Remove usage of .construct() method

.github/workflows/ci_tests.yml

@@ -140,11 +140,28 @@ jobs:
 
     - name: Start the Docker services
       run: |
-        docker-compose -f docker-compose_dev.yml  --verbose -- up &
+        docker-compose -f docker-compose_dev.yml --verbose -- up &
         .github/utils/wait_for_it.sh localhost:${{ env.PORT }} -t 120
         sleep 5
         curl -X "GET" -i "http://localhost:${{ env.PORT }}${{ env.OTEAPI_prefix }}/session"
       env:
         PORT: 8123
         OTEAPI_prefix: /api/ci/v1
         DOCKER_OTEAPI_TARGET: ${{ matrix.docker-target }}
+
+    - name: Start the Docker services with local `oteapi-core`
+      if: matrix.docker-target == 'development'
+      run: |
+        git clone https://github.com/EMMC-ASBL/oteapi-core ${PATH_TO_OTEAPI_CORE}
+        docker-compose -f docker-compose_dev.yml down
+        docker-compose -f docker-compose_dev.yml --verbose -- up &
+        .github/utils/wait_for_it.sh localhost:${{ env.PORT }} -t 120
+        # Sleep for longer, since it takes a while to install `oteapi-core`
+        # And the port will be available as soon as the CMD is reached in the Dockerfile.
+        sleep 40
+        curl -X "GET" -i "http://localhost:${{ env.PORT }}${{ env.OTEAPI_prefix }}/session"
+      env:
+        PORT: 8123
+        OTEAPI_prefix: /api/ci/v1
+        DOCKER_OTEAPI_TARGET: ${{ matrix.docker-target }}
+        PATH_TO_OTEAPI_CORE: /tmp/oteapi-core

Dockerfile

@@ -36,9 +36,9 @@ RUN pip install --trusted-host pypi.org --trusted-host files.pythonhosted.org -r
 
 # Run app with reload option
 EXPOSE 8080
-CMD hypercorn asgi:app --bind 0.0.0.0:8080 --reload --debug --log-level debug
+CMD if [ "${PATH_TO_OTEAPI_CORE}" != "/dev/null" ] && [ -n "${PATH_TO_OTEAPI_CORE}" ]; then pip install -U --force-reinstall -e /oteapi_core; fi && hypercorn asgi:app --bind 0.0.0.0:8080 --reload --debug --log-level debug
 
-################# PRODUCTION ####################################
+################# PRODUCTION #####################################
 FROM base as production
 
 # Run app

README.md

@@ -63,6 +63,22 @@ docker run \
 
 Open the following URL in a browser [http://localhost:8080/redoc](http://localhost:8080/redoc).
 
+One can also use a local `oteapi-core` repository by specifying the `PATH_TO_OTEAPI_CORE` environment variable:
+
+```shell
+export PATH_TO_OTEAPI_CORE=/local/path/to/oteapi-core
+docker run \
+    --rm \
+    --network otenet \
+    --detach \
+    --volume ${PWD}:/app \
+    --publish 8080:8080 \
+    --env OTEAPI_REDIS_TYPE=redis \
+    --env OTEAPI_REDIS_HOST=redis \
+    --env OTEAPI_REDIS_PORT=6379 \
+    ontotrans/oteapi-development:latest
+```
+
 ### Run oteapi (production)
 
 Run the services by attaching to the otenet network and set the environmental variables for connecting to Redis.
@@ -112,6 +128,12 @@ Note that default values will be used if certain environment variables are not p
 To inspect which environment variables can be specified, please inspect the [Docker Compose file](docker-compose_dev.yml).
 
 This Docker Compose file will use your local files for the application, meaning updates in your local files (under `app/`) should be reflected in the running application after hypercorn reloads.
+You can go one step further and use your local files also for the `oteapi-core` repository by specifying the `PATH_TO_OTEAPI_CORE` environment variable:
+
+```shell
+export PATH_TO_OTEAPI_CORE=/local/path/to/oteapi-core
+docker-compose -f docker-compose_dev.yml up --build -d  # Run the OTE Services detached, build if necessary
+```
 
 To see the logs (in real time) from the server, run:
 

app/routers/datafilter.py

@@ -68,10 +68,7 @@ async def get_filter(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = FilterConfig.construct(**json.loads(await cache.get(filter_id)))
+    config = FilterConfig(**json.loads(await cache.get(filter_id)))
 
     strategy = create_strategy("filter", config)
     session_data = None if not session_id else json.loads(await cache.get(session_id))
@@ -103,10 +100,7 @@ async def initialize_filter(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = FilterConfig.construct(**json.loads(await cache.get(filter_id)))
+    config = FilterConfig(**json.loads(await cache.get(filter_id)))
 
     strategy = create_strategy("filter", config)
     session_data = None if not session_id else json.loads(await cache.get(session_id))

app/routers/dataresource.py

@@ -85,10 +85,7 @@ async def info_dataresource(
     if not await cache.exists(resource_id):
         raise httpexception_404_item_id_does_not_exist(resource_id, "resource_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    return ResourceConfig.construct(**json.loads(await cache.get(resource_id)))
+    return ResourceConfig(**json.loads(await cache.get(resource_id)))
 
