Dev (#345)

* 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

---------

Co-authored-by: Kiran Sen <[email protected]>
Co-authored-by: Kiran Sen <[email protected]>

Author: HadleyKing

biocompute/apis.py

@@ -910,35 +910,27 @@ def post(self, request):
         accepted_requests = True
         data = request.data
 
-        for index, comparison in enumerate(data):
-            new_bco, old_bco = comparison
-            identifier = new_bco["object_id"]+ " vs " + old_bco["object_id"]
-
-            # new_results = validator.parse_and_validate(bco=new_bco)
-            # old_results = validator.parse_and_validate(bco=old_bco)
-            # import pdb; pdb.set_trace()
-            # new_identifier, new_results = new_results.popitem()
-            # old_identifier, old_results = bco_results.popitem()
-
-            # if results["number_of_errors"] > 0:
-            #     rejected_requests = True
-            #     bco_status = "FAILED"
-            #     status_code = 400
-            #     message = "BCO not valid"
-
-            # else:
-            #     accepted_requests = True
-            #     bco_status = "SUCCESS"
-            #     status_code = 200
-            #     message = "BCO valid"
+        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'])
+                }
 
-            response_data.append(bulk_response_constructor(
-                identifier = identifier,
-                status="SUCCESS",
-                code=200,
-                # message=message,
-                data=DeepDiff(new_bco, old_bco).to_json()
-            ))
+                response_data.append(bulk_response_constructor(
+                    identifier = identifier,
+                    status="SUCCESS",
+                    code=200,
+                    data=parsed_results
+                ))
 
-        status_code = response_status(accepted_requests, rejected_requests)
-        return Response(status=status_code, data=response_data)
+            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={})