From 312835014d8d243c72f3520bb116eb3c36cd6b85 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 28 Sep 2020 02:33:09 +0300
Subject: Convert None to "" in if statement

* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork
error: float argument required, not NoneType)"
---
 wqflask/base/trait.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7666348e..bdd9c3d6 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -599,12 +599,11 @@ 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
-- 
cgit v1.2.3


From d34258bed3ef13350499414100401df3bf08a105 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 28 Sep 2020 18:08:34 +0300
Subject: Fix casting error

* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
---
 wqflask/base/trait.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index bdd9c3d6..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
-- 
cgit v1.2.3


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')

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