 
 @ROUTER.get(
@@ -114,10 +111,7 @@ async def read_dataresource(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = ResourceConfig.construct(**json.loads(await cache.get(resource_id)))
+    config = ResourceConfig(**json.loads(await cache.get(resource_id)))
 
     session_data: "Optional[Dict[str, Any]]" = (
         None if not session_id else json.loads(await cache.get(session_id))
@@ -165,10 +159,7 @@ async def initialize_dataresource(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = ResourceConfig.construct(**json.loads(await cache.get(resource_id)))
+    config = ResourceConfig(**json.loads(await cache.get(resource_id)))
 
     session_data: "Optional[Dict[str, Any]]" = (
         None if not session_id else json.loads(await cache.get(session_id))

app/routers/mapping.py

@@ -72,10 +72,7 @@ async def get_mapping(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = MappingConfig.construct(**json.loads(await cache.get(mapping_id)))
+    config = MappingConfig(**json.loads(await cache.get(mapping_id)))
 
     mapping_strategy = create_strategy("mapping", config)
     session_data: "Optional[Dict[str, Any]]" = (
@@ -109,10 +106,7 @@ async def initialize_mapping(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = MappingConfig.construct(**json.loads(await cache.get(mapping_id)))
+    config = MappingConfig(**json.loads(await cache.get(mapping_id)))
 
     mapping_strategy = create_strategy("mapping", config)
     session_data: "Optional[Dict[str, Any]]" = (

app/routers/session.py

@@ -159,10 +159,7 @@ async def update_session(
     if not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    session = Session.construct(**json.loads(await cache.get(session_id)))
+    session = Session(**json.loads(await cache.get(session_id)))
     session.update(updated_session)
     await cache.set(session_id, session.json().encode("utf-8"))
     return session
@@ -183,10 +180,7 @@ async def get_session(
     if not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    return Session.construct(**json.loads(await cache.get(session_id)))
+    return Session(**json.loads(await cache.get(session_id)))
 
 
 @ROUTER.delete(

app/routers/transformation.py

@@ -74,12 +74,7 @@ async def get_transformation_status(
             transformation_id, "transformation_id"
         )
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = TransformationConfig.construct(
-        **json.loads(await cache.get(transformation_id))
-    )
+    config = TransformationConfig(**json.loads(await cache.get(transformation_id)))
 
     strategy: "ITransformationStrategy" = create_strategy("transformation", config)
     return strategy.status(task_id=task_id)
@@ -105,12 +100,7 @@ async def get_transformation(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = TransformationConfig.construct(
-        **json.loads(await cache.get(transformation_id))
-    )
+    config = TransformationConfig(**json.loads(await cache.get(transformation_id)))
 
     strategy: "ITransformationStrategy" = create_strategy("transformation", config)
     session_data: "Optional[Dict[str, Any]]" = (
@@ -147,12 +137,7 @@ async def execute_transformation(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = TransformationConfig.construct(
-        **json.loads(await cache.get(transformation_id))
-    )
+    config = TransformationConfig(**json.loads(await cache.get(transformation_id)))
 
     strategy: "ITransformationStrategy" = create_strategy("transformation", config)
     session_data: "Optional[Dict[str, Any]]" = (
@@ -189,12 +174,7 @@ async def initialize_transformation(
     if session_id and not await cache.exists(session_id):
         raise httpexception_404_item_id_does_not_exist(session_id, "session_id")
 
-    # Using `.construct` here to avoid validation of already validated data.
-    # This is a slight speed up.
-    # https://pydantic-docs.helpmanual.io/usage/models/#creating-models-without-validation
-    config = TransformationConfig.construct(
-        **json.loads(await cache.get(transformation_id))
-    )
+    config = TransformationConfig(**json.loads(await cache.get(transformation_id)))
 
     strategy: "ITransformationStrategy" = create_strategy("transformation", config)
     session_data: "Optional[Dict[str, Any]]" = (

docker-compose_dev.yml

@@ -12,12 +12,14 @@ services:
       OTEAPI_REDIS_HOST: redis
       OTEAPI_REDIS_PORT: 6379
       OTEAPI_prefix: "${OTEAPI_prefix:-/api/v1}"
+      PATH_TO_OTEAPI_CORE: "${PATH_TO_OTEAPI_CORE:-/dev/null}"
     depends_on:
       - redis
     networks:
       - otenet
     volumes:
-      - ${PWD}:/app
+      - "${PWD}:/app"
+      - "${PATH_TO_OTEAPI_CORE:-/dev/null}:/oteapi_core"
 
   redis:
     image: redis:latest