From 9a1e7270bc9c2130a4cb9405f2de24053dea6582 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 11 Aug 2021 20:26:45 +0000 Subject: Sort by attribute ID instead of name in initialize_show_trait_tables.js when defining attribute columns --- wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') 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..49311f87 100644 --- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js +++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -93,7 +93,7 @@ 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( { @@ -101,7 +101,7 @@ build_columns = function() { '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])){ -- cgit v1.2.3 From 67bab7f9cd12ceb7ea0b0ac4b0b98c24935f3ab5 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 11 Aug 2021 20:28:35 +0000 Subject: Fixed issue that caused case attribute columns to become unaligned if some strains didn't have values for all case attributes + changed ordering to use attribute ID instead of name --- wqflask/wqflask/show_trait/SampleList.py | 44 ++++++++++++++++++-------------- 1 file changed, 25 insertions(+), 19 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 92cea550..e4bbe5b9 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) @@ -128,12 +128,13 @@ class SampleList: 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 self.attributes[key] = Bunch() + self.attributes[key].id = key self.attributes[key].name = name self.attributes[key].distinct_values = [ item.Value for item in values] @@ -168,10 +169,13 @@ 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 +183,10 @@ 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): -- cgit v1.2.3 From eecaad2dac6efa885540287a7ef5a273c6d18be2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 21:55:26 +0000 Subject: Get case attribute descriptions from DB and display them as mouseover titles in the sample table headers for the trait page --- wqflask/wqflask/show_trait/SampleList.py | 7 ++++--- .../wqflask/static/new/javascript/initialize_show_trait_tables.js | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index e4bbe5b9..ae30aa59 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -124,18 +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 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( 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 49311f87..4de1b0ac 100644 --- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js +++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -97,7 +97,7 @@ build_columns = function() { for (i = 0; i < attr_keys.length; i++){ column_list.push( { - 'title': "
" + js_data.attributes[attr_keys[i]].name + "
", + 'title': "
" + js_data.attributes[attr_keys[i]].name + "
", 'type': "natural", 'data': null, 'render': function(data, type, row, meta) { -- cgit v1.2.3 From f4fbb6d53419a19c6ee67977d18605cdcbb09c0e Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 22:35:53 +0000 Subject: add function for reading in JSON file that lists sample lists unique to each study within a group (in this case only BXD Longevity for now) --- wqflask/base/data_set.py | 9 +++++++++ wqflask/wqflask/show_trait/show_trait.py | 1 + 2 files changed, 10 insertions(+) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4cb82665..b8f2f9fb 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -398,6 +398,15 @@ class DatasetGroup: if maternal and paternal: self.parlist = [maternal, paternal] + def get_study_samplelists(self): + study_sample_file = "%s/study_sample_lists/%s.json" % (webqtlConfig.GENODIR, self.name) + try: + f = open(study_sample_file) + except: + return None + study_samples = json.load(f) + return study_samples + def get_genofiles(self): jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) try: diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index c07430dd..d3356bc3 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -192,6 +192,7 @@ class ShowTrait: [self.dataset.species.chromosomes.chromosomes[this_chr].name, i]) self.genofiles = self.dataset.group.get_genofiles() + self.study_samplelists = self.dataset.group.get_study_samplelists() # ZS: No need to grab scales from .geno file unless it's using # a mapping method that reads .geno files -- cgit v1.2.3 From 308860f05b87e5fc3899230b7312be9543e6c299 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:16:02 +0000 Subject: Add option to filter samples by study to template --- .../templates/show_trait_transform_and_filter.html | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index 20f78b48..56c3c30e 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -45,6 +45,25 @@ {% endif %} + {% if study_samplelists|length > 0 %} +
+ + + + +
+ {% endif %}
{% if (numerical_var_list|length > 0) or js_data.se_exists %} -- cgit v1.2.3 From 98683bd5cc809aa03e0bd58a67733498b4f56a9d Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:17:04 +0000 Subject: Fix the way the study_sample_lists path is set and checked --- wqflask/base/data_set.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index b8f2f9fb..1042e1bd 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -399,7 +399,7 @@ class DatasetGroup: self.parlist = [maternal, paternal] def get_study_samplelists(self): - study_sample_file = "%s/study_sample_lists/%s.json" % (webqtlConfig.GENODIR, self.name) + study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists') try: f = open(study_sample_file) except: -- cgit v1.2.3 From 810b2ace0a9cb2511cf0ef6f0c01f70a0ce11915 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:19:38 +0000 Subject: Return empty list instead of None in get_study_samplelists --- wqflask/base/data_set.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1042e1bd..0ea61faa 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -403,7 +403,7 @@ class DatasetGroup: try: f = open(study_sample_file) except: - return None + return [] study_samples = json.load(f) return study_samples -- cgit v1.2.3 From 11d5e9ffbf48c6a2fa7a59f10a9d7fe44cee0c23 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:20:28 +0000 Subject: Get list of study titles to use for the dropdown menu and store the full list of study samplelists as a hddn input (don't like this, but no easy alternative right now) --- wqflask/wqflask/show_trait/show_trait.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index d3356bc3..bc97d417 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -192,7 +192,8 @@ class ShowTrait: [self.dataset.species.chromosomes.chromosomes[this_chr].name, i]) self.genofiles = self.dataset.group.get_genofiles() - self.study_samplelists = self.dataset.group.get_study_samplelists() + 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 @@ -281,6 +282,7 @@ 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: -- cgit v1.2.3 From 88c9f4f9bd2adca23052fc3f5c5b965accf6722d Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:20:52 +0000 Subject: Add JS for filtering sample table rows by study samplelist --- wqflask/wqflask/static/new/javascript/show_trait.js | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 77ef1720..3957175b 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -713,10 +713,24 @@ 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 block_group = $('#filter_study_group').val(); + let study_sample_data = JSON.parse($('input[name=study_samplelists]').val()) + let filter_samples = study_sample_data[parseInt(this_study)]['samples'] + 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(); @@ -1690,6 +1704,11 @@ $('#block_by_index').click(function(){ edit_data_change(); }); +$('#filter_by_study').click(function(){ + filter_by_study(); + edit_data_change(); +}) + $('#filter_by_value').click(function(){ filter_by_value(); edit_data_change(); -- cgit v1.2.3 From 9ae4c8d0370137c3a698d57566305d815929d4ce Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:28:08 +0000 Subject: Fixed issue where 1 was added to the loop.index instead of subtracted + only show the sample group selection if there are more than one sample groups --- wqflask/wqflask/templates/show_trait_transform_and_filter.html | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index 56c3c30e..064fd3e5 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -50,9 +50,10 @@ + {% if sample_groups|length != 1 %} + {% endif %}
