Infer WorkflowRun from CreateAction in five-safes SHACL profiles by EttoreM · Pull Request #104 · eScienceLab/rocrate-validator

EttoreM · 2026-03-20T10:52:06Z

Closes #43.

This PR implements a solution for treating the workflow-execution CreateAction as a dedicated ro-crate:WorkflowRun entity across the Five Safes SHACL profiles.

At a high level:

A hidden SHACL rule was added to the relevant TTL files to infer the triple CreateAction -> rdf:type -> ro-crate:WorkflowRun for the CreateAction whose instrument matches RootDataEntity -> mainEntity.
All SHACL constraints that are really about the actual workflow run were then retargeted from generic CreateAction to WorkflowRun, with corresponding updates on shapes' names and messages.
Tests were updated accordingly.

One important testing detail:

In the Python tests, the graph mutations still target entities of type CreateAction, not WorkflowRun.
This is intentional: WorkflowRun is inferred by SHACL during validation, so it is safer for the tests to alter the source CreateAction nodes in the RO-Crate metadata graph.
This remains correct as long as the tests are understood to target the specific CreateAction that is effectively the workflow run, and not any other CreateAction that may also be present in the crate.

A separate consistency note:

In prefixes.ttl, the RO-Crate namespace is exposed in SPARQL via rocrate (without the dash), while elsewhere in the codebase we also use ro-crate.
This did not originate in this PR, but it is something we may want to clean up in future to align prefix syntax across the codebase.

douglowe

I've had a read of Eli's original issue, and I think I understand now what we're doing (I didn't before - which I think may have led me to think we were doing something different here).

Many of the changes look sensible to me, and should do what we want. I've a couple of changes I'd request though.

Should we use five-safes-crate:WorkflowRun instead of ro-crate:WorkflowRun?
We should be able to transform the RDF graph once, and then use the ro-crate:WorkflowRun tag in all our tests after that. Can you create a 0_workflowrun.ttl file in the 'must' folder, which contains only this transformation - perhaps that would work?
Should we be mentioning WorkflowRun in the message strings which tests return? If this is an internal tag then will this confuse users?

rocrate_validator/profiles/five-safes-crate/may/11_workflow_execution_phase.ttl

alexhambley

Happy with this I think, just a bit concerned about the maintainability of the duplicated code block across the rules. :)

rocrate_validator/profiles/five-safes-crate/may/11_workflow_execution_phase.ttl

EttoreM · 2026-03-25T16:40:14Z

@alexhambley @douglowe

OK, I managed to centralise the WorkflowRun inference used across five-safes-crate into a single hidden SHACL rule in 0_workflow_run_inference.ttl, and removed the duplicated FindWorkflowRunAction blocks from the individual requirement files.

Also made the dependency on the RO-Crate root explicit: FindRootDataEntity in 2_root_data_entity_metadata.ttl now has sh:order 0, while FindWorkflowRunAction has sh:order 1 and targets ro-crate:RootDataEntity rather than re-deriving the root from schema:Dataset. This ensures the root is inferred first, then the WorkflowRun, before the other validation shapes run.

tests/integration/profiles/five-safes-crate/test_5src_7_requesting_workflow_run.py

rocrate_validator/profiles/five-safes-crate/must/11_workflow_execution_phase.ttl

douglowe

Thanks for merging the definition into one file - that looks good.

Can you review the messages that rules return, as well as the tests you've removed? I think we should make sure that the messages that the end user gets mention CreateAction not WorkflowRun.

… TO BE COMPLETED.

douglowe · 2026-03-27T17:44:29Z

@elichad & @alexhambley - I've finished off the last couple of message strings for Ettore, as he's on leave now. If you're okay with the PR now I'll merge it.

elichad · 2026-04-01T11:15:53Z

rocrate_validator/profiles/five-safes-crate/must/7_requested_workflow_run.ttl

        """ ;
-        sh:message "`CreateAction` --> `instrument` MUST reference the same entity as `Root Data Entity` --> `mainEntity`" ;
-    ] ;
+        sh:message "The crate MUST contain at least one `CreateAction` (corresponding to the workflow run)" ;


This message could be clearer about how the user can resolve the issue - combine the new message with the old message?

elichad · 2026-04-01T11:17:17Z

rocrate_validator/profiles/five-safes-crate/must/7_requested_workflow_run.ttl

        """ ;
-        sh:message "Each `object` in `CreateAction` MUST reference an existing entity." ;
-    ] .
+        sh:message "Each `object` in the `CreateAction` entity corresponding to the workflow run MUST reference an existing entity." ;


Suggested change

sh:message "Each `object` in the `CreateAction` entity corresponding to the workflow run MUST reference an existing entity." ;

sh:message "In the `CreateAction` entity corresponding to the workflow run, each `object` MUST reference an existing entity." ;

elichad · 2026-04-01T11:19:09Z

rocrate_validator/profiles/five-safes-crate/should/11_workflow_execution_phase.ttl

