bug fix

build

@@ -1 +1 @@
-c256c884
+dd11dfcb

command/consumers.py

@@ -154,7 +154,8 @@ def ws_connect(message):
         Group("admin").add(message.reply_channel)
     for db in CompendiumDatabase.objects.all():
         Group("compendium_" + str(db.id)).add(message.reply_channel)
-    message.http_session['channel_name'] = message.reply_channel.name
+    if message.http_session:
+        message.http_session['channel_name'] = message.reply_channel.name
     message.reply_channel.send({"accept": True})
 
 

command/lib/anno/ontology_helper.py

@@ -30,7 +30,7 @@ def get_neighbourhood(self, node_id, level=1):
                 Q(source_id__in=node_ids) & Q(target_id__in=node_ids))
         for e in edges_qr:
             edges.append({'data': {
-                'id': e.id,
+                'id': 'edge_' + str(e.id),
                 'source': e.source.id,
                 'target': e.target.id
             }})

command/lib/anno/owl_file_parser.py

@@ -0,0 +1,13 @@
+
+import networkx
+from onto2nx import OWLParser, parse_owl
+
+from command.lib.anno.base_parser import BaseParser
+
+
+class OWLFileParser(BaseParser):
+    FILE_TYPE_NAME = 'OWL'
+
+    def parse(self, filename):
+        graph = parse_owl(filename)
+        return networkx.readwrite.cytoscape_data(graph)

command/lib/db/compendium/bio_feature_annotation.py

@@ -1,16 +1,17 @@
 from django.db import models
 
+from command.lib.db.compendium.annotation_value import AnnotationValue
 from command.lib.db.compendium.bio_feature import BioFeature
 from command.lib.db.compendium.ontology_node import OntologyNode
 
 
 class BioFeatureAnnotation(models.Model):
     bio_feature = models.ForeignKey(BioFeature, on_delete=models.CASCADE, default=1, null=False, blank=False)
-    ontology_node = models.ForeignKey(OntologyNode, on_delete=models.CASCADE, default=1, null=False, blank=False)
+    annotation_value = models.ForeignKey(AnnotationValue, on_delete=models.CASCADE, null=False, default=1)
 
     class Meta:
-        unique_together = ('bio_feature', 'ontology_node',)
+        unique_together = ('bio_feature', 'annotation_value')
 
     def to_dict(self):
-        fields = ['id', 'bio_feature_id', 'ontology_node_id']
+        fields = ['id', 'bio_feature_id', 'annotation_value_id']
         return {k: self.__dict__[k] for k in fields}

command/lib/db/compendium/raw_data.py

@@ -2,15 +2,14 @@
 
 from command.lib.db.compendium.bio_feature_reporter import BioFeatureReporter
 from command.lib.db.compendium.sample import Sample
+from command.lib.db.compendium.value_type import ValueType
 
 
 class RawData(models.Model):
     sample = models.ForeignKey(Sample, db_index=True, on_delete=models.CASCADE, null=False, default=1)
     bio_feature_reporter = models.ForeignKey(BioFeatureReporter, db_index=True, on_delete=models.CASCADE, null=False, default=1)
     value = models.FloatField(blank=True, null=True)
-
-    class Meta:
-        unique_together = ("sample", "bio_feature_reporter")
+    value_type = models.ForeignKey(ValueType, on_delete=models.CASCADE, default=1, null=True, blank=True)
 
     def to_dict(self, reduced=False):
         fields = ['id', 'value']

command/lib/tasks/annotation.py

@@ -10,6 +10,7 @@
 
 from command.lib.anno.annotation_parser import BaseAnnotationParser
 from command.lib.db.admin.compendium_database import CompendiumDatabase
+from command.lib.db.compendium.annotation_value import AnnotationValue
 from command.lib.db.compendium.bio_feature import BioFeature
 from command.lib.db.compendium.bio_feature_annotation import BioFeatureAnnotation
 from command.lib.db.compendium.message_log import MessageLog
@@ -82,11 +83,24 @@ def annotation_task(self, user_id, compendium_id, ontology_id, filename, file_ty
     ann_map = dict(OntologyNode.objects.using(compendium.compendium_nick_name).filter(ontology=ontology).values_list('original_id', 'id'))
     for chunk in parser.parse(filename):
         annotations = []
+        annotation_values = []
         for ann in chunk:
-            bfa = BioFeatureAnnotation()
             if ann[0] in bf_map and ann[1] in ann_map:
+                ann_val = AnnotationValue(
+                    ontology_node_id=ann_map[ann[1]],
+                    value='True',
+                    value_type='boolean'
+                )
+                annotation_values.append(ann_val)
+        AnnotationValue.objects.using(compendium.compendium_nick_name).bulk_create(annotation_values)
+        annotation_values_map = dict(AnnotationValue.objects.using(compendium.compendium_nick_name).filter(ontology_node__ontology=ontology).
+                                     values_list('ontology_node_id', 'id')
+                                     )
+        for ann in chunk:
+            if ann[0] in bf_map and ann[1] in ann_map:
+                bfa = BioFeatureAnnotation()
                 bfa.bio_feature_id = bf_map[ann[0]]
-                bfa.ontology_node_id = ann_map[ann[1]]
+                bfa.annotation_value_id = annotation_values_map[ann_map[ann[1]]]
                 annotations.append(bfa)
         BioFeatureAnnotation.objects.using(compendium.compendium_nick_name).bulk_create(annotations)
 

