22.11 (#150)

* Changes to be committed: modified: bco_api/bco_api/settings.py modified: bco_api/server.conf * Enable Group and Prefix to be open to all users. Changes to be committed: modified: bco_api/api/permissions.py modified: bco_api/server.conf * Enable Prefix creation from the ui Changes to be committed: modified: bco_api/api/model/groups.py modified: bco_api/api/model/prefix.py modified: bco_api/api/scripts/method_specific/POST_api_objects_drafts_modify.py modified: bco_api/api/views.py modified: bco_api/bco_api/settings.py * Docker building Changes to be committed: modified: Dockerfile modified: admin_only/bco_api.conf modified: bco_api/bco_api/settings.py modified: bco_api/server.conf new file: docker-compose.yml * Docker support on release Changes to be committed: new file: .github/workflows/publish-Docker-image * testing Changes to be committed: renamed: .github/workflows/publish-Docker-image -> .github/workflows/release-package.yml * Push to dockerhub Changes to be committed: modified: Dockerfile deleted: apitests.py deleted: apitests_new.py deleted: bco_api/static/img/android-chrome-192x192.png deleted: bco_api/static/img/android-chrome-512x512.png deleted: bco_api/static/img/apple-touch-icon.png deleted: bco_api/static/img/favicon-16x16.png deleted: bco_api/static/img/favicon-32x32.png deleted: bco_api/static/img/favicon.ico deleted: cag.sh deleted: curl_fetch.txt modified: docker-compose.yml * Fix Extension domain validation * linting Changes to be committed: modified: bco_api/api/model/groups.py modified: bco_api/api/model/prefix.py modified: bco_api/api/models.py modified: bco_api/api/permissions.py modified: bco_api/api/scripts/utilities/JsonUtils.py modified: bco_api/bco_api/settings.py modified: bco_api/server.conf
biocompute-objects · Nov 16, 2022 · e22f99e · e22f99e
1 parent d9e059f
commit e22f99e
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Showing 7 changed files with 28 additions and 27 deletions.
diff --git a/bco_api/api/model/groups.py b/bco_api/api/model/groups.py
@@ -337,7 +337,9 @@ def post_api_groups_modify(request):
 
                     if "owner_user" in action_set:
                         # Make sure the provided owner user exists.
-                        if usr_utils.check_user_exists(user_name=action_set["owner_user"]):
+                        if usr_utils.check_user_exists(
+                            user_name=action_set["owner_user"]
+                        ):
                             group_information.owner_user = User.objects.get(
                                 username=action_set["owner_user"]
                             )

diff --git a/bco_api/api/model/prefix.py b/bco_api/api/model/prefix.py
@@ -22,7 +22,7 @@
 # Generic meta data model
 # TODO: rename to prefix_meta
 class prefix_table(models.Model):
-    """ The number of objects for a given prefix."""
+    """The number of objects for a given prefix."""
 
     # Field is required.
     n_objects = models.IntegerField()
@@ -93,8 +93,8 @@ def post_api_prefixes_create(request):
     return_data = []
     any_failed = False
     for creation_object in bulk_request:
-        owner_user = User.objects.get(username=creation_object['owner_user'])
-        if creation_object['owner_group'] == 'bco_drafter':
+        owner_user = User.objects.get(username=creation_object["owner_user"])
+        if creation_object["owner_group"] == "bco_drafter":
             is_public = True
         else:
             is_public = False
@@ -136,9 +136,9 @@ def post_api_prefixes_create(request):
                     is not None
                 ):
                     return_data.append(
-                    db_utils.messages(parameters={"expiration_date": prfx["expiration_date"]})[
-                        "400_invalid_expiration_date"
-                    ]
+                        db_utils.messages(
+                            parameters={"expiration_date": prfx["expiration_date"]}
+                        )["400_invalid_expiration_date"]
                     )
                     any_failed = True
                     continue
@@ -157,7 +157,7 @@ def post_api_prefixes_create(request):
                     owner_user.groups.add(drafters)
                     GroupInfo.objects.create(
                         delete_members_on_group_deletion=False,
-                        description=prfx['description'],
+                        description=prfx["description"],
                         group=drafters,
                         max_n_members=-1,
                         owner_user=owner_user,
@@ -172,13 +172,13 @@ def post_api_prefixes_create(request):
                     owner_user.groups.add(publishers)
                     GroupInfo.objects.create(
                         delete_members_on_group_deletion=False,
-                        description=prfx['description'],
+                        description=prfx["description"],
                         group=publishers,
                         max_n_members=-1,
                         owner_user=owner_user,
                     )
                 if is_public is True:
-                    owner_group = 'bco_drafter'
+                    owner_group = "bco_drafter"
                 else:
                     owner_group = publish
 
