates_string += this_trait + ":" + this_dataset + "," - //this_covariate_display_string = this_trait + ": " + this_description this_covariate_display_string = this_trait_display if (this_covariate_display_string.length > 50) { this_covariate_display_string = this_covariate_display_string.substring(0, 45) + "..." } - covariates_display_string += this_covariate_display_string + "\n" + covariates_as_set.add(this_trait + ":" + this_dataset + "," + this_covariate_display_string) + }); + + covariates_as_list = Array.from(covariates_as_set) + + // Removed the starting "No covariates selected" option before adding options for each covariate + if (covariates_as_list.length > 0){ + $(".selected-covariates option[value='']").each(function() { + $(this).remove(); + }); + } + + $(".selected-covariates option").each(function() { + $(this).remove(); }); - // Trim the last newline from display_string - covariates_display_string = covariates_display_string.replace(/\n$/, "") - // Trim the last comma - covariates_string = covariates_string.substring(0, covariates_string.length - 1) - //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2) + covariate_list_for_form = [] + $.each(covariates_as_list, function (index, value) { + option_value = value.split(",")[0] + option_text = value.split(",")[1] + $(".selected-covariates").append($("<option/>", { + value: option_value, + text: option_text + })) + covariate_list_for_form.push(option_value) + }); - $("input[name=covariates]").val(covariates_string) - $(".selected-covariates").val(covariates_display_string) + $("input[name=covariates]").val(covariate_list_for_form.join(",")); + + cofactor_count = $(".selected-covariates:first option").length; + if (cofactor_count > 10){ + $(".selected-covariates").attr("size", 10); + } else { + $(".selected-covariates").attr("size", cofactor_count); + } return $.colorbox.close(); }; @@ -186,9 +209,8 @@ color_by_trait = function(trait_sample_data, textStatus, jqXHR) { process_traits = function(trait_data, textStatus, jqXHR) { var the_html, trait, _i, _len; console.log('in process_traits with trait_data:', trait_data); - the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>"; - the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>"; - the_html += " <button id='submit' class='btn btn-primary btn-small'> Submit </button>"; + the_html = "<button class='btn btn-success btn-small submit'> Submit </button>"; + the_html += "<button id='back_to_collections' class='btn btn-inverse btn-small' style='float: right;'>Back</button>"; the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>"; the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>"; the_html += "<tbody>"; @@ -221,6 +243,6 @@ back_to_collections = function() { }; $(".collection_line").on("click", collection_click); -$("#submit").on("click", submit_click); +$(".submit").on("click", submit_click); $(".trait").on("click", trait_click); -$("#back_to_collections").on("click", back_to_collections); \ No newline at end of file +$("#back_to_collections").on("click", back_to_collections); diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js index 9fe61abe..897f79ff 100644 --- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js +++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -132,16 +132,16 @@ build_columns = function() { } } - attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name.toLowerCase() > js_data.attributes[b].name.toLowerCase()) ? 1 : -1) + attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].id > js_data.attributes[b].id) ? 1 : -1) for (i = 0; i < attr_keys.length; i++){ column_list.push( { - 'title': "<div style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>", + 'title': "<div title='" + js_data.attributes[attr_keys[i]].description + "' style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>", 'type': "natural", 'data': null, 'targets': attr_start + i, 'render': function(data, type, row, meta) { - attr_name = Object.keys(data.extra_attributes).sort()[meta.col - data.first_attr_col] + attr_name = Object.keys(data.extra_attributes).sort((a, b) => (parseInt(a) > parseInt(b)) ? 1 : -1)[meta.col - data.first_attr_col] if (attr_name != null && attr_name != undefined){ if (Array.isArray(data.extra_attributes[attr_name])){ diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 77ef1720..f050d4ae 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -98,11 +98,54 @@ sample_group_types = js_data.sample_group_types; $(".select_covariates").click(function () { open_covariate_selection(); }); + $(".remove_covariates").click(function () { - $("input[name=covariates]").val("") - $(".selected-covariates").val("") + $(".selected-covariates option:selected").each(function() { + this_val = $(this).val(); + $(".selected-covariates option").each(function(){ + if ($(this).val() == this_val){ + $(this).remove(); + } + }) + cofactor_count = $(".selected-covariates:first option").length + if (cofactor_count > 2 && cofactor_count < 11){ + $(".selected-covariates").each(function() { + $(this).attr("size", $(".selected-covariates:first option").length) + }); + } else if (cofactor_count > 10) { + $(".selected-covariates").each(function() { + $(this).attr("size", 10) + }); + } else { + $(".selected-covariates").each(function() { + $(this).attr("size", 2) + }); + } + if (cofactor_count == 0){ + $(".selected-covariates").each(function() { + $(this).append($("<option/>", { + value: "", + text: "No covariates selected" + })) + }) + } + }); + + covariates_list = []; + $(".selected-covariates:first option").each(function() { + covariates_list.push($(this).val()); + }) + $("input[name=covariates]").val(covariates_list.join(",")) }); +$(".remove_all_covariates").click(function() { + $(".selected-covariates option").each(function() { + $(this).remove(); + }); + $(".selected-covariates").attr("size", 2) + $("input[name=covariates]").val(""); +}) + open_trait_selection = function() { return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) { return function() { @@ -608,13 +651,14 @@ $(".corr_compute").on("click", (function(_this) { create_value_dropdown = function(value) { return "<option val=" + value + ">" + value + "</option>"; }; + populate_sample_attributes_values_dropdown = function() { var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results; $('#attribute_values').empty(); sample_attributes = []; var attributes_as_list = Object.keys(js_data.attributes).map(function(key) { - return [key, js_data.attributes[key].name.toLowerCase()]; + return [key, js_data.attributes[key].id]; }); attributes_as_list.sort(function(first, second) { @@ -628,7 +672,7 @@ populate_sample_attributes_values_dropdown = function() { }); for (i=0; i < attributes_as_list.length; i++) { - attribute_info = js_data.attributes[attributes_as_list[i][0]] + attribute_info = js_data.attributes[attributes_as_list[i][1]] sample_attributes.push(attribute_info.distinct_values); } @@ -667,11 +711,13 @@ block_by_attribute_value = function() { let exclude_val_nodes = table_api.column(attribute_start_pos + parseInt(exclude_column)).nodes().to$(); for (i = 0; i < exclude_val_nodes.length; i++) { - let this_col_value = exclude_val_nodes[i].childNodes[0].data; - let this_val_node = val_nodes[i].childNodes[0]; + if (exclude_val_nodes[i].hasChildNodes()) { + let this_col_value = exclude_val_nodes[i].childNodes[0].data; + let this_val_node = val_nodes[i].childNodes[0]; - if (this_col_value == exclude_by_value){ - this_val_node.value = "x"; + if (this_col_value == exclude_by_value){ + this_val_node.value = "x"; + } } } @@ -713,10 +759,34 @@ block_by_index = function() { for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) { index = index_list[_k]; val_nodes[index - 1].childNodes[0].value = "x"; - } }; +filter_by_study = function() { + let this_study = $('#filter_study').val(); + + let study_sample_data = JSON.parse($('input[name=study_samplelists]').val()) + let filter_samples = study_sample_data[parseInt(this_study)]['samples'] + + if ($('#filter_study_group').length){ + let block_group = $('#filter_study_group').val(); + if (block_group === "other") { + table_api = $('#samples_other').DataTable(); + } else { + table_api = $('#samples_primary').DataTable(); + } + } + + let sample_nodes = table_api.column(2).nodes().to$(); + let val_nodes = table_api.column(3).nodes().to$(); + for (i = 0; i < sample_nodes.length; i++) { + this_sample = sample_nodes[i].childNodes[0].innerText; + if (!filter_samples.includes(this_sample)){ + val_nodes[i].childNodes[0].value = "x"; + } + } +} + filter_by_value = function() { let filter_logic = $('#filter_logic').val(); let filter_column = $('#filter_column').val(); @@ -748,7 +818,7 @@ filter_by_value = function() { var this_col_value = filter_val_nodes[i].childNodes[0].value; } else { if (filter_val_nodes[i].childNodes[0] !