diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 40 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 15 |
2 files changed, 12 insertions, 43 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 295f5c48..0d4ac24b 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -150,10 +150,12 @@ Publish or ProbeSet. E.g. "geno": "Geno", } + group_name = name if t in ['pheno', 'other_pheno']: - name = name.replace("Publish", "") + group_name = name.replace("Publish", "") - if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())): + results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone() + if results: self.datasets[name] = dataset_name_mapping[t] self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) return True @@ -1154,40 +1156,6 @@ class TempDataSet(DataSet): self.fullname = 'Temporary Storage' self.shortname = 'Temp' - @staticmethod - def handle_pca(desc): - if 'PCA' in desc: - # Todo: Modernize below lines - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - return desc - - def get_desc(self): - query = 'SELECT description FROM Temp WHERE Name=%s' % self.name - logger.sql(query) - g.db.execute(query) - desc = g.db.fetchone()[0] - desc = self.handle_pca(desc) - return desc - - def retrieve_sample_data(self, trait): - query = """ - SELECT - Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id - FROM - TempData, Temp, Strain - WHERE - TempData.StrainId = Strain.Id AND - TempData.Id = Temp.DataId AND - Temp.name = '%s' - Order BY - Strain.Name - """ % escape(trait.name) - - logger.sql(query) - results = g.db.execute(query).fetchall() - def geno_mrna_confidentiality(ob): dataset_table = ob.type + "Freeze" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index a493cfbf..cfc02f8b 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -132,7 +132,7 @@ class GeneralTrait(object): @property def description_fmt(self): - '''Return a text formated description''' + """Return a text formated description""" if self.dataset.type == 'ProbeSet': if self.description: formatted = self.description @@ -153,7 +153,7 @@ class GeneralTrait(object): @property def alias_fmt(self): - '''Return a text formatted alias''' + """Return a text formatted alias""" alias = 'Not available' if getattr(self, "alias", None): @@ -164,7 +164,7 @@ class GeneralTrait(object): @property def wikidata_alias_fmt(self): - '''Return a text formatted alias''' + """Return a text formatted alias""" alias = 'Not available' if self.symbol: @@ -194,12 +194,12 @@ class GeneralTrait(object): @property def location_fmt(self): - '''Return a text formatted location + """Return a text formatted location While we're at it we set self.location in case we need it later (do we?) - ''' + """ if self.chr and self.mb: self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb) @@ -542,7 +542,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if (str(description_display or "") != "" and description_display != 'N/A' and - str(target_string or "") != "" and target_string != 'None'): + str(target_string or "") != "" and target_string != 'None'): description_display = description_display + '; ' + target_string.strip() # Save it for the jinja2 template @@ -631,7 +631,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: trait.locus = trait.lrs = trait.additive = "" if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "": - trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb)) + trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( + trait.locus_chr, float(trait.locus_mb)) if str(trait.lrs or "") != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: |