Add path for extra RO-Crate profiles

README.md

@@ -21,6 +21,7 @@ This project presents a Flask-based API for validating RO-Crates.
 |------------|-----------|-------------------------|-----------------------------------------------------------------------|
 | root_path | optional  | string                 | Root path which contains the RO-Crate  |
 | webhook_url | optional  | string                 | Webhook to send validation result to  |
+| profile_name | optional | string                 | RO-Crate profile to validate against  |
 | minio_config | required  | dictionary                 | MinIO Configuration Details    |
 
 `minio_config`
@@ -167,12 +168,24 @@ curl -X 'POST' \
 
 2. Create the `.env` file for shared environment information. An example environment file is included (`example.env`), which can be copied for this purpose. But make sure to change any security settings (username and passwords).
 
-3. Build and start the services using Docker Compose:
+3. A directory containing RO-Crate profiles to replace the default RO-Crate profiles for validation may be provided. Note that this will need to contain all profile files, as the default profile data will not be used. An example of this is given in the `docker-compose-develop.yml` file, and described here:
+   1. Store the profiles in a convenient directory, e.g.: `./local/rocrate_validator_profiles`
+   2. Add a volume to the celery worker container for these, e.g.:
+   ```
+    volumes:
+      - ./local/rocrate_validator_profiles:/app/profiles:ro
+   ```
+   3. Provide the `PROFILES_PATH` environment to the flask container (not the celery worker container) to match the internal path, e.g.:
+   ```
+      - PROFILES_PATH=/app/profiles
+   ```
+
+4. Build and start the services using Docker Compose:
     ```bash
    docker compose up --build
    ```
 
-4. Set up the MinIO bucket
+5. Set up the MinIO bucket
    1. Open the MinIO web interface at `http://localhost:9000`.  
    2. Log in with your MinIO credentials.  
    3. Create a new bucket named `ro-crates`.  

app/ro_crates/routes/post_routes.py

@@ -7,7 +7,7 @@
 from apiflask import APIBlueprint, Schema
 from apiflask.fields import String, Boolean
 from marshmallow.fields import Nested
-from flask import Response
+from flask import Response, current_app
 
 from app.services.validation_service import (
     queue_ro_crate_validation_task,
@@ -81,7 +81,10 @@ def validate_ro_crate_via_id(json_data, crate_id) -> tuple[Response, int]:
     else:
         profile_name = None
 
-    return queue_ro_crate_validation_task(minio_config, crate_id, root_path, profile_name, webhook_url)
+    profiles_path = current_app.config["PROFILES_PATH"]
+
+    return queue_ro_crate_validation_task(minio_config, crate_id, root_path, profile_name,
+                                          webhook_url, profiles_path)
 
 
 @post_routes_bp.post("/validate_metadata")

app/services/validation_service.py

@@ -25,7 +25,8 @@
 
 
 def queue_ro_crate_validation_task(
-    minio_config, crate_id, root_path=None, profile_name=None, webhook_url=None
+    minio_config, crate_id, root_path=None, profile_name=None, webhook_url=None,
+    profiles_path=None
 ) -> tuple[Response, int]:
     """
     Queues an RO-Crate for validation with Celery.
@@ -51,7 +52,8 @@ def queue_ro_crate_validation_task(
         raise InvalidAPIUsage(f"No RO-Crate with prefix: {crate_id}", 400)
 
     try:
-        process_validation_task_by_id.delay(minio_config, crate_id, root_path, profile_name, webhook_url)
+        process_validation_task_by_id.delay(minio_config, crate_id, root_path,
+                                            profile_name, webhook_url, profiles_path)
         return jsonify({"message": "Validation in progress"}), 202
 
     except Exception as e:

app/tasks/validation_tasks.py

@@ -29,7 +29,8 @@
 
 @celery.task
 def process_validation_task_by_id(
-    minio_config: dict, crate_id: str, root_path: str, profile_name: str | None, webhook_url: str | None
+    minio_config: dict, crate_id: str, root_path: str, profile_name: str | None,
+    webhook_url: str | None, profiles_path: str | None
 ) -> None:
     """
     Background task to process the RO-Crate validation by ID.
@@ -56,7 +57,7 @@ def process_validation_task_by_id(
         logging.info(f"Processing validation task for {file_path}")
 
         # Perform validation:
-        validation_result = perform_ro_crate_validation(file_path, profile_name)
+        validation_result = perform_ro_crate_validation(file_path, profile_name, profiles_path=profiles_path)
 
         if isinstance(validation_result, str):
             logging.error(f"Validation failed: {validation_result}")
@@ -158,14 +159,15 @@ def process_validation_task_by_metadata(
 
 
 def perform_ro_crate_validation(
-    file_path: str, profile_name: str | None, skip_checks_list: Optional[list] = None
+    file_path: str, profile_name: str | None, skip_checks_list: Optional[list] = None, profiles_path: Optional[str] = None
 ) -> ValidationResult | str:
     """
     Validates an RO-Crate using the provided file path and profile name.
 