== undefined){ - var this_col_value = filter_val_nodes[i].childNodes[0].data; + var this_col_value = filter_val_nodes[i].innerText; } else { continue } @@ -1690,6 +1760,11 @@ $('#block_by_index').click(function(){ edit_data_change(); }); +$('#filter_by_study').click(function(){ + filter_by_study(); + edit_data_change(); +}) + $('#filter_by_value').click(function(){ filter_by_value(); edit_data_change(); diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 09e9d024..e42fe8c4 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -141,11 +141,11 @@ $('input[name=display_all]').change((function(_this) { })(this)); //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping -var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals', - 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', - 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'do_control', 'genofile', - 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', - 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] +var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + 'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', + 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', + 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', + 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'primary_samples'] $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) { return function() { diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index c0b99e75..692a7abc 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -81,7 +81,7 @@ <tr> <td><input type="checkbox" name="read" value="{{ group.id }}"></td> <td>{{ loop.index }}</td> - <td>{{ group.name }}</td> + <td><a href="/groups/view?id={{ group.id }}">{{ group.name }}</a></td> <td>{{ group.admins|length + group.members|length }}</td> <td>{{ group.created_timestamp }}</td> <td>{{ group.changed_timestamp }}</td> diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 1a0335b6..d30c575a 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -87,6 +87,7 @@ <li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li> <li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li> <li><a href="http://power.genenetwork.org">BXD Power Calculator</a></li> + <li><a href="http://notebook.genenetwork.org/">Jupyter Notebook Launcher</a></li> <li><a href="http://datafiles.genenetwork.org">Interplanetary File System</a></li> </ul> </li> @@ -208,7 +209,7 @@ <a href="http://joss.theoj.org/papers/10.21105/joss.00025"><img src="https://camo.githubusercontent.com/846b750f582ae8f1d0b4f7e8fee78bed705c88ba/687474703a2f2f6a6f73732e7468656f6a2e6f72672f7061706572732f31302e32313130352f6a6f73732e30303032352f7374617475732e737667" alt="JOSS" data-canonical-src="http://joss.theoj.org/papers/10.21105/joss.00025/status.svg" style="max-width:100%;"></a> </p> <p> - Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <span class="broken_link" href="https://webchat.freenode.net/">IRC</span> (#genenetwork channel). + Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <span class="broken_link" href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</span> and find us on <a href="https://webchat.freenode.net#genenetwork">IRC</a> (#genenetwork channel). {% if version: %} <p><small>GeneNetwork {{ version }}</small></p> {% endif %} diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html index 0398c6e4..8640fdb8 100644 --- a/wqflask/wqflask/templates/collections/add.html +++ b/wqflask/wqflask/templates/collections/add.html @@ -5,7 +5,7 @@ or add to an existing collection.</p> </div> <div class="modal-body" style="margin-left: 20px;"> - <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form"> + <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form" class="form-inline"> {% if traits is defined %} <input type="hidden" name="traits" value="{{ traits }}" /> {% else %} @@ -14,10 +14,8 @@ {% if collections|length > 0 %} <fieldset> <legend>1. Add to an existing collection</legend> - <div style="margin-left: 20px;"> - <!--<label>Existing collection name:</label>--> - <select name="existing_collection" class="form-control"> - <!--<option selected disabled>Select Collection</option>--> + <div style="margin-left: 20px;"> + <select name="existing_collection" class="form-control" style="width: 80%;"> {% for col in collections %} {% if loop.index == 1 %} <option value="{{ col.id }}:{{ col.name }}" selected>{{ col.name }}</option> @@ -26,8 +24,9 @@ {% endif %} {% endfor %} </select> - <br /> - <button type="submit" name="add_to_existing" class="btn btn-primary">Add to existing collection</button> + <input type="button" style="display: inline;" id="make_default" value="Make Default"> + <br><br> + <button type="submit" name="add_to_existing" class="btn btn-primary">Add</button> </div> </fieldset> {% endif %} @@ -35,7 +34,6 @@ <fieldset> <legend>{% if collections|length > 0 %}2. {% else %}{% endif %}Create a new collection</legend> <div style="margin-left: 20px;"> - <!--<label>Collection name:</label>--> <input type="text" name="new_collection" placeholder=" Name of new collection..." data-trigger="change" data-minlength="5" data-maxlength="50" style="width: 100%"> <button type="submit" name="create_new" class="btn btn-primary" style="margin-top: 20px;">Create collection</button> @@ -54,6 +52,21 @@ parent.jQuery.colorbox.close(); }); + make_default = function() { + alert("The current collection is now your default collection.") + let uc_id = $('[name=existing_collection] option:selected').val().split(":")[0] + $.cookie('default_collection', uc_id, { + expires: 365, + path: '/' + }); + + let default_collection_id = $.cookie('default_collection'); + }; + + $("#make_default").on("click", function(){ + make_default(); + }); + apply_default = function() { let default_collection_id = $.cookie('default_collection'); if (default_collection_id) { diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 9ec98ab1..a3090bcf 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -49,7 +49,7 @@ <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> <button id="remove" class="btn btn-danger" data-url="/collections/remove" type="button" disabled><i class="icon-minus-sign"></i> Delete Rows</button> - <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button> + <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" type="button" title="Delete this collection" > Delete Collection</button> </form> </div> <div style="margin-top: 10px; margin-bottom: 5px;"> diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 4cad2749..f66eb4bd 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -17,9 +17,9 @@ <hr style="height: 1px; background-color: #A9A9A9;"> </div> <div style="max-width: 100%;"> - <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a> + <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if this_dataset.accession_id != 'None' %}GN_AccessionId={{ this_dataset.accession_id }}{% else %}InfoPageName={{ this_dataset.name }}{% endif %}">{{ this_dataset.fullname }}</a> dataset were compared to all records in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if target_dataset.accession_id != 'None' %}GN_AccessionId={{ target_dataset.accession_id }}{% else %}InfoPageName={{ target_dataset.name }}{% endif %}">{{ target_dataset.fullname }}</a> - dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed. + dataset. The top {{ return_results }} correlations ranked by the {{ formatted_corr_type }} are displayed. You can resort this list by clicking the headers. Select the Record ID to open the trait data and analysis page. </p> @@ -30,7 +30,7 @@ <input type="hidden" name="form_url" value="" /> <input type="hidden" name="trait_list" id="trait_list" value= " {% for this_trait in trait_list %} - {{ this_trait.name }}:{{ this_trait.dataset }}, + {{ this_trait }}:{{ this_dataset.name }}, {% endfor %}" > {% include 'tool_buttons.html' %} </form> @@ -43,7 +43,7 @@ <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <input type="hidden" name="database_name" id="database_name" value="None"> <input type="hidden" name="export_data" id="export_data" value=""> - <input type="hidden" name="file_name" id="file_name" value="{{ this_trait.name }}_{{ dataset.name }}_correlation"> + <input type="hidden" name="file_name" id="file_name" value="{{ this_trait.name }}_{{ this_dataset.name }}_correlation"> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> @@ -146,7 +146,7 @@ <script type="text/javascript" charset="utf-8"> - var table_json = {{ json_results | safe }} + var table_json = {{ table_json | safe }} </script> <script type="text/javascript" charset="utf-8"> @@ -313,7 +313,7 @@ 'orderSequence': [ "desc", "asc"], 'render': function(data, type, row, meta) { if (data.sample_r != "N/A") { - return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" + return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if this_dataset.name == 'Temp' %}Temp_{{ this_dataset.group }}{% else %}{{ this_dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" } else { return data.sample_r } @@ -441,7 +441,7 @@ 'orderSequence': [ "desc", "asc"], 'render': function(data, type, row, meta) { if (data.sample_r != "N/A") { - return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" + return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if this_dataset.name== 'Temp' %}Temp_{{ this_dataset.group }}{% else %}{{ this_dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" } else { return data.sample_r } @@ -495,7 +495,7 @@ 'orderSequence': [ "desc", "asc"], 'render': function(data, type, row, meta) { if (data.sample_r != "N/A") { - return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" + return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if this_dataset.name == 'Temp' %}Temp_{{ this_dataset.group }}{% else %}{{ this_dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" } else { return data.sample_r } diff --git a/wqflask/wqflask/templates/display_files_admin.html b/wqflask/wqflask/templates/display_files_admin.html new file mode 100644 index 00000000..4b4babc4 --- /dev/null +++ b/wqflask/wqflask/templates/display_files_admin.html @@ -0,0 +1,32 @@ +{% extends "base.html" %} +{% block title %}Trait Submission{% endblock %} +{% block content %} +<!