Infer WorkflowRun from CreateAction in five-safes SHACL profiles - NEW

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

@@ -34,11 +34,11 @@ five-safes-crate:WorkflowexecutionObjectHasStartTimeIfBegun
         a sh:SPARQLTarget ;
         sh:select """
             PREFIX schema: <http://schema.org/>
-            PREFIX rdf:    <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+            PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/>
 
             SELECT ?this
             WHERE {
-                ?this rdf:type schema:CreateAction ;
+                ?this a rocrate:WorkflowRunAction ;
                       schema:actionStatus ?status .
                 FILTER(?status IN (
                     "http://schema.org/CompletedActionStatus",

rocrate_validator/profiles/five-safes-crate/may/1_responsible_project.ttl

@@ -30,7 +30,7 @@ five-safes-crate:ResponsibleProject
         sh:prefixes ro-crate:sparqlPrefixes ;
         sh:select """
             SELECT DISTINCT ?this WHERE {
-              ?action a schema:CreateAction ;
+              ?action a ro-crate:WorkflowRunAction ;
                       schema:agent ?agent .
               ?agent schema:memberOf ?this .
             }
@@ -53,4 +53,4 @@ five-safes-crate:ResponsibleProject
         sh:minCount 1 ;
         sh:severity sh:Info ;
         sh:message """The Responsible Project does not have the property `member`.""" ;
-    ] .
+    ] .

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

@@ -0,0 +1,47 @@
+# 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-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/> .
+
+
+ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape;
+    sh:order 1 ; # load this check after ro-crate:FindRootDataEntity; pySHACL sorts rules by sh:order before execution
+    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 .
+            }
+        """
+    ] ;
+
+    sh:rule [
+        a sh:TripleRule ;
+        sh:subject sh:this ;
+        sh:predicate rdf:type ;
+        sh:object ro-crate:WorkflowRunAction ;
+    ] .

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

@@ -26,30 +26,30 @@
 five-safes-crate:WorkflowMustHaveDescriptiveName
     a sh:NodeShape ;
     sh:name "WorkflowExecution" ;
-    sh:targetClass schema:CreateAction ;
+    sh:targetClass ro-crate:WorkflowRunAction ;
 
     sh:property [
         a sh:PropertyShape ;
         sh:name "name" ;
         sh:minCount 1 ;    
-        sh:description "Workflow (CreateAction) MUST have a name string of at least 10 characters." ;
+        sh:description "The `CreateAction` corresponding to the workflow run MUST have a name string of at least 10 characters." ;
         sh:path schema:name ;
         sh:datatype xsd:string ;
         sh:minLength 10 ;
         sh:severity sh:Violation ;
-        sh:message "Workflow (CreateAction) MUST have a name string of at least 10 characters." ;
+        sh:message "The `CreateAction` corresponding to the workflow run MUST have a name string of at least 10 characters." ;
     ] .
 
 
 five-safes-crate:WorkflowMustHaveActionStatusWithAllowedValues
     a sh:NodeShape ;
     sh:name "WorkflowExecution" ;
-    sh:targetClass schema:CreateAction ;
+    sh:targetClass ro-crate:WorkflowRunAction ;
     sh:property [
         a sh:PropertyShape ;
         sh:minCount 1 ;
         sh:name "actionStatus" ;
-        sh:description "WorkflowExecution MUST have an actionStatus with an allowed value (see https://schema.org/ActionStatusType)." ;
+        sh:description "`CreateAction` MUST have an actionStatus with an allowed value (see https://schema.org/ActionStatusType)." ;
         sh:path schema:actionStatus ;
         sh:in (
             "http://schema.org/PotentialActionStatus"
@@ -58,5 +58,5 @@ five-safes-crate:WorkflowMustHaveActionStatusWithAllowedValues
             "http://schema.org/FailedActionStatus"
         ) ;
         sh:severity sh:Violation ;
-        sh:message "WorkflowExecution MUST have an actionStatus with an allowed value (see https://schema.org/ActionStatusType)." ;
+        sh:message "`CreateAction` MUST have an actionStatus with an allowed value (see https://schema.org/ActionStatusType)." ;
     ] .