{% endif %} -- cgit v1.2.3 From 6acafff1b22089916b8323afb872e2ebed37943a Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:28:49 +0000 Subject: Account for user selecting one of the two sample groups if more than one exist --- wqflask/wqflask/static/new/javascript/show_trait.js | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 3957175b..845ed907 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -718,9 +718,19 @@ block_by_index = function() { filter_by_study = function() { let this_study = $('#filter_study').val(); - let block_group = $('#filter_study_group').val(); + let study_sample_data = JSON.parse($('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++) { -- cgit v1.2.3 From e2ee1c489f0eb59c3efbf81d42f43a1f74cd1adb Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 6 Aug 2021 15:31:30 +0300 Subject: wqflask: show_trait:: Remove debug comment --- wqflask/wqflask/show_trait/show_trait.py | 3 +++ 1 file changed, 3 insertions(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index c07430dd..b640ec27 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -520,6 +520,9 @@ 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 -- cgit v1.2.3 From 579ae94b08f0b1cef00350b54dadc12869ad70de Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 6 Aug 2021 16:15:17 +0300 Subject: base: data_set: Remove unnecessary comments and logging statements --- wqflask/base/data_set.py | 12 ------------ 1 file changed, 12 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4cb82665..edc22540 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 = {} @@ -737,7 +735,6 @@ 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 +905,6 @@ 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 +934,6 @@ class PhenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -1005,7 +1000,6 @@ 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 +1120,6 @@ 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 +1139,6 @@ 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 +1170,6 @@ 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 +1180,6 @@ 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 +1213,6 @@ 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, -- cgit v1.2.3 From 2071107566d89a12fe27fdcc94dd16b7b8680f83 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 16 Aug 2021 11:38:05 +0300 Subject: wqflask: views: Remove commented out code blocks --- wqflask/wqflask/views.py | 28 ---------------------------- 1 file changed, 28 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 44560427..08e895cb 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -365,20 +365,6 @@ def wcgna_setup(): return render_template("wgcna_setup.html", **request.form) -# @app.route("/wgcna_results", methods=('POST',)) -# def wcgna_results(): -# logger.info("In wgcna, request.form is:", request.form) -# logger.info(request.url) -# # Start R, load the package and pointers and create the analysis -# wgcna = wgcna_analysis.WGCNA() -# # Start the analysis, a wgcnaA object should be a separate long running thread -# wgcnaA = wgcna.run_analysis(request.form) -# # After the analysis is finished store the result -# result = wgcna.process_results(wgcnaA) -# # Display them using the template -# return render_template("wgcna_results.html", **result) - - @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): # We are going to get additional user input for the analysis @@ -388,20 +374,6 @@ 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) -- cgit v1.2.3 From 923d849d640e3048422e3cdfa6ce24716cfa7904 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 16 Aug 2021 18:54:16 +0300 Subject: wqflask: views: Use "inbredset_id" in the "Edit Trait" URL --- wqflask/wqflask/views.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 08e895cb..3f0ab93f 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -408,9 +408,9 @@ def submit_trait_form(): version=GN_VERSION) -@app.route("/trait//edit/phenotype-id/") +@app.route("/trait//edit/inbredset-id/") @admin_login_required -def edit_phenotype(name, phenotype_id): +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"), @@ -419,7 +419,7 @@ 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", -- cgit v1.2.3 From 82a7ccf6d2e5e18dcbd83f8070fd88ddc34ad419 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 16 Aug 2021 19:00:34 +0300 Subject: Update URL for editing published trait --- wqflask/wqflask/templates/show_trait_details.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index bb30c54c..53e16aa0 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -236,7 +236,7 @@ {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} {% if this_trait.dataset.type == 'Publish' %} - + {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} -- cgit v1.2.3 From 83af88a4bbf9d8a67f4d11c3546ba64f09efb6d2 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 17 Aug 2021 09:15:04 +0300 Subject: wqflask: wsgi: Remove it * wqflask/wsgi.py: Delete file. Not used anywhere. --- wqflask/wsgi.py | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 wqflask/wsgi.py (limited to 'wqflask') diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py deleted file mode 100644 index 755da333..00000000 --- a/wqflask/wsgi.py +++ /dev/null @@ -1,4 +0,0 @@ -from run_gunicorn import app as application # expect application as a name - -if __name__ == "__main__": - application.run() -- cgit v1.2.3 From b0610024e7cb5dec73742fd461cd662881869214 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 17 Aug 2021 09:15:47 +0300 Subject: wqflask: views: Re-enable admin access in edit probeset --- wqflask/wqflask/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3f0ab93f..7095c392 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -466,7 +466,7 @@ def edit_phenotype(name, inbredset_id): @app.route("/trait/edit/probeset-name/") -# @admin_login_required +@admin_login_required def edit_probeset(dataset_name): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), -- cgit v1.2.3 From d89a13ef9f3f4da47432eb3555df3ada7bbfbb8b Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 17 Aug 2021 12:41:24 +0300 Subject: wqflask: runserver: Add DebugToolbar when running in DEBUG mode --- wqflask/runserver.py | 3 +++ 1 file changed, 3 insertions(+) (limited to 'wqflask') 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, -- cgit v1.2.3 From b70bf1250bc93a47c3e3e32d4d2f4a116121d11f Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 17 Aug 2021 12:43:50 +0300 Subject: wqflask:.DS_Store: Delete it --- wqflask/.DS_Store | Bin 6148 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 wqflask/.DS_Store (limited to 'wqflask') diff --git a/wqflask/.DS_Store b/wqflask/.DS_Store deleted file mode 100644 index d992942f..00000000 Binary files a/wqflask/.DS_Store and /dev/null differ -- cgit v1.2.3 From 94f278b68817fb22d363fdfd1b416f9c674c3226 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 18 Aug 2021 09:42:48 +0300 Subject: Revert "wqflask: wsgi: Remove it" This reverts commit 83af88a4bbf9d8a67f4d11c3546ba64f09efb6d2. --- wqflask/wsgi.py | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 wqflask/wsgi.py (limited to 'wqflask') diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py new file mode 100644 index 00000000..755da333 --- /dev/null +++ b/wqflask/wsgi.py @@ -0,0 +1,4 @@ +from run_gunicorn import app as application # expect application as a name + +if __name__ == "__main__": + application.run() -- cgit v1.2.3 From f5f1b3e64db18dbdde39860f1f86a4bf408e3dd6 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 16 Aug 2021 19:50:24 +0000 Subject: Replace textarea with multiple select element for displaying mapping covariates --- wqflask/wqflask/templates/show_trait_mapping_tools.html | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 3dd44c85..3f0557aa 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -77,7 +77,9 @@ - + {% endif %} @@ -320,7 +322,9 @@ - + {% endif %} -- cgit v1.2.3 From eb7863b540bda56f3e0a769440ebc16c675d4adb Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 16 Aug 2021 19:51:07 +0000 Subject: Update get_covariates_from_collection.js to properly interact with the select element instead of the previous textarea --- .../javascript/get_covariates_from_collection.js | 55 +++++++++++++++------- 1 file changed, 39 insertions(+), 16 deletions(-) (limited to 'wqflask') 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..62590aaf 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] + $(".selected-covariates").append($(" -- cgit v1.2.3 From e98ef60db6d0986360e6c8aa920241bbb268af8e Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 17 Aug 2021 03:07:18 +0000 Subject: Add some CSS changing the way the colorbox pop-up for adding covariates looks on the trait page --- wqflask/wqflask/static/new/css/show_trait.css | 30 +++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'wqflask') 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; +} -- cgit v1.2.3 From 5c879337593366005d07f390b8e0da901ec23881 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 17 Aug 2021 18:34:50 +0000 Subject: Changed Remove All button to Clear and changed Select and Clear button colors --- wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index cc472914..e63d0195 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -74,9 +74,9 @@ No collections available. Please add traits to a collection to use them as covariates. {% else %}
- + - +

- + {% endif %} -- cgit v1.2.3 From fc15b67ca15a8f08833a8b1e479c152bc4a2b723 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 17 Aug 2021 20:35:50 +0000 Subject: Added option to make collection default in the colorbox pop-up --- wqflask/wqflask/templates/collections/add.html | 29 +++++++++++++++++++------- 1 file changed, 21 insertions(+), 8 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html index cb4172ac..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.

