Merge branch 'release/5.12.0'

Author: JeltevanBoheemen

.github/workflows/backend-test.yml

@@ -1,4 +1,4 @@
-# This workflow will run backend tests on the Python version defined in the Dockerfiles
+# This workflow will run backend tests on the Python version defined in the backend/Dockerfile
 
 name: Backend unit tests
 
@@ -13,15 +13,45 @@ on:
       - 'hotfix/**'
       - 'release/**'
       - 'dependabot/**'
-    paths-ignore:
-      - 'frontend/**'
-      - '**.md'
+    paths:
+      - 'backend/**'
+      - '.github/workflows/backend*'
+      - 'docker-compose.yaml'
 
 jobs:
   backend-test:
     name: Test Backend
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    - name: Login to GitHub Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    - name: Build and push Elasticsearch image
+      uses: docker/build-push-action@v6
+      with:
+        context: .
+        file: DockerfileElastic
+        push: true
+        tags: ghcr.io/uudigitalhumanitieslab/ianalyzer-elastic:latest
+        cache-from: type=registry,ref=ghcr.io/uudigitalhumanitieslab/ianalyzer-elastic:latest
+        cache-to: type=inline
+    - name: Build and push Backend
+      uses: docker/build-push-action@v6
+      with:
+        context: backend/.
+        push: true
+        tags: ghcr.io/uudigitalhumanitieslab/ianalyzer-backend:latest
+        cache-from: type=registry,ref=ghcr.io/uudigitalhumanitieslab/ianalyzer-backend:latest
+        cache-to: type=inline
     - name: Run backend tests
-      run: sudo mkdir -p /ci-data && sudo docker-compose --env-file .env-ci run backend pytest
+      run: |
+        sudo mkdir -p /ci-data
+        docker compose pull elasticsearch
+        docker compose pull backend
+        docker compose --env-file .env-ci run --rm backend pytest

.github/workflows/frontend-test.yml

@@ -13,15 +13,34 @@ on:
       - 'hotfix/**'
       - 'release/**'
       - 'dependabot/**'
-    paths-ignore:
-      - 'backend/**'
-      - '**.md'
+    paths:
+      - 'frontend/**'
+      - '.github/workflows/frontend*'
+      - 'docker-compose.yaml'
 
 jobs:
   frontend-test:
     name: Test Frontend
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Run frontend tests
-      run: sudo docker-compose --env-file .env-ci run frontend yarn test
+    - uses: actions/checkout@v4
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    - name: Login to GitHub Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    - name: Build frontend image, using cache from Github registry
+      uses: docker/build-push-action@v6
+      with:
+        context: frontend/.
+        push: true
+        tags: ghcr.io/uudigitalhumanitieslab/ianalyzer-frontend:latest
+        cache-from: type=registry,ref=ghcr.io/uudigitalhumanitieslab/ianalyzer-frontend:latest
+        cache-to: type=inline
+    - name: Run frontend unit tests
+      run: |
+        docker compose pull frontend
+        docker compose --env-file .env-ci run --rm frontend yarn test

.github/workflows/release.yml

@@ -61,6 +61,16 @@
             }
         },
         {
+            "name": "Python: Debug Tests",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": [
+                "debug-test"
+            ],
+            "console": "internalConsole",
+            "justMyCode": false
+        }, {
             "name": "celery",
             "type": "debugpy",
             "request": "launch",

.vscode/launch.json

@@ -35,5 +35,5 @@ keywords:
   - elasticsearch
   - natural language processing
 license: MIT
-version: 5.9.0
-date-released: '2024-07-05'
+version: 5.12.0
+date-released: '2024-08-30'

CITATION.cff

@@ -7,7 +7,6 @@ RUN apt-get -y update && apt-get -y upgrade
 RUN apt-get install -y pkg-config libxml2-dev libxmlsec1-dev libxmlsec1-openssl default-libmysqlclient-dev
 
 RUN pip install --upgrade pip
-RUN pip install pip-tools
 # make a directory in the container
 WORKDIR /backend
 # copy requirements from the host system to the directory in the container

backend/Dockerfile

@@ -49,9 +49,18 @@ class VisualizationType(Enum):
     'scan',
     'tab-scan'
     'p',
+    'tags',
+    'context',
+    'tab',
 ]
 '''
-Field names that cannot be used because they are also query parameters in frontend routes.
+Field names that cannot be used because they interfere with other functionality.
 
