Release 1.5.0

applications/accounts-api/backend/accounts_api/__main__.py

@@ -9,4 +9,4 @@
 
 
 if __name__ == '__main__':
-    main()
+    main()

applications/accounts-api/backend/accounts_api/controllers/security_controller_.py

@@ -13,4 +13,3 @@ def info_from_bearerAuth(token):
     :rtype: dict | None
     """
     return {'uid': 'user_id'}
-

applications/accounts-api/backend/accounts_api/controllers/users_controller.py

@@ -93,6 +93,7 @@ def users_username_password_put(username, update_password: UpdatePassword = None
     user_service.update_password(username, update_password.new_password)
     return "OK", 204
 
+
 def users_username_orcid_put(username, body):  # noqa: E501
     """users_username_orcid_put
 
@@ -108,5 +109,5 @@ def users_username_orcid_put(username, body):  # noqa: E501
     if not user_service.validate_orcid_id(body):
         return "Invalid ORCID ID", 400
     user_service.associate_orcid_id(username, body)
-    
+
     return "OK", 204

applications/accounts-api/backend/accounts_api/services/user_service.py

@@ -20,9 +20,11 @@ class UserNotFound(Exception):
 class UserNotAuthorized(Exception):
     pass
 
+
 class ValidationError(Exception):
     pass
 
+
 def get_user(userid: str) -> User:
     try:
         client = AuthClient()
@@ -112,7 +114,7 @@ def update_user(userid, user: User):
             }
         }
 
-        admin_client.update_user(userid,  updated_user)
+        admin_client.update_user(userid, updated_user)
         return get_user(userid)
     except KeycloakError as e:
         if e.response_code == 404:
@@ -145,13 +147,14 @@ def update_password(username: str, new_password: str):
         raise Exception(
             "Unhandled Keycloak exception while updating user") from e
 
+
 def associate_orcid_id(userid: str, orcid: str):
     client = AuthClient()
     admin_client = client.get_admin_client()
     try:
         orcid_no_prefix = orcid.replace("https://orcid.org/", "")
 
-        admin_client.update_user(userid,  {"attributes": {"orcid": orcid}})
+        admin_client.update_user(userid, {"attributes": {"orcid": orcid}})
         admin_client.add_user_social_login(userid, "orcid", orcid_no_prefix, orcid_no_prefix)
     except KeycloakError as e:
         try:
@@ -161,5 +164,6 @@ def associate_orcid_id(userid: str, orcid: str):
             raise Exception(
                 "Unhandled Keycloak exception while updating user") from e
 
-def validate_orcid_id( orcid: str) -> bool:
+
+def validate_orcid_id(orcid: str) -> bool:
     return re.match(r'^https://orcid.org/\d{4}-\d{4}-\d{4}-\d{3}[0-9X]$', orcid)

applications/accounts-api/backend/accounts_api/util.py

@@ -68,8 +68,8 @@ def deserialize_date(string):
     :rtype: date
     """
     if string is None:
-      return None
-    
+        return None
+
     try:
         from dateutil.parser import parse
         return parse(string).date()
@@ -88,8 +88,8 @@ def deserialize_datetime(string):
     :rtype: datetime
     """
     if string is None:
-      return None
-    
+        return None
+
     try:
         from dateutil.parser import parse
         return parse(string)

applications/accounts-api/backend/setup.py

@@ -37,4 +37,3 @@
     accounts_api
     """
 )
-

applications/portal/api/templates/main.jinja2

@@ -51,7 +51,7 @@ app.add_middleware(
     allow_headers=["*"],
 )
 
-from cloudharness.middleware import set_authentication_token, get_authentication_token
+from cloudharness.middleware import set_authentication_token, get_authentication_token # noqa E402
 
