Moved a bunch of functions out of the GeneralTrait class that didn't need to be there and changed the code that calls them accordingly

Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static)

Removed some unused code from show_trait.py

changed appearance of table headers some, though needs a little more work

Updated dataset_menu_structure.json

1 files changed, 17 insertions, 16 deletions

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 542c0d83..e5726656 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -95,13 +95,13 @@ def get_groups(species):
     for species_name, _species_full_name in species:
         Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet,
                        Species,
-                       ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s
+                       ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = '%s'
                        and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and
                        (PublishFreeze.InbredSetId = InbredSet.Id
                         or GenoFreeze.InbredSetId = InbredSet.Id
                         or ProbeFreeze.InbredSetId = InbredSet.Id)
                         group by InbredSet.Name
-                        order by InbredSet.Name""", (species_name))
+                        order by InbredSet.Name""" % species_name)
         groups[species_name] = list(Cursor.fetchall())
     return groups
 
@@ -133,7 +133,7 @@ def get_types(groups):
 def phenotypes_exist(group_name):
     #print("group_name:", group_name)
     Cursor.execute("""select Name from PublishFreeze
-                      where PublishFreeze.Name = %s""", (group_name+"Publish"))
+                      where PublishFreeze.Name = '%s'""" % (group_name+"Publish"))
 
     results = Cursor.fetchone()
     #print("RESULTS:", results)
@@ -146,7 +146,7 @@ def phenotypes_exist(group_name):
 def genotypes_exist(group_name):
     #print("group_name:", group_name)
     Cursor.execute("""select Name from GenoFreeze
-                      where GenoFreeze.Name = %s""", (group_name+"Geno"))
+                      where GenoFreeze.Name = '%s'""" % (group_name+"Geno"))
 
     results = Cursor.fetchone()
     #print("RESULTS:", results)
@@ -166,13 +166,14 @@ def build_types(species, group):
 
     Cursor.execute("""select distinct Tissue.Name
                        from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
-                       where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
-                       InbredSet.Name = %s and
+                       where Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and
+                       InbredSet.Name = '%s' and
                        ProbeFreeze.TissueId = Tissue.Id and
                        ProbeFreeze.InbredSetId = InbredSet.Id and
                        ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-                       ProbeSetFreeze.public > 0
-                       order by Tissue.Name""", (species, group))
+                       ProbeSetFreeze.public > 0 and
+                       ProbeSetFreeze.confidentiality < 1
+                       order by Tissue.Name""" % (species, group))
 
     results = []
     for result in Cursor.fetchall():
@@ -205,12 +206,12 @@ def build_datasets(species, group, type_name):
     if type_name == "Phenotypes":
         print("GROUP:", group)
         Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
-                    InbredSet.Name = %s and
+                    InbredSet.Name = '%s' and
                     PublishFreeze.InbredSetId = InbredSet.Id and
                     InfoFiles.InfoPageName = PublishFreeze.Name and
                     PublishFreeze.public > 0 and
                     PublishFreeze.confidentiality < 1 order by
-                    PublishFreeze.CreateTime desc""", (group))
+                    PublishFreeze.CreateTime desc""" % group)
 
         results = Cursor.fetchone()
         if results != None:
@@ -225,12 +226,12 @@ def build_datasets(species, group, type_name):
 
     elif type_name == "Genotypes":
         Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
-                    InbredSet.Name = %s and
+                    InbredSet.Name = '%s' and
                     GenoFreeze.InbredSetId = InbredSet.Id and
                     InfoFiles.InfoPageName = GenoFreeze.ShortName and
                     GenoFreeze.public > 0 and
                     GenoFreeze.confidentiality < 1 order by
-                    GenoFreeze.CreateTime desc""", (group))
+                    GenoFreeze.CreateTime desc""" % group)
 
         results = Cursor.fetchone()
         if results != None:
@@ -245,12 +246,12 @@ def build_datasets(species, group, type_name):
     else:
         Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
                     ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
-                    Species.Name = %s and Species.Id = InbredSet.SpeciesId and
-                    InbredSet.Name = %s and
-                    ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s and
+                    Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and
+                    InbredSet.Name = '%s' and
+                    ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '%s' and
                     ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and
                     ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 order by
-                    ProbeSetFreeze.CreateTime desc""", (species, group, type_name))
+                    ProbeSetFreeze.CreateTime desc""" % (species, group, type_name))
 
         dataset_results = Cursor.fetchall()
         datasets = []