-- Start of body --> +{% with messages = get_flashed_messages(with_categories=true) %} +{% if messages %} +{% for category, message in messages %} +<div class="container-fluid bg-{{ category }}"> + <p>{{ message }}</p> +</div> +{% endfor %} +{% endif %} +{% endwith %} +Show files for approval + +<div> + <ul> + {% for file in files %} + <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/> + <button><a href="/data-samples/approve/{{ file }}">Approve</a></button> + <button><a href="/data-samples/reject/{{ file }}">Reject</a></button></li> + {% endfor %} + </ul> +</div> +{%endblock%} + +{% block js %} +<script> + gn_server_url = "{{ gn_server_url }}"; + +</script> +{% endblock %} diff --git a/wqflask/wqflask/templates/display_files_user.html b/wqflask/wqflask/templates/display_files_user.html new file mode 100644 index 00000000..b6bab709 --- /dev/null +++ b/wqflask/wqflask/templates/display_files_user.html @@ -0,0 +1,31 @@ +{% extends "base.html" %} +{% block title %}Trait Submission{% endblock %} +{% block content %} +<!-- Start of body --> +{% with messages = get_flashed_messages(with_categories=true) %} +{% if messages %} +{% for category, message in messages %} +<div class="container-fluid bg-{{ category }}"> + <p>{{ message }}</p> +</div> +{% endfor %} +{% endif %} +{% endwith %} +Show files for approval + +<div> + <ul> + {% for file in files %} + <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/> + <button><a href="/data-samples/reject/{{ file }}">Reject</a></button></li> + {% endfor %} + </ul> +</div> +{%endblock%} + +{% block js %} +<script> + gn_server_url = "{{ gn_server_url }}"; + +</script> +{% endblock %} diff --git a/wqflask/wqflask/templates/edit_trait.html b/wqflask/wqflask/templates/edit_phenotype.html index 7d4c65f8..7a841793 100644 --- a/wqflask/wqflask/templates/edit_trait.html +++ b/wqflask/wqflask/templates/edit_phenotype.html @@ -2,8 +2,18 @@ {% block title %}Trait Submission{% endblock %} {% block content %} <!-- Start of body --> -Edit Trait for Published Database -Submit Trait | Reset +{% with messages = get_flashed_messages(with_categories=true) %} +{% if messages %} +{% for category, message in messages %} +<div class="container-fluid bg-{{ category }}"> + <p>{{ message }}</p> +</div> +{% endfor %} +{% endif %} +{% endwith %} +<div class="page-header text-center"> + <h1>Edit Trait for Published Database</h1> +</div> {% if diff %} @@ -53,7 +63,7 @@ Submit Trait | Reset {% endif %} -<form id="edit-form" class="form-horizontal" method="post" action="/trait/update"> +<form id="edit-form" class="form-horizontal" method="post" action="/trait/update" enctype=multipart/form-data> <h2 class="text-center">Trait Information:</h2> <div class="form-group"> <label for="pubmed-id" class="col-sm-2 control-label">Pubmed ID:</label> @@ -207,10 +217,18 @@ Submit Trait | Reset <input name="old_sequence" class="changed" type="hidden" value="{{ publication.sequence |default('', true) }}"/> </div> </div> - <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;"> + <div style="margin-left: 13%;"> + <a href="/trait/{{ publish_xref.id_ }}/sampledata/{{ publish_xref.phenotype_id }}" class="btn btn-link btn-sm"> + Sample Data(CSV Download) + </a> + </div> + <div class="form-group"> + <input type = "file" class="col-sm-4 control-label" name = "file" /> + </div> + <div class="controls center-block" style="width: max-content;"> <input name="dataset-name" class="changed" type="hidden" value="{{ publish_xref.id_ }}"/> - <input name="phenotype-id" class="changed" type="hidden" value="{{ publish_xref.phenotype_id }}"/> <input name="inbred-set-id" class="changed" type="hidden" value="{{ publish_xref.inbred_set_id }}"/> + <input name="phenotype-id" class="changed" type="hidden" value="{{ publish_xref.phenotype_id }}"/> <input name="comments" class="changed" type="hidden" value="{{ publish_xref.comments }}"/> <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change"> <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset"> diff --git a/wqflask/wqflask/templates/edit_probeset.html b/wqflask/wqflask/templates/edit_probeset.html new file mode 100644 index 00000000..85d49561 --- /dev/null +++ b/wqflask/wqflask/templates/edit_probeset.html @@ -0,0 +1,239 @@ +{% extends "base.html" %} +{% block title %}Trait Submission{% endblock %} +{% block content %} +<!-- Start of body --> +Edit Trait for Probeset +Submit Trait | Reset + +{% if diff %} + +<div class="container"> + <details class="col-sm-12 col-md-10 col-lg-12"> + <summary> + <h2>Update History</h2> + </summary> + <table class="table"> + <tbody> + <tr> + <th>Timestamp</th> + <th>Editor</th> + <th>Field</th> + <th>Diff</th> + </tr> + {% set ns = namespace(display_cell=True) %} + + {% for timestamp, group in diff %} + {% set ns.display_cell = True %} + {% for i in group %} + <tr> + {% if ns.display_cell and i.timestamp == timestamp %} + + {% set author = i.author %} + {% set timestamp_ = i.timestamp %} + + {% else %} + + {% set author = "" %} + {% set timestamp_ = "" %} + + {% endif %} + <td>{{ timestamp_ }}</td> + <td>{{ author }}</td> + <td>{{ i.diff.field }}</td> + <td><pre>{{ i.diff.diff }}</pre></td> + {% set ns.display_cell = False %} + </tr> + {% endfor %} + {% endfor %} + </tbody> + </table> + </details> + +</div> + +{% endif %} + +<form id="edit-form" class="form-horizontal" method="post" action="/probeset/update"> + <h2 class="text-center">Probeset Information:</h2> + <div class="form-group"> + <label for="symbol" class="col-sm-2 control-label">Symbol:</label> + <div class="col-sm-4"> + <textarea name="symbol" class="form-control" rows="1">{{ probeset.symbol |default('', true) }}</textarea> + <input name="old_symbol" class="changed" type="hidden" value="{{ probeset.symbol |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="description" class="col-sm-2 control-label">Description:</label> + <div class="col-sm-5"> + <textarea name="description" class="form-control" rows="3">{{ probeset.description |default('', true) }}</textarea> + <input name="old_description" class="changed" type="hidden" value="{{ probeset.description |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_target_description" class="col-sm-2 control-label">Probe Target Description:</label> + <div class="col-sm-4"> + <textarea name="probe_target_description" class="form-control" rows="4">{{ probeset.probe_target_description |default('', true) }}</textarea> + <input name="old_probe_target_description" class="changed" type="hidden" value="{{ probeset.probe_target_description |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="chr" class="col-sm-2 control-label">Chr:</label> + <div class="col-sm-4"> + <textarea name="chr" class="form-control" rows="1">{{ probeset.chr_ |default('', true) }}</textarea> + <input name="old_chr_" class="changed" type="hidden" value="{{ probeset.chr_ |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="mb" class="col-sm-2 control-label">Mb:</label> + <div class="col-sm-4"> + <textarea name="mb" class="form-control" rows="1">{{ probeset.mb |default('', true) }}</textarea> + <input name="old_mb" class="changed" type="hidden" value="{{ probeset.mb |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="alias" class="col-sm-2 control-label"> + Alias: + </label> + <div class="col-sm-4"> + <textarea name="alias" class="form-control" rows="1">{{ probeset.alias |default('', true) }}</textarea> + <input name="old_alias" class="changed" type="hidden" value="{{ probeset.alias |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="geneid" class="col-sm-2 control-label"> + Gene Id: + </label> + <div class="col-sm-4"> + <textarea name="geneid" class="form-control" rows="1">{{ probeset.geneid |default('', true) }}</textarea> + <input name="old_geneid" class="changed" type="hidden" value="{{ probeset.geneid |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="homologeneid" class="col-sm-2 control-label"> + Homolegene Id: + </label> + <div class="col-sm-4"> + <textarea name="homologeneid" class="form-control" rows="1">{{ probeset.homologeneid |default('', true) }}</textarea> + <input name="old_homologeneid" class="changed" type="hidden" value="{{ probeset.homologeneid |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="unigeneid" class="col-sm-2 control-label"> + Unigene Id: + </label> + <div