Fixed the transaction related errors

Author: Sentient07

pgd/settings.py

@@ -185,6 +185,7 @@
     }
 }
 
+DJANGO_SETTINGS_MODULE = 'pgd.settings'
 # PGD Specific settings
 QUERY_LIMIT = config('QUERY_LIMIT', default=50000000, cast=int)
 SEGMENT_SIZE = config('SEGMENT_SIZE', default=10, cast=int)

pgd/wsgi.py

@@ -14,9 +14,12 @@
 
 """
 import os
+import sys
+from django.core.wsgi import get_wsgi_application
 
-os.environ.setdefault("DJANGO_SETTINGS_MODULE", "pgd.settings")
 
+#os.environ.setdefault("DJANGO_SETTINGS_MODULE", "pgd.settings")
+os.environ['DJANGO_SETTINGS_MODULE'] = 'pgd.settings'
 # This application object is used by any WSGI server configured to use this
 # file. This includes Django's development server, if the WSGI_APPLICATION
 # setting points here.

pgd_search/plot/ConfDistFuncs.py

@@ -312,7 +312,7 @@ def query_bins(self):
                 annotations[avg] = Avg(field[1])
                 annotations[stddev] = StdDev(field[1])
         annotated_query = querySet.annotate(**annotations)
-        print annotated_query
+
         # sort and group by bins using an aggregate function that calculates
         # bin index based on bin size (in field units ie. degrees) and bin count.
         #
@@ -325,27 +325,20 @@ def query_bins(self):
         # XXX in Django 1.2+ aggregates were changed to require connection and
         # SQLCompiler objects to generate sql.  We must initialize this all
         # manually to be able to grab the SQL for just our aggregate.
-        print "xTextString is :"
-        print self.xTextString
-        print "yTextString is "
-        print self.yTextString
-        print querySet
+
         sortx = BinSort(self.xTextString, offset=x, bincount=xbin, max=x1)
         sorty = BinSort(self.yTextString, offset=y, bincount=ybin, max=y1)
 
-        pgdaggr = PGDAggregate(self.xTextString, offset=x, bincount=xbin, max=x1)
-        print "Checking Attribute for PGDAggregate"
-        print hasattr(pgdaggr, 'aggr')
         annotated_query.annotate(x=sortx, y=sorty)
 
         cn = connections['default']
         qn = SQLCompiler(annotated_query.query, cn, 'default').quote_name_unless_alias
-        if not hasattr(sortx, 'queryObj'):
-            print "doesn't have queryObj"
-        else :
-            print "has queryObj"
+
+        #Hack : Using the BinSortSQL class directly instead of BinSort
+        #this overrides l:329 and l:330
         sortx = BinSortSQL(('pgd_core_residue', 'psi'), offset=x, bincount=xbin, max=x1)
         sorty = BinSortSQL(('pgd_core_residue', 'phi'), offset=y, bincount=ybin, max=y1)
+
         sortx_sql = sortx.as_sql(qn, cn)[0]
         sorty_sql = sorty.as_sql(qn, cn)[0]
 

pgd_search/plot/PlotForm.py

@@ -168,7 +168,9 @@ def clean(self):
         if not data['background_color'] :
             data['background_color'] = 'Transparent'
         if not data['graph_color'] :
-            data['graph_color'] = 'Transparent'
+            data['graph_color'] = 'Dark Gray'
         if not data['hash_color'] :
-            data['hash_color'] = 'Transparent'
+            data['hash_color'] = 'Gray'
+        if not data['text_color'] :
+            data['text_color'] = 'Black'
         return data

pgd_search/plot/views.py

@@ -194,7 +194,6 @@ def renderToSVG(request):
             return HttpResponse(_json)
 
         else:
-            print form.errors
             """
             Errors in the form - repackage the error list as a list of errors
             This list can then be json serialized and processed by the javascript

pgd_search/statistics/aggregates.py

@@ -29,15 +29,6 @@ def add_to_query(self, query, alias, col, source, is_summary):
         klass = globals()['%sSQL' % self.name]
         aggregate = klass(col, source=source, is_summary=is_summary, **self.extra)
 
-        print self.extra
-
-        print "alias is :"
-        print alias
-        print "col is :"
-        print col
-        print "source is : "
-        print source
-
         # Validate that the backend has a fully supported, correct
         # implementation of this aggregate
         self.aggr = aggregate

pgd_splicer/ProcessPDBTask.py

@@ -32,6 +32,7 @@
 from Bio.PDB import calc_angle as pdb_calc_angle
 from Bio.PDB import calc_dihedral as pdb_calc_dihedral
 from django.db import transaction
+import django
 
 from pgd_core.models import (Protein as ProteinModel, Chain as ChainModel,
                              Residue as ResidueModel, Sidechain_ARG,
@@ -45,6 +46,7 @@
 from pgd_splicer.chi import CHI_MAP, CHI_CORRECTIONS_TESTS, CHI_CORRECTIONS
 from pgd_splicer.sidechain import bond_angles, bond_lengths
 
+django.setup()
 
 def NO_VALUE(field):
     """
@@ -195,12 +197,12 @@ def workhorse(data):
         return False
 
 
-@transaction.commit_manually
+
 def process_pdb(data):
     """
     Process an individual pdb file
     """
-
+    transaction.set_autocommit(False)
     # create a copy of the data.  This dict will have a large amount of data
     # added to it as the protein is processed.  This prevents memory leaks
     # due to the original dict having a reference held outside this method.
@@ -233,8 +235,10 @@ def process_pdb(data):
         protein.rfactor    = float(data['rfactor'])
         protein.rfree      = float(data['rfree'])
         protein.pdb_date   = data['pdb_date']
-        protein.save()
+        with transaction.atomic():
+            protein.save()
 
+        transaction.commit()
         # 3) Get/Create Chains and save values
         chains = {}
         for chaincode, residues in data['chains'].items():
@@ -248,9 +252,10 @@ def process_pdb(data):
                 chain.id      = chainId
                 chain.protein = protein
                 chain.code    = chaincode
-                chain.save()
+                with transaction.atomic():
+                    chain.save()
 
-                protein.chains.add(chain)
+                    protein.chains.add(chain)
             #create dictionary of chains for quick access
             chains[chaincode] = chain
 
@@ -288,17 +293,20 @@ def process_pdb(data):
                     except:
                         sidechain = klass()
                     sidechain.__dict__.update(residue_props['sidechain'])
-                    sidechain.save()
+                    with transaction.atomic():
+                        sidechain.save()
                     residue.__setattr__(name, sidechain)
 
                 # 4e) save
-                residue.save()
-                chain.residues.add(residue)
+                with transaction.atomic():
+                    residue.save()
+                    chain.residues.add(residue)
 
                 # 4f) Update old_residue.next
                 if "prev" in residue_props:
                     old_residue.next = residue
-                    old_residue.save()
+                    with transaction.atomic():
+                        old_residue.save()
 
 
                 old_residue = residue