Upgrade

docker-compose.yml

@@ -40,4 +40,4 @@ networks:
     front-tier:
         driver: bridge
     back-tier:
-        driver: bridge
+        driver: bridge

pgd/settings.py

@@ -4,9 +4,10 @@
 import os
 PROJECT_ROOT = os.path.dirname(os.path.abspath(os.path.dirname(__file__)))
 
-DEBUG = config('DEBUG', default=False, cast=bool)
+DEBUG = True
 TEMPLATE_DEBUG = DEBUG
 
+
 ADMINS = (
     # ('Your Name', 'your_email@domain.com'),
 )
@@ -122,6 +123,7 @@
     'django.contrib.sessions.middleware.SessionMiddleware',
     'django.contrib.auth.middleware.AuthenticationMiddleware',
     'django.contrib.messages.middleware.MessageMiddleware',
+    'django_pdb.middleware.PdbMiddleware',
 )
 
 ROOT_URLCONF = config('ROOT_URLCONF', default='pgd.urls')
@@ -130,11 +132,12 @@
 WSGI_APPLICATION = 'pgd.wsgi.application'
 
 TEMPLATE_DIRS = (
-    '%s/templates' % DOC_ROOT
+    '%s/templates' % DOC_ROOT, 
 )
 
 INSTALLED_APPS = (
     'django.contrib.auth',
+    'django_pdb',
     'django.contrib.contenttypes',
     'django.contrib.sessions',
     'django.contrib.sites',
@@ -175,6 +178,7 @@
     }
 }
 
+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/urls.py

@@ -5,6 +5,8 @@
 from django.core.urlresolvers import reverse_lazy
 from views import ReferencesView, ContactUsView, NewsView, WelcomeView
 admin.autodiscover()
+import pgd_search.urls
+import pgd_core.urls
 
 #from pgd import VERSION
 #from pgd_splicer.models import pdb_select_settings
@@ -20,9 +22,9 @@
     # Uncomment the next line to enable the admin:
     #(r'^admin/', include(admin.site.urls)),
 
-    url(r'^search/', include('pgd_search.urls'), name='pgd_search'),
+    url(r'^search/', include(pgd_search.urls), name='pgd_search'),
 
-    url(r'^accounts/', include('pgd_core.urls')),
+    url(r'^accounts/', include(pgd_core.urls)),
 
     # Static pages:
     (r'^references/$', ReferencesView.as_view()),

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

@@ -9,15 +9,16 @@
 from django.db import connections
 from django.db.backends.mysql.compiler import SQLCompiler
 
-from django.db.models import Count, Avg, StdDev
+from django.db.models import Count, Avg, StdDev, FloatField
 
 from pgd_constants import *
 from pgd_core.models import *
 from pgd_search.models import *
-from pgd_search.statistics.aggregates import DirectionalAvg, DirectionalStdDev, BinSort
+from pgd_search.statistics.aggregates import DirectionalAvg, DirectionalStdDev, BinSort, PGDAggregate, BinSortSQL
 from pgd_splicer.sidechain import sidechain_length_relationship_list, sidechain_angle_relationship_list
 from svg import *
 
+import sys
 ANGLES = ('ome', 'phi', 'psi', 'chi1','chi2','chi3','chi4','chi5','zeta')
 NON_FIELDS = ('Observations', 'all')
 
@@ -311,7 +312,7 @@ def query_bins(self):
                 annotations[avg] = Avg(field[1])
                 annotations[stddev] = StdDev(field[1])
         annotated_query = querySet.annotate(**annotations)
-        
+
         # 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.
         #
@@ -324,14 +325,24 @@ 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.
+
         sortx = BinSort(self.xTextString, offset=x, bincount=xbin, max=x1)
         sorty = BinSort(self.yTextString, offset=y, bincount=ybin, max=y1)
+
         annotated_query.annotate(x=sortx, y=sorty)
 
         cn = connections['default']
         qn = SQLCompiler(annotated_query.query, cn, 'default').quote_name_unless_alias
-        sortx_sql = sortx.aggregate.as_sql(qn, cn)[0]
-        sorty_sql = sorty.aggregate.as_sql(qn, cn)[0]
+
+        #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]
+
+
 