-
+ {% if traits is defined %} {% else %} @@ -14,10 +14,8 @@ {% if collections|length > 0 %}
1. Add to an existing collection -
- - {% for col in collections %} {% if loop.index == 1 %} @@ -26,8 +24,9 @@ {% endif %} {% endfor %} -
- + +

+
{% endif %} @@ -35,7 +34,6 @@
{% if collections|length > 0 %}2. {% else %}{% endif %}Create a new collection
- @@ -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) { -- cgit v1.2.3 From 1393d777bd0fee4a25ba4b1f6af6ccb9ae24c0f8 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 17 Aug 2021 20:49:16 +0000 Subject: Added hash of sample values and table of changed values to the loading page --- wqflask/wqflask/templates/loading.html | 36 ++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 6d6136ac..b02605ee 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -25,6 +25,8 @@
transformation = {{ start_vars.transform }} {% endif %} +
+ hash of sample values = {{ start_vars.vals_hash }}

Mapping Metadata
@@ -68,6 +70,29 @@
+ {% if start_vars.vals_diff|length != 0 and start_vars.transform == "" %} +

+ +
+ + {% endif %}
@@ -79,4 +104,15 @@ $("#loading_form").attr("action", "{{ start_vars.form_url }}"); setTimeout(function(){ $("#loading_form").submit()}, 350); + +$('#show_full_diff').click(function() { + if ($('#diff_table_container').is(':visible')){ + $('#diff_table_container').hide(); + } else { + $('#diff_table_container').show(); + } +}) + + + -- cgit v1.2.3 From 26958694322855f4ee91beb3b01e73afe75066cf Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 17 Aug 2021 20:50:31 +0000 Subject: Added function for getting the diff of sample values before and after user changes to show_trait.py --- wqflask/wqflask/show_trait/show_trait.py | 40 ++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 4120c801..96f6901a 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 @@ -805,3 +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 = float(new_vals[sample]) + except: + new_val = "x" + try: + old_val = float(old_vals[sample]) + except: + old_val = "x" + + if new_val != old_val: + diff_dict[sample] = { + "new_val": new_val, + "old_val": old_val + } + + return diff_dict -- cgit v1.2.3 From 71e6c7483c8675e96376295927133c370478bbba Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 17 Aug 2021 20:51:26 +0000 Subject: Removed some unnecessary empty lines from loading.html JS --- wqflask/wqflask/templates/loading.html | 4 ---- 1 file changed, 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index b02605ee..1edde31e 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -101,7 +101,6 @@ -- cgit v1.2.3 From ab3b838b99b58693f3f187093e78f492e7cf392b Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 18 Aug 2021 00:13:55 +0000 Subject: Exclude attributes with only one distinct value as well --- wqflask/wqflask/templates/show_trait_transform_and_filter.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index 064fd3e5..8d21b0b0 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 @@ {% endif %} -- cgit v1.2.3 From 041354b4c278c4784119da60ace2c3d4ad981354 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 19 Aug 2021 18:28:31 +0000 Subject: Fixed issue in JS that caused filter_by_value to not work for case attributes --- wqflask/wqflask/static/new/javascript/show_trait.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index be9e2089..f050d4ae 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -818,7 +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 } -- cgit v1.2.3 From 0e0f25a71d2fab7395af007643b908af51bd7ca2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 19 Aug 2021 18:29:45 +0000 Subject: Fixed R/qtl 'select covariates' buttons to be the same as the changed ones for GEMMA --- wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index ddcc3edf..4c0efecb 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -320,9 +320,9 @@ No collections available. Please add traits to a collection to use them as covariates. {% else %}
- + - +
+ {% if categorical_vars is defined %} + + {% endif %} -- cgit v1.2.3 From 0bbe9072566397942a6db034cb11203bcb43b78f Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 23 Aug 2021 19:03:10 +0000 Subject: Fix the way categorical_var_list is set to account for case attribute Ids being keys now instead of names --- wqflask/wqflask/show_trait/show_trait.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 96f6901a..36e69fa3 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -701,7 +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 -- cgit v1.2.3 From 654b35c2050e89f9ba533a3713d40465cf6fcd47 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 23 Aug 2021 19:05:10 +0000 Subject: Fix get_perm_strata to usethe Ids for case attributes instead of names + allow perm_strata to be passed to the template --- wqflask/wqflask/marker_regression/run_mapping.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index f601201b..ebad7d36 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -220,7 +220,7 @@ 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 +229,7 @@ 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 +243,10 @@ 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: @@ -765,9 +765,9 @@ 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: -- cgit v1.2.3 From fff90d1a1b194fe5e65e99506bc4fe6fffc9a255 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 23 Aug 2021 19:06:01 +0000 Subject: Account for situations where the minimum permutation value is also above webqtlConfig.MAXLRS; previously threw an error --- wqflask/utility/Plot.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') 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 -- cgit v1.2.3 From 7546da17cc5b7a2f97b490e1593b41609b281a43 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 23 Aug 2021 19:29:38 +0000 Subject: Fixed issue with the way categorical_vars and perm_strata were being passed to the template --- wqflask/wqflask/templates/mapping_results.html | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 7baac000..81eb1ba1 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -45,8 +45,10 @@ {% if categorical_vars is defined %} - - + + {% endif %} + {% if perm_strata is defined %} + {% endif %} -- cgit v1.2.3 From 629aab0ef51c2c6f7d4f479e51a7168d9aa14d41 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 23 Aug 2021 19:31:18 +0000 Subject: Removed unused variable from list of 'wanted' variables for mapping --- wqflask/wqflask/views.py | 1 - 1 file changed, 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 957c34be..11a9380c 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1067,7 +1067,6 @@ def mapping_results_page(): 'num_perm', 'permCheck', 'perm_strata', - 'strat_var', 'categorical_vars', 'perm_output', 'num_bootstrap', -- cgit v1.2.3 From 3fd1d766fcf38f5a147c01b1c397469139c9080d Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Aug 2021 17:39:02 +0000 Subject: Fix issue that could cause mapping_scale to not be set correctly in show_trait.py --- wqflask/wqflask/show_trait/show_trait.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 36e69fa3..80f5d117 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -300,7 +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] -- cgit v1.2.3 From ae634a36891ddba9748e0f75ff1cf51e95e4a8a7 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Aug 2021 17:39:16 +0000 Subject: Fix issue that could cause an error when doing cM mapping --- wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index f941267e..3986c441 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2113,7 +2113,7 @@ 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: -- cgit v1.2.3 From 3327c9dc95d2c4d295dc8dbf4839c01294b53ada Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Aug 2021 17:46:02 +0000 Subject: Add map scale option that was missing for groups with only a single genotype file --- wqflask/wqflask/templates/show_trait_mapping_tools.html | 11 +++++++++++ 1 file changed, 11 insertions(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 4c0efecb..5365140d 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -229,6 +229,17 @@ + {% else %} +