-Using them would make routing ambiguous.
+This is usually because they are also query parameters in frontend routes, and using them
+would make routing ambiguous.
+
+`query` is also forbidden because it is a reserved column in CSV downloads. Likewise,
+`context` is forbidden because it's used in download requests.
+
+`scan` and `tab-scan` are added because they interfere with element IDs in the DOM.
 '''

backend/addcorpus/constants.py

@@ -268,8 +268,9 @@ def has_named_entities(self):
         try:
             mapping = client.indices.get_mapping(
                 index=self.es_index)
-            fields = mapping[self.es_index].get(
-                'mappings', {}).get('properties', {}).keys()
+            # in production, the index name can be different from the object's es_index value
+            index_name = list(mapping.keys())[0]
+            fields = mapping[index_name].get('mappings', {}).get('properties', {}).keys()
             if any(field.endswith(':ner') for field in fields):
                 return True
         except:
@@ -473,6 +474,13 @@ class PageType(models.TextChoices):
         help_text='markdown contents of the documentation'
     )
 
+    @property
+    def page_index(self):
+        '''Numerical index to determine the order in which pages should be displayed.
+        Based on the order in which `PageType` choices are declared.'''
+        indexed_values = enumerate(__class__.PageType.values)
+        return next((i for (i, value) in indexed_values if value == self.type), None)
+
     def __str__(self):
         return f'{self.corpus_configuration.corpus.name} - {self.type}'
 

backend/addcorpus/models.py

@@ -1,7 +1,6 @@
 from rest_framework import permissions
 from rest_framework.exceptions import NotFound
-from users.models import CustomUser
-from typing import List
+from rest_framework.request import Request
 from addcorpus.models import Corpus
 
 def corpus_name_from_request(request):
@@ -25,20 +24,7 @@ def corpus_name_from_request(request):
     return corpus
 
 
-def filter_user_corpora(corpora: List[Corpus], user: CustomUser) -> List[Corpus]:
-    '''
-    Filter all available corpora to only
-    include the ones the user has access to
-    '''
-
-    return [
-         corpus
-         for corpus in corpora
-         if user.has_access(corpus.name)
-    ]
-
-
-class CorpusAccessPermission(permissions.BasePermission):
+class CanSearchCorpus(permissions.BasePermission):
     message = 'You do not have permission to access this corpus'
 
     def has_permission(self, request, view):
@@ -48,9 +34,32 @@ def has_permission(self, request, view):
         # check if the corpus exists
         try:
             corpus = Corpus.objects.get(name=corpus_name)
-            assert corpus.active
         except:
             raise NotFound('Corpus does not exist')
 
         # check if the user has access
-        return user.has_access(corpus)
+        return user.can_search(corpus)
+
+
+class IsCurator(permissions.BasePermission):
+    '''
+    The user is permitted to use the corpus definition API.
+    '''
+
+    message = 'You do not have permission to manage corpus definitions'
+
+    def has_permission(self, request: Request, view):
+        return request.user.is_staff
+
+class IsCuratorOrReadOnly(permissions.BasePermission):
+    '''
+    The user is permitted to edit the corpus, or it is a read-only request.
+    '''
+
+    message = 'You do not have permission to edit this corpus'
+
+    def has_permission(self, request: Request, view):
+        if request.method in permissions.SAFE_METHODS:
+            return True
+
+        return request.user.is_staff

