diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 21 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 8 |
2 files changed, 14 insertions, 15 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4cb82665..8906ab69 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -277,7 +277,6 @@ class Markers: filtered_markers = [] for marker in self.markers: if marker['name'] in p_values: - # logger.debug("marker {} IS in p_values".format(i)) marker['p_value'] = p_values[marker['name']] if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 @@ -298,7 +297,6 @@ class HumanMarkers(Markers): self.markers = [] for line in marker_data_fh: splat = line.strip().split() - # logger.debug("splat:", splat) if len(specified_markers) > 0: if splat[1] in specified_markers: marker = {} @@ -398,6 +396,15 @@ class DatasetGroup: if maternal and paternal: self.parlist = [maternal, paternal] + def get_study_samplelists(self): + study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists') + try: + f = open(study_sample_file) + except: + return [] + study_samples = json.load(f) + return study_samples + def get_genofiles(self): jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) try: @@ -737,7 +744,6 @@ class DataSet: and Strain.SpeciesId=Species.Id and Species.name = '{}' """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) - logger.sql(query) results = dict(g.db.execute(query).fetchall()) sample_ids = [results[item] for item in self.samplelist] @@ -908,7 +914,6 @@ class PhenotypeDataSet(DataSet): Geno.Name = '%s' and Geno.SpeciesId = Species.Id """ % (species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -938,7 +943,6 @@ class PhenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -1005,7 +1009,6 @@ class GenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() @@ -1126,8 +1129,6 @@ class MrnaAssayDataSet(DataSet): ProbeSet.Name = '%s' """ % (escape(str(this_trait.dataset.id)), escape(this_trait.name))) - - logger.sql(query) result = g.db.execute(query).fetchone() mean = result[0] if result else 0 @@ -1147,7 +1148,6 @@ class MrnaAssayDataSet(DataSet): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -1179,7 +1179,6 @@ class MrnaAssayDataSet(DataSet): Order BY Strain.Name """ % (escape(trait), escape(self.name)) - logger.sql(query) results = g.db.execute(query).fetchall() return results @@ -1190,7 +1189,6 @@ class MrnaAssayDataSet(DataSet): where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) - logger.sql(query) results = g.db.execute(query).fetchall() return dict(results) @@ -1224,7 +1222,6 @@ def geno_mrna_confidentiality(ob): query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name) - logger.sql(query) result = g.db.execute(query) (dataset_id, diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 10851e00..96a09302 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -27,11 +27,13 @@ def create_trait(**kw): assert bool(kw.get('name')), "Needs trait name" - if kw.get('dataset_name'): + if bool(kw.get('dataset')): + dataset = kw.get('dataset') + else: if kw.get('dataset_name') != "Temp": dataset = create_dataset(kw.get('dataset_name')) - else: - dataset = kw.get('dataset') + else: + dataset = create_dataset("Temp", group_name=kw.get('group_name')) if dataset.type == 'Publish': permissions = check_resource_availability( |