Infer WorkflowRun from CreateAction in five-safes SHACL profiles #104
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| # 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. | ||
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| @prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-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/> . | ||
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| ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape; | ||
| sh:order 1 ; | ||
| sh:name "Identify the CreateAction Entity that corresponds to the Workflow run" ; | ||
| sh:description """The Workflow Run is the CreateAction entity that refers to Workflow run. | ||
| This is identified by checking that the CreateAction entity has an `instrument` property | ||
| that references the same entity as the `mainEntity` property of the Root Data Entity.""" ; | ||
| sh:target [ | ||
| a sh:SPARQLTarget ; | ||
| sh:prefixes ro-crate:sparqlPrefixes ; | ||
| sh:select """ | ||
| SELECT ?this | ||
| WHERE { | ||
| ?this a schema:CreateAction ; | ||
| schema:instrument ?instrument . | ||
| ?root a ro-crate:RootDataEntity ; | ||
| schema:mainEntity ?instrument . | ||
| } | ||
| """ | ||
| ] ; | ||
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| sh:rule [ | ||
| a sh:TripleRule ; | ||
| sh:subject sh:this ; | ||
| sh:predicate rdf:type ; | ||
| sh:object ro-crate:WorkflowRun ; | ||
| ] . | ||
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| @@ -0,0 +1,37 @@ | ||
| # Copyright (c) 2024-2026 CRS4 | ||
| # | ||
| # 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. | ||
|
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| @prefix ro: <./> . | ||
| @prefix owl: <http://www.w3.org/2002/07/owl#> . | ||
| @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . | ||
| @prefix xml: <http://www.w3.org/XML/1998/namespace#> . | ||
| @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . | ||
| @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | ||
| @prefix schema: <http://schema.org/> . | ||
| @prefix rocrate: <https://w3id.org/ro/crate/1.1/> . | ||
| @prefix bioschemas: <https://bioschemas.org/> . | ||
| @prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> . | ||
| @prefix isa-ro-crate: <https://github.com/crs4/rocrate-validator/profiles/isa-ro-crate/> . | ||
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| <urn:absolute:.> rdf:type owl:Ontology ; | ||
| owl:versionIRI <urn:absolute:1.0> . | ||
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| # # ################################################################# | ||
| # # # Classes | ||
| # # ################################################################# | ||
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| # Declare a WorkflowRun class | ||
| ro-crate:WorkflowRun rdf:type owl:Class ; | ||
|
There was a problem hiding this comment. might be too late for this, but I think a slightly preferable name for this class would be |
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| rdfs:subClassOf schema:CreateAction ; | ||
| rdfs:label "WorkflowRun"@en . | ||
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@@ -22,20 +22,19 @@ | |
| @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . | ||
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| five-safes-crate:WorkflowRunHasResultIfActionCompleted | ||
| a sh:NodeShape ; | ||
| sh:name "WorkflowRun" ; | ||
| sh:description "The `CreateAction` corresponding to the workflow run, with CompletedActionStatus, SHOULD have the `schema:result` property." ; | ||
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| sh:target [ | ||
| a sh:SPARQLTarget ; | ||
| sh:name "WorkflowRun" ; | ||
| sh:description "The `CreateAction` corresponding to the workflow run, with CompletedActionStatus, SHOULD have the `result` property." ; | ||
| sh:prefixes ro-crate:sparqlPrefixes ; | ||
| sh:select """ | ||
| SELECT ?this WHERE { | ||
| ?this a ro-crate:WorkflowRun ; | ||
| schema:actionStatus "http://schema.org/CompletedActionStatus" . | ||
| } | ||
| """ | ||
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@@ -48,22 +47,22 @@ five-safes-crate:CreateActionHasResultIfActionCompleted | |
| sh:path schema:result ; | ||
| sh:minCount 1 ; | ||
| sh:severity sh:Warning ; | ||
| sh:message "The `CreateAction` corresponding to the workflow run, with CompletedActionStatus, SHOULD have the `result` property." ; | ||
| ] . | ||
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| five-safes-crate:WorkflowRunResultOutputsHaveAllowedTypes | ||
| a sh:NodeShape ; | ||