class="col-sm-4"> + <textarea name="unigeneid" class="form-control" rows="1">{{ probeset.unigeneid |default('', true) }}</textarea> + <input name="old_unigeneid" class="changed" type="hidden" value="{{ probeset.unigeneid |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="omim" class="col-sm-2 control-label">OMIM:</label> + <div class="col-sm-4"> + <textarea name="omim" class="form-control" rows="1">{{ probeset.omim |default('', true) }}</textarea> + <input name="old_omim" class="changed" type="hidden" value="{{ probeset.omim |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="refseq_transcriptid" class="col-sm-2 control-label"> + Refseq TranscriptId: + </label> + <div class="col-sm-4"> + <textarea name="refseq_transcriptid" class="form-control" rows="1">{{ probeset.refseq_transcriptid |default('', true) }}</textarea> + <input name="old_refseq_transcriptid" class="changed" type="hidden" value="{{ probeset.refseq_transcriptid |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="blatseq" class="col-sm-2 control-label">BlatSeq:</label> + <div class="col-sm-8"> + <textarea name="blatseq" class="form-control" rows="6">{{ probeset.blatseq |default('', true) }}</textarea> + <input name="old_blatseq" class="changed" type="hidden" value="{{ probeset.blatseq |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="targetseq" class="col-sm-2 control-label">TargetSeq:</label> + <div class="col-sm-8"> + <textarea name="targetseq" class="form-control" rows="6">{{ probeset.targetseq |default('', true) }}</textarea> + <input name="old_targetseq" class="changed" type="hidden" value="{{ probeset.targetseq |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="strand_probe" class="col-sm-2 control-label">Strand Probe:</label> + <div class="col-sm-2"> + <textarea name="strand_probe" class="form-control" rows="1">{{ probeset.strand_probe |default('', true) }}</textarea> + <input name="old_strand_probe" class="changed" type="hidden" value="{{ probeset.strand_probe |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_target_region" class="col-sm-2 control-label">Probe Set Target Region:</label> + <div class="col-sm-8"> + <textarea name="probe_set_target_region" class="form-control" rows="1">{{ probeset.probe_set_target_region |default('', true) }}</textarea> + <input name="old_probe_set_target_region" class="changed" type="hidden" value="{{ probeset.probe_set_target_region_ |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_specificity" class="col-sm-2 control-label">Probeset Specificity:</label> + <div class="col-sm-8"> + <textarea name="probe_set_specificity" class="form-control" rows="1">{{ probeset.probe_set_specificity |default('', true) }}</textarea> + <input name="old_probe_set_specificity" class="changed" type="hidden" value="{{ probeset.probe_set_specificity |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_blat_score" class="col-sm-2 control-label">Probeset Blat Score:</label> + <div class="col-sm-8"> + <textarea name="probe_set_blat_score" class="form-control" rows="1">{{ probeset.probe_set_blat_score |default('', true) }}</textarea> + <input name="old_probe_set_blat_score" class="changed" type="hidden" value="{{ probeset.probe_set_blat_score |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_blat_mb_start" class="col-sm-2 control-label"> + Probeset Blat Mb Start:</label> + <div class="col-sm-8"> + <textarea name="probe_set_blat_mb_start" class="form-control" rows="1">{{ probeset.probe_set_blat_mb_start |default('', true) }}</textarea> + <input name="old_probe_set_blat_mb_start" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_start |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_blat_mb_end" class="col-sm-2 control-label">Probeset Blat Mb End:</label> + <div class="col-sm-8"> + <textarea name="probe_set_blat_mb_end" class="form-control" rows="6">{{ probeset.probe_set_blat_mb_end |default('', true) }}</textarea> + <input name="old_probe_set_blat_mb_end" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_end |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_strand" class="col-sm-2 control-label">Probeset Strand:</label> + <div class="col-sm-8"> + <textarea name="probe_set_strand" class="form-control" rows="6">{{ probeset.probe_set_strand |default('', true) }}</textarea> + <input name="old_probe_set_strand" class="changed" type="hidden" value="{{ probeset.probe_set_strand |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_note_by_rw" class="col-sm-2 control-label">Probeset Strand:</label> + <div class="col-sm-8"> + <textarea name="probe_set_note_by_rw" class="form-control" rows="6">{{ probeset.probe_set_note_by_rw |default('', true) }}</textarea> + <input name="old_probe_set_note_by_rw" class="changed" type="hidden" value="{{ probeset.probe_set_note_by_rw |default('', true) }}"/> + </div> + </div> + <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;"> + <input name="id" class="changed" type="hidden" value="{{ probeset.id_ }}"/> + <input name="old_id_" class="changed" type="hidden" value="{{ probeset.id_ }}"/> + <input name="probeset_name" class="changed" type="hidden" value="{{ probeset.name }}"/> + <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change"> + <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset"> + </div> +</form> + +{%endblock%} + +{% block js %} +<script> + gn_server_url = "{{ gn_server_url }}"; + function MarkAsChanged(){ + $(this).addClass("changed"); + } + $(":input").blur(MarkAsChanged).change(MarkAsChanged); + + $("input[type=submit]").click(function(){ + $(":input:not(.changed)").attr("disabled", "disabled"); + }); +</script> +{% endblock %} diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 6d6136ac..ccf810b0 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -12,6 +12,8 @@ {% if start_vars.tool_used == "Mapping" %} <h1>Computing the Maps</h1> <br> + <b>Time Elapsed:</b> <span class="timer"></span> + <br> <b>Trait Metadata</b> <br> species = <b><i>{{ start_vars.species[0] | upper }}{{ start_vars.species[1:] }}</i></b> @@ -25,6 +27,8 @@ <br> transformation = <b><i>{{ start_vars.transform }}</i></b> {% endif %} + <br> + hash of sample values = <b><i>{{ start_vars.vals_hash }}</i></b> <br><br> <b>Mapping Metadata</b> <br> @@ -68,6 +72,29 @@ <div style="text-align: center;"> <img align="center" src="/static/gif/89.gif"> </div> + {% if start_vars.vals_diff|length != 0 and start_vars.transform == "" %} + <br><br> + <button id="show_full_diff">Show Full Diff</button> + <br> + <div id="diff_table_container" style="display: none; height:200px; overflow:auto;"> + <table class="table table-hover"> + <thead> + <th>Sample</th> + <th>New Value</th> + <th>Old Value</th> + </thead> + <tbody> + {% for sample in start_vars.vals_diff %} + <tr> + <td>{{ sample }}</td> + <td>{{ start_vars.vals_diff[sample].new_val }}</td> + <td>{{ start_vars.vals_diff[sample].old_val }}</td> + </tr> + {% endfor %} + </tbody> + </table> + </div> + {% endif %} </div> </div> </div> @@ -76,6 +103,30 @@ <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script> <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script> <script type="text/javascript"> +$('#show_full_diff').click(function() { + if ($('#diff_table_container').is(':visible')){ + $('#diff_table_container').hide(); + } else { + $('#diff_table_container').show(); + } +}) + +var start = new Date; + +setInterval(function() { + minutes = Math.floor((new Date - start) / 1000 / 60) + seconds = Math.round(((new Date - start) / 1000) % 60) + if (seconds < 10 && minutes >= 1){ + seconds_text = "0" + seconds.toString() + } else { + seconds_text = seconds.toString() + } + if (minutes < 1) { + $('.timer').text(seconds_text + " seconds"); + } else { + $('.timer').text(minutes.toString() + ":" + seconds_text); + } +}, 100); $("#loading_form").attr("action", "{{ start_vars.form_url }}"); setTimeout(function(){ $("#loading_form").submit()}, 350); diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index d6fc6e37..f2d11e89 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -34,6 +34,7 @@ <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> <input type="hidden" name="sample_vals" value="{{ sample_vals }}"> + <input type="hidden" name="vals_hash" value="{{ vals_hash }}"> <input type="hidden" name="n_samples" value="{{ n_samples }}"> <input type="hidden" name="maf" value="{{ maf }}"> <input type="hidden" name="use_loco" value="{{ use_loco }}"> @@ -44,7 +45,12 @@ {% endif %} <input type="hidden" name="num_perm" value="{{ nperm }}"> <input type="hidden" name="perm_info" value=""> - <input type="hidden" name="perm_strata" value="{{ perm_strata }}"> + {% if categorical_vars is defined %} + <input type="hidden" name="categorical_vars" value="{{ categorical_vars|join(',') }}"> + {% endif %} + {% if perm_strata is defined %} + <input type="hidden" name="perm_strata" value="True"> + {% endif %} <input type="hidden" name="num_bootstrap" value="{{ nboot }}"> <input type="hidden" name="do_control" value="{{ doControl }}"> <input type="hidden" name="control_marker" value="{{ controlLocus }}"> @@ -62,15 +68,16 @@ <h2>Map Viewer: Whole