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/base/data_set.py')

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 217f527e873d5197c7efcaec627e1df5afadefa4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 15:32:18 -0500
Subject: Fixed issue where new phenotype groups wouldn't be saved to the
 self.datasets property because the group name was used as the key (instead of
 the group name + "Publish", which is the full dataset name for phenotypes)

* wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets
---
 wqflask/base/data_set.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'wqflask/base/data_set.py')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index e0ef559c..aeafc027 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -150,10 +150,11 @@ 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())):
+        if bool(len(g.db.execute(sql_query_mapping[t].format(group_name)).fetchone())):
             self.datasets[name] = dataset_name_mapping[t]
             self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
             return True
-- 
cgit v1.2.3


From 3d444c29ab975e313534dd7c57747b3e79f06c26 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 15:40:18 -0500
Subject: Fixed remaining issue that applies to all dataset types

* wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results
---
 wqflask/base/data_set.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'wqflask/base/data_set.py')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index aeafc027..2f1549ae 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -154,7 +154,8 @@ Publish or ProbeSet. E.g.
         if t in ['pheno', 'other_pheno']:
             group_name = name.replace("Publish", "")
 
-        if bool(len(g.db.execute(sql_query_mapping[t].format(group_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
-- 
cgit v1.2.3