Merge pull request #415 from ImagingDataCommons/idc-prod-sp

Release 46 / v21

Author: s-paquette

accounts/models.py

@@ -24,7 +24,7 @@
 from datetime import datetime, timezone, timedelta
 import pytz
 
-logger = logging.getLogger('main_logger')
+logger = logging.getLogger(__name__)
 
 
 def utc_now_plus_expiry():

accounts/service_obj.py

@@ -23,7 +23,7 @@
 
 from jsonschema import validate as schema_validate, ValidationError
 
-logger = logging.getLogger('main_logger')
+logger = logging.getLogger(__name__)
 
 class ServiceObjectBase(object):
     """

accounts/urls.py

@@ -14,15 +14,15 @@
 # limitations under the License.
 # 
 
-from django.conf.urls import url, include
+from django.urls import include, re_path, path
 from allauth import urls as allauth_urls
 from allauth.socialaccount.providers.google import urls as google_urls, views as google_views
 
 from . import views
 
 
 urlpatterns = [
-    url(r'^', include(google_urls)),
-    url(r'^', include(allauth_urls)),
-    url(r'^logout', views.extended_logout_view, name='account_logout'),
+    # re_path(r'^', include(google_urls)),
+    # re_path(r'^', include(allauth_urls)),
+    re_path(r'^logout', views.extended_logout_view, name='account_logout'),
 ]

accounts/views.py

@@ -26,7 +26,7 @@
 
 from .models import *
 
-logger = logging.getLogger('main_logger')
+logger = logging.getLogger(__name__)
 
 
 @login_required

cohorts/decorators.py

@@ -22,7 +22,7 @@
 from django.http import JsonResponse
 
 import logging
-logger = logging.getLogger('main_logger')
+logger = logging.getLogger(__name__)
 
 
 # Adapted from the Django REST Framework's TokenAuthentization class

cohorts/models.py

@@ -35,7 +35,7 @@
 from functools import reduce
 from google_helpers.bigquery.bq_support import BigQuerySupport
 
-logger = logging.getLogger('main_logger')
+logger = logging.getLogger(__name__)
 
 
 class CohortQuerySet(models.QuerySet):

cohorts/urls.py

@@ -15,55 +15,53 @@
 # 
 from __future__ import absolute_import
 
-from django.conf.urls import url
+from django.urls import include, re_path, path
 from . import views
 