Genome</h2><br> <b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br> <b>Database:</b> {{ dataset.fullname }}<br> - {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.name }}</a><br> + {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.display_name }}</a><br> + <b>Trait Hash: </b> {{ vals_hash }}<br> {% if dataset.type == "ProbeSet" %} <b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br> <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb<br> {% endif %} - {% if genofile_string is defined %} - <b>Genotypes:</b> {{ genofile_string.split(":")[1] }} + {% if genofile_string != "" %} + <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}<br> {% endif %} - <br> + <b>Current Date/Time:</b> {{ current_datetime }}<br> <br> <a class="export_mapping_results" href="#" target="_blank" >Download Full Results</a> </div> @@ -357,7 +364,9 @@ {% endif %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='purescript-genome-browser/js/purescript-genetics-browser.js') }}"></script> @@ -409,13 +418,12 @@ "info": "Showing from _START_ to _END_ of " + js_data.total_markers + " records", }, "order": [[1, "asc" ]], - "sDom": "iRZtir", - "iDisplayLength": -1, - "autoWidth": false, - "deferRender": true, + "sDom": "itir", + "autoWidth": true, "bSortClasses": false, - "scrollCollapse": false, - "paging": false + "scrollY": "100vh", + "scroller": true, + "scrollCollapse": true } ); {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %} $('#trait_table').dataTable( { @@ -523,7 +531,7 @@ }); {% endif %} - {% if mapping_method != "gemma" and mapping_method != "plink" %} + {% if mapping_method != "gemma" and mapping_method != "plink" and nperm > 0 and permChecked == "ON" %} $('#download_perm').click(function(){ perm_info_dict = { perm_data: js_data.perm_results, diff --git a/wqflask/wqflask/templates/new_security/_scripts.html b/wqflask/wqflask/templates/new_security/_scripts.html deleted file mode 100644 index 5fefe305..00000000 --- a/wqflask/wqflask/templates/new_security/_scripts.html +++ /dev/null @@ -1 +0,0 @@ -<!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>--> diff --git a/wqflask/wqflask/templates/new_security/forgot_password.html b/wqflask/wqflask/templates/new_security/forgot_password.html index e5c42a45..60a221da 100644 --- a/wqflask/wqflask/templates/new_security/forgot_password.html +++ b/wqflask/wqflask/templates/new_security/forgot_password.html @@ -48,6 +48,5 @@ {% endblock %} {% block js %} - {% include "new_security/_scripts.html" %} {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/forgot_password_step2.html b/wqflask/wqflask/templates/new_security/forgot_password_step2.html index b4bf41c7..1835fd4c 100644 --- a/wqflask/wqflask/templates/new_security/forgot_password_step2.html +++ b/wqflask/wqflask/templates/new_security/forgot_password_step2.html @@ -20,7 +20,6 @@ {% endblock %} {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html index 095036f0..88eab6bc 100644 --- a/wqflask/wqflask/templates/new_security/login_user.html +++ b/wqflask/wqflask/templates/new_security/login_user.html @@ -114,31 +114,5 @@ label.error,div.error{ {% endblock %} {% block js %} - <!-- Disable plugin, see https://github.com/genenetwork/genenetwork2/issues/310 - - <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script> - <script> - $(document).ready(function () { - $("#loginUserForm").validate({ - onkeyup: false, - onsubmit: true, - onfocusout: function(element) { $(element).valid(); }, - rules: { - email_address: { - required: true, - email: true - }, - password: { - required: true - } - } - }); - }); - - </script> - - --> - - {% include "new_security/_scripts.html" %} {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/password_reset.html b/wqflask/wqflask/templates/new_security/password_reset.html index 684c12b1..e21f075c 100644 --- a/wqflask/wqflask/templates/new_security/password_reset.html +++ b/wqflask/wqflask/templates/new_security/password_reset.html @@ -73,7 +73,6 @@ {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/register_user.html b/wqflask/wqflask/templates/new_security/register_user.html index 3ae4488b..c2895517 100644 --- a/wqflask/wqflask/templates/new_security/register_user.html +++ b/wqflask/wqflask/templates/new_security/register_user.html @@ -100,7 +100,6 @@ {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/registered.html b/wqflask/wqflask/templates/new_security/registered.html index f2f58ec1..29889a97 100644 --- a/wqflask/wqflask/templates/new_security/registered.html +++ b/wqflask/wqflask/templates/new_security/registered.html @@ -19,7 +19,6 @@ {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/thank_you.html b/wqflask/wqflask/templates/new_security/thank_you.html index 0ff7ee8d..d4f5e574 100644 --- a/wqflask/wqflask/templates/new_security/thank_you.html +++ b/wqflask/wqflask/templates/new_security/thank_you.html @@ -18,7 +18,6 @@ {% endblock %} {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/verification_still_needed.html b/wqflask/wqflask/templates/new_security/verification_still_needed.html index dc0f9e68..1f91fd8d 100644 --- a/wqflask/wqflask/templates/new_security/verification_still_needed.html +++ b/wqflask/wqflask/templates/new_security/verification_still_needed.html @@ -21,7 +21,6 @@ {% endblock %} {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index e5eea4d1..72a4b560 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -54,6 +54,7 @@ A total of {{ results|count }} records were found. </p> + {% if results|count > 0 %} {% if go_term is not none %} <p><b>The associated genes include:</b><br><br>{% for word in search_terms %}{{ word.search_term[0] }}{% endfor %}</p> {% endif %} @@ -134,8 +135,11 @@ </div> </div> {% endif %} + {% else %} + <br> + <button type="button" onclick="window.location.href='/'">Return To Index Page</button> + {% endif %} </div> - <div id="myModal"></div> <!-- End of body --> @@ -172,6 +176,7 @@ return params; }; + {% if results|count > 0 %} var tableId = "trait_table"; var width_change = 0; //ZS: For storing the change in width so overall table width can be adjusted by that amount @@ -501,6 +506,7 @@ var table = $('#' + tableId).DataTable(); table.colReorder.reset() }); + {% endif %} submit_special = function(url) { $("#trait_submission_form").attr("action", url); diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index e623a968..16a819fa 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -7,8 +7,10 @@ <div class="col-xs-3 controls"> <select name="corr_type" class="form-control"> <option value="sample">Sample r</option> + {% if dataset.type == 'ProbeSet' %} <option value="lit">Literature r</option> <option value="tissue">Tissue r</option> + {% endif %} </select> </div> </div> @@ -70,7 +72,7 @@ <select name="corr_sample_method" class="form-control"> <option value="pearson">Pearson</option> <option value="spearman">Spearman Rank</option> - <!-- <option value="bicor">Biweight Midcorrelation</option> --> + <option value="bicor">Biweight Midcorrelation</option> </select> </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 83f7b0ac..2a21dd24 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -235,7 +235,16 @@ {% endif %} <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button> {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} - <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/{{ this_trait.dataset.id }}', '_blank')">Edit</button> + {% if this_trait.dataset.type == 'Publish' %} + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/inbredset-id/{{ this_trait.dataset.id }}', '_blank')">Edit</button> + {% endif %} + + {% if this_trait.dataset.type == 'ProbeSet' %} + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/edit/probeset-name/{{ this_trait.name }}', '_blank')">Edit</button> + {% endif %} + {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit Privileges</button> + {% endif %} {% endif %} </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 3dd44c85..3af94ed6 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -74,17 +74,20 @@ No collections available. Please add traits to a collection to use them as covariates. {% else %} <div class="select-covar-div"> - <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button> + <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button> <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button> + <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button> </div> - <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea> + <select size="2" name="selected_covariates_gemma" class="form-control selected-covariates" multiple> + <option value="">No covariates selected</option> + </select> {% endif %} </div> </div> <div class="mapping_method_fields form-group"> <label class="col-xs-3 control-label"></label> <div class="col-xs-6"> - <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button> + <button id="gemma_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button> </div> </div> </div> @@ -93,15 +96,6 @@ <div class="tab-pane" id="interval_mapping"> <div class="form-horizontal section-form-div"> <div class="mapping_method_fields form-group"> - <label