24.08.30 (#348)

* BCO scoring changes * Add New Production Deployment md Changes to be committed: deleted: docs/bco_scores.json modified: docs/deployment/productionDeployment.md new file: docs/newProductionInstance.md * Update config.md * Add API endpoint for basic comaprison Changes to be committed: modified: biocompute/apis.py modified: biocompute/urls.py modified: requirements.txt * Fix Django CI issue (#340) biocompute-objects/portal_userdb#380 Changes to be committed: modified: .github/workflows/django.yml modified: biocompute/apis.py modified: biocompute/models.py modified: config/settings.py modified: config/urls.py * Update to BcoValidator.load_schema (#341) Updated the function to check locally for the most used schemas. Improves testing and speed in BCO validation. Changes to be committed: modified: biocompute/services.py renamed: config/IEEE/2791object.json -> config/schemas/2791object.json new file: config/schemas/dataset_extension.json renamed: config/IEEE/description_domain.json -> config/schemas/description_domain.json renamed: config/IEEE/error_domain.json -> config/schemas/error_domain.json renamed: config/IEEE/execution_domain.json -> config/schemas/execution_domain.json new file: config/schemas/fhir_extension.json new file: config/schemas/galaxy_extension.json renamed: config/IEEE/io_domain.json -> config/schemas/io_domain.json new file: config/schemas/license_extension.json renamed: config/IEEE/parametric_domain.json -> config/schemas/parametric_domain.json renamed: config/IEEE/provenance_domain.json -> config/schemas/provenance_domain.json new file: config/schemas/scm_extension.json renamed: config/IEEE/usability_domain.json -> config/schemas/usability_domain.json * Add additional schema files and reorganize Changes to be committed: modified: biocompute/services.py new file: config/schemas/1.1.0/dataset_extension.json new file: config/schemas/1.1.0/fhir_extension.json new file: config/schemas/1.1.0/galaxy_extension.json new file: config/schemas/1.1.0/license_extension.json new file: config/schemas/1.1.0/scm_extension.json renamed: config/schemas/dataset_extension.json -> config/schemas/1.2.0/dataset_extension.json renamed: config/schemas/fhir_extension.json -> config/schemas/1.2.0/fhir_extension.json renamed: config/schemas/galaxy_extension.json -> config/schemas/1.2.0/galaxy_extension.json renamed: config/schemas/license_extension.json -> config/schemas/1.2.0/license_extension.json renamed: config/schemas/scm_extension.json -> config/schemas/1.2.0/scm_extension.json renamed: config/schemas/2791object.json -> config/schemas/2791/2791object.json renamed: config/schemas/description_domain.json -> config/schemas/2791/description_domain.json renamed: config/schemas/error_domain.json -> config/schemas/2791/error_domain.json renamed: config/schemas/execution_domain.json -> config/schemas/2791/execution_domain.json renamed: config/schemas/io_domain.json -> config/schemas/2791/io_domain.json renamed: config/schemas/parametric_domain.json -> config/schemas/2791/parametric_domain.json renamed: config/schemas/provenance_domain.json -> config/schemas/2791/provenance_domain.json renamed: config/schemas/usability_domain.json -> config/schemas/2791/usability_domain.json modified: config/settings.py modified: requirements.txt * Add instructions for Docker deployment Changes to be committed: modified: Dockerfile modified: docker-compose.yml modified: docs/deployment/dockerDeployment.md new file: entrypoint.sh * Update comparison API (#344) Changes to be committed: modified: biocompute/apis.py * Add API for LDH (#347) #333 Changes to be committed: modified: biocompute/apis.py modified: biocompute/selectors.py modified: biocompute/services.py modified: biocompute/urls.py --------- Co-authored-by: Kiran Sen <[email protected]> Co-authored-by: Kiran Sen <[email protected]>
biocompute-objects · Aug 30, 2024 · 30d2e95 · 30d2e95
1 parent 2ca9b40
commit 30d2e95
Show file tree

Hide file tree

Showing 4 changed files with 123 additions and 24 deletions.
diff --git a/biocompute/apis.py b/biocompute/apis.py
@@ -19,7 +19,9 @@
     user_can_publish_draft,
     user_can_publish_prefix,
     prefix_from_object_id,
+    get_authorized_bcos
 )
+from biocompute.services import convert_to_ldh
 from config.services import (
     legacy_api_converter,
     bulk_response_constructor,
@@ -910,27 +912,71 @@ def post(self, request):
         accepted_requests = True
         data = request.data
 
-        try:
-
-            for index, comparison in enumerate(data):
-                new_bco, old_bco = comparison
-                identifier = new_bco["object_id"]+ " vs " + old_bco["object_id"]
-
-                result = DeepDiff(new_bco, old_bco)
-                parsed_results = {
-                    'dictionary_item_removed': list(result['dictionary_item_removed']),
-                    'values_changed': list(result['values_changed']),
-                    'iterable_item_removed': list(result['iterable_item_removed'])
-                }
+        for index, comparison in enumerate(data):
+            new_bco, old_bco = comparison
+            identifier = new_bco["object_id"]+ " vs " + old_bco["object_id"]
 