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

@@ -22,7 +22,7 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 
-five-safes-crate:RootDataEntityMentionsCreateAction
+five-safes-crate:RootDataEntityMentionsWorkflowRunAction
     a sh:NodeShape ;
     sh:name "RootDataEntity" ;
     sh:targetClass ro-crate:RootDataEntity ;
@@ -33,42 +33,43 @@ five-safes-crate:RootDataEntityMentionsCreateAction
         sh:name "mentions" ;
         sh:path schema:mentions;
         sh:qualifiedValueShape [
-            sh:class schema:CreateAction ;
+            sh:class ro-crate:WorkflowRunAction ;
         ] ;
         sh:qualifiedMinCount 1 ;
         sh:severity sh:Violation ;
-        sh:message "`RootDataEntity` MUST reference at least one `CreateAction` through `mentions`" ;
+        sh:message "`RootDataEntity` MUST reference at least one `CreateAction` (corresponding to the workflow run) through `mentions`" ;
     ] .
 
 
-five-safes-crate:CreateActionInstrumentAndStatus
+five-safes-crate:WorkflowRunActionExistence
     a sh:NodeShape ;
-    sh:name "CreateAction" ;
-    sh:targetClass schema:CreateAction ;
-    sh:description "" ; 
-    sh:severity sh:Violation ; # Apply to all property shapes / constraints below
+    sh:name "RootDataEntity" ;
+    sh:targetClass ro-crate:RootDataEntity ;
+    sh:description "" ;
 
-    sh:property [
-        a sh:PropertyShape ;
-        sh:name "instrument" ;
-        sh:path schema:instrument;
-        sh:minCount 1 ;
-        sh:message "`CreateAction` MUST have the `instrument` property" ;
-    ]  ;
     sh:sparql [
         a sh:SPARQLConstraint ;
-        sh:name "instrument" ;
+        sh:name "WorkflowRunAction" ;
         sh:prefixes ro-crate:sparqlPrefixes ;
         sh:select """
-        SELECT $this ?main ?instrument
-        WHERE {
-            ?root schema:mainEntity ?main .
-            $this schema:instrument ?instrument .
-            FILTER (?instrument != ?main)
-        }
+            SELECT $this
+            WHERE {
+                FILTER NOT EXISTS {
+                    ?workflowRunAction a ro-crate:WorkflowRunAction .
+                }
+            }
         """ ;
-        sh:message "`CreateAction` --> `instrument` MUST reference the same entity as `Root Data Entity` --> `mainEntity`" ;
-    ] ;
+        sh:message "The CreateAction entity corresponding to the workflow MUST reference, as an instrument, the entity that is referenced as mainEntity by the RO-Crate" ;
+    ] .
+
+
+five-safes-crate:WorkflowRunObject
+    a sh:NodeShape ;
+    sh:name "WorkflowRunAction" ;
+    sh:targetClass ro-crate:WorkflowRunAction ;
+    sh:description "" ; 
+    sh:severity sh:Violation ; # Apply to all property shapes / constraints below
+
     sh:sparql [
         a sh:SPARQLConstraint ;
         sh:prefixes ro-crate:sparqlPrefixes ;
@@ -80,5 +81,5 @@ five-safes-crate:CreateActionInstrumentAndStatus
                 FILTER NOT EXISTS {  ?object a ?type . }
             }
         """ ;
-        sh:message "Each `object` in `CreateAction` MUST reference an existing entity." ;
-    ] .
+        sh:message "In the `CreateAction` entity corresponding to the workflow run, each `object`  MUST reference an existing entity." ;
+    ] .

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

@@ -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.
+
+@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/> .
+
+<urn:absolute:.> rdf:type owl:Ontology ;
+                  owl:versionIRI <urn:absolute:1.0> .
+
+# # #################################################################
+# # #    Classes
+# # #################################################################
+
+# Declare a WorkflowRunAction class
+ro-crate:WorkflowRunAction rdf:type owl:Class ;
+  rdfs:subClassOf schema:CreateAction ;
+  rdfs:label "WorkflowRunAction"@en .

rocrate_validator/profiles/five-safes-crate/should/10_outputs.ttl

@@ -22,20 +22,19 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 
-
-five-safes-crate:CreateActionHasResultIfActionCompleted
+five-safes-crate:WorkflowRunActionHasResultIfActionCompleted
   a sh:NodeShape ;
-  sh:name "CreateAction" ;
-  sh:description "`CreateAction` with CompletedActionStatus SHOULD have the `schema:result` property." ;
+  sh:name "WorkflowRunAction" ;
+  sh:description "The `CreateAction` corresponding to the workflow run, with CompletedActionStatus, SHOULD have the `schema:result` property." ;
 