 
 urlpatterns = [
-    url(r'^$', views.cohorts_list, name='cohort_list'),
-    url(r'^manifests/fetch/(?P<file_name>[A-Za-z\-0-9]+\/manifest_[0-9_]+(aws|gcs|gcp)\.s5cmd)', views.fetch_user_manifest, name='fetch_user_manifest'),
-    url(r'^manifests/check/(?P<file_name>[A-Za-z\-0-9]+\/manifest_[0-9_]+(aws|gcs|gcp)\.s5cmd)', views.check_manifest_ready, name='check_user_manifest'),
-    url(r'^manifests/fetch/$', views.fetch_user_manifest, name='fetch_user_manifest_base'),
-    url(r'^manifests/check/$', views.check_manifest_ready, name='check_user_manifest_base'),
-    url(r'^api/$', views.views_api_v1.cohort_list_api, name='cohort_list_api'),
-    url(r'^api/v1/$', views.views_api_v1.cohort_list_api, name='cohort_list_api'),
-    url(r'^api/v2/$', views.views_api_v2.cohort_list_api, name='cohort_list_api'),
-    #    url(r'^api/preview/$', views.cohort_preview_api, name='cohort_preview_api'),
-    url(r'^api/preview/manifest/$', views.views_api_v1.cohort_preview_manifest_api, name='cohort_preview_manifest_api'),
-    url(r'^api/v1/preview/manifest/$', views.views_api_v1.cohort_preview_manifest_api, name='cohort_preview_manifest_api'),
-    # url(r'^api/v2/preview/manifest/$', views.views_api_v2.cohort_preview_manifest_api, name='cohort_preview_manifest_api'),
-    url(r'^api/preview/query/$', views.views_api_v1.cohort_preview_query_api, name='cohort_preview_query_api'),
-    url(r'^api/v1/preview/query/$', views.views_api_v1.cohort_preview_query_api, name='cohort_preview_query_api'),
-    url(r'^api/v2/preview/query/$', views.views_api_v2.cohort_preview_query_api, name='cohort_preview_query_api'),
-    url(r'^(?P<cohort_id>\d+)/$', views.cohort_detail, name='cohort_details'),
-#    url(r'^api/(?P<cohort_id>\d+)/$', views.cohort_detail_api, name='cohort_detail_api'),
-    url(r'^(?P<cohort_id>\d+)/stats/$', views.get_cohort_stats, name='cohort_stats'),
+    # re_path(r'^$', views.cohorts_list, name='cohort_list'),
+    re_path(r'^manifests/fetch/(?P<file_name>[A-Za-z\-0-9]+\/manifest_(cohort_)?[0-9_]+(aws|gcs|gcp)?\.(s5cmd|json|csv|tsv))', views.fetch_user_manifest, name='fetch_user_manifest'),
+    re_path(r'^manifests/check/(?P<file_name>[A-Za-z\-0-9]+\/manifest_(cohort_)?[0-9_]+(aws|gcs|gcp)?\.(s5cmd|json|csv|tsv))', views.check_manifest_ready, name='check_user_manifest'),
+    re_path(r'^manifests/fetch/$', views.fetch_user_manifest, name='fetch_user_manifest_base'),
+    re_path(r'^manifests/check/$', views.check_manifest_ready, name='check_user_manifest_base'),
+    # re_path(r'^api/$', views.views_api_v1.cohort_list_api, name='cohort_list_api'),
+    # re_path(r'^api/v1/$', views.views_api_v1.cohort_list_api, name='cohort_list_api'),
+    # re_path(r'^api/v2/$', views.views_api_v2.cohort_list_api, name='cohort_list_api'),
+    # re_path(r'^api/preview/$', views.cohort_preview_api, name='cohort_preview_api'),
+    re_path(r'^api/preview/manifest/$', views.views_api_v1.cohort_preview_manifest_api, name='cohort_preview_manifest_api'),
+    re_path(r'^api/v1/preview/manifest/$', views.views_api_v1.cohort_preview_manifest_api, name='cohort_preview_manifest_api'),
+    # re_path(r'^api/v2/preview/manifest/$', views.views_api_v2.cohort_preview_manifest_api, name='cohort_preview_manifest_api'),
+    re_path(r'^api/preview/query/$', views.views_api_v1.cohort_preview_query_api, name='cohort_preview_query_api'),
+    re_path(r'^api/v1/preview/query/$', views.views_api_v1.cohort_preview_query_api, name='cohort_preview_query_api'),
+    re_path(r'^api/v2/preview/query/$', views.views_api_v2.cohort_preview_query_api, name='cohort_preview_query_api'),
+    # re_path(r'^(?P<cohort_id>\d+)/$', views.cohort_detail, name='cohort_details'),
+    # re_path(r'^api/(?P<cohort_id>\d+)/$', views.cohort_detail_api, name='cohort_detail_api'),
+    # re_path(r'^(?P<cohort_id>\d+)/stats/$', views.get_cohort_stats, name='cohort_stats'),
 
