Merge pull request #75 from JSv4/JSv4/add-gui-elements-to-create-meta…

…data-labels

Add GUI Elements to Filter on Metadata and Thumbnails for Docs

.github/workflows/backend.yml

@@ -4,6 +4,7 @@ name: Backend CI
 env:
   DOCKER_BUILDKIT: 1
   COMPOSE_DOCKER_CLI_BUILD: 1
+  SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL: True
 
 defaults:
  run:

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
       - id: black
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
 

compose/local/django/Dockerfile

@@ -87,7 +87,10 @@ RUN apt-get update && apt-get install --no-install-recommends -y \
   git \
   poppler-utils \
   tesseract-ocr \
-  libtesseract-dev \
+  libtesseract-dev  \
+  ffmpeg \
+  libsm6 \
+  libxext6 \
   # cleaning up unused files
   && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false \
   && rm -rf /var/lib/apt/lists/*

config/graphql/base.py

@@ -2,14 +2,16 @@
 import logging
 from abc import ABC
 
+import django.db.models
 import graphene
 from graphene.relay import Node
+from graphene_django import DjangoObjectType
 from graphql_jwt.decorators import login_required
-from graphql_relay import from_global_id
+from graphql_relay import from_global_id, to_global_id
 
 from opencontractserver.shared.resolvers import resolve_single_oc_model_from_id
-from opencontractserver.utils.data_types import PermissionTypes
-from opencontractserver.utils.permissioning_utils import (
+from opencontractserver.types.enums import PermissionTypes
+from opencontractserver.utils.permissioning import (
     set_permissions_for_obj_to_user,
     user_has_permission_for_obj,
 )
@@ -115,22 +117,25 @@ def mutate(cls, root, info, *args, **kwargs):
 
 class DRFMutation(graphene.Mutation):
     class IOSettings(ABC):
-        pk_fields = []
+        pk_fields: list[str | int] = []
         lookup_field = "id"
-        model = None
+        model: django.db.models.Model = None
+        graphene_model: DjangoObjectType = None
         serializer = None
 
     class Arguments(ABC):
         pass
 
     ok = graphene.Boolean()
     message = graphene.String()
+    obj_id = graphene.ID()
 
     @classmethod
     @login_required
     def mutate(cls, root, info, *args, **kwargs):
 
         ok = False
+        obj_id = None
 
         try:
             logger.info("Test if context has user")
@@ -196,6 +201,9 @@ def mutate(cls, root, info, *args, **kwargs):
                 obj_serializer.save()
                 ok = True
                 message = "Success"
+                obj_id = to_global_id(
+                    cls.IOSettings.graphene_model.__class__.__name__, obj.id
+                )
                 logger.info("Succeeded updating obj")
 
             else:
@@ -215,8 +223,11 @@ def mutate(cls, root, info, *args, **kwargs):
 
                 ok = True
                 message = "Success"
+                obj_id = to_global_id(
+                    cls.IOSettings.graphene_model.__class__.__name__, obj.id
+                )
 
         except Exception as e:
             message = f"Mutation failed due to error: {e}"
 
-        return cls(ok=ok, message=message)
+        return cls(ok=ok, message=message, obj_id=obj_id)

config/graphql/mutations.py

@@ -12,7 +12,7 @@
 from django.utils import timezone
 from graphene.types.generic import GenericScalar
 from graphql_jwt.decorators import login_required, user_passes_test
-from graphql_relay import from_global_id
+from graphql_relay import from_global_id, to_global_id
 
 from config.graphql.base import DRFDeletion, DRFMutation
 from config.graphql.graphene_types import (
@@ -56,9 +56,9 @@
     make_analysis_public_task,
     make_corpus_public_task,
 )
+from opencontractserver.types.enums import PermissionTypes
 from opencontractserver.users.models import UserExport
-from opencontractserver.utils.data_types import PermissionTypes
-from opencontractserver.utils.permissioning_utils import (
+from opencontractserver.utils.permissioning import (
     set_permissions_for_obj_to_user,
     user_has_permission_for_obj,
 )
@@ -132,6 +132,7 @@ class IOSettings:
         lookup_field = "id"
         serializer = LabelsetSerializer
         model = LabelSet
+        graphene_model = LabelSetType
 
     class Arguments:
         id = graphene.String(required=True)
@@ -303,6 +304,7 @@ class IOSettings:
         lookup_field = "id"
         serializer = DocumentSerializer
         model = Document
+        graphene_model = DocumentType
 
     class Arguments:
         id = graphene.String(required=True)
@@ -883,6 +885,7 @@ class IOSettings:
         lookup_field = "id"
         serializer = AnnotationSerializer
         model = Annotation
+        graphene_model = AnnotationType
 