         annotated_query = annotated_query.extra(select={'x':sortx_sql, 'y':sorty_sql})
         annotated_query = annotated_query.order_by('x','y')

pgd_search/plot/PlotForm.py

@@ -3,7 +3,7 @@
 from pgd_search.views import RESIDUE_INDEXES
 
 #choice for occurence of property
-ATTRIBUTE_CHOICES = [
+ATTRIBUTE_CHOICES = (
                     ("Observations",'Observations'),
                     ("L1",u'C<sup>-1</sup>N'),
                     ("L2",u'NC<sup>&alpha;</sup>'),
@@ -28,10 +28,10 @@
                     ("psi",u'&psi;'),
                     ('zeta',u'&zeta;'),
                     #('h_bond_energy','H Bond'),
-                    ]
+                    )
 
 # choices for properties mapped to axis
-PROPERTY_CHOICES = [
+PROPERTY_CHOICES = (
                     ("L1",u'C<sup>-1</sup>N'),
                     ("L2",u'NC<sup>&alpha;</sup>'),
                     ("L3",u'C<sup>&alpha;</sup>C<sup>&beta;</sup>'),
@@ -55,50 +55,50 @@
                     ("psi",u'&psi;'),
                     ('zeta',u'&zeta;'),
                     #('h_bond_energy','H Bond'),
-                    ]
+                    )
 
 
 PROPERTY_CHOICES_DICT = {}
 for prop, label in PROPERTY_CHOICES:
     PROPERTY_CHOICES_DICT[prop] = label          
 
 
-BACKGROUND_CHOICES = [
+BACKGROUND_CHOICES = (
                     ('#ffffff','White'),
                     ('#000000','Black'),
                     ('#666666','Gray'),
                     ('#222222','Dark Gray'),
                     (None,'Transparent'),
-]
+)
 
-GRAPH_CHOICES = [
+GRAPH_CHOICES = (
                     ('#222222','Dark Gray'),
                     ('#666666','Gray'),
                     ('#000000','Black'),
                     ('#ffffff','White'),
                     (None,'Transparent'),
-]
+)
 
-TEXT_CHOICES = [
+TEXT_CHOICES = (
                     ('#000000','Black'),
                     ('#ffffff','White'),
                     ('#666666','Gray'),
                     ('#222222','Dark Gray'),
-]
+)
 
-HUE_CHOICES = [
+HUE_CHOICES = (
                     ('green','Green'),
                     ('blue','Blue'),
                     ('red','Red'),
                     ('black','Black/White'),
-]
+)
 
-HASH_CHOICES = [
+HASH_CHOICES = (
                     ('#666666','Gray'),
                     ('#222222','Dark Gray'),
                     ('#000000','Black'),
                     ('#ffffff','White'),
-]
+)
 
 
 """
@@ -147,11 +147,11 @@ class PlotForm(forms.Form):
                                        widget=forms.TextInput(attrs={'size':4}))
 
     #custom plot properties
-    background_color= forms.ChoiceField(choices=BACKGROUND_CHOICES)
-    graph_color     = forms.ChoiceField(choices=GRAPH_CHOICES)
-    text_color      = forms.ChoiceField(choices=TEXT_CHOICES)
+    background_color= forms.ChoiceField(required=False, choices=BACKGROUND_CHOICES)
+    graph_color     = forms.ChoiceField(required=False, choices=GRAPH_CHOICES)
+    text_color      = forms.ChoiceField(required=False, choices=TEXT_CHOICES)
     plot_hue        = forms.ChoiceField(choices=HUE_CHOICES)
-    hash_color      = forms.ChoiceField(choices=HASH_CHOICES)
+    hash_color      = forms.ChoiceField(required=False, choices=HASH_CHOICES)
     height          = forms.IntegerField(initial=470,
                                          widget=forms.TextInput(attrs={'size':4}))
     width           = forms.IntegerField(initial=560,
@@ -165,4 +165,10 @@ def clean(self):
             data['attribute'] = data['attribute'].replace('-','_')
         except KeyError:
             pass
+        if not data['graph_color'] :
+            data['graph_color'] = '#222222'
+        if not data['hash_color'] :
+            data['hash_color'] = '#666666'
+        if not data['text_color'] :
+            data['text_color'] = '#000000'
         return data

pgd_search/plot/views.py

@@ -6,13 +6,13 @@
 from django.conf import settings
 from django.shortcuts import render_to_response
 import json
-
 from PlotForm import PlotForm, ATTRIBUTE_CHOICES, PROPERTY_CHOICES
 from ConfDistFuncs import *
 from pgd_constants import AA_CHOICES
 from pgd_search.views import settings_processor
 from pgd_splicer.sidechain import sidechain_string_dict
 
