Merge pull request #172 from isb-cgc/prod-sp

Sprint 18

Author: s-paquette

api_3/isb_cgc_api_CCLE/users_get.py

@@ -39,21 +39,23 @@ def build_queries(self, program, genomic_builds):
 
         sample_query_str = 'select sample_barcode ' \
                            'from {}_metadata_biospecimen ' \
-                           'where case_barcode=%s'.format(program)
+                           'where case_barcode=%s ' \
+                           'group by sample_barcode ' \
+                           'order by sample_barcode'.format(program)
 
         aliquot_query_str = ''
         for genomic_build in genomic_builds:
             part_aliquot_query_str = 'select aliquot_barcode ' \
                                 'from {}_metadata_data_{} ' \
                                 'where case_barcode=%s and aliquot_barcode is not null ' \
-                                'group by aliquot_barcode'.format(program, genomic_build)
+                                'group by aliquot_barcode ' \
+                                'order by aliquot_barcode'.format(program, genomic_build)
             if 0 < len(aliquot_query_str):
                 aliquot_query_str += ' union '
             aliquot_query_str += part_aliquot_query_str
 
         return clinical_query_str, sample_query_str, aliquot_query_str
 
-
 class CasesGetHelper(remote.Service):
 
     GET_RESOURCE = endpoints.ResourceContainer(case_barcode=messages.StringField(1, required=True))

api_3/patients_get_helper.py

@@ -70,7 +70,7 @@ def get(self, program):
                         allowed = True
                 if not allowed:
                     das = DatasetAccessSupportFactory.from_webapp_django_settings()
-                    authorized_datasets = das.get_datasets_for_era_login(user_email)
+                    authorized_datasets = das.get_datasets_for_era_login(nih_user.NIH_username)
                     for dataset in authorized_datasets:
                         try:
                             ad = AuthorizedDataset.objects.get(whitelist_id=dataset.dataset_id)

api_3/users_get_common.py

@@ -44,7 +44,6 @@
 from api_3.isb_cgc_api_CCLE.patients_get import CCLE_CasesGetAPI
 from api_3.isb_cgc_api_CCLE.samples_get import CCLE_SamplesGetAPI
 from api_3.isb_cgc_api_CCLE.samples_cloudstoragefilepaths import CCLE_SamplesCloudStorageFilePathsAPI
-from api_3.isb_cgc_api_CCLE.users_get import CCLE_UserGetAPI
 
 package = 'isb-cgc-api'
 
@@ -75,7 +74,6 @@
     CCLE_CohortsCreateAPI,
     CCLE_CasesGetAPI,
     CCLE_SamplesGetAPI,
-    CCLE_SamplesCloudStorageFilePathsAPI,
-    CCLE_UserGetAPI
+    CCLE_SamplesCloudStorageFilePathsAPI
 ])
 

cgc_api.py

@@ -23,15 +23,16 @@
     os.environ.get('ALLOWED_HOST')
 ]
 
-### check if we are running in app engine
+### Check what we're running in
+APP_ENGINE_FLEX = 'aef-'
 APP_ENGINE = 'Google App Engine/'
+IS_APP_ENGINE_FLEX = os.getenv('GAE_INSTANCE', '').startswith(APP_ENGINE_FLEX)
 IS_APP_ENGINE = os.getenv('SERVER_SOFTWARE', '').startswith(APP_ENGINE)
+IS_DEV = bool(os.environ.get('IS_DEV', False))
 
 ### added for connecting to CloudSQL with SSL certs on MVM platform
 SSL_DIR = os.path.abspath(os.path.dirname(__file__))+os.sep
 
-APP_ENGINE = 'ae-'
-IS_APP_ENGINE = os.getenv('GAE_INSTANCE', '').startswith(APP_ENGINE)
 
 #ADMINS = (
     # ('Your Name', 'your_email@example.com'),
@@ -45,7 +46,6 @@
 
 BASE_URL = os.environ.get('CLOUD_BASE_URL')
 BASE_API_URL = os.environ.get('CLOUD_API_URL')
-SITE_ID = 4
 
 # Compute services
 PAIRWISE_SERVICE_URL = os.environ.get('PAIRWISE_SERVICE_URL')
@@ -63,8 +63,6 @@
 
 NIH_AUTH_ON = os.environ.get('NIH_AUTH_ON', False)
 
-IS_DEV = os.environ.get('IS_DEV', False)
-
 DATABASES = {
     'default': {
         'ENGINE': os.environ.get('DATABASE_ENGINE', 'django.db.backends.mysql'),
@@ -86,17 +84,14 @@
 
 DB_SOCKET = DATABASES['default']['HOST'] if 'cloudsql' in DATABASES['default']['HOST'] else None
 
-IS_DEV = bool(os.environ.get('IS_DEV', False))
-
 # Default to localhost for the site ID
 SITE_ID = 3
 
-if IS_APP_ENGINE:
+if IS_APP_ENGINE_FLEX or IS_APP_ENGINE:
     print >> sys.stdout, "[STATUS] AppEngine detected."
     SITE_ID = 4
 
 # For running local unit tests for models
-import sys
 if 'test' in sys.argv:
     DATABASES = os.environ.get('TEST_DATABASE')