Merge branch 'master' into dev

Conflicts:
	project/epi2/models.py

project/animal/exports.py

@@ -89,19 +89,16 @@ class EndpointFlatDataPivot(FlatFileExporter):
 
     def _get_header_row(self):
         return [
-            'study',
-            'study_url',
-            'Study HAWC ID',
-            'Study Published',
-
-            'Experiment ID',
-            'experiment',
-            'experiment_url',
+            'study id',
+            'study name',
+            'study published',
+
+            'experiment id',
+            'experiment name',
             'chemical',
 
-            'Animal Group ID',
-            'animal_group',
-            'animal_group_url',
+            'animal group id',
+            'animal group name',
             'lifestage exposed',
             'lifestage assessed',
             'species',
@@ -114,20 +111,19 @@ def _get_header_row(self):
             'treatment period',
             'duration exposure',
 
-            'endpoint_name',
-            'endpoint_url',
+            'endpoint id',
+            'endpoint name',
             'system',
             'organ',
             'effect',
             'effect subtype',
             'diagnostic',
             'tags',
-            'observation_time',
-            'data_type',
+            'observation time',
+            'data type',
             'doses',
-            'dose_units',
-            'response_units',
-            'Endpoint Key',
+            'dose units',
+            'response units',
 
             'low_dose',
             'NOEL',
@@ -141,16 +137,16 @@ def _get_header_row(self):
             'BMDU',
             'CSF',
 
-            'Row Key',
-            'dose_index',
+            'key',
+            'dose index',
             'dose',
-            'n',
+            'N',
             'incidence',
             'response',
-            'stdev',
-            'percentControlMean',
-            'percentControlLow',
-            'percentControlHigh'
+            'variance',
+            'percent control mean',
+            'percent control low',
+            'percent control high'
         ]
 
     def _get_data_rows(self):
@@ -201,19 +197,16 @@ def get_tags(e):
 
             # build endpoint-group independent data
             row = [
-                ser['animal_group']['experiment']['study']['short_citation'],
-                ser['animal_group']['experiment']['study']['url'],
                 ser['animal_group']['experiment']['study']['id'],
+                ser['animal_group']['experiment']['study']['short_citation'],
                 ser['animal_group']['experiment']['study']['published'],
 
                 ser['animal_group']['experiment']['id'],
                 ser['animal_group']['experiment']['name'],
-                ser['animal_group']['experiment']['url'],
                 ser['animal_group']['experiment']['chemical'],
 
                 ser['animal_group']['id'],
                 ser['animal_group']['name'],
-                ser['animal_group']['url'],
                 ser['animal_group']['lifestage_exposed'],
                 ser['animal_group']['lifestage_assessed'],
                 ser['animal_group']['species'],
@@ -227,8 +220,8 @@ def get_tags(e):
                                      ser['animal_group']['dosing_regime']),
                 ser['animal_group']['dosing_regime']['duration_exposure_text'],
 
+                ser['id'],
                 ser['name'],
-                ser['url'],
                 ser['system'],
                 ser['organ'],
                 ser['effect'],
@@ -240,7 +233,6 @@ def get_tags(e):
                 get_doses_str(doses),
                 get_dose_units(doses),
                 ser['response_units'],
-                ser['id']
             ]
 
             # dose-group specific information

project/animal/migrations/0011_auto_20150723_1600.py

@@ -9,7 +9,7 @@ class Migration(migrations.Migration):
     dependencies = [
         ('animal', '0010_auto_20150723_1536'),
         ('bmd', '0002_auto_20150723_1557'),
-        ('epi', '0003_auto_20150723_1544'),
+        ('epi', '0001_initial'),
         ('invitro', '0002_auto_20150723_1542'),
         ('summary', '0003_auto_20150723_1557'),
     ]

project/assessment/models.py

@@ -473,8 +473,8 @@ def get_json(self, *args, **kwargs):
         return an empty object.
         """
         d = {}
-        if hasattr(self, 'assessedoutcome'):
-            d = self.assessedoutcome.get_json(*args, **kwargs)
+        if hasattr(self, 'outcome'):
+            d = self.outcome.get_json(*args, **kwargs)
         elif hasattr(self, 'endpoint'):
             d = self.endpoint.d_response(*args, **kwargs)
         elif hasattr(self, 'ivendpoint'):

project/assessment/views.py

@@ -325,17 +325,12 @@ def get_context_data(self, **kwargs):
             .filter(assessment_id=self.assessment.id)\
             .count()
 