     class Arguments:
         id = graphene.String(required=True)
@@ -979,6 +982,7 @@ class IOSettings:
         pk_fields = ["label_set"]
         serializer = CorpusSerializer
         model = Corpus
+        graphene_model = CorpusType
 
     class Arguments:
         title = graphene.String(required=False)
@@ -993,6 +997,7 @@ class IOSettings:
         pk_fields = ["label_set"]
         serializer = CorpusSerializer
         model = Corpus
+        graphene_model = CorpusType
 
     class Arguments:
         id = graphene.String(required=True)
@@ -1016,6 +1021,7 @@ class IOSettings:
         pk_fields = []
         serializer = AnnotationLabelSerializer
         model = AnnotationLabel
+        graphene_model = AnnotationLabelType
 
     class Arguments:
         text = graphene.String(required=False)
@@ -1031,6 +1037,7 @@ class IOSettings:
         serializer = AnnotationLabelSerializer
         lookup_field = "id"
         model = AnnotationLabel
+        graphene_model = AnnotationLabelType
 
     class Arguments:
         id = graphene.String(required=True)
@@ -1094,12 +1101,14 @@ class Arguments:
     ok = graphene.Boolean()
     message = graphene.String()
     obj = graphene.Field(AnnotationLabelType)
+    obj_id = graphene.ID()
 
     @login_required
     def mutate(root, info, labelset_id, text, description, color, icon, label_type):
 
         ok = False
         obj = None
+        obj_id = None
 
         try:
             labelset = LabelSet.objects.get(
@@ -1114,6 +1123,7 @@ def mutate(root, info, labelset_id, text, description, color, icon, label_type):
                 label_type=label_type,
                 creator=info.context.user,
             )
+            obj_id = to_global_id("AnnotationLabelType", obj.id)
             logger.debug("CreateLabelForLabelsetMutation - mutate / Created label", obj)
 
             set_permissions_for_obj_to_user(
@@ -1131,7 +1141,9 @@ def mutate(root, info, labelset_id, text, description, color, icon, label_type):
         except Exception as e:
             message = f"Failed to create label for labelset due to error: {e}"
 
-        return CreateLabelForLabelsetMutation(obj=obj, message=message, ok=ok)
+        return CreateLabelForLabelsetMutation(
+            obj=obj, obj_id=obj_id, message=message, ok=ok
+        )
 
 
 class StartCorpusAnalysisMutation(graphene.Mutation):

config/graphql/permission_annotator/mixins.py

@@ -8,7 +8,7 @@
 from config.graphql.permission_annotator.middleware import (
     get_permissions_for_user_on_model_in_app,
 )
-from opencontractserver.utils.data_types import PermissionTypes
+from opencontractserver.types.enums import PermissionTypes
 
 User = get_user_model()
 

config/graphql/queries.py

@@ -50,8 +50,8 @@
 from opencontractserver.corpuses.models import Corpus
 from opencontractserver.documents.models import Document
 from opencontractserver.shared.resolvers import resolve_oc_model_queryset
+from opencontractserver.types.enums import LabelType
 from opencontractserver.users.models import Assignment, UserExport, UserImport
-from opencontractserver.utils.data_types import LabelType
 
 logger = logging.getLogger(__name__)
 
@@ -109,7 +109,7 @@ def resolve_bulk_doc_relationships_in_corpus(self, info, corpus_id, document_id)
 
     bulk_doc_annotations_in_corpus = graphene.Field(
         graphene.List(AnnotationType),
-        corpus_id=graphene.String(required=True),
+        corpus_id=graphene.ID(required=True),
         document_id=graphene.ID(required=False),
         for_analysis_ids=graphene.String(required=False),
         label_type=graphene.List(label_type_enum),

config/graphql_api_key_auth/__init__.py

@@ -1,14 +0,0 @@
-#  Copyright (C) 2022  John Scrudato / Gordium Knot Inc. d/b/a OpenSource.Legal
-#
-#  This program is free software: you can redistribute it and/or modify
-#  it under the terms of the GNU Affero General Public License as
-#  published by the Free Software Foundation, either version 3 of the
-#  License, or (at your option) any later version.
-
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU Affero General Public License for more details.
-
-#  You should have received a copy of the GNU Affero General Public License
-#  along with this program.  If not, see <https://www.gnu.org/licenses/>.

