diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 34 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 14 |
2 files changed, 7 insertions, 41 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index afffe780..e0ef559c 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -1173,40 +1173,6 @@ 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 7666348e..8f8b5b70 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -507,13 +507,14 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') - if len(description_string) > 1 and description_string != 'None': + if str(description_string or "") != "" and description_string != 'None': description_display = description_string else: description_display = trait.symbol - if (len(description_display) > 1 and description_display != 'N/A' and - len(target_string) > 1 and target_string != 'None'): + if (str(description_display or "") != "" and + description_display != 'N/A' and + str(target_string or "") != "" and target_string != 'None'): description_display = description_display + '; ' + target_string.strip() # Save it for the jinja2 template @@ -599,12 +600,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" else: trait.locus = trait.lrs = trait.additive = "" - - if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "": + 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)) - if trait.lrs != "": + if str(trait.lrs or "") != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: raise KeyError, `trait.name`+' information is not found in the database.' - return trait
\ No newline at end of file + return trait |