-        aos = self.model.assessedoutcome\
+        os = self.model.outcome\
             .related.related_model.objects\
             .filter(assessment_id=self.assessment.id)\
             .count()
 
-        aos2 = self.model.outcome\
-            .related.related_model.objects\
-            .filter(assessment_id=self.assessment.id)\
-            .count()
-
-        mrs = get_model('epi', 'metaresult')\
+        mrs = get_model('epimeta', 'metaresult')\
             .objects\
             .filter(protocol__study__assessment_id=self.assessment.id)\
             .count()
@@ -345,13 +340,12 @@ def get_context_data(self, **kwargs):
             .filter(assessment_id=self.assessment.id)\
             .count()
 
-        alleps = eps + aos + aos2 + mrs + iveps
+        alleps = eps + os + mrs + iveps
 
         context.update({
             "ivendpoints": iveps,
             "endpoints": eps,
-            "assessed_outcomes": aos,
-            "outcomes": aos2,
+            "outcomes": os,
             "meta_results": mrs,
             "total_endpoints": alleps
         })

project/epi/admin.py

@@ -3,11 +3,34 @@
 from . import models
 
 
-class StatisticalMetricAdmin(admin.ModelAdmin):
-    list_display = ('metric', 'abbreviation', 'isLog', 'order', )
+class CriteriaAdmin(admin.ModelAdmin):
+    pass
 
-    def has_delete_permission(self, request, obj=None):
-        return False
 
+class CountryAdmin(admin.ModelAdmin):
 
-admin.site.register(models.StatisticalMetric, StatisticalMetricAdmin)
+    search_fields = (
+        'name',
+    )
+
+
+class AdjustmentFactorAdmin(admin.ModelAdmin):
+    pass
+
+
+class EthnicityAdmin(admin.ModelAdmin):
+    pass
+
+
+class ResultMetricAdmin(admin.ModelAdmin):
+    list_display = (
+        "metric", "abbreviation", "showForestPlot",
+        "isLog", "reference_value", "order",
+    )
+
+
+admin.site.register(models.Criteria, CriteriaAdmin)
+admin.site.register(models.Country, CountryAdmin)
+admin.site.register(models.AdjustmentFactor, AdjustmentFactorAdmin)
+admin.site.register(models.Ethnicity, EthnicityAdmin)
+admin.site.register(models.ResultMetric, ResultMetricAdmin)

project/epi/api.py

@@ -5,12 +5,6 @@
 from . import models, serializers
 
 
-class MetaResult(AssessmentViewset):
-    assessment_filter_args = "protocol__study__assessment"
-    model = models.MetaResult
-    serializer_class = serializers.MetaResultSerializer
-
-
 class StudyPopulation(AssessmentViewset):
     assessment_filter_args = "study__assessment"
     model = models.StudyPopulation
@@ -20,10 +14,28 @@ class StudyPopulation(AssessmentViewset):
 class Exposure(AssessmentViewset):
     assessment_filter_args = "study_population__study__assessment"
     model = models.Exposure
-    serializer_class = serializers.ExposureVerboseSerializer
+    serializer_class = serializers.ExposureSerializer
 
 
-class AssessedOutcome(AssessmentViewset):
+class Outcome(AssessmentViewset):
     assessment_filter_args = "assessment"
-    model = models.AssessedOutcome
-    serializer_class = serializers.AssessedOutcomeSerializer
+    model = models.Outcome
+    serializer_class = serializers.OutcomeSerializer
+
+
+class Result(AssessmentViewset):
+    assessment_filter_args = "outcome__assessment"
+    model = models.Result
+    serializer_class = serializers.ResultSerializer
+
+
+class ComparisonSet(AssessmentViewset):
+    assessment_filter_args = "assessment"  # todo: fix
+    model = models.ComparisonSet
+    serializer_class = serializers.ComparisonSetSerializer
+
+
+class Group(AssessmentViewset):
+    assessment_filter_args = "assessment"  # todo: fix
+    model = models.Group
+    serializer_class = serializers.GroupSerializer