config/graphql_api_key_auth/backends.py

@@ -1,25 +1,10 @@
-#  Copyright (C) 2022  John Scrudato / Gordium Knot Inc. d/b/a OpenSource.Legal
-#
-#  This program is free software: you can redistribute it and/or modify
-#  it under the terms of the GNU Affero General Public License as
-#  published by the Free Software Foundation, either version 3 of the
-#  License, or (at your option) any later version.
 from django.conf import settings
-
-#  You should have received a copy of the GNU Affero General Public License
-#  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 from django.contrib.auth import get_user_model
 from django.utils.translation import gettext_lazy as _
 from rest_framework import exceptions
 
 from config.graphql_api_key_auth.utils import get_authorization_header
 
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU Affero General Public License for more details.
-
-
 UserModel = get_user_model()
 
 

config/graphql_api_key_auth/middleware.py

@@ -1,10 +1,16 @@
-from django.contrib.auth import authenticate
+from django.contrib.auth import authenticate, get_user_model
 
 from config.graphql_api_key_auth.utils import get_http_authorization, get_token_argument
 
+User = get_user_model()
+
+
+def _context_has_user(request):
+    return hasattr(request, "user") and request.user.is_authenticated
+
 
 def _authenticate(request):
-    is_anonymous = not hasattr(request, "user") or request.user.is_anonymous
+    is_anonymous = _context_has_user(request)
     return is_anonymous and get_http_authorization(request) is not None
 
 
@@ -21,16 +27,30 @@ def authenticate_context(self, info, **kwargs):
 
     def resolve(self, next, root, info, **kwargs):
 
+        # Check to see if user already on context
+
+        if "user" in info.context.POST:
+            existing_user = info.context.POST["user"]
+            if (
+                existing_user is not None
+                and isinstance(existing_user, User)
+                and existing_user.is_authenticated
+            ):
+                return next(root, info, **kwargs)
+
         context = info.context
         token_argument = get_token_argument(context, **kwargs)
 
         if (
             _authenticate(context) or token_argument is not None
         ) and self.authenticate_context(info, **kwargs):
 
-            user = authenticate(request=context, **kwargs)
+            # If we already have an authenticated user for our request, don't bother re-authenticating
+            # same request. This was causing a massive performance hit.
+            if not _context_has_user(context):
+                user = authenticate(request=context, **kwargs)
 
-            if user is not None:
-                context.user = user
+                if user is not None:
+                    context.user = user
 
         return next(root, info, **kwargs)

config/settings/base.py

@@ -403,10 +403,10 @@
 CELERY_RESULT_SERIALIZER = "json"
 # http://docs.celeryproject.org/en/latest/userguide/configuration.html#task-time-limit
 # TODO: set to whatever value is adequate in your circumstances
-CELERY_TASK_TIME_LIMIT = 5 * 3600
+# CELERY_TASK_TIME_LIMIT = 5 * 3600
 # http://docs.celeryproject.org/en/latest/userguide/configuration.html#task-soft-time-limit
 # TODO: set to whatever value is adequate in your circumstances
-CELERY_TASK_SOFT_TIME_LIMIT = 3600
+# CELERY_TASK_SOFT_TIME_LIMIT = 3600
 # http://docs.celeryproject.org/en/latest/userguide/configuration.html#beat-scheduler
 CELERY_BEAT_SCHEDULER = "django_celery_beat.schedulers:DatabaseScheduler"
 CELERY_WORKER_MAX_MEMORY_PER_CHILD = 1024000

config/settings/local.py

@@ -39,7 +39,7 @@
 # django-extensions
 # ------------------------------------------------------------------------------
 # https://django-extensions.readthedocs.io/en/latest/installation_instructions.html#configuration
-INSTALLED_APPS += ["django_extensions"]  # noqa F405
+INSTALLED_APPS += ["django_extensions", "silk"]  # noqa F405
 
 # Celery
 # ------------------------------------------------------------------------------
@@ -57,3 +57,8 @@
 
 # Your stuff...
 # ------------------------------------------------------------------------------
+MIDDLEWARE += [
+    "django_cprofile_middleware.middleware.ProfilerMiddleware",
+    "silk.middleware.SilkyMiddleware",
+]
+SILKY_PYTHON_PROFILER = True

config/urls.py

@@ -3,7 +3,7 @@
 from django.conf import settings
 from django.conf.urls.static import static
 from django.contrib import admin
-from django.urls import path
+from django.urls import include, path
 from django.views import defaults as default_views
 from django.views.decorators.csrf import csrf_exempt
 from graphene_django.views import GraphQLView
@@ -26,6 +26,7 @@
         []
         if not settings.DEBUG
         else [
+            path("silk/", include("silk.urls", namespace="silk")),
             path(
                 "400/",
                 default_views.bad_request,

frontend/src/assets/configurations/menus.ts

@@ -18,7 +18,7 @@ export const header_menu_items = [
     id: "label_set_menu_button",
   },
   {
-    title: "Provisions",
+    title: "Annotations",
     route: "/annotations/",
     protected: false,
     id: "annotation_menu_button",