Merge branch 'master' into 'production'

Master

See merge request !38

.gitlab-ci.yml

@@ -26,7 +26,7 @@ stages:
 
 build-job:
   stage: build
-  image: python:3.10.9
+  image: python:3.10.6
   script:
     - python -V
     - pip install virtualenv
@@ -40,14 +40,14 @@ build-job:
 
 test-job1:
   stage: test
-  image: python:3.10.9
+  image: python:3.10.6
   script:
     - source venv/bin/activate
     - flake8 --config .flake8
 
 test-job2:
   stage: test
-  image: python:3.10.9
+  image: python:3.10.6
   script:
     - source venv/bin/activate
     - which python
@@ -57,7 +57,7 @@ test-job2:
 deploy-to-production:
   stage: deploy
   tags:
-    - bare-metal
+    - vm,bare-metal
   script:
     - echo "Current working directory and user"
     - pwd
@@ -71,10 +71,9 @@ deploy-to-production:
     - git config --global user.email gitlab-runner@gitlab.pik-potsdam.de
     - git config --global -l --show-origin
     - echo "Go to deployment location"
-    - cd /home/nacsos/nacsos-core
+    - cd /var/www/nacsos2/nacsos-core
     - ls -lisah
-    - sudo chown -R gitlab-runner /home/nacsos/nacsos-core
-    - sudo chgrp -R gitlab-runner /home/nacsos/nacsos-core
+    - sudo chown -R gitlab-runner:gitlab-runner /var/www/nacsos2/nacsos-core
     - ls -lisah
     - echo "Stopping NACSOS-core service"
     - sudo systemctl stop nacsos-core.service
@@ -91,16 +90,10 @@ deploy-to-production:
     - echo "Installing requirements"
     - pip install -r requirements.txt
     - echo "Handling migrations"
-    - nacsos_migrate upgrade --revision head --root-path=/home/nacsos/nacsos-core/venv/lib/python3.10/site-packages/nacsos_data --ini-file=/home/nacsos/nacsos-core/config/alembic.ini
-    - sudo chown -R nacsos /home/nacsos/nacsos-core
-    - sudo chgrp -R nacsos /home/nacsos/nacsos-core
+    - nacsos_migrate upgrade --revision head --root-path=/var/www/nacsos2/nacsos-core/venv/lib/python3.10/site-packages/nacsos_data --ini-file=/var/www/nacsos2/nacsos-core/config/alembic.ini
+    - sudo chown -R nacsos:nacsos /var/www/nacsos2/nacsos-core
     - echo "Starting NACSOS-core service"
     - sudo systemctl start nacsos-core.service
-# DEPRECATED
-#    - echo "Run as nacsos user"
-#    - sudo -u nacsos bash ./deploy.sh $CI_JOB_TOKEN
-#    - echo "Becoming 'nacsos' user"
-#    - sudo -u nacsos -s
   when: manual
   only:
     - production

requirements.txt

-fastapi==0.95.0
+fastapi==0.95.1
 hypercorn==0.14.3
 toml==0.10.2
-email-validator==1.3.1
+email-validator==2.0.0.post1
 python-dotenv==1.0.0
 passlib[bcrypt]==1.7.4
-httpx[http2]==0.23.3
+httpx[http2]==0.24.0
 pymitter==0.4.0
 uvicorn==0.21.1
 python-multipart==0.0.6
-nacsos_data[scripts,server] @ git+ssh://git@gitlab.pik-potsdam.de/mcc-apsis/nacsos/nacsos-data.git@v0.5.1
+nacsos_data[scripts,server] @ git+ssh://git@gitlab.pik-potsdam.de/mcc-apsis/nacsos/nacsos-data.git@v0.5.2

requirements_dev.txt

 flake8==6.0.0
-tox==4.4.8
-pytest==7.2.2
+tox==4.4.12
+pytest==7.3.1
 pytest-cov==4.0.0
-mypy==1.1.1
+mypy==1.2.0
 types-toml==0.10.8.6
 types-PyYAML==6.0.12.9
\ No newline at end of file

server/api/routes/highlight.py

 from typing import TYPE_CHECKING
 
-from nacsos_data.util.auth import UserPermissions
-from sqlalchemy import select
 from fastapi import APIRouter, Depends
+from sqlalchemy import select
+from sqlalchemy import func as F
 
-from nacsos_data.db.schemas.annotations import AssignmentScope
-from nacsos_data.db.schemas.highlight import Highlighter
-from nacsos_data.models.highlight import HighlighterModel
-
+from server.data import db_engine
 from server.api.errors import \
     NoDataForKeyError, \
     DataNotFoundWarning
-from server.util.security import UserPermissionChecker, InsufficientPermissions
-from server.data import db_engine
+from server.util.security import \
+    UserPermissionChecker, \
+    InsufficientPermissions
+
+from nacsos_data.util.auth import UserPermissions
+from nacsos_data.db.schemas.annotations import AssignmentScope
+from nacsos_data.db.schemas.highlight import Highlighter
+from nacsos_data.models.highlight import HighlighterModel
 
 if TYPE_CHECKING:
     from sqlalchemy.ext.asyncio import AsyncSession  # noqa F401
@@ -20,19 +23,21 @@ if TYPE_CHECKING:
 router = APIRouter()
 
 
-@router.get('/scope/{assignment_scope_id}', response_model=HighlighterModel | None)
-async def get_scope_highlighter(assignment_scope_id: str,
-                                permissions: UserPermissions = Depends(UserPermissionChecker('annotations_read'))) \
-        -> HighlighterModel:
+@router.get('/scope/{assignment_scope_id}', response_model=list[HighlighterModel] | None)
+async def get_scope_highlighters(assignment_scope_id: str,
+                                 permissions: UserPermissions = Depends(UserPermissionChecker('annotations_read'))) \
+        -> list[HighlighterModel]:
     async with db_engine.session() as session:  # type: AsyncSession
+        highlighter_ids = select(F.unnest(AssignmentScope.highlighter_ids).label('highlighter_id')) \
+            .where(AssignmentScope.assignment_scope_id == assignment_scope_id) \
+            .subquery()
         stmt = select(Highlighter) \
-            .join(AssignmentScope,
-                  AssignmentScope.highlighter_id == Highlighter.highlighter_id) \
-            .where(Highlighter.project_id == permissions.permissions.project_id,
-                   AssignmentScope.assignment_scope_id == assignment_scope_id)
-        result = (await session.scalars(stmt)).one_or_none()
-        if result is not None:
-            return HighlighterModel.parse_obj(result.__dict__)
+            .join(highlighter_ids, highlighter_ids.c.highlighter_id == Highlighter.highlighter_id) \
+            .where(Highlighter.project_id == permissions.permissions.project_id)
+
+        result = (await session.scalars(stmt)).all()
+        if result is not None and len(result) > 0:
+            return [HighlighterModel.parse_obj(r.__dict__) for r in result]
         raise DataNotFoundWarning(f'No highlighter in project {permissions.permissions.project_id} '
                                   f'for scope with id {assignment_scope_id}!')