+
 AA_CHOICES = [aa[1].upper() for aa in filter(lambda x: x[1].upper() in sidechain_string_dict, AA_CHOICES)]
 
 def drawGraph(request, height=470, width=560, xStart=None, yStart=None, xEnd=None, yEnd=None, attribute='Observations', xProperty='phi', yProperty='psi', reference=None, sigmaVal=3, residue_attribute=None, residue_xproperty=None, residue_yproperty=None, xBin=None, yBin=None, background_color='#ffffff',graph_color='#222222',text_color='#000000', hue='green', hash_color='666666'):
@@ -74,15 +74,12 @@ def drawGraph(request, height=470, width=560, xStart=None, yStart=None, xEnd=Non
                 text_color,
                 hash_color
         )
-
         svg = cdp.Plot()
     except Exception, e:
-        print 'exception', e
         import traceback, sys
         exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
         print "*** print_tb:"
         traceback.print_tb(exceptionTraceback, limit=10, file=sys.stdout)
-
         raise e
     return (svg, xStart, xEnd, xBin, yStart, yEnd, yBin)
 

pgd_search/search/views.py

@@ -1,12 +1,11 @@
 import math
 import re
 import pickle
-
 from django.http import HttpResponse, HttpResponseRedirect
 from django.template import RequestContext
 from django.shortcuts import render_to_response, redirect
 from django.conf import settings
-from django.forms.util import ErrorList
+from django.forms.utils import ErrorList
 from django.core.paginator import Paginator, InvalidPage, EmptyPage
 import json
 from datetime import datetime
@@ -24,7 +23,6 @@
 json_sidechain_angles_lookup = json.dumps(bond_angles_string_dict)
 
 
-
 def search(request):
     """
     Handler for search form.
@@ -43,10 +41,10 @@ def search(request):
             #at least for now limit the size of the result set
             count = search_object.querySet().count()
             if count > settings.QUERY_LIMIT:
-                form._errors['Result Size'] = ErrorList(['Your query returned more than 20,000 records, refine your search'])
+                form.error['Result Size'] = ErrorList(['Your query returned more than 20,000 records, refine your search'])
 
             elif count == 0 and False:
-                form._errors['Result Size'] = ErrorList(['Your query returned no results'])
+                form.error['Result Size'] = ErrorList(['Your query returned no results'])
 
             else:
                 #store search in session

pgd_search/statistics/aggregates.py

@@ -6,6 +6,7 @@ class PGDAggregate(Aggregate):
     Modified to allow Aggregate functions outside of the Django module
     """
 
+
     def add_to_query(self, query, alias, col, source, is_summary):
         """Add the aggregate to the nominated query.
 
@@ -24,13 +25,15 @@ def add_to_query(self, query, alias, col, source, is_summary):
          * is_summary is a boolean that is set True if the aggregate is a
            summary value rather than an annotation.
         """
+        self.queryObj = query
         klass = globals()['%sSQL' % self.name]
         aggregate = klass(col, source=source, is_summary=is_summary, **self.extra)
-        
+
         # Validate that the backend has a fully supported, correct
         # implementation of this aggregate
+        self.aggr = aggregate
         query.aggregates[alias] = aggregate
-        self.aggregate = aggregate
+
 
 
 class DirectionalStdDev(PGDAggregate):
@@ -63,3 +66,4 @@ class BinSort(PGDAggregate):
 class BinSortSQL(SQLAggregate):
     sql_function = ''
     sql_template = '%(function)sFLOOR((IF(%(field)s<%(offset).16f,360,0)+%(field)s-%(offset).16f)/%(bincount).16f)-IF(%(field)s=%(max).16f,1,0)'
+