        """ ;
      sh:severity sh:Warning ;
-      sh:message "RootDataEntity SHOULD mention workflow execution object (typed CreateAction)." ;
+      sh:message "RootDataEntity SHOULD mention a workflow run object (typed CreateAction)." ;


Suggested change

sh:message "RootDataEntity SHOULD mention a workflow run object (typed CreateAction)." ;

sh:message "RootDataEntity SHOULD reference a workflow run entity (typed CreateAction) through `mentions`." ;

after making this comment I just noticed there's a very similar message in some of our tests - https://github.com/eScienceLab/rocrate-validator/pull/104/changes#diff-ddb895f3dbdf2ce99bcefe65919fb782c019baca128c2410f57823c73c8f84a9R88 - do we have two tests doing the same thing?

elichad · 2026-04-01T11:19:36Z

rocrate_validator/profiles/five-safes-crate/should/2_requesting_agent.ttl

        sh:severity sh:Warning ;
-        sh:message "The agent of a CreateAction entity SHOULD have an affiliation" ;
-    ] .
+        sh:message "The agent of the `CreateAction` corresponding to the workflowrun SHOULD have an affiliation" ;


Suggested change

sh:message "The agent of the `CreateAction` corresponding to the workflowrun SHOULD have an affiliation" ;

sh:message "The agent of the `CreateAction` corresponding to the workflow run SHOULD have an affiliation" ;

elichad · 2026-04-01T11:22:27Z

rocrate_validator/profiles/ro-crate/must/2_root_data_entity_metadata.ttl



 ro-crate:FindRootDataEntity a sh:NodeShape, validator:HiddenShape;
+    sh:order 0 ;


I don't think sh:order does anything for us here. From https://www.w3.org/TR/shacl/#order (emphasis added):

Property shapes may have one value for the property sh:order to indicate the relative order of the property shape for purposes such as form building. The values of sh:order are decimals. sh:order is not used for validation purposes and may be used with any type of subjects. If present at property shapes, the recommended use of sh:order is to sort the property shapes in an ascending order, for example so that properties with smaller order are placed above (or to the left) of properties with larger order.

elichad · 2026-04-01T11:28:43Z

rocrate_validator/profiles/five-safes-crate/ontology.ttl

+# # #################################################################
+
+# Declare a WorkflowRun class
+ro-crate:WorkflowRun rdf:type owl:Class ;


might be too late for this, but I think a slightly preferable name for this class would be WorkflowRunAction - signifying to devs that it's a subclass of Action.

elichad · 2026-04-01T11:29:04Z

rocrate_validator/profiles/five-safes-crate/must/0_workflow_run_inference.ttl

+
+
+ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape;
+    sh:order 1 ;


Same comment about sh:order here

Infer WorkflowRun from CreateAction in five-safes SHACL profiles

b7df62f

EttoreM self-assigned this Mar 20, 2026

EttoreM linked an issue Mar 20, 2026 that may be closed by this pull request

Run CreateAction checks only against the CreateAction(s) that the profile cares about #43

Open

EttoreM requested review from douglowe and elichad March 20, 2026 11:08

douglowe requested a review from alexhambley March 24, 2026 15:40

douglowe requested changes Mar 24, 2026

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Modification of @graph is now centralised

a15258e

EttoreM requested review from alexhambley and douglowe March 25, 2026 16:40

douglowe reviewed Mar 26, 2026

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EttoreM and others added 4 commits March 27, 2026 11:59

PARTIALLY amended the error messages that appear as validation fails.…

2bd4354

… TO BE COMPLETED.

completion of amended error messages for workflowrun / createaction

8f19274

linting test files

5b948c1

update 5s-rocrate tests

08dd31e

elichad reviewed Apr 1, 2026

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	sh:message "Each `object` in the `CreateAction` entity corresponding to the workflow run MUST reference an existing entity." ;
	sh:message "In the `CreateAction` entity corresponding to the workflow run, each `object` MUST reference an existing entity." ;

	sh:message "RootDataEntity SHOULD mention a workflow run object (typed CreateAction)." ;
	sh:message "RootDataEntity SHOULD reference a workflow run entity (typed CreateAction) through `mentions`." ;

	sh:message "The agent of the `CreateAction` corresponding to the workflowrun SHOULD have an affiliation" ;
	sh:message "The agent of the `CreateAction` corresponding to the workflow run SHOULD have an affiliation" ;



		ro-crate:FindRootDataEntity a sh:NodeShape, validator:HiddenShape;
		sh:order 0 ;



		ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape;
		sh:order 1 ;

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EttoreM commented Mar 20, 2026 •

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