-                response_data.append(bulk_response_constructor(
-                    identifier = identifier,
-                    status="SUCCESS",
-                    code=200,
-                    data=parsed_results
-                ))
+            response_data.append(bulk_response_constructor(
+                identifier = identifier,
+                status="SUCCESS",
+                code=200,
+                data=DeepDiff(new_bco, old_bco).to_json()
+            ))
+
+        status_code = response_status(accepted_requests, rejected_requests)
+        return Response(status=status_code, data=response_data)
+
+
+class ConverToLDH(APIView):
+    """Convert BCO to LDH Format
+
+    -------------------
+    Provides an API endpoint for converting BioCompute Objects (BCOs) to a LDH 
+    compatable format.
+
+    Example usage with curl:
+    ```shell
+    curl -X GET "http://localhost:8000/api/objects/?contents=review&prefix=BCO&owner=tester&object_id=BCO" -H "accept: application/json"
+    ```
+
+    This API view is accessible to any user without authentication requirements.
+    """
+    authentication_classes = []
+    permission_classes = [AllowAny]
 
-            status_code = response_status(accepted_requests, rejected_requests)
-            return Response(status=status_code, data=response_data)
-        except Exception:
-            return Response(status=status.HTTP_400_BAD_REQUEST, data={})
+    @swagger_auto_schema(
+        operation_id="convert_to_ldh",
+        manual_parameters=[
+            openapi.Parameter("object_id",
+                openapi.IN_QUERY,
+                description="Object ID to be converted.",
+                type=openapi.TYPE_STRING,
+                default="http://127.0.0.1:8000/BCO_000000/1.0"
+            )
+        ],
+        responses={
+            200: "Success. Object contents converted",
+            404: "Not found. That BCO could not be found on the server or The "\
+                 "requestor does not have appropriate permissions."
+        },
+        tags=["BCO Management"],
+    )
+
+    def get(self, request):
+        authorized_bcos = get_authorized_bcos(request.user.id)
+
+        object_id = request.GET["object_id"]
+        if object_id in authorized_bcos:
+            data  = convert_to_ldh(
+                object_id=object_id,
+                username=request.user.username
+            )
+
+            return Response(status=status.HTTP_200_OK, data=data)
+        else:
+            return Response(
+                status=status.HTTP_404_NOT_FOUND,
+                data={"message": f"{object_id}, could not be found "\
+                      + "on the server or user does not have permissions."
+                }
+            )
diff --git a/biocompute/selectors.py b/biocompute/selectors.py
@@ -237,7 +237,7 @@ def get_authorized_bcos(user: User):
 
     Returns:
     - QuerySet: 
-        A Django QuerySet containing the BCOs the user is authorized to access.
+        A Django QuerySet containing the BCO object_ids the user is authorized to access.
     """
 
     bcos = Bco.objects.filter(

diff --git a/biocompute/services.py b/biocompute/services.py
@@ -1,6 +1,9 @@
 #!/usr/bin/env python3
 # biocopmute/services.py
 
+import datetime
+import os
+import glob
 import copy
 import json
 import jsonref
@@ -654,3 +657,51 @@ def bco_score(bco_instance: Bco) -> Bco:
     bco_instance.score = base_score
 
     return bco_instance
+
+def convert_to_ldh(object_id, username):
+    """
+    """
+
+    data = Bco.objects.get(object_id=object_id).contents
+    contents = {}
+    contents['entType'] = 'BioCompute Object'
+    contents['entIri'] = data['object_id']
+    contents['entId'] = data['object_id'].split('/')[-2]
+    contents['modified'] = datetime.datetime.utcnow().isoformat()+'Z'
+    contents['modifier'] = username
+    contents['entContent'] = {}
+
+
+    # contents['id'] = get_id()
+    # contents['IdFor'] = get_id_for()
+    contents['entAliases'] = [contents['entId'], contents['entIri'], contents['entType']]
+
+
+    try:
+        contents['entContent']['provenance'] = data['provenance_domain']
+    except KeyError:
+        pass
+    try:
+        contents['entContent']['usability'] = data['usability_domain']
+    except KeyError:
+        pass
+    try:
+        contents['entContent']['description'] = data['description_domain']
+    except KeyError:
+        pass
+    try:
+        contents['entContent']['execution'] = data['execution_domain']
+    except KeyError:
+        pass
+    try:
+        contents['entContent']['io'] = data['io_domain']
+    except KeyError:
+        pass
+    try:
+        contents['entContent']['parametric'] = data['parametric_domain']
+    except KeyError:
+        pass
+
+    print(contents)
+    return contents
+
diff --git a/biocompute/urls.py b/biocompute/urls.py
@@ -2,14 +2,15 @@
 """BioCompute URLs
 """
 
-from django.urls import path
+from django.urls import path, re_path
 from biocompute.apis import (
     DraftsCreateApi,
     DraftsModifyApi,
     DraftsPublishApi,
     PublishBcoApi,
     ValidateBcoApi,
     CompareBcoApi,
+    ConverToLDH,
 )
 
 urlpatterns = [
@@ -19,4 +20,5 @@
     path("objects/validate/", ValidateBcoApi.as_view()),
     path("objects/publish/", PublishBcoApi.as_view()),
     path("objects/compare/", CompareBcoApi.as_view()),
+    re_path("objects/convert_to_ldh/$", ConverToLDH.as_view()),
 ]