 @app.middleware("http")
 async def add_process_time_header(request: Request, call_next):
@@ -67,8 +67,8 @@ async def add_process_time_header(request: Request, call_next):
 if os.environ.get('KUBERNETES_SERVICE_HOST', None):
     # init the auth service when running in/for k8s
     import threading 
-    from cloudharness_django.services import get_auth_service, init_services
-    from cloudharness import log
+    from cloudharness_django.services import get_auth_service, init_services # noqa E402
+    from cloudharness import log # noqa E402
     import time
     def start_auth_service():
         try:
@@ -146,6 +146,6 @@ app.mount("/", get_asgi_application())
 #    import uvicorn
 #    uvicorn.run(app, host="0.0.0.0", port=8000)
 
-from api.helpers import init_sentry
+from api.helpers import init_sentry # noqa E402
 
 init_sentry()

applications/portal/backend/api/admin.py

@@ -13,6 +13,7 @@
 from django.utils.html import escape, format_html, format_html_join, mark_safe
 from django.utils.text import format_lazy
 from import_export.admin import ImportExportModelAdmin
+from simple_history.admin import SimpleHistoryAdmin
 from keycloak.exceptions import KeycloakGetError
 from cloudharness_django.models import Member
 
@@ -36,13 +37,14 @@
 def id_with_ab(obj: Antibody):
     return f"AB_{obj.ab_id}"
 
+
 @cache
 def get_user_by_kc_id(kc_id) -> User:
     try:
         return Member.objects.get(kc_id=kc_id).user
     except Member.DoesNotExist:
         return None
-    
+
 
 class VerboseManyToManyRawIdWidget(ManyToManyRawIdWidget):
     """
@@ -100,20 +102,21 @@ class AntibodyFilesAdmin(admin.TabularInline):
     extra = 1
 
 
-# not in fields - catalog_num_search 
+# not in fields - catalog_num_search
 antibody_fields_shown = (
-    "ab_name", "ab_id", "accession", "commercial_type", "catalog_num", "cat_alt", "citation", "vendor", 
-    "url","ab_target", "entrez_id", "uniprot_id", "target_species_raw", "subregion", 
+    "ab_name", "ab_id", "accession", "commercial_type", "catalog_num", "cat_alt", "citation", "vendor",
+    "url", "ab_target", "entrez_id", "uniprot_id", "target_species_raw", "subregion",
     "modifications", "epitope", "source_organism", "clonality", "clone_id", "product_isotype",
     "product_conjugate", "defining_citation", "product_form", "comments",
     "kit_contents", "feedback", "curator_comment", "disc_date", "status", "show_link",
     # also in the read-only fields
     "uid", "uid_legacy", "insert_time", "lastedit_time", "curate_time",
 )
 
+
 @admin.register(Antibody)
-class AntibodyAdmin(ImportExportModelAdmin):
-    
+class AntibodyAdmin(ImportExportModelAdmin, SimpleHistoryAdmin):
+
     change_form_template = "admin/antibody_change_form.html"
 
     # Import/Export module settings
@@ -130,7 +133,7 @@ class AntibodyAdmin(ImportExportModelAdmin):
     fields = antibody_fields_shown
 
     inlines = [TargetSpeciesInlineAdmin, AntibodyFilesAdmin, ApplicationsInlineAdmin]
-    
+
     readonly_fields = (
         "submitter_name",
         "submitter_email",
@@ -143,11 +146,11 @@ class AntibodyAdmin(ImportExportModelAdmin):
     )
     autocomplete_fields = ("vendor", "source_organism")
     save_on_top = True
-    show_save=False
+    show_save = False
 
     formfield_overrides = {
-        models.CharField: {'widget': TextInput(attrs={'size':'120'})},
-        models.TextField: {'widget': Textarea(attrs={'rows':2, 'cols':120})}
+        models.CharField: {'widget': TextInput(attrs={'size': '120'})},
+        models.TextField: {'widget': Textarea(attrs={'rows': 2, 'cols': 120})}
     }
 