backend/addcorpus/permissions.py

@@ -36,8 +36,6 @@ class NewReader(CSVReader):
                   for f in corpus.configuration.fields.all()]
 
         def sources(self, *args, **kwargs):
-            return (
-                (fn, {}) for fn in glob.glob(f'{self.data_directory}/**/*.csv', recursive=True)
-            )
+            return glob.glob(f'{self.data_directory}/**/*.csv', recursive=True)
 
     return NewReader()

backend/addcorpus/reader.py

@@ -65,6 +65,16 @@ def to_representation(self, value):
         key = super().to_representation(value)
         return self.choices[key]
 
+    def to_internal_value(self, data):
+        # If the data provides a display name, get the corresponding key.
+        # The browsable API sends keys instead of labels; use the original data if no
+        # matching label is found.
+        value = next(
+            (key for (key, label) in self.choices.items() if label == data),
+            data
+        )
+        return super().to_internal_value(value)
+
 class CorpusConfigurationSerializer(serializers.ModelSerializer):
     fields = FieldSerializer(many=True, read_only=True)
     languages = serializers.ListField(child=LanguageField())
@@ -123,11 +133,18 @@ def to_representation(self, value):
 
 class CorpusDocumentationPageSerializer(serializers.ModelSerializer):
     type = PrettyChoiceField(choices = CorpusDocumentationPage.PageType.choices)
-    content = DocumentationTemplateField()
+    index = serializers.IntegerField(source='page_index', read_only=True)
+    content = DocumentationTemplateField(read_only=True)
+    content_template = serializers.CharField(source='content')
+    corpus = serializers.SlugRelatedField(
+        source='corpus_configuration',
+        queryset=CorpusConfiguration.objects.all(),
+        slug_field='corpus__name',
+    )
 
     class Meta:
         model = CorpusDocumentationPage
-        fields = ['corpus_configuration', 'type', 'content']
+        fields = ['id', 'corpus', 'type', 'content', 'content_template', 'index']
 
 
 class JSONDefinitionField(serializers.Field):

backend/addcorpus/serializers.py

@@ -1,24 +1,33 @@
 from users.models import CustomUser, CustomAnonymousUser
+from addcorpus.models import Corpus
 
 def test_access_through_group(db, basic_mock_corpus, group_with_access):
     user = CustomUser.objects.create(username='nice-user', password='secret')
     user.groups.add(group_with_access)
     user.save()
-    assert user.has_access(basic_mock_corpus)
+    corpus = Corpus.objects.get(name=basic_mock_corpus)
+    assert user.can_search(corpus)
+    assert corpus in user.searchable_corpora()
 
 def test_superuser_access(basic_mock_corpus, admin_user):
-    assert admin_user.has_access(basic_mock_corpus)
+    corpus = Corpus.objects.get(name=basic_mock_corpus)
+    assert admin_user.can_search(corpus)
+    assert corpus in admin_user.searchable_corpora()
 
 def test_no_corpus_access(db, basic_mock_corpus):
     user = CustomUser.objects.create(username='bad-user', password='secret')
-    assert not user.has_access(basic_mock_corpus)
-
+    corpus = Corpus.objects.get(name=basic_mock_corpus)
+    assert not user.can_search(corpus)
+    assert corpus not in user.searchable_corpora()
 
 def test_public_corpus_access(db, basic_corpus_public):
     user = CustomUser.objects.create(username='new-user', password='secret')
-    assert user.has_access(basic_corpus_public)
+    corpus = Corpus.objects.get(name=basic_corpus_public)
+    assert user.can_search(corpus)
+    assert corpus in user.searchable_corpora()
     anon = CustomAnonymousUser()
-    assert anon.has_access(basic_corpus_public)
+    assert anon.can_search(corpus)
+    assert corpus in anon.searchable_corpora()
 
 def test_api_access(db, basic_mock_corpus, group_with_access, auth_client, auth_user):
     # default: no access