diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 33 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 25 |
2 files changed, 39 insertions, 19 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 6dc44829..8906ab69 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -277,7 +277,6 @@ class Markers: filtered_markers = [] for marker in self.markers: if marker['name'] in p_values: - # logger.debug("marker {} IS in p_values".format(i)) marker['p_value'] = p_values[marker['name']] if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 @@ -298,7 +297,6 @@ class HumanMarkers(Markers): self.markers = [] for line in marker_data_fh: splat = line.strip().split() - # logger.debug("splat:", splat) if len(specified_markers) > 0: if splat[1] in specified_markers: marker = {} @@ -398,6 +396,15 @@ class DatasetGroup: if maternal and paternal: self.parlist = [maternal, paternal] + def get_study_samplelists(self): + study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists') + try: + f = open(study_sample_file) + except: + return [] + study_samples = json.load(f) + return study_samples + def get_genofiles(self): jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) try: @@ -557,6 +564,7 @@ class DataSet: self.fullname = None self.type = None self.data_scale = None # ZS: For example log2 + self.accession_id = None self.setup() @@ -573,6 +581,17 @@ class DataSet: self.group.get_samplelist() self.species = species.TheSpecies(self) + def as_dict(self): + return { + 'name': self.name, + 'shortname': self.shortname, + 'fullname': self.fullname, + 'type': self.type, + 'data_scale': self.data_scale, + 'group': self.group.name, + 'accession_id': self.accession_id + } + def get_accession_id(self): if self.type == "Publish": results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where @@ -725,7 +744,6 @@ class DataSet: and Strain.SpeciesId=Species.Id and Species.name = '{}' """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) - logger.sql(query) results = dict(g.db.execute(query).fetchall()) sample_ids = [results[item] for item in self.samplelist] @@ -896,7 +914,6 @@ class PhenotypeDataSet(DataSet): Geno.Name = '%s' and Geno.SpeciesId = Species.Id """ % (species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -926,7 +943,6 @@ class PhenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -993,7 +1009,6 @@ class GenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() @@ -1114,8 +1129,6 @@ class MrnaAssayDataSet(DataSet): ProbeSet.Name = '%s' """ % (escape(str(this_trait.dataset.id)), escape(this_trait.name))) - - logger.sql(query) result = g.db.execute(query).fetchone() mean = result[0] if result else 0 @@ -1135,7 +1148,6 @@ class MrnaAssayDataSet(DataSet): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -1167,7 +1179,6 @@ class MrnaAssayDataSet(DataSet): Order BY Strain.Name """ % (escape(trait), escape(self.name)) - logger.sql(query) results = g.db.execute(query).fetchall() return results @@ -1178,7 +1189,6 @@ class MrnaAssayDataSet(DataSet): where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) - logger.sql(query) results = g.db.execute(query).fetchall() return dict(results) @@ -1212,7 +1222,6 @@ def geno_mrna_confidentiality(ob): query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name) - logger.sql(query) result = g.db.execute(query) (dataset_id, diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index d09cfd40..96a09302 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -27,11 +27,13 @@ def create_trait(**kw): assert bool(kw.get('name')), "Needs trait name" - if kw.get('dataset_name'): + if bool(kw.get('dataset')): + dataset = kw.get('dataset') + else: if kw.get('dataset_name') != "Temp": dataset = create_dataset(kw.get('dataset_name')) - else: - dataset = kw.get('dataset') + else: + dataset = create_dataset("Temp", group_name=kw.get('group_name')) if dataset.type == 'Publish': permissions = check_resource_availability( @@ -284,17 +286,19 @@ def get_sample_data(): return None -def jsonable(trait): +def jsonable(trait, dataset=None): """Return a dict suitable for using as json Actual turning into json doesn't happen here though""" - dataset = create_dataset(dataset_name=trait.dataset.name, - dataset_type=trait.dataset.type, - group_name=trait.dataset.group.name) + if not dataset: + dataset = create_dataset(dataset_name=trait.dataset.name, + dataset_type=trait.dataset.type, + group_name=trait.dataset.group.name) if dataset.type == "ProbeSet": return dict(name=trait.name, + view=trait.view, symbol=trait.symbol, dataset=dataset.name, dataset_name=dataset.shortname, @@ -308,37 +312,44 @@ def jsonable(trait): elif dataset.type == "Publish": if trait.pubmed_id: return dict(name=trait.name, + view=trait.view, dataset=dataset.name, dataset_name=dataset.shortname, description=trait.description_display, abbreviation=trait.abbreviation, authors=trait.authors, + pubmed_id=trait.pubmed_id, pubmed_text=trait.pubmed_text, pubmed_link=trait.pubmed_link, + mean=trait.mean, lrs_score=trait.LRS_score_repr, lrs_location=trait.LRS_location_repr, additive=trait.additive ) else: return dict(name=trait.name, + view=trait.view, dataset=dataset.name, dataset_name=dataset.shortname, description=trait.description_display, abbreviation=trait.abbreviation, authors=trait.authors, pubmed_text=trait.pubmed_text, + mean=trait.mean, lrs_score=trait.LRS_score_repr, lrs_location=trait.LRS_location_repr, additive=trait.additive ) elif dataset.type == "Geno": return dict(name=trait.name, + view=trait.view, dataset=dataset.name, dataset_name=dataset.shortname, location=trait.location_repr ) elif dataset.name == "Temp": return dict(name=trait.name, + view=trait.view, dataset="Temp", dataset_name="Temp") else: |