     @property
@@ -163,7 +166,7 @@ def get_user(self, user_id):
     def submitter_name(self, obj: Antibody):
         if not obj.uid:
             return "Unknown"
-        
+
         dj_user: User = get_user_by_kc_id(obj.uid)
         if dj_user:
             return f"{dj_user.get_full_name()} ({dj_user.username})"
@@ -185,7 +188,7 @@ def submitter_email(self, obj: Antibody):
         dj_user: User = get_user_by_kc_id(obj.uid)
         if dj_user:
             return dj_user.email
-            
+
         try:
             submitter = self.get_user(user_id=obj.uid)
             return f"{submitter['email']}"
@@ -337,10 +340,10 @@ def queryset(self, request, queryset):
         if self.value():
             return queryset.filter(vendor__commercial_type=self.value())
         return queryset
-        
+
 
 @admin.register(VendorDomain)
-class VendorDomainAdmin(admin.ModelAdmin):
+class VendorDomainAdmin(SimpleHistoryAdmin):
     list_display = (
         "base_url",
         "vendor",
@@ -350,8 +353,9 @@ class VendorDomainAdmin(admin.ModelAdmin):
     list_editable = ("is_domain_visible",)
     list_filter = [CommercialTypeFilter]
 
+
 @admin.register(Vendor)
-class VendorAdmin(admin.ModelAdmin):
+class VendorAdmin(SimpleHistoryAdmin):
     delete_confirmation_template = "admin/vendor/delete_confirmation.html"
     search_fields = ("name",)
     list_display = ("id", "name", "commercial_type", "nif_id", "eu_id")

applications/portal/backend/api/controllers/antibody_controller.py

@@ -17,6 +17,7 @@
 from openapi.models import UpdateAntibody as UpdateAntibodyDTO
 from openapi.models import Antibody as AntibodyDTO
 
+
 def get_antibodies(page: int, size: int, updated_from: datetime, updated_to: datetime, status=str) -> PaginatedAntibodies:
     if page is None:
         page = 1
@@ -82,9 +83,10 @@ def update_user_antibody(accession_number: str, body: UpdateAntibodyDTO) -> Anti
 
 
 def delete_antibody(antibody_id: str) -> None:
-    #FIXME this must be protected
+    # FIXME this must be protected
     return antibody_service.delete_antibody(antibody_id)
 
+
 def get_by_accession(accession_number: int) -> AntibodyDTO:
     try:
         return antibody_service.get_antibody_by_accession(accession_number)
@@ -104,7 +106,6 @@ def get_antibodies_export():
     # return FileResponse(fname, filename="antibodies_export.csv")
 
 
-
 def get_antibodies_export_admin():
     """
     Export all fields of all antibodies to a CSV file - Only for admin users
@@ -119,6 +120,3 @@ def get_antibodies_export_admin():
     if filesystem_service.check_if_file_exists_and_recent(fname) and is_admin:
         generate_all_antibodies_fields_to_csv(fname)
     return RedirectResponse("/" + fname)
-
-
-

applications/portal/backend/api/controllers/api_controller.py

@@ -1,5 +1,6 @@
 from openapi.models import DataInfo
 from api.services import antibody_service
 
+
 def get_datainfo():
-    return DataInfo(total=antibody_service.count(), lastupdate=antibody_service.last_update())
+    return DataInfo(total=antibody_service.count(), lastupdate=antibody_service.last_update())

applications/portal/backend/api/controllers/ingest_controller.py

@@ -15,9 +15,6 @@ def ingest(body: IngestRequest):
                                 detail="You are not authorized to ingest data.")
     except:
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED,
-                                detail="You are not authorized to ingest data.")
+                            detail="You are not authorized to ingest data.")
     execute_ingestion_workflow(body.driveLinkOrId, body.hot)
     return status.HTTP_200_OK
-
-
-

applications/portal/backend/api/helpers/__init__.py

@@ -1 +1 @@
-from .sentry import init_sentry
+from .sentry import init_sentry

applications/portal/backend/api/helpers/sentry.py

@@ -4,9 +4,10 @@
 import re
 from cloudharness import log
 
+
 def init_sentry():
     try:
-        
+
         app_cfg = get_current_configuration()
         sentry_cfg = app_cfg.get("sentry", {})
         resources_extensions = set(["css", "js", "png", "jpg", "jpeg", "gif", "svg", "ico", "xml"])
@@ -24,7 +25,7 @@ def traces_sampler(sampling_context):
             extension = "." in url and url.split(".")[-1]
             if extension in resources_extensions:
                 return sentry_cfg.get("traces_sample_rate_resources", 0.0)
-            
+
             return sentry_cfg.get("traces_sample_rate", 1.0)
 
         sentry.init(

applications/portal/backend/api/import_export/AntibodyResource.py

@@ -21,6 +21,7 @@
 CLONALITIES = {c[0] for c in AntibodyClonality.choices}
 COMMERCIAL_TYPES = {c[0] for c in CommercialType.choices}
 