   sh:target [
         a sh:SPARQLTarget ;
-        sh:name "Result" ;
-        sh:description "`CreateAction` with CompletedActionStatus SHOULD have the `schema:result` property." ;
+        sh:name "WorkflowRunAction" ;
+        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 schema:CreateAction ;
+              ?this a ro-crate:WorkflowRunAction ;
                       schema:actionStatus "http://schema.org/CompletedActionStatus" .
             }
         """
@@ -48,22 +47,22 @@ five-safes-crate:CreateActionHasResultIfActionCompleted
     sh:path schema:result ;
     sh:minCount 1 ;
     sh:severity sh:Warning ;
-    sh:message "`CreateAction` with CompletedActionStatus SHOULD have the `result` property." ;
+    sh:message "The `CreateAction` corresponding to the workflow run, with CompletedActionStatus, SHOULD have the `result` property." ;
   ] .
 
 
-five-safes-crate:CreateActionResultOutputsHaveAllowedTypes
+five-safes-crate:WorkflowRunActionResultOutputsHaveAllowedTypes
   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 """
-        PREFIX schema: <http://schema.org/>
         SELECT ?this
         WHERE {
-          ?createAction a schema:CreateAction .
-          ?createAction schema:result ?this .
+          ?workflowRunAction a ro-crate:WorkflowRunAction .
+          ?workflowRunAction schema:result ?this .
         }
       """ ;
     ] ;
@@ -86,4 +85,3 @@ five-safes-crate:CreateActionResultOutputsHaveAllowedTypes
         sh:class schema:PropertyValue;
       ]
     ) .
-

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

@@ -23,47 +23,20 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 
-
-five-safes-crate:RootDataEntityShouldMentionWorkflow 
-    a sh:NodeShape ;
-    sh:name "RootDataEntity" ;
-    sh:description "RootDataEntity SHOULD mention workflow execution object (typed CreateAction)." ;
-    sh:targetClass ro-crate:RootDataEntity ;
-    sh:sparql [
-        a sh:SPARQLConstraint ; 
-        sh:name "mentions" ;
-        sh:select """
-        PREFIX schema: <http://schema.org/>
-        PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-        SELECT $this 
-        WHERE {
-
-            FILTER NOT EXISTS {
-                $this schema:mentions ?workflowExecution .
-                ?workflowExecution rdf:type schema:CreateAction .
-            }
-        }
-        """ ;
-      sh:severity sh:Warning ;
-      sh:message "RootDataEntity SHOULD mention workflow execution object (typed CreateAction)." ;
-   ] .
-
-
-
 five-safes-crate:WorkflowexecutionObjectHasEndTimeIfEnded
     a sh:NodeShape ;
     sh:name "WorkflowExecution" ;
-    sh:description "The workflow execution object SHOULD have an endTime property if it has ended." ;
+    sh:description "The workflow run object SHOULD have an endTime property if it has ended." ;
 
     sh:target [
         a sh:SPARQLTarget ;
         sh:select """
             PREFIX schema: <http://schema.org/>
-            PREFIX rdf:    <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+            PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/>
 
             SELECT ?this
             WHERE {
-                ?this rdf:type schema:CreateAction ;
+                ?this a rocrate:WorkflowRunAction ;
                       schema:actionStatus ?status .
                 FILTER(?status IN (
                     "http://schema.org/CompletedActionStatus",
@@ -82,4 +55,4 @@ 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." ;
-    ] .
+    ] .

rocrate_validator/profiles/five-safes-crate/should/1_requesting_agent.ttl

@@ -30,7 +30,7 @@ five-safes-crate:AgentIsMemberOf
         sh:prefixes ro-crate:sparqlPrefixes ;
         sh:select """
             SELECT DISTINCT ?this WHERE {
-              ?action a schema:CreateAction ;
+              ?action a rocrate:WorkflowRunAction ;
                       schema:agent ?this .
             }
         """
@@ -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.""" ;
-    ] .
+    ] .

rocrate_validator/profiles/five-safes-crate/should/1_responsible_project.ttl

@@ -33,7 +33,7 @@ five-safes-crate:ResponsibleProjectMemberAndSourceOrganizationIntersection
         sh:prefixes ro-crate:sparqlPrefixes ;
         sh:select """
             SELECT DISTINCT ?this WHERE {
-              ?action a schema:CreateAction ;
+              ?action a ro-crate:WorkflowRunAction ;
                       schema:agent ?this .
               ?this a schema:Person ;
                     schema:memberOf ?project ;
@@ -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.""" ;
-    ] .
+    ] .