+ +
+ +
+
{% endif %}
-- cgit v1.2.3 From 582893c0cc87f87e5dfc7fe0209b2e4a3f85d4a4 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Aug 2021 18:02:31 +0000 Subject: Fixed issue in get_diff_of_vals that caused the diff to be calculated wrong (due to one set of values being rounded to 3 digits and the other not --- wqflask/wqflask/show_trait/show_trait.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 80f5d117..3f93bae0 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -830,11 +830,11 @@ def get_diff_of_vals(new_vals: Dict, trait_id: str) -> Dict: diff_dict = {} for sample in shared_samples: try: - new_val = float(new_vals[sample]) + new_val = round(float(new_vals[sample]), 3) except: new_val = "x" try: - old_val = float(old_vals[sample]) + old_val = round(float(old_vals[sample]), 3) except: old_val = "x" -- cgit v1.2.3 From cc7c392198f73ac8e8419be1367ce566d85a873c Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Aug 2021 19:05:07 +0000 Subject: Fix issue where correlation results weren't included parents/f1s --- wqflask/wqflask/correlation/correlation_gn3_api.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index a78cb0b9..d0d4bcba 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -148,7 +148,7 @@ 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()) if target_dataset.type == "ProbeSet": target_dataset.get_probeset_data(list(sample_data.keys())) -- cgit v1.2.3 From 5ebe36d5ff685e6b663b14c130606aa60b0123c2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 3 Sep 2021 14:58:05 +0000 Subject: Fix issue where values written to phenotype file for R/qtl sometimes had trailing decimal values by grounding to 3 places past the decimal --- wqflask/wqflask/marker_regression/rqtl_mapping.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 09afb8d1..cd578870 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -89,7 +89,7 @@ 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 +126,7 @@ 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") -- cgit v1.2.3 From 8af212bc7eac5b39e8e6838df446a4003633a55e Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 3 Sep 2021 14:59:14 +0000 Subject: Fix issue that caused javascript to not work on the R/qtl mapping result page when permutations weren't used (because it wrongly expected the permutation histogram to always exist) --- wqflask/wqflask/templates/mapping_results.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 81eb1ba1..d446745d 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -529,7 +529,7 @@ }); {% 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, -- cgit v1.2.3 From f4297bc9e4c49f58e0759d02d3e7aea392ba5615 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 3 Sep 2021 15:01:34 +0000 Subject: Allow categorical_var_list to be passed as a template variable --- wqflask/wqflask/show_trait/show_trait.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 3f93bae0..c4d1ae1c 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -178,11 +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]) @@ -287,8 +287,8 @@ class ShowTrait: 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: @@ -323,7 +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, -- cgit v1.2.3 From f81a5629ab6ea7e39893af00e59c3ac6d79d7892 Mon Sep 17 00:00:00 2001 From: zsloan Date: Sun, 5 Sep 2021 17:03:51 +0000 Subject: Fixed issue that caused sample data to not be fetched correctly; there's something wrong with the 'get_probeset_data' function (not sure why this function exists) --- wqflask/wqflask/correlation/correlation_gn3_api.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index d0d4bcba..a18bceaf 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -150,10 +150,7 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset): sample_data = process_samples( start_vars, this_dataset.group.all_samples_ordered()) - if target_dataset.type == "ProbeSet": - target_dataset.get_probeset_data(list(sample_data.keys())) - else: - target_dataset.get_trait_data(list(sample_data.keys())) + target_dataset.get_trait_data(list(sample_data.keys())) this_trait = retrieve_sample_data(this_trait, this_dataset) this_trait_data = { "trait_sample_data": sample_data, -- cgit v1.2.3 From 25a5fe8027a00a64513855630a4365480cf567d7 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 7 Sep 2021 18:21:34 +0000 Subject: Add timer to loading page to track how long the process has been running --- wqflask/wqflask/templates/loading.html | 25 ++++++++++++++++++++++--- 1 file changed, 22 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 1edde31e..ccf810b0 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -12,6 +12,8 @@ {% if start_vars.tool_used == "Mapping" %}

Computing the Maps


+ Time Elapsed: +
Trait Metadata
species = {{ start_vars.species[0] | upper }}{{ start_vars.species[1:] }} @@ -101,9 +103,6 @@ -- cgit v1.2.3 From d243e3a69b26d60709fe10ab0b70a0e1d53ba50d Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 7 Sep 2021 18:22:44 +0000 Subject: Add trait hash and datetime to mapping figure --- .../marker_regression/display_mapping_results.py | 68 ++++++++++++++-------- wqflask/wqflask/marker_regression/run_mapping.py | 1 + .../new/javascript/show_trait_mapping_tools.js | 10 ++-- wqflask/wqflask/templates/mapping_results.html | 1 + wqflask/wqflask/views.py | 1 + 5 files changed, 51 insertions(+), 30 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 3986c441..5f5fe6a3 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'] @@ -651,7 +653,7 @@ 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 +663,7 @@ 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 +1197,47 @@ class DisplayMappingResults: dataset_label = "%s - %s" % (self.dataset.group.name, self.dataset.fullname) - string1 = 'Dataset: %s' % (dataset_label) + + current_datetime = datetime.datetime.now() + string1 = 'UTC Timestamp: %s' % (current_datetime.strftime("%b %d %Y %H:%M:%S")) + 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 - 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: @@ -1260,7 +1266,9 @@ class DisplayMappingResults: 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 +1277,9 @@ 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 +1306,22 @@ 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): diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index ebad7d36..2f90b475 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): 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..b75d658e 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', 'reaper_version', 'primary_samples'] $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) { return function() { diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index d446745d..162ae810 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -34,6 +34,7 @@ + diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 11a9380c..707b18e1 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1051,6 +1051,7 @@ def mapping_results_page(): 'samples', 'vals', 'sample_vals', + 'vals_hash', 'first_run', 'output_files', 'geno_db_exists', -- cgit v1.2.3 From 1f2e32a91727abab77ecdf501fcc5040b17dfece Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 9 Sep 2021 17:07:06 +0000 Subject: Replaced trait name with trait display name in display_mapping_results so the group codes will be includes in phenotype IDs --- wqflask/wqflask/marker_regression/display_mapping_results.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 5f5fe6a3..e9ba7dff 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1249,18 +1249,18 @@ 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( -- cgit v1.2.3 From 5020158b3ab7cf14a5809af65d2c616d32714a22 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 9 Sep 2021 17:07:47 +0000 Subject: Change trait name to display name in the metadata at the top of the page (so group codes will be includes in phenotype IDs --- wqflask/wqflask/templates/mapping_results.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 162ae810..7f865056 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -68,7 +68,7 @@