for="reaper_version" class="col-xs-3 control-label">Version<sup><a href="https://github.com/chfi/rust-qtlreaper" target="_blank" title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label> - <div class="col-xs-3 controls"> - <select name="reaper_version" class="form-control reaper-ver-select"> - <option value="new">New</option> - <option value="original">Original</option> - </select> - </div> - </div> - <div class="mapping_method_fields form-group"> <label for="chr_select" class="col-xs-3 control-label">Chromosome</label> <div class="col-xs-2 controls"> <select id="chr_reaper" class="form-control chr-select"> @@ -187,7 +181,7 @@ <div class="mapping_method_fields form-group"> <label class="col-xs-3 control-label"></label> <div class="col-xs-6"> - <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button> + <button id="interval_mapping_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button> </div> </div> </div> @@ -226,6 +220,17 @@ </select> </div> </div> + {% else %} + <div class="mapping_method_fields form-group"> + <label for="scale_select" class="col-xs-3 control-label">Map Scale</label> + <div class="col-xs-2 controls"> + <select id="scale_rqtl_geno" class="form-control scale-select"> + {% for item in scales_in_geno[dataset.group.name + ".geno"] %} + <option value="{{ item[0] }}">{{ item[1] }}</option> + {% endfor %} + </select> + </div> + </div> {% endif %} <div class="mapping_method_fields form-group"> <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label> @@ -249,21 +254,6 @@ </div> {% endif %} <div class="mapping_method_fields form-group"> - <label for="control_for" class="col-xs-3 control-label">Control for</label> - <div class="col-xs-6 controls"> - <input name="control_rqtl_geno" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" /> - <label class="radio-inline"> - <input type="radio" name="do_control_rqtl" value="true"> - Yes - </label> - <label class="radio-inline"> - <input type="radio" name="do_control_rqtl" value="false" checked=""> - No - </label> - </div> - </div> - - <div class="mapping_method_fields form-group"> <label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label> <div class="col-xs-4 controls"> <select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control"> @@ -317,17 +307,20 @@ No collections available. Please add traits to a collection to use them as covariates. {% else %} <div class="select-covar-div"> - <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button> + <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button> <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button> + <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button> </div> - <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea> + <select size="2" name="selected_covariates_rqtl" class="form-control selected-covariates" multiple> + <option value="">No covariates selected</option> + </select> {% endif %} </div> </div> <div class="mapping_method_fields form-group"> <label class="col-xs-3 control-label"></label> <div class="col-xs-6 controls"> - <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button> + <button id="rqtl_geno_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button> </div> </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index 20f78b48..5e6ed2cf 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -25,7 +25,7 @@ <label for="exclude_column">Block samples by group:</label> <select id="exclude_column" size=1> {% for attribute in sample_groups[0].attributes %} - {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 %} + {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 and sample_groups[0].attributes[attribute].distinct_values|length > 1 %} <option value="{{ loop.index }}"> {{ sample_groups[0].attributes[attribute].name }} </option> @@ -45,6 +45,27 @@ <input type="button" id="exclude_by_attr" class="btn btn-danger" value="Block"> </div> {% endif %} + {% if study_samplelists|length > 0 %} + <div id="filterMenuSpan" class="input-append block-div-2"> + <label for="filter_study_select">Filter samples by study: </label> + <select id="filter_study"> + {% for study in study_samplelists %} + <option value="{{ loop.index - 1 }}">{{ study }}</option> + {% endfor %} + </select> + {% if sample_groups|length != 1 %} + <select id="filter_study_group" size="1"> + <option value="primary"> + {{ sample_group_types['samples_primary'] }} + </option> + <option value="other"> + {{ sample_group_types['samples_other'] }} + </option> + </select> + {% endif %} + <input type="button" id="filter_by_study" class="btn btn-danger" value="Filter"> + </div> + {% endif %} <div id="filterMenuSpan" class="input-append block-div-2"> <label for="filter_samples_field">Filter samples by {% if (numerical_var_list|length == 0) and (not js_data.se_exists) %}value{% endif %} </label> {% if (numerical_var_list|length > 0) or js_data.se_exists %} @@ -53,10 +74,12 @@ {% if js_data.se_exists %} <option value="stderr">SE</option> {% endif %} - {% for attribute in numerical_var_list %} + {% for attribute in sample_groups[0].attributes %} + {% if sample_groups[0].attributes[attribute].name in numerical_var_list %} <option value="{{ loop.index }}"> - {{ attribute }} + {{ sample_groups[0].attributes[attribute].name }} </option> + {% endif %} {% endfor %} </select> {% endif %} diff --git a/wqflask/wqflask/templates/test_correlation_page.html b/wqflask/wqflask/templates/test_correlation_page.html index 0809b65e..991773a2 100644 --- a/wqflask/wqflask/templates/test_correlation_page.html +++ b/wqflask/wqflask/templates/test_correlation_page.html @@ -113,7 +113,7 @@ console.log(correlationResults) {"data":corr_type=="sample"?null:"fd","width":"25px"}, { "data": "index","width":"120px","title":"Index" }, { "data": "trait_name","title":"TraitName"}, - { "data": "corr_coeffient","defaultContent": "--"}, + { "data": "corr_coefficient","defaultContent": "--"}, { "data": "p_value","defaultContent":"--"}, { "data": "num_overlap","defaultContent":"--"}, {"data":"tissue_corr","defaultContent":"--","title":"Tissue r"}, diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index b9181368..5067ca0e 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -27,6 +27,8 @@ from zipfile import ZIP_DEFLATED from wqflask import app +from gn3.commands import run_cmd +from gn3.computations.gemma import generate_hash_of_string from gn3.db import diff_from_dict from gn3.db import fetchall from gn3.db import fetchone @@ -34,12 +36,17 @@ from gn3.db import insert from gn3.db import update from gn3.db.metadata_audit import MetadataAudit from gn3.db.phenotypes import Phenotype +from gn3.db.phenotypes import Probeset from gn3.db.phenotypes import Publication from gn3.db.phenotypes import PublishXRef +from gn3.db.phenotypes import probeset_mapping +from gn3.db.traits import get_trait_csv_sample_data +from gn3.db.traits import update_sample_data from flask import current_app from flask import g +from flask import flash from flask import Response from flask import request from flask import make_response @@ -57,6 +64,7 @@ from wqflask import server_side from base.data_set import create_dataset # Used by YAML in marker_regression from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data +from wqflask.show_trait.show_trait import get_diff_of_vals from wqflask.heatmap import heatmap from wqflask.external_tools import send_to_bnw from wqflask.external_tools import send_to_webgestalt @@ -65,7 +73,7 @@ from wqflask.comparison_bar_chart import comparison_bar_chart from wqflask.marker_regression import run_mapping from wqflask.marker_regression import display_mapping_results from wqflask.network_graph import network_graph -from wqflask.correlation import show_corr_results +from wqflask.correlation.show_corr_results import set_template_vars from wqflask.correlation.correlation_gn3_api import compute_correlation from wqflask.correlation_matrix import show_corr_matrix from wqflask.correlation import corr_scatter_plot @@ -77,7 +85,7 @@ from wqflask.export_traits import export_search_results_csv from wqflask.gsearch import GSearch from wqflask.update_search_results import GSearch as UpdateGSearch from wqflask.docs import Docs, update_text -from wqflask.decorators import admin_login_required +from wqflask.decorators import edit_access_required from wqflask.db_info import InfoPage from utility import temp_data @@ -152,28 +160,37 @@ def shutdown_session(exception=None): @app.errorhandler(Exception) -def handle_bad_request(e): +def handle_generic_exceptions(e): + import werkzeug err_msg = str(e) - logger.error(err_msg) - logger.error(request.url) - # get the stack trace and send it to the logger - exc_type, exc_value, exc_traceback = sys.exc_info() - logger.error(traceback.format_exc()) now = datetime.datetime.utcnow() time_str = now.strftime('%l:%M%p UTC %b %d, %Y') - formatted_lines = [request.url - + " (" + time_str + ")"] + traceback.format_exc().splitlines() - + # get the stack trace and send it to the logger + exc_type, exc_value, exc_traceback = sys.exc_info() + formatted_lines = {f"{request.url} ({time_str}) " + f" {traceback.format_exc().splitlines()}"} + + _message_templates = { + werkzeug.exceptions.NotFound: ("404: Not Found: " + f"{time_str}: {request.url}"), + werkzeug.exceptions.BadRequest: ("400: Bad Request: " + f"{time_str}: {request.url}"), + werkzeug.exceptions.RequestTimeout: ("408: Request Timeout: " + f"{time_str}: {request.url}")} + # Default to the lengthy stack trace! + logger.error(_message_templates.get(exc_type, + formatted_lines)) # Handle random animations # Use a cookie to have one animation on refresh animation = request.cookies.get(err_msg[:32]) if not animation: - list = [fn for fn in os.listdir( - "./wqflask/static/gif/error") if fn.endswith(".gif")] - animation = random.choice(list) + animation = random.choice([fn for fn in os.listdir( + "./wqflask/static/gif/error") if fn.endswith(".gif")]) resp = make_response(render_template("error.html", message=err_msg, - stack=formatted_lines, error_image=animation, version=GN_VERSION)) + stack=formatted_lines, + error_image=animation, + version=GN_VERSION)) # logger.error("Set cookie %s with %s" % (err_msg, animation)) resp.set_cookie(err_msg[:32], animation) @@ -300,6 +317,7 @@ def gsearchact(): elif type == "phenotype": return render_template("gsearch_pheno.html", **result) + @app.route("/gsearch_table", methods=('GET',)) def gsearchtable(): logger.info(request.url) @@ -314,6 +332,7 @@ def gsearchtable(): return flask.jsonify(current_page) + @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): logger.info("REQUEST ARGS:", request.values) @@ -357,20 +376,6 @@ def wcgna_setup(): return render_template("wgcna_setup.html", **request.form) -# @app.route("/wgcna_results", methods=('POST',)) -# def wcgna_results(): -# logger.info("In wgcna, request.form is:", request.form) -# logger.info(request.url) -# # Start R, load the package and pointers and create the analysis -# wgcna = wgcna_analysis.WGCNA() -# # Start the analysis, a wgcnaA object should be a separate long running thread -# wgcnaA = wgcna.run_analysis(request.form) -# # After the analysis is finished store the result -# result = wgcna.process_results(wgcnaA) -# # Display them using the template -# return render_template("wgcna_results.html", **result) - - @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): # We are going to get additional user input for the analysis @@ -380,20 +385,6 @@ def ctl_setup(): return render_template("ctl_setup.html", **request.form) -# @app.route("/ctl_results", methods=('POST',)) -# def ctl_results(): -# logger.info("In ctl, request.form is:", request.form) -# logger.info(request.url) -# # Start R, load the package and pointers and create the analysis -# ctl = ctl_analysis.CTL() -# # Start the analysis, a ctlA object should be a separate long running thread -# ctlA = ctl.run_analysis(request.form) -# # After the analysis is finished store the result -# result = ctl.process_results(ctlA) -# # Display them using the template -# return render_template("ctl_results.html", **result) - - @app.route("/intro") def intro(): doc = Docs("intro", request.args) @@ -428,9 +419,9 @@ def submit_trait_form(): version=GN_VERSION) -@app.route("/trait/<name>/edit/<inbred_set_id>") -@admin_login_required -def edit_trait(name, inbred_set_id): +@app.route("/trait/<name>/edit/inbredset-id/<inbredset_id>") +@edit_access_required +def edit_phenotype(name, inbredset_id): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), passwd=current_app.config.get("DB_PASS"), @@ -439,7 +430,7 @@ def edit_trait(name, inbred_set_id): conn=conn, table="PublishXRef", where=PublishXRef(id_=name, - inbred_set_id=inbred_set_id)) + inbred_set_id=inbredset_id)) phenotype_ = fetchone( conn=conn, table="Phenotype", @@ -476,7 +467,7 @@ def edit_trait(name, inbred_set_id): if len(diff_data) > 0: diff_data_ = groupby(diff_data, lambda x: x.timestamp) return render_template( - "edit_trait.html", + "edit_phenotype.html", diff=diff_data_, publish_xref=publish_xref, phenotype=phenotype_, @@ -485,13 +476,119 @@ def edit_trait(name, inbred_set_id): ) +@app.route("/trait/edit/probeset-name/<dataset_name>") +@edit_access_required +def edit_probeset(dataset_name): + conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), + user=current_app.config.get("DB_USER"), + passwd=current_app.config.get("DB_PASS"), + host=current_app.config.get("DB_HOST")) + probeset_ = fetchone(conn=conn, + table="ProbeSet", + columns=list(probeset_mapping.values()), + where=Probeset(name=dataset_name)) + json_data = fetchall( + conn, + "metadata_audit", + where=MetadataAudit(dataset_id=probeset_.id_)) + Edit = namedtuple("Edit", ["field", "old", "new", "diff"]) + Diff = namedtuple("Diff", ["author", "diff", "timestamp"]) + diff_data = [] + for data in json_data: + json_ = json.loads(data.json_data) + timestamp = json_.get("timestamp") + author = json_.get("author") + for key, value in json_.items(): + if isinstance(value, dict): + for field, data_ in value.items(): + diff_data.append( + Diff(author=author, + diff=Edit(field, + data_.get("old"), + data_.get("new"), + "\n".join(difflib.ndiff( + [data_.get("old")], + [data_.get("new")]))), + timestamp=timestamp)) + diff_data_ = None + if len(diff_data) > 0: + diff_data_ = groupby(diff_data, lambda x: x.timestamp) + return render_template( + "edit_probeset.html", + diff=diff_data_, + probeset=probeset_) + + @app.route("/trait/update", methods=["POST"]) -def update_trait(): +@edit_access_required +def update_phenotype(): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), passwd=current_app.config.get("DB_PASS"), host=current_app.config.get("DB_HOST")) data_ = request.form.to_dict() + TMPDIR = current_app.config.get("TMPDIR") + author = g.user_session.record.get(b'user_name') + if 'file' not in request.files: + flash("No sample-data has been uploaded", "warning") + else: + file_ = request.files['file'] + trait_name = str(data_.get('dataset-name')) + phenotype_id = str(data_.get('phenotype-id', 35)) + SAMPLE_DATADIR = os.path.join(TMPDIR, "sample-data") + if not os.path.exists(SAMPLE_DATADIR): + os.makedirs(SAMPLE_DATADIR) + if not os.path.exists(os.path.join(SAMPLE_DATADIR, + "diffs")): + os.makedirs(os.path.join(SAMPLE_DATADIR, + "diffs")) + if not os.path.exists(os.path.join(SAMPLE_DATADIR, + "updated")): + os.makedirs(os.path.join(SAMPLE_DATADIR, + "updated")) + current_time = str(datetime.datetime.now().isoformat()) + new_file_name = (os.path.join(TMPDIR, + "sample-data/updated/", + (f"{author.decode('utf-8')}." + f"{trait_name}.{phenotype_id}." + f"{current_time}.csv"))) + uploaded_file_name = (os.path.join( + TMPDIR, + "sample-data/updated/", + (f"updated.{author.decode('utf-8')}." + f"{trait_name}.{phenotype_id}." + f"{current_time}.csv"))) + file_.save(new_file_name) + publishdata_id = "" + lines = [] + with open(new_file_name, "r") as f: + lines = f.read() + first_line = lines.split('\n', 1)[0] + publishdata_id = first_line.split("Id:")[-1].strip() + with open(new_file_name, "w") as f: + f.write(lines.split("\n\n")[-1]) + csv_ = get_trait_csv_sample_data(conn=conn, + trait_name=str(trait_name), + phenotype_id=str(phenotype_id)) + with open(uploaded_file_name, "w") as f_: + f_.write(csv_.split("\n\n")[-1]) + r = run_cmd(cmd=("csvdiff " + f"'{uploaded_file_name}' '{new_file_name}' " + "--format json")) + diff_output = (f"{TMPDIR}/sample-data/diffs/" + f"{trait_name}.{author.decode('utf-8')}." + f"{phenotype_id}.{current_time}.json") + with open(diff_output, "w") as f: + dict_ = json.loads(r.get("output")) + dict_.update({ + "author": author.decode('utf-8'), + "publishdata_id": publishdata_id, + "dataset_id": data_.get("dataset-name"), + "timestamp": datetime.datetime.now().strftime( + "%Y-%m-%d %H:%M:%S") + }) + f.write(json.dumps(dict_)) + flash("Sample-data has been successfully uploaded", "success") # Run updates: phenotype_ = { "pre_pub_description": data_.get("pre-pub-desc"), @@ -533,7 +630,6 @@ def update_trait(): diff_data.update({"Publication": diff_from_dict(old={ k: data_.get(f"old_{k}") for k, v in publication_.items() if v is not None}, new=publication_)}) - author = g.user_session.record.get(b'user_name') if diff_data: diff_data.update({"dataset_id": data_.get("dataset-name")}) diff_data.update({"author": author.decode('utf-8')}) @@ -544,7 +640,66 @@ def update_trait(): data=MetadataAudit(dataset_id=data_.get("dataset-name"), editor=author.decode("utf-8"), json_data=json.dumps(diff_data))) - return redirect("/trait/10007/edit/1") + flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success") + return redirect(f"/trait/{data_.get('dataset-name')}" + f"/edit/inbredset-id/{data_.get('inbred-set-id')}") + + +@app.route("/probeset/update", methods=["POST"]) +@edit_access_required +def update_probeset(): + conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), + user=current_app.config.get("DB_USER"), + passwd=current_app.config.get("DB_PASS"), + host=current_app.config.get("DB_HOST")) + data_ = request.form.to_dict() + probeset_ = { + "id_": data_.get("id"), + "symbol": data_.get("symbol"), + "description": data_.get("description"), + "probe_target_description": data_.get("probe_target_description"), + "chr_": data_.get("chr"), + "mb": data_.get("mb"), + "alias": data_.get("alias"), + "geneid": data_.get("geneid"), + "homologeneid": data_.get("homologeneid"), + "unigeneid": data_.get("unigeneid"), + "omim": data_.get("OMIM"), + "refseq_transcriptid": data_.get("refseq_transcriptid"), + "blatseq": data_.get("blatseq"), + "targetseq": data_.get("targetseq"), + "strand_probe": data_.get("Strand_Probe"), + "probe_set_target_region": data_.get("probe_set_target_region"), + "probe_set_specificity": data_.get("probe_set_specificity"), + "probe_set_blat_score": data_.get("probe_set_blat_score"), + "probe_set_blat_mb_start": data_.get("probe_set_blat_mb_start"), + "probe_set_blat_mb_end": data_.get("probe_set_blat_mb_end"), + "probe_set_strand": data_.get("probe_set_strand"), + "probe_set_note_by_rw": data_.get("probe_set_note_by_rw"), + "flag": data_.get("flag") + } + updated_probeset = update( + conn, "ProbeSet", + data=Probeset(**probeset_), + where=Probeset(id_=data_.get("id"))) + + diff_data = {} + author = g.user_session.record.get(b'user_name') + if updated_probeset: + diff_data.update({"Probeset": diff_from_dict(old={ + k: data_.get(f"old_{k}") for k, v in probeset_.items() + if v is not None}, new=probeset_)}) + if diff_data: + diff_data.update({"probeset_name": data_.get("probeset_name")}) + diff_data.update({"author": author.decode('utf-8')}) + diff_data.update({"timestamp": datetime.datetime.now().strftime( + "%Y-%m-%d %H:%M:%S")}) + insert(conn, + table="metadata_audit", + data=MetadataAudit(dataset_id=data_.get("id"), + editor=author.decode("utf-8"), + json_data=json.dumps(diff_data))) + return redirect(f"/trait/edit/probeset-name/{data_.get('probeset_name')}") @app.route("/create_temp_trait", methods=('POST',)) @@ -852,16 +1007,16 @@ def loading_page(): if key in wanted: start_vars[key] = value + sample_vals_dict = json.loads(start_vars['sample_vals']) if 'n_samples' in start_vars: n_samples = int(start_vars['n_samples']) else: - sample_vals_dict = json.loads(start_vars['sample_vals']) if 'group' in start_vars: dataset = create_dataset( start_vars['dataset'], group_name=start_vars['group']) else: dataset = create_dataset(start_vars['dataset']) - samples = start_vars['primary_samples'].split(",") + samples = dataset.group.samplelist if 'genofile' in start_vars: if start_vars['genofile'] != "": genofile_string = start_vars['genofile'] @@ -877,6 +1032,10 @@ def loading_page(): n_samples += 1 start_vars['n_samples'] = n_samples + start_vars['vals_hash'] = generate_hash_of_string(str(sample_vals_dict)) + if start_vars['dataset'] != "Temp": # Currently can't get diff for temp traits + start_vars['vals_diff'] = get_diff_of_vals(sample_vals_dict, str(start_vars['trait_id'] + ":" + str(start_vars['dataset']))) + start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs'] start_vars_container['start_vars'] = start_vars @@ -901,6 +1060,7 @@ def mapping_results_page(): 'samples', 'vals', 'sample_vals', + 'vals_hash', 'first_run', 'output_files', 'geno_db_exists', @@ -917,7 +1077,6 @@ def mapping_results_page(): 'num_perm', 'permCheck', 'perm_strata', - 'strat_var', 'categorical_vars', 'perm_output', 'num_bootstrap', @@ -947,7 +1106,6 @@ def mapping_results_page(): 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', - 'reaper_version', 'n_samples', 'transform' ) @@ -1006,9 +1164,8 @@ def mapping_results_page(): gn1_template_vars = display_mapping_results.DisplayMappingResults( result).__dict__ - with Bench("Rendering template"): - rendered_template = render_template( - "mapping_results.html", **gn1_template_vars) + rendered_template = render_template( + "mapping_results.html", **gn1_template_vars) return rendered_template @@ -1021,7 +1178,7 @@ def export_mapping_results(): results_csv = open(file_path, "r").read() response = Response(results_csv, mimetype='text/csv', - headers={"Content-Disposition": "attachment;filename=mapping_results.csv"}) + headers={"Content-Disposition": "attachment;filename=" + os.path.basename(file_path)}) return response @@ -1082,22 +1239,17 @@ def network_graph_page(): @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): - logger.info("In corr_compute, request.form is:", pf(request.form)) - logger.info(request.url) - template_vars = show_corr_results.CorrelationResults(request.form) - return render_template("correlation_page.html", **template_vars.__dict__) - - # to test/disable the new correlation api uncomment these lines - - # correlation_results = compute_correlation(request.form) - # return render_template("test_correlation_page.html", correlation_results=correlation_results) + correlation_results = compute_correlation(request.form, compute_all=True) + correlation_results = set_template_vars(request.form, correlation_results) + return render_template("correlation_page.html", **correlation_results) @app.route("/test_corr_compute", methods=["POST"]) def test_corr_compute_page(): - correlation_data = compute_correlation(request.form) + correlation_data = compute_correlation(request.form, compute_all=True) return render_template("test_correlation_page.html", **correlation_data) - + + @app.route("/corr_matrix", methods=('POST',)) def corr_matrix_page(): logger.info("In corr_matrix, request.form is:", pf(request.form)) @@ -1195,8 +1347,6 @@ def browser_inputs(): return flask.jsonify(file_contents) -########################################################################## - def json_default_handler(obj): """Based on http://stackoverflow.com/a/2680060/1175849""" @@ -1212,3 +1362,112 @@ def json_default_handler(obj): else: raise TypeError('Object of type %s with value of %s is not JSON serializable' % ( type(obj), repr(obj))) + + +@app.route("/trait/<trait_name>/sampledata/<phenotype_id>") +def get_sample_data_as_csv(trait_name: int, phenotype_id: int): + conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), + user=current_app.config.get("DB_USER"), + passwd=current_app.config.get("DB_PASS"), + host=current_app.config.get("DB_HOST")) + csv_ = get_trait_csv_sample_data(conn, str(trait_name), + str(phenotype_id)) + return Response( + csv_, + mimetype="text/csv", + headers={"Content-disposition": + "attachment; filename=myplot.csv"} + ) + + +@app.route("/admin/data-sample/diffs/") +@edit_access_required +def display_diffs_admin(): + TMPDIR = current_app.config.get("TMPDIR") + DIFF_DIR = f"{TMPDIR}/sample-data/diffs" + files = [] + if os.path.exists(DIFF_DIR): + files = os.listdir(DIFF_DIR) + files = filter(lambda x: not(x.endswith((".approved", ".rejected"))), + files) + return render_template("display_files_admin.html", + files=files) + + +@app.route("/user/data-sample/diffs/") +def display_diffs_users(): + TMPDIR = current_app.config.get("TMPDIR") + DIFF_DIR = f"{TMPDIR}/sample-data/diffs" + files = [] + author = g.user_session.record.get(b'user_name').decode("utf-8") + if os.path.exists(DIFF_DIR): + files = os.listdir(DIFF_DIR) + files = filter(lambda x: not(x.endswith((".approved", ".rejected"))) \ + and author in x, + files) + return render_template("display_files_user.html", + files=files) + + +@app.route("/data-samples/approve/<name>") +def approve_data(name): + sample_data = {} + conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), + user=current_app.config.get("DB_USER"), + passwd=current_app.config.get("DB_PASS"), + host=current_app.config.get("DB_HOST")) + TMPDIR = current_app.config.get("TMPDIR") + with open(os.path.join(f"{TMPDIR}/sample-data/diffs", + name), 'r') as myfile: + sample_data = json.load(myfile) + PUBLISH_ID = sample_data.get("publishdata_id") + modifications = [d for d in sample_data.get("Modifications")] + row_counts = len(modifications) + for modification in modifications: + if modification.get("Current"): + (strain_id, + strain_name, + value, se, count) = modification.get("Current").split(",") + update_sample_data( + conn=conn, + strain_name=strain_name, + strain_id=int(strain_id), + publish_data_id=int(PUBLISH_ID), + value=value, + error=se, + count=count + ) + insert(conn, + table="metadata_audit", + data=MetadataAudit( + dataset_id=name.split(".")[0], # use the dataset name + editor=sample_data.get("author"), + json_data=json.dumps(sample_data))) + if modifications: + # Once data is approved, rename it! + os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", name), + os.path.join(f"{TMPDIR}/sample-data/diffs", + f"{name}.approved")) + flash((f"Just updated data from: {name}; {row_counts} " + "row(s) modified!"), + "success") + return redirect("/admin/data-sample/diffs/") + + +@app.route("/data-samples/reject/<name>") +def reject_data(name): + TMPDIR = current_app.config.get("TMPDIR") + os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", name), + os.path.join(f"{TMPDIR}/sample-data/diffs", + f"{name}.rejected")) + flash(f"{name} has been rejected!", "success") + return redirect("/admin/data-sample/diffs/") + + +@app.route("/display-file/<name>") +def display_file(name): + TMPDIR = current_app.config.get("TMPDIR") + with open(os.path.join(f"{TMPDIR}/sample-data/diffs", + name), 'r') as myfile: + content = myfile.read() + return Response(content, mimetype='text/json') |