-#    url(r'^api/(?P<cohort_id>\d+)/$', views.cohort_detail_api, name='cohort_detail_api'),
-    url(r'^api/(?P<cohort_id>\d+)/manifest/$', views.views_api_v1.cohort_manifest_api, name='cohort_manifest_api'),
-    url(r'^api/v1/(?P<cohort_id>\d+)/manifest/$', views.views_api_v1.cohort_manifest_api, name='cohort_manifest_api'),
-    # url(r'^api/v2/(?P<cohort_id>\d+)/manifest/$', views.views_api_v2.cohort_manifest_api, name='cohort_manifest_api'),
-    url(r'^api/(?P<cohort_id>\d+)/query/$', views.views_api_v1.cohort_query_api, name='cohort_query_api'),
-    url(r'^api/v1/(?P<cohort_id>\d+)/query/$', views.views_api_v1.cohort_query_api, name='cohort_query_api'),
-    url(r'^api/v2/(?P<cohort_id>\d+)/query/$', views.views_api_v2.cohort_query_api, name='cohort_query_api'),
-    url(r'^save_cohort/', views.save_cohort, name='save_cohort'),
-    url(r'^api/save_cohort/', views.views_api_v1.save_cohort_api, name='save_cohort_api'),
-    url(r'^api/v1/save_cohort/', views.views_api_v1.save_cohort_api, name='save_cohort_api'),
-    url(r'^api/v2/save_cohort/', views.views_api_v2.save_cohort_api, name='save_cohort_api'),
-    url(r'^delete_cohort/', views.delete_cohort, name='delete_cohort'),
-    url(r'^api/delete_cohort/', views.views_api_v1.delete_cohort_api, name='delete_cohort_api'),
-    url(r'^api/v1/delete_cohort/', views.views_api_v1.delete_cohort_api, name='delete_cohort_api'),
-    url(r'^api/v2/delete_cohort/', views.views_api_v2.delete_cohort_api, name='delete_cohort_api'),
-    #url(r'^clone_cohort/(?P<cohort_id>\d+)/', views.clone_cohort, name='clone_cohort'),
-    #url(r'^share_cohort/$', views.share_cohort, name='share_cohorts'),
-    #url(r'^share_cohort/(?P<cohort_id>\d+)/', views.share_cohort, name='share_cohort'),
-    #url(r'^unshare_cohort/$', views.unshare_cohort, name='unshare_cohorts'),
-    #url(r'^unshare_cohort/(?P<cohort_id>\d+)/', views.unshare_cohort, name='unshare_cohort'),
-    #url(r'^set_operation/', views.set_operation, name='set_operation'),
-    #url(r'^save_cohort_comment/', views.save_comment, name='save_cohort_comment'),
-    url(r'^download_manifest/(?P<cohort_id>\d+)/', views.download_cohort_manifest, name='cohort_manifest'),
-    url(r'bq_string/(?P<cohort_id>\d+)/', views.get_query_str_response, name='bq_string'),
-    url(r'^download_manifest/', views.download_cohort_manifest, name='cohort_manifest_base'),
-    url(r'^download_ids/(?P<cohort_id>\d+)/', views.cohort_uuids, name='download_ids'),
-    url(r'^get_metadata_ajax/$', views.get_metadata, name='metadata_count_ajax')
+    # re_path(r'^api/(?P<cohort_id>\d+)/$', views.cohort_detail_api, name='cohort_detail_api'),
+    # re_path(r'^api/(?P<cohort_id>\d+)/manifest/$', views.views_api_v1.cohort_manifest_api, name='cohort_manifest_api'),
+    # re_path(r'^api/v1/(?P<cohort_id>\d+)/manifest/$', views.views_api_v1.cohort_manifest_api, name='cohort_manifest_api'),
+    # re_path(r'^api/v2/(?P<cohort_id>\d+)/manifest/$', views.views_api_v2.cohort_manifest_api, name='cohort_manifest_api'),
+    # re_path(r'^api/(?P<cohort_id>\d+)/query/$', views.views_api_v1.cohort_query_api, name='cohort_query_api'),
+    # re_path(r'^api/v1/(?P<cohort_id>\d+)/query/$', views.views_api_v1.cohort_query_api, name='cohort_query_api'),
+    # re_path(r'^api/v2/(?P<cohort_id>\d+)/query/$', views.views_api_v2.cohort_query_api, name='cohort_query_api'),
+    # re_path(r'^save_cohort/', views.save_cohort, name='save_cohort'),
+    # re_path(r'^api/save_cohort/', views.views_api_v1.save_cohort_api, name='save_cohort_api'),
+    # re_path(r'^api/v1/save_cohort/', views.views_api_v1.save_cohort_api, name='save_cohort_api'),
+    # re_path(r'^api/v2/save_cohort/', views.views_api_v2.save_cohort_api, name='save_cohort_api'),
+    # re_path(r'^delete_cohort/', views.delete_cohort, name='delete_cohort'),
+    # re_path(r'^api/delete_cohort/', views.views_api_v1.delete_cohort_api, name='delete_cohort_api'),
+    # re_path(r'^api/v1/delete_cohort/', views.views_api_v1.delete_cohort_api, name='delete_cohort_api'),
+    # re_path(r'^api/v2/delete_cohort/', views.views_api_v2.delete_cohort_api, name='delete_cohort_api'),
+    # re_path(r'^clone_cohort/(?P<cohort_id>\d+)/', views.clone_cohort, name='clone_cohort'),
+    # re_path(r'^share_cohort/$', views.share_cohort, name='share_cohorts'),
+    # re_path(r'^share_cohort/(?P<cohort_id>\d+)/', views.share_cohort, name='share_cohort'),
+    # re_path(r'^unshare_cohort/$', views.unshare_cohort, name='unshare_cohorts'),
+    # re_path(r'^unshare_cohort/(?P<cohort_id>\d+)/', views.unshare_cohort, name='unshare_cohort'),
+    # re_path(r'^set_operation/', views.set_operation, name='set_operation'),
+    # re_path(r'^save_cohort_comment/', views.save_comment, name='save_cohort_comment'),
+    # re_path(r'^download_manifest/(?P<cohort_id>\d+)/', views.download_cohort_manifest, name='cohort_manifest'),
+    # re_path(r'bq_string/(?P<cohort_id>\d+)/', views.get_query_str_response, name='bq_string'),
+    # re_path(r'^download_manifest/', views.download_cohort_manifest, name='cohort_manifest_base'),
 ]