Map Viewer: Whole Genome


Population: {{ dataset.group.species|capitalize }} {{ dataset.group.name }}
Database: {{ dataset.fullname }}
- {% if dataset.type == "ProbeSet" %}Trait ID:{% else %}Record ID:{% endif %} {{ this_trait.name }}
+ {% if dataset.type == "ProbeSet" %}Trait ID:{% else %}Record ID:{% endif %} {{ this_trait.display_name }}
{% if dataset.type == "ProbeSet" %} Gene Symbol: {{ this_trait.symbol }}
Location: Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb
-- cgit v1.2.3 From f51569c80a4e00ad7dcd99ed9bf3ed6d9aaf4051 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 10 Sep 2021 18:54:44 +0000 Subject: Removed encoding, since it's apparently not needed since the Python 3 switchover (and was causing there to be no matches between user IDs and groups) --- wqflask/utility/redis_tools.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index ff125bd2..99295c67 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -135,10 +135,8 @@ def get_user_groups(user_id): for key in groups_list: try: group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin.encode( - 'utf-8') if this_admin else None for this_admin in group_ob['admins']]) - group_members = set([this_member.encode( - 'utf-8') if this_member else None for this_member in group_ob['members']]) + group_admins = set([this_admin if this_admin else None for this_admin in group_ob['admins']]) + group_members = set([this_member if this_member else None for this_member in group_ob['members']]) if user_id in group_admins: admin_group_ids.append(group_ob['id']) elif user_id in group_members: -- cgit v1.2.3 From d76e1ec30195074cf8dfd0f8396285d31faa8984 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 10 Sep 2021 19:02:10 +0000 Subject: Fix issue with the way the template was checking if genofile_string was set; it was receiving an empty string, so the previous logic made it think there was a genofile string when there wasn't one --- wqflask/wqflask/templates/mapping_results.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 7f865056..7a222d0c 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -73,7 +73,7 @@ Gene Symbol: {{ this_trait.symbol }}
Location: Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb
{% endif %} - {% if genofile_string is defined %} + {% if genofile_string != "" %} Genotypes: {{ genofile_string.split(":")[1] }} {% endif %}
-- cgit v1.2.3 From f414cd4109229546bfb8c56fea95b6729121f0b3 Mon Sep 17 00:00:00 2001 From: jgart Date: Thu, 9 Sep 2021 22:28:02 -0500 Subject: Add Jupyter Notebook Launcher to Tools dropdown menu --- wqflask/wqflask/templates/base.html | 1 + 1 file changed, 1 insertion(+) (limited to 'wqflask') 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 @@
  • Systems Genetics PheWAS
  • Genome Browser
  • BXD Power Calculator
    • +
  • Jupyter Notebook Launcher
  • Interplanetary File System
    • -- cgit v1.2.3 From 38a8544553506651a263b0134ab5372c6a62c629 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 13 Sep 2021 18:58:10 +0000 Subject: Temporarily point the View in GN1 button to gn1-lily.genenetwork.org since some features aren't working on gn1.genenetwork.org yet --- wqflask/wqflask/templates/show_trait_details.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 53e16aa0..36d3c15a 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -233,7 +233,7 @@ {% endif %} {% endif %} - + {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} {% if this_trait.dataset.type == 'Publish' %} -- cgit v1.2.3 From 6a94f7a3a4893f087af53c2d39685d9dcb4b733d Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 13 Sep 2021 19:41:19 +0000 Subject: Change Genotype File text to only show the meaningful genotype deescription --- wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index e9ba7dff..a9ebeb64 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1206,7 +1206,7 @@ class DisplayMappingResults: if self.genofile_string == "": string4 = 'Genotype File: %s.geno' % self.dataset.group.name else: - string4 = 'Genotype File: %s' % self.genofile_string + string4 = 'Genotype File: %s' % self.genofile_string.split(":")[1] string6 = '' if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": -- cgit v1.2.3 From 75132a5382d32d9332f743aca0e406ae6137d7e5 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 13 Sep 2021 19:49:05 +0000 Subject: Include some extra metadata in the mapping page details (in addition to the figure itself) --- wqflask/wqflask/marker_regression/display_mapping_results.py | 4 ++-- wqflask/wqflask/templates/mapping_results.html | 5 +++-- 2 files changed, 5 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index a9ebeb64..77d6e2db 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1198,8 +1198,8 @@ class DisplayMappingResults: self.dataset.fullname) - current_datetime = datetime.datetime.now() - string1 = 'UTC Timestamp: %s' % (current_datetime.strftime("%b %d %Y %H:%M:%S")) + 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) diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 7a222d0c..f2d11e89 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -69,14 +69,15 @@ Population: {{ dataset.group.species|capitalize }} {{ dataset.group.name }}
    Database: {{ dataset.fullname }}
    {% if dataset.type == "ProbeSet" %}Trait ID:{% else %}Record ID:{% endif %} {{ this_trait.display_name }}
    + Trait Hash: {{ vals_hash }}
    {% if dataset.type == "ProbeSet" %} Gene Symbol: {{ this_trait.symbol }}
    Location: Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb
    {% endif %} {% if genofile_string != "" %} - Genotypes: {{ genofile_string.split(":")[1] }} + Genotypes: {{ genofile_string.split(":")[1] }}
    {% endif %} -
    + Current Date/Time: {{ current_datetime }}

    Download Full Results
    -- cgit v1.2.3 From 2ef7cad06cc1dcde61c91d2eafef002d25cb194e Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 13 Sep 2021 19:58:43 +0000 Subject: Add trait name and trait hash to exported mapping results --- wqflask/wqflask/marker_regression/run_mapping.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 2f90b475..b101b948 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -422,8 +422,9 @@ class RunMapping: total_markers = len(self.qtl_results) with Bench("Exporting Results"): - export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, - self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) + export_mapping_results(self.dataset, self.this_trait, self.qtl_results, + self.mapping_results_path, self.mapping_scale, self.score_type, + self.transform, self.covariates, self.n_samples, self.vals_hash) with Bench("Trimming Markers for Figure"): if len(self.qtl_results) > 30000: @@ -541,13 +542,15 @@ class RunMapping: return trimmed_genotype_data -def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples): +def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples, vals_hash): with open(results_path, "w+") as output_file: output_file.write( "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") output_file.write( "Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") output_file.write("Data Set: " + dataset.fullname + "\n") + output_file.write("Trait: " + trait.display_name + "\n") + output_file.write("Trait Hash: " + vals_hash + "\n") output_file.write("N Samples: " + str(n_samples) + "\n") if len(transform) > 0: transform_text = "Transform - " -- cgit v1.2.3 From 91d04e5b573107aead1da8482dd9184d9869b82a Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 13 Sep 2021 20:03:45 +0000 Subject: Change mapping export filename to use the trait hash --- wqflask/wqflask/marker_regression/run_mapping.