@@ -212,9 +212,9 @@ def post_api_prefixes_create(request):
                     continue
 
                 return_data.append(
-                    db_utils.messages(
-                        parameters={"prefix": standardized}
-                    )["201_prefix_create"]
+                    db_utils.messages(parameters={"prefix": standardized})[
+                        "201_prefix_create"
+                    ]
                 )
                 # Created the prefix.
                 # errors["201_prefix_create"] = db_utils.messages(
@@ -223,7 +223,7 @@ def post_api_prefixes_create(request):
 
             # Append the possible "errors".
     if any_failed and len(return_data) == 1:
-        return Response(status=return_data[0]['status_code'], data=return_data)
+        return Response(status=return_data[0]["status_code"], data=return_data)
 
     if any_failed and len(return_data) > 1:
         return Response(status=status.HTTP_207_MULTI_STATUS, data=return_data)

diff --git a/bco_api/api/models.py b/bco_api/api/models.py
@@ -51,7 +51,7 @@ class BCO(models.Model):
     schema: str
         schema to which the BCO should be validated. Default is 'IEEE'
     state:str
-        State of object. PUBLISHED, DRAFT, and DELETE are currently accepted values.
+        State of object. REFERENCED, PUBLISHED, DRAFT, and DELETE are currently accepted values.
     last_update: DateTime
         Date Time object for the last database change to this object
     """

diff --git a/bco_api/api/permissions.py b/bco_api/api/permissions.py
@@ -19,11 +19,12 @@
 
 class RequestorInGroupAdminsGroup(permissions.BasePermission):
     """Class docstring"""
+
     def has_permission(self, request, view):
         """Check to see if the requester is in the group admins group.
-            Get the groups for this token (user).
-            This means getting the user ID for the token,
-            then the username."""
+        Get the groups for this token (user).
+        This means getting the user ID for the token,
+        then the username."""
 
         user_id = Token.objects.get(
             key=request.META.get("HTTP_AUTHORIZATION").split(" ")[1]
@@ -64,9 +65,7 @@ def has_permission(self, request, view):
             ).user_id
 
             username = User.objects.get(id=user_id)
-
             prefix_admins = Group.objects.filter(user=username, name="prefix_admins")
-            import pdb; pdb.set_trace()
             return len(prefix_admins) > 0
 
         else:

diff --git a/bco_api/api/scripts/utilities/JsonUtils.py b/bco_api/api/scripts/utilities/JsonUtils.py
@@ -123,7 +123,7 @@ def parse_bco(bco, results):
 
     results = validate(spec_version, bco, results)
     if "extension_domain" in bco.keys():
-        if bco["extension_domain"] is not list:
+        if isinstance(bco["extension_domain"], list) is False:
             results[identifier]["extension_domain"] = {
                 "number_of_errors": 1,
                 "error_detail": ["extension_doamin invalid"],

diff --git a/bco_api/bco_api/settings.py b/bco_api/bco_api/settings.py
@@ -42,12 +42,12 @@
 HUMAN_READABLE_HOSTNAME = server_config["HRHOSTNAME"]["hrnames"]
 
 if server_config["GROUP_PREFIX"]["allow_all_creation"] == "True":
-    GROUP=True
-    PREFIX=True
+    GROUP = True
+    PREFIX = True
 elif server_config["GROUP_PREFIX"]["allow_group_creation"] == "True":
-    GROUP=True
+    GROUP = True
 elif server_config["GROUP_PREFIX"]["allow_prefix_creation"] == "True":
-    PREFIX=True
+    PREFIX = True
 
 # The publicly accessible hostname.
 if server_config["PRODUCTION"]["production"] == "True":
@@ -185,7 +185,7 @@
     "SECURITY_DEFINITIONS": {
         "Bearer": {"type": "apiKey", "name": "Authorization", "in": "header"}
     },
-    "DEEP_LINKING": True
+    "DEEP_LINKING": True,
 }
 
 REDOC_SETTINGS = {"LAZY_RENDERING": False}

diff --git a/bco_api/server.conf b/bco_api/server.conf
@@ -7,7 +7,7 @@ production=False
 
 # DB Version
 [VERSION]
-version=22.08
+version=22.11
 
 # NOTE:  Valid values are True or False (note the capitalization).
 # Is this a publish-only server?