cohorts/utils.py

@@ -36,7 +36,7 @@
 from idc_collections.collex_metadata_utils import get_collex_metadata, filter_manifest
 from idc_collections.models import DataSetType,DataSource
 
-logger = logging.getLogger('main_logger')
+logger = logging.getLogger(__name__)
 DENYLIST_RE = settings.DENYLIST_RE
 
 
@@ -142,7 +142,7 @@ def _save_cohort(user, filters=None, name=None, cohort_id=None, version=None, de
 
         cohort_details = {}
         if name or desc:
-            denylist = re.compile(DENYLIST_RE, re.UNICODE)
+            denylist = re.compile(DENYLIST_RE, re.UNICODE|re.IGNORECASE)
             check = {'name': {'val': name, 'match': denylist.search(str(name))},
                      'description': {'val': desc, 'match': denylist.search(str(desc))}}
             if len([check[x]['match'] for x in check if check[x]['match'] is not None]):

cohorts/utils_api_v1.py

@@ -25,7 +25,7 @@
 from google_helpers.bigquery.bq_support import BigQuerySupport
 
 
-logger = logging.getLogger('main_logger')
+logger = logging.getLogger(__name__)
 DENYLIST_RE = settings.DENYLIST_RE
 
 # Get the current if none specified

cohorts/utils_api_v2.py

@@ -22,7 +22,7 @@
 from idc_collections.models import ImagingDataCommonsVersion
 from idc_collections.collex_metadata_utils import get_bq_metadata, get_bq_string
 
-logger = logging.getLogger('main_logger')
+logger = logging.getLogger(__name__)
 DENYLIST_RE = settings.DENYLIST_RE
 
 NUMERIC_OPS = ('_btw', '_ebtw', '_btwe', '_ebtwe', '_gte', '_lte', '_gt', '_lt', '_eq')