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index b101b948..361c413b 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -104,9 +104,7 @@ class RunMapping: if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] else: - mapping_results_filename = self.dataset.group.name + "_" + \ - ''.join(random.choice(string.ascii_uppercase + string.digits) - for _ in range(6)) + mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash]) self.mapping_results_path = "{}{}.csv".format( webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) -- cgit v1.2.3 From 24e0de14969edb220a03e22d1c9b7e6ed33f6b82 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 13 Sep 2021 20:04:30 +0000 Subject: Change mapping export filename to use the path passed from run_mapping, instead of the generic mapping_results.csv --- wqflask/wqflask/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 707b18e1..54314a20 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1170,7 +1170,7 @@ 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 -- cgit v1.2.3 From c0fbbb42a79baa823b517ee8f537cec1edc057c8 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 14 Sep 2021 18:09:36 +0000 Subject: Replace / with _ in the file hashes in rqtl_mapping.py, since they get translated to directories --- wqflask/wqflask/marker_regression/rqtl_mapping.py | 1 + 1 file changed, 1 insertion(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index cd578870..a148b49c 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -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 -- cgit v1.2.3 From 8d54d1871e1319f7db46132d3eed61a817d5dc4c Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 14 Sep 2021 18:14:33 +0000 Subject: Replace / with _ in the mapping results filename, due to / causing issues with being translated to directories --- wqflask/wqflask/marker_regression/run_mapping.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 361c413b..1df53fef 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -104,7 +104,7 @@ class RunMapping: if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] else: - mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash]) + mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash]).replace("/", "_") self.mapping_results_path = "{}{}.csv".format( webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) -- cgit v1.2.3 From b6c0885007d516b257d1027b97df66c11b8672dd Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 16 Sep 2021 13:26:53 +0300 Subject: wqflask: views: Redirect to the correct URL after phenotype update --- wqflask/wqflask/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 54314a20..85aa6b17 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -633,7 +633,7 @@ 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"]) -- cgit v1.2.3 From 719b256996facb1f4bee2a0288bce1f18168f99b Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 16 Sep 2021 17:59:49 +0000 Subject: Added back the option to edit privileges on trait pages, since the metadata edit button had replaced it --- wqflask/wqflask/templates/show_trait_details.html | 3 +++ 1 file changed, 3 insertions(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 36d3c15a..6a541c8c 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -242,6 +242,9 @@ {% if this_trait.dataset.type == 'ProbeSet' %} {% endif %} + {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} + + {% endif %} {% endif %} -- cgit v1.2.3 From a9509a01191883e61cd5013453d18e89db022df2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 20 Sep 2021 17:34:26 +0000 Subject: Removed the reaper_version selection option, since original qtlreaper is no longer supported --- wqflask/wqflask/templates/show_trait_mapping_tools.html | 9 --------- 1 file changed, 9 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 5365140d..c6b6c0e1 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -95,15 +95,6 @@ {% elif mapping_method == "QTLReaper" %}
    -
    - -
    - -
    -
    -- cgit v1.2.3 From 2ad5b87f1c9bc5ce5bd3f54f7d83f18123ce3c3e Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 20 Sep 2021 17:37:18 +0000 Subject: Returned the GN1 url to gn1.genenetwork.org since it's apparently working well enough again now that some issues have been fixed --- wqflask/wqflask/templates/show_trait_details.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 6a541c8c..2a21dd24 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -233,7 +233,7 @@ {% endif %} {% endif %} - + {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} {% if this_trait.dataset.type == 'Publish' %} -- cgit v1.2.3 From 92df90d68c3d3067f6856c6894be92c7c5dbcaa6 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 22 Sep 2021 17:41:53 +0000 Subject: Remove references to reaper_version and code for running old qtlreaper --- .../marker_regression/display_mapping_results.py | 3 +- .../wqflask/marker_regression/qtlreaper_mapping.py | 95 ---------------------- wqflask/wqflask/marker_regression/run_mapping.py | 59 +++++--------- .../new/javascript/show_trait_mapping_tools.js | 2 +- wqflask/wqflask/views.py | 1 - 5 files changed, 24 insertions(+), 136 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 77d6e2db..6254b9b9 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -357,8 +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']]) 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/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 1df53fef..290c4a14 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -271,47 +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 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 b75d658e..e42fe8c4 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -145,7 +145,7 @@ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form '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', 'reaper_version', 'primary_samples'] + '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/views.py b/wqflask/wqflask/views.py index 85aa6b17..980b9362 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1097,7 +1097,6 @@ def mapping_results_page(): 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', - 'reaper_version', 'n_samples', 'transform' ) -- cgit v1.2.3 From 7cb23fe9c03e4f8051340e2a8f32645e88acce3a Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 22 Sep 2021 17:52:37 +0000 Subject: Added type='button' to the Delete Collection button within collections/view, since without it it attempts to submit the form encapsulating the button (export in this case) --- wqflask/wqflask/templates/collections/view.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') 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 @@ - +
    -- cgit v1.2.3 From 9bd85361d58eb67ef9e59eff6031ed9fd00a3411 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 22 Sep 2021 18:30:13 +0000 Subject: Only show most search page options if results exist; otherwise provide a link back to the home page --- wqflask/wqflask/templates/search_result_page.html | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) (limited to 'wqflask') 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.