     :param file_path: The path to the RO-Crate file to validate
     :param profile_name: The name of the validation profile to use. Defaults to None. If None, the CRS4 validator will
         attempt to determine the profile.
+    :param profiles_path: The path to the profiles definition directory
     :param skip_checks_list: A list of checks to skip, if needed
     :return: The validation result.
     :raises Exception: If an error occurs during the validation process.
@@ -183,7 +185,8 @@ def perform_ro_crate_validation(
         settings = services.ValidationSettings(
             rocrate_uri=full_file_path,
             **({"profile_identifier": profile_name} if profile_name else {}),
-            **({"skip_checks": skip_checks_list} if skip_checks_list else {})
+            **({"skip_checks": skip_checks_list} if skip_checks_list else {}),
+            **({"profiles_path": profiles_path} if profiles_path else {})
         )
 
         return services.validate(settings)

app/utils/config.py

@@ -10,34 +10,32 @@
 from flask import Flask
 
 
+def get_env(name: str, default=None, required=False):
+    value = os.environ.get(name, default)
+    if required and value is None:
+        raise RuntimeError(f"Missing required environment variable: {name}")
+    return value
+
+
 class Config:
     """Base configuration class for the Flask application."""
 
-    SECRET_KEY = os.getenv("SECRET_KEY", "my_precious")
-
     # Celery configuration:
-    CELERY_BROKER_URL = os.getenv("CELERY_BROKER_URL")
-    CELERY_RESULT_BACKEND = os.getenv("CELERY_RESULT_BACKEND")
+    CELERY_BROKER_URL = get_env("CELERY_BROKER_URL", required=False)
+    CELERY_RESULT_BACKEND = get_env("CELERY_RESULT_BACKEND", required=False)
 
-    # MinIO configuration:
-    MINIO_ENDPOINT = os.getenv("MINIO_ENDPOINT")
-    MINIO_ACCESS_KEY = os.getenv("MINIO_ACCESS_KEY")
-    MINIO_SECRET_KEY = os.getenv("MINIO_SECRET_KEY")
-    MINIO_BUCKET_NAME = os.getenv("MINIO_BUCKET_NAME", "bucket-name")
+    # rocrate validator configuration:
+    PROFILES_PATH = get_env("PROFILES_PATH", required=False)
 
 
 class DevelopmentConfig(Config):
     """Development configuration class."""
-
     DEBUG = True
-    ENV = "development"
 
 
 class ProductionConfig(Config):
     """Production configuration class."""
-
     DEBUG = False
-    ENV = "production"
 
 
 class InvalidAPIUsage(Exception):
@@ -63,10 +61,13 @@ def make_celery(app: Flask = None) -> Celery:
     :param app: The Flask application to use.
     :return: The Celery instance.
     """
+    env = os.environ.get("FLASK_ENV", "development")
+    config_cls = ProductionConfig if env == "production" else DevelopmentConfig
+
     celery = Celery(
         app.import_name if app else __name__,
-        broker=os.getenv("CELERY_BROKER_URL"),
-        backend=os.getenv("CELERY_RESULT_BACKEND"),
+        broker=config_cls.CELERY_BROKER_URL,
+        backend=config_cls.CELERY_RESULT_BACKEND,
     )
 
     if app:

docker-compose-develop.yml

@@ -16,6 +16,7 @@ services:
       - MINIO_ROOT_USER=${MINIO_ROOT_USER}
       - MINIO_ROOT_PASSWORD=${MINIO_ROOT_PASSWORD}
       - MINIO_BUCKET_NAME=${MINIO_BUCKET_NAME}
+      - PROFILES_PATH=/app/profiles
     depends_on:
       - redis
       - minio
@@ -28,13 +29,11 @@ services:
     environment:
       - CELERY_BROKER_URL=redis://redis:6379/0
       - CELERY_RESULT_BACKEND=redis://redis:6379/0
-      - MINIO_ENDPOINT=${MINIO_ENDPOINT}
-      - MINIO_ROOT_USER=${MINIO_ROOT_USER}
-      - MINIO_ROOT_PASSWORD=${MINIO_ROOT_PASSWORD}
-      - MINIO_BUCKET_NAME=${MINIO_BUCKET_NAME}
     depends_on:
       - redis
       - minio
+    volumes:
+      - ./tests/data/rocrate_validator_profiles:/app/profiles:ro
 
   redis:
     image: "redis:alpine"

