diff options
Diffstat (limited to 'wqflask')
44 files changed, 623 insertions, 454 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 4cb82665..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: @@ -737,7 +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] @@ -908,7 +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: @@ -938,7 +943,6 @@ class PhenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -1005,7 +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() @@ -1126,8 +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 @@ -1147,7 +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: @@ -1179,7 +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 @@ -1190,7 +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) @@ -1224,7 +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 10851e00..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( 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/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index 4003d68f..58a44b2a 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -81,10 +81,12 @@ class TestGemmaMapping(unittest.TestCase): def test_gen_pheno_txt_file(self): """add tests for generating pheno txt file""" with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ - "x", "w", "q", "we", "R"], trait_filename="fitr.re") + gen_pheno_txt_file( + this_dataset=AttributeSetter({"name": "A"}), + genofile_name="", vals=[ + "x", "w", "q", "we", "R"]) mock_open.assert_called_once_with( - '/home/user/data/gn2/fitr.re.txt', 'w') + '/home/user/data/gn2/PHENO_KiAEKlCvM6iGTM9Kh_TAlQ.txt', 'w') filehandler = mock_open() values = ["x", "w", "q", "we", "R"] write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call( @@ -112,7 +114,7 @@ class TestGemmaMapping(unittest.TestCase): create_trait.side_effect = create_trait_side_effect group = MockGroup({"name": "group_X", "samplelist": samplelist}) - this_dataset = AttributeSetter({"group": group}) + this_dataset = AttributeSetter({"group": group, "name": "A"}) flat_files.return_value = "Home/Genenetwork" with mock.patch("builtins.open", mock.mock_open())as mock_open: @@ -132,7 +134,7 @@ class TestGemmaMapping(unittest.TestCase): flat_files.assert_called_once_with('mapping') mock_open.assert_called_once_with( - 'Home/Genenetwork/group_X_covariates.txt', 'w') + 'Home/Genenetwork/COVAR_anFZ_LfZYV0Ulywo+7tRCw.txt', 'w') filehandler = mock_open() filehandler.write.assert_has_calls([mock.call( '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py index c220a072..868b0b0b 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -43,11 +43,11 @@ class TestRunMapping(unittest.TestCase): }) } self.dataset = AttributeSetter( - {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) + {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"}) self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) self.trait = AttributeSetter( - {"symbol": "IGFI", "chr": "X1", "mb": 123313}) + {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"}) def tearDown(self): self.dataset = AttributeSetter( @@ -180,34 +180,36 @@ class TestRunMapping(unittest.TestCase): with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock): export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers, - results_path="~/results", mapping_scale="physic", score_type="-log(p)", - transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100") + results_path="~/results", mapping_method="gemma", mapping_scale="physic", + score_type="-logP", transform="qnorm", + covariates="Dataset1:Trait1,Dataset2:Trait2", + n_samples="100", vals_hash="") write_calls = [ mock.call('Time/Date: 09/01/19 / 10:12:12\n'), mock.call('Population: Human GP1_\n'), mock.call( - 'Data Set: dataser_1\n'), - mock.call('N Samples: 100\n'), mock.call( - 'Transform - Quantile Normalized\n'), + 'Data Set: dataset_1\n'), + mock.call('Trait: Test Name\n'), + mock.call('Trait Hash: \n'), + mock.call('N Samples: 100\n'), + mock.call('Mapping Tool: gemma\n'), + mock.call('Transform - Quantile Normalized\n'), mock.call('Gene Symbol: IGFI\n'), mock.call( 'Location: X1 @ 123313 Mb\n'), mock.call('Cofactors (dataset - trait):\n'), mock.call('Trait1 - Dataset1\n'), mock.call('Trait2 - Dataset2\n'), mock.call('\n'), mock.call('Name,Chr,'), - mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), + mock.call('Mb,-logP'), mock.call(',Additive'), mock.call(',Dominance'), mock.call('\n'), mock.call('MK1,C1,'), - mock.call('12000,'), mock.call('1,'), - mock.call('3'), mock.call(',VA'), - mock.call(',TT'), mock.call('\n'), - mock.call('MK2,C2,'), mock.call('10000,'), - mock.call('15,'), mock.call('7'), + mock.call('12000,'), mock.call('3'), + mock.call(',VA'), mock.call(',TT'), + mock.call('\n'), mock.call('MK2,C2,'), + mock.call('10000,'), mock.call('7'), mock.call('\n'), mock.call('MK1,C3,'), - mock.call('1,'), mock.call('45,'), - mock.call('7'), mock.call(',VE'), - mock.call(',Tt') - + mock.call('1,'), mock.call('7'), + mock.call(',VE'), mock.call(',Tt') ] mock_open.assert_called_once_with("~/results", "w+") filehandler = mock_open() @@ -232,25 +234,20 @@ class TestRunMapping(unittest.TestCase): "c1": "c1_value", "c2": "c2_value", "w1": "w1_value" - }, "S2": { "w1": "w2_value", "w2": "w2_value" - }, "S3": { "c1": "c1_value", "c2": "c2_value" - }, - }}) - results = get_perm_strata(this_trait={}, sample_list=sample_list, categorical_vars=categorical_vars, used_samples=used_samples) - self.assertEqual(results, [2, 1]) + self.assertEqual(results, [1, 1]) def test_get_chr_length(self): """test for getting chromosome length""" 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/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_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index f7c06a46..a18bceaf 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -148,14 +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) + start_vars, this_dataset.group.all_samples_ordered()) - sample_data = test_process_data(this_trait, this_dataset, start_vars) - - 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, 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 f941267e..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: @@ -1195,43 +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: @@ -1243,24 +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, @@ -1269,7 +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 - " @@ -1296,14 +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): @@ -2113,7 +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: 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 f601201b..80094057 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.mapping_method, 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 @@ -422,7 +406,8 @@ class RunMapping: 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) + self.mapping_method, 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: @@ -540,14 +525,21 @@ 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_method, mapping_scale, score_type, transform, covariates, n_samples, vals_hash): + if mapping_scale == "physic": + scale_string = "Mb" + else: + scale_string = "cM" 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") + output_file.write("Mapping Tool: " + str(mapping_method) + "\n") if len(transform) > 0: transform_text = "Transform - " if transform == "qnorm": @@ -577,10 +569,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Name,Chr,") if score_type.lower() == "-logP": score_type = "-logP" - if 'Mb' in markers[0]: - output_file.write("Mb," + score_type) - if 'cM' in markers[0]: - output_file.write("Cm," + score_type) + output_file.write(scale_string + "," + score_type) if "additive" in list(markers[0].keys()): output_file.write(",Additive") if "dominance" in list(markers[0].keys()): @@ -588,11 +577,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("\n") for i, marker in enumerate(markers): output_file.write(marker['name'] + "," + str(marker['chr']) + ",") - if 'Mb' in marker: - output_file.write(str(marker['Mb']) + ",") - if 'cM' in marker: - output_file.write(str(marker['cM']) + ",") - if "lod_score" in marker.keys(): + output_file.write(str(marker[scale_string]) + ",") + if score_type == "-logP": output_file.write(str(marker['lod_score'])) else: output_file.write(str(marker['lrs_value'])) @@ -765,9 +751,9 @@ 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/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 782dabc2..b0514e01 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -260,3 +260,33 @@ 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 6ca92fb6..0a060cdc 100644 --- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js +++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -93,15 +93,15 @@ 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, '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])){ @@ -130,6 +130,7 @@ var primary_table = $('#samples_primary').DataTable( { $(row).addClass("value_se"); if (data.outlier) { $(row).addClass("outlier"); + $(row).attr("style", "background-color: orange;"); } $('td', row).eq(1).addClass("column_name-Index") $('td', row).eq(2).addClass("column_name-Sample") @@ -189,6 +190,7 @@ if (js_data.sample_lists.length > 1){ $(row).addClass("value_se"); if (data.outlier) { $(row).addClass("outlier"); + $(row).attr("style", "background-color: orange;"); } $('td', row).eq(1).addClass("column_name-Index") $('td', row).eq(2).addClass("column_name-Sample") 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 049ebe6d..14e6bc88 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> 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/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 35d8a157..