    + {% if results|count > 0 %} {% if go_term is not none %}

    The associated genes include:

    {% for word in search_terms %}{{ word.search_term[0] }}{% endfor %}

    {% endif %} @@ -133,8 +134,11 @@
    {% endif %} + {% else %} +
    + + {% endif %}
    -
    @@ -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); -- cgit v1.2.3 From cbb9905aa4406551973bfe47dcdb00f6b8ce9628 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 22 Sep 2021 18:39:38 +0000 Subject: Fixed issue where the control marker parameter was being passed incorrectly to GN3 (should be just 'control' but was previously passed as 'control_marker') --- wqflask/wqflask/marker_regression/rqtl_mapping.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index a148b49c..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 -- cgit v1.2.3 From cb9422ec5fc985530fcb4fb44d2729e460424d60 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 22 Sep 2021 18:44:01 +0000 Subject: Removed the Control for (marker) option from R/qtl for now since Danny mentioned it isn't working correctly --- wqflask/wqflask/templates/show_trait_mapping_tools.html | 15 --------------- 1 file changed, 15 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index c6b6c0e1..3af94ed6 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -253,21 +253,6 @@
    {% endif %} -
    - -
    - - - -
    -
    -
    -- cgit v1.2.3 From 3494a9af7f82691f419ba1e3bd616be5ce68a00a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Sep 2021 13:07:11 +0300 Subject: Remove lengthy stack trace for 404, 400, 408 status codes The stack trace causes the log file to grow into unmanageable sizes over time. --- wqflask/wqflask/views.py | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 980b9362..1139ad43 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -160,18 +160,26 @@ 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]) -- cgit v1.2.3 From 8135bd22898130ae6f58aa74cb80c83ab334d0d4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Sep 2021 13:08:49 +0300 Subject: Remove variable-- named after a python keyword-- called "list" --- wqflask/wqflask/views.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 1139ad43..007b0f9e 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -184,9 +184,8 @@ def handle_generic_exceptions(e): # 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)) -- cgit v1.2.3 From 16947a15bd955be7da45bb5f078870649b1b63e5 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Sep 2021 13:09:24 +0300 Subject: Apply pep-8 formatting --- wqflask/wqflask/views.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 007b0f9e..b297da08 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -188,7 +188,9 @@ def handle_generic_exceptions(e): "./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) -- cgit v1.2.3 From 266d4c4a425ca0a215c8d789e2978d213d5ff37d Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 21 Sep 2021 21:25:13 +0300 Subject: Rename "admin_login_required" to "edit_access_required" --- wqflask/wqflask/decorators.py | 2 +- wqflask/wqflask/views.py | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/decorators.py b/wqflask/wqflask/decorators.py index f0978fd3..f6e3eb8a 100644 --- a/wqflask/wqflask/decorators.py +++ b/wqflask/wqflask/decorators.py @@ -3,7 +3,7 @@ from flask import g from functools import wraps -def admin_login_required(f): +def edit_access_required(f): """Use this for endpoints where admins are required""" @wraps(f) def wrap(*args, **kwargs): diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index b297da08..5067ca0e 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -85,7 +85,7 @@ from wqflask.export_traits import export_search_results_csv from wqflask.gsearch import GSearch from wqflask.update_search_results import GSearch as UpdateGSearch from wqflask.docs import Docs, update_text -from wqflask.decorators import admin_login_required +from wqflask.decorators import edit_access_required from wqflask.db_info import InfoPage from utility import temp_data @@ -420,7 +420,7 @@ def submit_trait_form(): @app.route("/trait//edit/inbredset-id/") -@admin_login_required +@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"), @@ -477,7 +477,7 @@ def edit_phenotype(name, inbredset_id): @app.route("/trait/edit/probeset-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"), @@ -520,7 +520,7 @@ 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"), @@ -646,7 +646,7 @@ def update_phenotype(): @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"), @@ -1381,7 +1381,7 @@ 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" -- cgit v1.2.3 From 7f317126d7d422b073cb4e4a8698757fe1e763f3 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 21 Sep 2021 21:36:32 +0300 Subject: Replace hard-coded e-mails with gn-proxy queries * wqflask/wqflask/decorators.py (edit_access_required.wrap): Query the proxy to see the access rights of a given user. --- wqflask/wqflask/decorators.py | 26 ++++++++++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/decorators.py b/wqflask/wqflask/decorators.py index f6e3eb8a..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 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 -- cgit v1.2.3 From ac14326be6695f185f843d29bf3ff016f5eb3016 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 22 Sep 2021 14:30:09 +0300 Subject: new_security: login_user.html: Delete commented out block --- .../wqflask/templates/new_security/login_user.html | 26 ---------------------- 1 file changed, 26 deletions(-) (limited to 'wqflask') 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 %} - - - {% include "new_security/_scripts.html" %} {% endblock %} -- cgit v1.2.3 From 84a0cce8a341b8b45b3b0037379818c32d5614b2 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 22 Sep 2021 14:32:03 +0300 Subject: Remove "_scripts.html" and all it's references --- wqflask/wqflask/templates/new_security/_scripts.html | 1 - wqflask/wqflask/templates/new_security/forgot_password.html | 1 - wqflask/wqflask/templates/new_security/forgot_password_step2.html | 1 - wqflask/wqflask/templates/new_security/password_reset.html | 1 - wqflask/wqflask/templates/new_security/register_user.html | 1 - wqflask/wqflask/templates/new_security/registered.html | 1 - wqflask/wqflask/templates/new_security/thank_you.html | 1 - wqflask/wqflask/templates/new_security/verification_still_needed.html | 1 - 8 files changed, 8 deletions(-) delete mode 100644 wqflask/wqflask/templates/new_security/_scripts.html (limited to 'wqflask') 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 @@ - 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" %} {% 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" %} {% 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" %} {% 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" %} {% 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" %} {% 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" %} {% endblock %} -- cgit v1.2.3 From edb6fe1b9dd98d84deb0925a2d83726e739d8677 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Sep 2021 16:28:12 +0300 Subject: wqflask: resource_manager: Remove logger --- wqflask/wqflask/resource_manager.py | 2 -- 1 file changed, 2 deletions(-) (limited to 'wqflask') 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')) -- cgit v1.2.3 From 609865fc42b7436d8c34cdcefd159c3352c5d91c Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 4 Oct 2021 20:58:14 +0000 Subject: Add group link for user member groups --- wqflask/wqflask/templates/admin/group_manager.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') 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 @@ {{ loop.index }} - {{ group.name }} + {{ group.name }} {{ group.admins|length + group.members|length }} {{ group.created_timestamp }} {{ group.changed_timestamp }} -- cgit v1.2.3 From 5b116de4aaf796be138ee0ad06c2242b3f3c33c7 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 4 Oct 2021 21:02:37 +0000 Subject: Changed get_user_groups to pull both the ID and details in the for loop from group_list by using group_list.items() --- wqflask/utility/redis_tools.