| sh:name "Output" ; | ||
| sh:description "Result SHOULD have a `@type` among an allowed set of values." ; | ||
| sh:target [ | ||
| a sh:SPARQLTarget ; | ||
| sh:prefixes ro-crate:sparqlPrefixes ; | ||
| sh:select """ | ||
| SELECT ?this | ||
| WHERE { | ||
| ?workflowRun a ro-crate:WorkflowRun . | ||
| ?workflowRun schema:result ?this . | ||
| } | ||
| """ ; | ||
| ] ; | ||
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@@ -86,4 +85,3 @@ five-safes-crate:CreateActionResultOutputsHaveAllowedTypes | |
| sh:class schema:PropertyValue; | ||
| ] | ||
| ) . | ||
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@@ -23,47 +23,46 @@ | |||||
| @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . | ||||||
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| five-safes-crate:RootDataEntityShouldMentionWorkflow | ||||||
| a sh:NodeShape ; | ||||||
| sh:name "RootDataEntity" ; | ||||||
| sh:description "RootDataEntity SHOULD mention a workflow run object (typed CreateAction)." ; | ||||||
| sh:targetClass ro-crate:RootDataEntity ; | ||||||
| sh:sparql [ | ||||||
| a sh:SPARQLConstraint ; | ||||||
| sh:name "mentions" ; | ||||||
| sh:select """ | ||||||
| PREFIX schema: <http://schema.org/> | ||||||
| PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> | ||||||
| SELECT $this | ||||||
| WHERE { | ||||||
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| FILTER NOT EXISTS { | ||||||
| $this schema:mentions ?workflowExecution . | ||||||
| ?workflowExecution a rocrate:WorkflowRun . | ||||||
| } | ||||||
| } | ||||||
| """ ; | ||||||
| sh:severity sh:Warning ; | ||||||
| sh:message "RootDataEntity SHOULD mention a workflow run object (typed CreateAction)." ; | ||||||
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There was a problem hiding this comment.
Suggested change
There was a problem hiding this comment. 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? |
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| ] . | ||||||
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| five-safes-crate:WorkflowexecutionObjectHasEndTimeIfEnded | ||||||
| a sh:NodeShape ; | ||||||
| sh:name "WorkflowExecution" ; | ||||||
| sh:description "The workflow run object SHOULD have an endTime property if it has ended." ; | ||||||
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| sh:target [ | ||||||
| a sh:SPARQLTarget ; | ||||||
| sh:select """ | ||||||
| PREFIX schema: <http://schema.org/> | ||||||
| PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> | ||||||
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| SELECT ?this | ||||||
| WHERE { | ||||||
| ?this a rocrate:WorkflowRun ; | ||||||
| schema:actionStatus ?status . | ||||||
| FILTER(?status IN ( | ||||||
| "http://schema.org/CompletedActionStatus", | ||||||
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@@ -82,4 +81,4 @@ five-safes-crate:WorkflowexecutionObjectHasEndTimeIfEnded | |||||
| sh:severity sh:Warning ; | ||||||
| sh:description "The workflow execution object SHOULD have an endTime property if it has ended." ; | ||||||
| sh:message "The workflow execution object SHOULD have an endTime property if it has ended." ; | ||||||
| ] . | ||||||
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@@ -30,7 +30,7 @@ five-safes-crate:AgentIsMemberOf | |
| sh:prefixes ro-crate:sparqlPrefixes ; | ||
| sh:select """ | ||
| SELECT DISTINCT ?this WHERE { | ||
| ?action a rocrate:WorkflowRun ; | ||
| schema:agent ?this . | ||
| } | ||
| """ | ||
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@@ -43,4 +43,4 @@ five-safes-crate:AgentIsMemberOf | |
| sh:minCount 1 ; | ||
| sh:severity sh:Warning ; | ||
| sh:message """The Requesting Agent SHOULD have a `memberOf` property.""" ; | ||
| ] . | ||
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@@ -33,7 +33,7 @@ five-safes-crate:ResponsibleProjectMemberAndSourceOrganizationIntersection | |
| sh:prefixes ro-crate:sparqlPrefixes ; | ||
| sh:select """ | ||
| SELECT DISTINCT ?this WHERE { | ||
| ?action a ro-crate:WorkflowRun ; | ||
| schema:agent ?this . | ||
| ?this a schema:Person ; | ||
| schema:memberOf ?project ; | ||
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@@ -59,4 +59,4 @@ five-safes-crate:ResponsibleProjectMemberAndSourceOrganizationIntersection | |
| } | ||
| """ ; | ||
| sh:message """At least one of the organisations that are members of the responsible project SHOULD be included in the Requesting Agent's affiliations, if such properties exist.""" ; | ||
| ] . | ||
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Same comment about
sh:orderhere