+
 class AntibodyIdentifier:
     def __init__(self, fields, condition: Callable, q: Callable, filter_dataset: Callable):
         """

applications/portal/backend/api/import_export/__init__.py

@@ -1 +1 @@
-from .AntibodyResource import AntibodyResource # noqa: F401
+from .AntibodyResource import AntibodyResource  # noqa: F401

applications/portal/backend/api/import_export/import_antibody_helpers.py

@@ -30,11 +30,13 @@ def get_antibody_q2(dataset, catalog_number_field, vendor_field) -> Q:
         **{"%s__%s__in" % (vendor_field.attribute, vendor_field.widget.field): remove_empty_string(
             dataset[vendor_field.column_name])})
 
+
 def filter_dataset_by_ix(dataset, negate, antibodies):
     values = (str(antibody.ix) for antibody in antibodies)
     condition = dataset.df['ix'].isin(values)
     return ~condition if negate else condition
 
+
 def filter_dataset_by_accession(dataset, negate, antibodies):
     values = (str(antibody.accession) for antibody in antibodies)
     condition = dataset.df['accession'].isin(values)
@@ -64,5 +66,5 @@ def filter_dataset_by_catnum_vendor(dataset, negate, antibodies, catalog_number_
         antibody_catalog_numbers.append(antibody.catalog_num)
         antibody_vendor_names.append(antibody.vendor.name)
     condition = dataset.df[catalog_number_field.column_name].isin(antibody_catalog_numbers) & \
-                dataset.df[vendor_field.column_name].isin(antibody_vendor_names)
+        dataset.df[vendor_field.column_name].isin(antibody_vendor_names)
     return ~condition if negate else condition

applications/portal/backend/api/import_export/widgets/many_to_many_widget.py

@@ -13,4 +13,4 @@ def clean(self, value, row=None, **kwargs):
             return self.model.objects.none()
         else:
             ids = value.split(self.separator)
-            return [self.get_or_create(**{self.field: i.strip()}) for i in ids]
+            return [self.get_or_create(**{self.field: i.strip()}) for i in ids]

applications/portal/backend/api/management/commands/ingest.py

@@ -20,14 +20,15 @@ def parse_drive_link(drive_link_or_id: str):
         except:
             # https://drive.google.com/file/d/FILE_ID/view?usp=drive_link
             return drive_link_or_id.split("/")[-2]
-
+
+
 class Command(BaseCommand):
     help = "Ingests antibody data into the database"
 
     def add_arguments(self, parser):
         parser.add_argument("file_id", type=str)
         parser.add_argument("--hot", action="store_true",
-            help="execute a hot load (no replacements)",)
+                            help="execute a hot load (no replacements)",)
 
     def handle(self, *args, **options):
         metadata = Preprocessor(parse_drive_link(options["file_id"])).preprocess()

applications/portal/backend/api/management/commands/scicrunch_citation.py

@@ -31,7 +31,7 @@ def log(self, msg):
 
     def handle(self, *args, **options):
         requests_per_second_limit = options.get('max_requests_per_second', 10)
-        
+
         antibodies_ids = get_curated_antibodies_ids()
 
         api_request_rate_limiter = RateLimiter(
@@ -64,8 +64,6 @@ def process_antibody_ingestion(self, ab_id):
             ingested = set_citation_metric(
                 ab_id, number_of_citations)
 
-
-
     def log_failed_antibodies(self, failed_antibody_ids):
         if failed_antibody_ids:
             antibodies_failed = (