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 99295c67..de9dde46 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -127,20 +127,20 @@ def check_verification_code(code): def get_user_groups(user_id): - # ZS: Get the groups where a user is an admin or a member and + # Get the groups where a user is an admin or a member and # return lists corresponding to those two sets of groups - admin_group_ids = [] # ZS: Group IDs where user is an admin - user_group_ids = [] # ZS: Group IDs where user is a regular user + admin_group_ids = [] # Group IDs where user is an admin + user_group_ids = [] # Group IDs where user is a regular user groups_list = Redis.hgetall("groups") - for key in groups_list: + for group_id, group_details in groups_list.items(): try: - group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin if this_admin else None for this_admin in group_ob['admins']]) - group_members = set([this_member if this_member else None for this_member in group_ob['members']]) + _details = json.loads(group_details) + group_admins = set([this_admin if this_admin else None for this_admin in _details['admins']]) + group_members = set([this_member if this_member else None for this_member in _details['members']]) if user_id in group_admins: - admin_group_ids.append(group_ob['id']) + admin_group_ids.append(group_id) elif user_id in group_members: - user_group_ids.append(group_ob['id']) + user_group_ids.append(group_id) else: continue except: -- cgit v1.2.3 From 2236508f24c8c266a6a9dff28a1307bb3d0dd31e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 5 Oct 2021 11:07:09 +0300 Subject: tests: test_run_mapping: Add missing positional argument "vals_hash" --- wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'wqflask') 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..31f56c07 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -181,7 +181,8 @@ 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") + 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'), -- cgit v1.2.3 From 321632bf70c72ed987ba7c4f605dd92deaa62380 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 5 Oct 2021 11:10:04 +0300 Subject: tests: test_run_mapping: Add missing attribute to "self.trait" --- wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') 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 31f56c07..26903eed 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -47,7 +47,7 @@ class TestRunMapping(unittest.TestCase): 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( -- cgit v1.2.3 From e97719eea27ede1b3e943e6d21d18e5d383679f0 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 5 Oct 2021 11:12:29 +0300 Subject: tests: test_run_mapping: Fix failing assert when getting perm strata --- wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) (limited to 'wqflask') 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 26903eed..3e9e4ef3 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -233,25 +233,20 @@ 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""" -- cgit v1.2.3 From 1f5be42d8f090fd4fe77a9275b12a9c9b1383d09 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 5 Oct 2021 11:19:52 +0300 Subject: tests: test_run_mapping: Add missing calls After adding the missing attribute to "self.trait", we need to also need to update some missing calls. --- wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py | 2 ++ 1 file changed, 2 insertions(+) (limited to 'wqflask') 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 3e9e4ef3..3747aeb8 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -188,6 +188,8 @@ class TestRunMapping(unittest.TestCase): mock.call('Time/Date: 09/01/19 / 10:12:12\n'), mock.call('Population: Human GP1_\n'), mock.call( 'Data Set: dataser_1\n'), + mock.call('Trait: Test Name\n'), + mock.call('Trait Hash: \n'), mock.call('N Samples: 100\n'), mock.call( 'Transform - Quantile Normalized\n'), mock.call('Gene Symbol: IGFI\n'), mock.call( -- cgit v1.2.3 From a4ec2505fb9dd6f0480c9b452fd623e038c07939 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 5 Oct 2021 11:28:33 +0300 Subject: tests: test_run_mapping: Add missing "name" attribute to tests --- .../unit/wqflask/marker_regression/test_gemma_mapping.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) (limited to 'wqflask') 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')]) -- cgit v1.2.3 From e473a210491620477898ba69f33f69f14fdf5893 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 8 Oct 2021 22:49:20 +0000 Subject: Fix issue where outliers weren't being highlighted for rows drawn by Scroller (so all rows beyond a certain point) --- wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js | 2 ++ wqflask/wqflask/templates/show_trait.html | 2 -- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') 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 4de1b0ac..0a060cdc 100644 --- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js +++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -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/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')) { -- cgit v1.2.3 From 9b28d111ad156f3862286e88bc220e02d5e1312b Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 8 Oct 2021 23:31:19 +0000 Subject: Fixed some issues with scale and score_type in mapping export + include mapping method in export filename --- wqflask/wqflask/marker_regression/run_mapping.py | 25 ++++++++++++------------ 1 file changed, 12 insertions(+), 13 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 290c4a14..80094057 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -104,7 +104,7 @@ class RunMapping: if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] else: - mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash]).replace("/", "_") + 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) @@ -405,8 +405,8 @@ class RunMapping: total_markers = len(self.qtl_results) with Bench("Exporting Results"): - export_mapping_results(self.dataset, self.this_trait, self.qtl_results, - self.mapping_results_path, self.mapping_scale, self.score_type, + export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, + 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"): @@ -525,7 +525,11 @@ class RunMapping: return trimmed_genotype_data -def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples, vals_hash): +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") @@ -535,6 +539,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, 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": @@ -564,10 +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()): @@ -575,11 +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'])) -- cgit v1.2.3 From a212ad123f902b6a9c74bcac1d98bc274cebbdda Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 12 Oct 2021 17:36:02 +0000 Subject: Fixed export_mapping_results test in test_run_mapping.py --- .../wqflask/marker_regression/test_run_mapping.py | 33 +++++++++++----------- 1 file changed, 16 insertions(+), 17 deletions(-) (limited to 'wqflask') 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 3747aeb8..868b0b0b 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -43,7 +43,7 @@ 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( @@ -180,37 +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", - vals_hash="") + 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'), + 'Data Set: dataset_1\n'), mock.call('Trait: Test Name\n'), mock.call('Trait Hash: \n'), - mock.call('N Samples: 100\n'), mock.call( - 'Transform - Quantile Normalized\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() -- cgit v1.2.3