command/lib/tasks/ontology.py

@@ -98,7 +98,7 @@ def create_ontology_task(self, user_id, compendium_id, ontology_name,
                 node.ontology = ontology
                 node.original_id = n['data']['id']
                 node.json = n['data']
-                if not ontology.json or 'columns' not in ontology.json:
+                if not ontology.json or 'columns' not in ontology.json or len(ontology.json['columns']) == 0:
                     ontology.json = {'columns': [{'text': x.title().replace('_', ' '), 'data_index': x} for x in n['data'].keys() if x != 'id']}
                     ontology.save(using=compendium.compendium_nick_name)
                 nodes.append(node)
@@ -107,12 +107,17 @@ def create_ontology_task(self, user_id, compendium_id, ontology_name,
         for c in chunks(structure['elements']['edges'], 10000):
             edges = []
             for e in c:
+                e_type = None
+                if 'key' in e['data']:
+                    e_type = e['data']['key']
+                elif 'type' in e['data']:
+                    e_type = e['data']['type']
                 edge = OntologyEdge()
                 edge.source_id = node_ids[e['data']['source']]
                 edge.target_id = node_ids[e['data']['target']]
                 edge.is_directed = True
                 edge.ontology = ontology
-                edge.edge_type = e['data']['key']
+                edge.edge_type = e_type
                 edges.append(edge)
             OntologyEdge.objects.using(compendium.compendium_nick_name).bulk_create(edges)
 

command/lib/utils/database.py

@@ -1,10 +1,15 @@
 from django.db import connection,connections
 
 
-def create_db(admin_db_name, admin_db_setting, db_name):
+def create_db(admin_db_name, admin_db_setting, db_name, db_user):
     connections.databases[admin_db_name] = admin_db_setting
     cur = connections[admin_db_name].cursor()
     cur.execute('CREATE DATABASE ' + db_name)
+    cur.execute('REVOKE CONNECT ON DATABASE ' + db_name + ' FROM PUBLIC')
+    cur.execute('GRANT CONNECT ON DATABASE ' + db_name + ' TO ' + db_user)
+    cur.execute('GRANT ALL ON ALL TABLES IN SCHEMA public TO ' + db_user)
+    cur.execute('GRANT ALL ON ALL SEQUENCES IN SCHEMA public TO ' + db_user)
+    cur.execute('GRANT ALL ON ALL FUNCTIONS IN SCHEMA public TO ' + db_user)
 
 
 def get_database_list():

command/lib/utils/init_compendium.py

@@ -7,6 +7,7 @@
 from django.core.management import call_command
 from django.db import connections, transaction
 
+from command.lib.db.compendium.annotation_value import AnnotationValue
 from command.lib.db.compendium.bio_feature_annotation import BioFeatureAnnotation
 from command.lib.db.compendium.normalization import Normalization
 from command.lib.db.compendium.normalization_experiment import NormalizationExperiment
@@ -31,6 +32,7 @@
 from command.lib.db.admin.compendium_database import CompendiumDatabase
 from command.lib.db.compendium.data_source import DataSource
 from command.lib.db.compendium.experiment import Experiment
+from command.lib.db.compendium.sample_annotation import SampleAnnotation
 from command.lib.db.compendium.status import Status
 from command.lib.db.compendium.message_log import MessageLog
 from command.lib.db.compendium.platform import Platform
@@ -140,6 +142,12 @@ def init_compendium(db_id):
                 pass
     call_command('migrate', database=key)
     if compendium.compendium_type.name == 'gene_expression':
+        ValueType(name='I', description='Intensity').save(using=key)
+        ValueType(name='BG', description='BackGround').save(using=key)
+        ValueType(name='IBG', description='Intensity Background corrected').save(using=key)
+        ValueType(name='M', description='M-value, Intensity log-ratio').save(using=key)
+        ValueType(name='A', description='A-value, Intensity average').save(using=key)
+        ValueType(name='C', description='Count').save(using=key)
         geo_db = DataSource(source_name='GEO',
                             python_class='command.lib.coll.public_database.GEOPublicDatabase',
                             is_local=False)
@@ -185,6 +193,12 @@ def init_compendium(db_id):
     status_platform_imported = Status(name='platform_imported', description='Platform is imported')
     status_platform_importing.save(using=key)
     status_platform_imported.save(using=key)
+    status_annotated = Status(name='experiment_annotated', description='Experiment samples have been annotated')
+    status_design_defined = Status(name='experiment_design_defined', description='Experiment design has been defined')
+    status_normalized = Status(name='experiment_normalized', description='Experiment has been normalized')
+    status_annotated.save(using=key)
+    status_design_defined.save(using=key)
+    status_normalized.save(using=key)
     # copy over data from platform type and biological features tables
     for plt_type_admin in PlatformTypeAdmin.objects.all():
         plt_type = PlatformType()

command/lib/views/bio_feature_anno.py

@@ -151,8 +151,8 @@ def read_bio_feature_anno(channel_name, view, request, user):
             b = bf.to_dict()
             b['annotation'] = []
             for bfa in bf.biofeatureannotation_set.all():
-                ontology = bfa.ontology_node.ontology
-                node = bfa.ontology_node
+                ontology = bfa.annotation_value.ontology_node.ontology
+                node = bfa.annotation_value.ontology_node
                 ann = node.to_dict()
                 ann['ontology'] = ontology.to_dict()
                 ann['columns'] = ontology.json['columns']

command/lib/views/compendium_manager.py

@@ -257,7 +257,7 @@ def create_compendium(request, *args, **kwargs):
             admin_db.compendium_nick_name = values['admin']['username']
             admin_db.db_user = values['admin']['username']
             admin_db.db_password = values['admin']['password']
-            create_db(values['admin']['username'], admin_db.get_setting_entry()[1], db.compendium_nick_name)
+            create_db(values['admin']['username'], admin_db.get_setting_entry()[1], db.compendium_nick_name, db.db_user)
         db.save()
         init_database_connections()
         Group('admin').send({