From 4bd5534658fe7ed2a9ffd50c137be81d7a7b190b Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 30 Sep 2020 13:32:54 -0500 Subject: Removed unused code from TempDataSet class * wqflask/base/data_set.py - TempDataSet class contained some code referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore --- wqflask/base/data_set.py | 34 ---------------------------------- 1 file changed, 34 deletions(-) (limited to 'wqflask') 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" -- cgit v1.2.3 From 8a01dca227aa03e794ced5f99513355f2a035f2f Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 30 Sep 2020 15:37:10 -0500 Subject: Changed the logic for adding 0 to the PCA results to do so when the shared samples are < 2 instead of 0; this fixed the error when running the correlation matrix, but results in the PCA traits having no values * wqflask/wqflask/correlation_matrx/show_corr_matrix.py - changed "if num_overlap == 0" to "if num_overlap < 2" because correlations can't be run if there are fewer than 2 shared samples (and previously would throw an error if there was exactly 1 shared sample) --- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 0ac94139..3beee84f 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -147,7 +147,7 @@ class CorrelationMatrix(object): if num_overlap < self.lowest_overlap: self.lowest_overlap = num_overlap - if num_overlap == 0: + if num_overlap < 2: corr_result_row.append([target_trait, 0, num_overlap]) pca_corr_result_row.append(0) else: -- cgit v1.2.3