docker-compose.yml

@@ -26,10 +26,6 @@ services:
     environment:
       - CELERY_BROKER_URL=redis://redis:6379/0
       - CELERY_RESULT_BACKEND=redis://redis:6379/0
-      - MINIO_ENDPOINT=${MINIO_ENDPOINT}
-      - MINIO_ROOT_USER=${MINIO_ROOT_USER}
-      - MINIO_ROOT_PASSWORD=${MINIO_ROOT_PASSWORD}
-      - MINIO_BUCKET_NAME=${MINIO_BUCKET_NAME}
     depends_on:
       - redis
       - minio

tests/data/rocrate_validator_profiles/alpha-crate/1_root_data_entity.ttl

@@ -0,0 +1,46 @@
+# Copyright (c) 2025 eScience Lab, The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix alpha-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/alpha-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix validator: <https://github.com/crs4/rocrate-validator/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+
+alpha-crate:RootDataEntityRequiredProperties
+    a sh:NodeShape ;
+    sh:name "RootDataEntity" ;
+    sh:targetClass ro-crate:RootDataEntity ;
+
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "sourceOrganization" ;
+        sh:path schema:sourceOrganization;
+        sh:minCount 1 ;
+        sh:severity sh:Violation ;
+        sh:message """The Root Data Entity MUST have a `sourceOrganization` property.""" ;
+    ] ;
+
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "sourceOrganization" ;
+        sh:path schema:sourceOrganization ;
+        sh:class schema:Project ;
+        sh:severity sh:Violation ;
+        sh:message """The `sourceOrganization` property of the RootDataEntity MUST point to a Project entity.""" ;
+    ] .

tests/data/rocrate_validator_profiles/alpha-crate/profile.ttl

@@ -0,0 +1,55 @@
+# Copyright (c) 2024-2025 CRS4, University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix dct: <http://purl.org/dc/terms/> .
+@prefix prof: <http://www.w3.org/ns/dx/prof/> .
+@prefix role: <http://www.w3.org/ns/dx/prof/role/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+<https://w3id.org/alpha-crate/0.1>
+    a prof:Profile ;
+
+    # the Profile's label
+    rdfs:label "Alpha RO-Crate 0.1" ;
+
+    # regular metadata, a basic description of the Profile
+    rdfs:comment """Alpha RO-Crate Metadata Specification 0.1"""@en ;
+
+    # URI of the publisher of the Metadata Specification
+    dct:publisher <https://w3id.org/alpha-crate> ;
+
+    # This profile is a transitive profile of the RO-Crate Metadata Specification
+    prof:isTransitiveProfileOf <https://w3id.org/ro/crate/1.1> ;
+
+    # this profile has a JSON-LD context resource
+    prof:hasResource [
+        a prof:ResourceDescriptor ;
+
+        # it's in JSON-LD format
+        dct:format <https://w3id.org/mediatype/application/ld+json> ;
+
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
+        dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
+
+        # this profile resource plays the role of "Vocabulary"
+        # described in this ontology's accompanying Roles vocabulary
+        prof:hasRole role:Vocabulary ;
+
+        # this profile resource's actual file
+        prof:hasArtifact <https://w3id.org/ro/terms/workflow-run/context> ;
+    ] ;
+
+    # a short code to refer to the Profile with when a URI can't be used
+    prof:hasToken "alpha-crate" ;
+.

tests/data/rocrate_validator_profiles/five-safes-crate/may/11_workflow_execution_phase.ttl

@@ -0,0 +1,64 @@
+# Copyright (c) 2025 eScience Lab, The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix five-safes-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/five-safes-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix validator: <https://github.com/crs4/rocrate-validator/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+
+five-safes-crate:WorkflowexecutionObjectHasStartTimeIfBegun
+    a sh:NodeShape ;
+    sh:name "WorkflowExecution" ;
+    sh:description (
+        "The workflow execution object MAY have a startTime if actionStatus is "
+        "either ActiveActionStatus, CompletedActionStatus or FailedActionStatus."
+    ) ;
+
+    sh:target [
+        a sh:SPARQLTarget ;
+        sh:select """
+            PREFIX schema: <http://schema.org/>
+            PREFIX rdf:    <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+            SELECT ?this
+            WHERE {
+                ?this rdf:type schema:CreateAction ;
+                      schema:actionStatus ?status .
+                FILTER(?status IN (
+                    "http://schema.org/CompletedActionStatus",
+                    "http://schema.org/FailedActionStatus",
+                    "http://schema.org/ActiveActionStatus"
+                ))
+            }
+        """ ;
+    ] ;
+
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "StartTime" ;
+        sh:path schema:startTime ;
+        sh:minCount 1 ;
+        sh:maxCount 1 ;
+        sh:severity sh:Info ;
+        sh:description (
+            "The workflow execution object MAY have a startTime if actionStatus is "
+            "either ActiveActionStatus, CompletedActionStatus or FailedActionStatus."
+        ) ;
+        sh:message "The workflow execution object MAY have a startTime if actionStatus is either ActiveActionStatus, CompletedActionStatus or FailedActionStatus." ;
+    ] .