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> @@ -524,7 +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 7ec335d5..c499aa8f 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -53,6 +53,7 @@ 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 %} @@ -133,8 +134,11 @@ </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 --> @@ -171,6 +175,7 @@ return params; }; + {% if results|count > 0 %} //ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters trait_table = $('#trait_table').DataTable( { 'drawCallback': function( settings ) { @@ -412,6 +417,7 @@ var table = $('#trait_table').DataTable(); table.colReorder.reset() }); + {% endif %} submit_special = function(url) { $("#trait_submission_form").attr("action", url); diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 3dbf5f57..f3fa1332 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -254,8 +254,6 @@ } ); {% endif %} - $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'orange') - $('.edit_sample_checkbox:checkbox').change(function() { if ($(this).is(":checked")) { if (!$(this).closest('tr').hasClass('selected')) { diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index bb30c54c..2a21dd24 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -236,12 +236,15 @@ <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" %} {% 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/{{ this_trait.dataset.id }}', '_blank')">Edit</button> + <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/views.py b/wqflask/wqflask/views.py index a462b31a..b0da1f21 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -28,6 +28,7 @@ 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 @@ -63,6 +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 @@ -84,7 +86,7 @@ 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 @@ -159,28 +161,37 @@ 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) @@ -372,7 +383,6 @@ def wcgna_results(): results = run_wgcna(dict(request.form)) return render_template("test_wgcna_results.html", **results) - @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): # We are going to get additional user input for the analysis @@ -382,20 +392,6 @@ 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) @@ -430,9 +426,9 @@ def submit_trait_form(): version=GN_VERSION) -@app.route("/trait/<name>/edit/phenotype-id/<phenotype_id>") -@admin_login_required -def edit_phenotype(name, phenotype_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"), @@ -441,7 +437,7 @@ def edit_phenotype(name, phenotype_id): conn=conn, table="PublishXRef", where=PublishXRef(id_=name, - phenotype_id=phenotype_id)) + inbred_set_id=inbredset_id)) phenotype_ = fetchone( conn=conn, table="Phenotype", @@ -488,7 +484,7 @@ def edit_phenotype(name, phenotype_id): @app.route("/trait/edit/probeset-name/<dataset_name>") -# @admin_login_required +@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"), @@ -531,7 +527,7 @@ def edit_probeset(dataset_name): @app.route("/trait/update", methods=["POST"]) -@admin_login_required +@edit_access_required def update_phenotype(): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), @@ -653,11 +649,11 @@ def update_phenotype(): json_data=json.dumps(diff_data))) flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success") return redirect(f"/trait/{data_.get('dataset-name')}" - f"/edit/phenotype-id/{data_.get('phenotype-id')}") + f"/edit/inbredset-id/{data_.get('inbred-set-id')}") @app.route("/probeset/update", methods=["POST"]) -@admin_login_required +@edit_access_required def update_probeset(): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), @@ -1018,10 +1014,10 @@ 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']) @@ -1043,6 +1039,10 @@ 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 @@ -1067,6 +1067,7 @@ def mapping_results_page(): 'samples', 'vals', 'sample_vals', + 'vals_hash', 'first_run', 'output_files', 'geno_db_exists', @@ -1083,7 +1084,6 @@ def mapping_results_page(): 'num_perm', 'permCheck', 'perm_strata', - 'strat_var', 'categorical_vars', 'perm_output', 'num_bootstrap', @@ -1113,7 +1113,6 @@ def mapping_results_page(): 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', - 'reaper_version', 'n_samples', 'transform' ) @@ -1186,7 +1185,7 @@ 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 @@ -1389,7 +1388,7 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int): @app.route("/admin/data-sample/diffs/") -@admin_login_required +@edit_access_required def display_diffs_admin(): TMPDIR = current_app.config.get("TMPDIR") DIFF_DIR = f"{TMPDIR}/sample-data/diffs" |