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Infer WorkflowRun from CreateAction in five-safes SHACL profiles #104

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Infer WorkflowRun from CreateAction in five-safes SHACL profiles #104

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33 changes: 31 additions & 2 deletions rocrate_validator/profiles/five-safes-crate/may/11_workflow_execution_phase.ttl
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Expand Up @@ -22,6 +22,35 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .


ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape;
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 schema:mainEntity ?instrument ;
a schema:Dataset .
?metadatafile schema:about ?root .
FILTER(contains(str(?metadatafile), "ro-crate-metadata.json"))
}
"""
] ;

sh:rule [
a sh:TripleRule ;
sh:subject sh:this ;
sh:predicate rdf:type ;
sh:object ro-crate:WorkflowRun ;
] .


five-safes-crate:WorkflowexecutionObjectHasStartTimeIfBegun
a sh:NodeShape ;
sh:name "WorkflowExecution" ;
Expand All @@ -34,11 +63,11 @@ 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:WorkflowRun ;
schema:actionStatus ?status .
FILTER(?status IN (
"http://schema.org/CompletedActionStatus",
Expand Down
33 changes: 31 additions & 2 deletions rocrate_validator/profiles/five-safes-crate/may/1_responsible_project.ttl
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Expand Up @@ -22,6 +22,35 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .


ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape;
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 schema:mainEntity ?instrument ;
a schema:Dataset .
?metadatafile schema:about ?root .
FILTER(contains(str(?metadatafile), "ro-crate-metadata.json"))
}
"""
] ;

sh:rule [
a sh:TripleRule ;
sh:subject sh:this ;
sh:predicate rdf:type ;
sh:object ro-crate:WorkflowRun ;
] .


five-safes-crate:ResponsibleProject
a sh:NodeShape ;
sh:name "Responsible Project" ;
Expand All @@ -30,7 +59,7 @@ five-safes-crate:ResponsibleProject
sh:prefixes ro-crate:sparqlPrefixes ;
sh:select """
SELECT DISTINCT ?this WHERE {
?action a schema:CreateAction ;
?action a ro-crate:WorkflowRun ;
schema:agent ?agent .
?agent schema:memberOf ?this .
}
Expand All @@ -53,4 +82,4 @@ five-safes-crate:ResponsibleProject
sh:minCount 1 ;
sh:severity sh:Info ;
sh:message """The Responsible Project does not have the property `member`.""" ;
] .
] .
41 changes: 35 additions & 6 deletions rocrate_validator/profiles/five-safes-crate/must/11_workflow_execution_phase.ttl
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Expand Up @@ -23,33 +23,62 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .


ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape;
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 schema:mainEntity ?instrument ;
a schema:Dataset .
?metadatafile schema:about ?root .
FILTER(contains(str(?metadatafile), "ro-crate-metadata.json"))
}
"""
] ;

sh:rule [
a sh:TripleRule ;
sh:subject sh:this ;
sh:predicate rdf:type ;
sh:object ro-crate:WorkflowRun ;
] .


five-safes-crate:WorkflowMustHaveDescriptiveName
a sh:NodeShape ;
sh:name "WorkflowExecution" ;
sh:targetClass schema:CreateAction ;
sh:targetClass ro-crate:WorkflowRun ;

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 "WorkflowRun 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 "WorkflowRun 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:WorkflowRun ;
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 "WorkflowRun MUST have an actionStatus with an allowed value (see https://schema.org/ActionStatusType)." ;
sh:path schema:actionStatus ;
sh:in (
"http://schema.org/PotentialActionStatus"
Expand All @@ -58,5 +87,5 @@ 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 "WorkflowRun MUST have an actionStatus with an allowed value (see https://schema.org/ActionStatusType)." ;
] .
83 changes: 57 additions & 26 deletions rocrate_validator/profiles/five-safes-crate/must/7_requested_workflow_run.ttl
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Expand Up @@ -22,7 +22,37 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .


five-safes-crate:RootDataEntityMentionsCreateAction
ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape;
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 schema:mainEntity ?instrument ;
a schema:Dataset .
?metadatafile schema:about ?root .
FILTER(contains(str(?metadatafile), "ro-crate-metadata.json"))
}
"""
] ;

# Expand data graph with triples from the file data entity
sh:rule [
a sh:TripleRule ;
sh:subject sh:this ;
sh:predicate rdf:type ;
sh:object ro-crate:WorkflowRun ;
] .


five-safes-crate:RootDataEntityMentionsWorkflowRun
a sh:NodeShape ;
sh:name "RootDataEntity" ;
sh:targetClass ro-crate:RootDataEntity ;
Expand All @@ -33,42 +63,43 @@ five-safes-crate:RootDataEntityMentionsCreateAction
sh:name "mentions" ;
sh:path schema:mentions;
sh:qualifiedValueShape [
sh:class schema:CreateAction ;
sh:class ro-crate:WorkflowRun ;
] ;
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 `WorkflowRun` through `mentions`" ;
] .


five-safes-crate:CreateActionInstrumentAndStatus
five-safes-crate:WorkflowRunExistence
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 "WorkflowRun" ;
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 {
?workflowRun a ro-crate:WorkflowRun .
}
}
""" ;
sh:message "`CreateAction` --> `instrument` MUST reference the same entity as `Root Data Entity` --> `mainEntity`" ;
] ;
sh:message "The crate MUST contain at least one `WorkflowRun` entity" ;
] .


five-safes-crate:WorkflowRunObject
a sh:NodeShape ;
sh:name "WorkflowRun" ;
sh:targetClass ro-crate:WorkflowRun ;
sh:description "" ;
sh:severity sh:Violation ; # Apply to all property shapes / constraints below

sh:sparql [
a sh:SPARQLConstraint ;
sh:prefixes ro-crate:sparqlPrefixes ;
Expand All @@ -80,5 +111,5 @@ five-safes-crate:CreateActionInstrumentAndStatus
FILTER NOT EXISTS { ?object a ?type . }
}
""" ;
sh:message "Each `object` in `CreateAction` MUST reference an existing entity." ;
] .
sh:message "Each `object` in `WorkflowRun` MUST reference an existing entity." ;
] .
37 changes: 37 additions & 0 deletions rocrate_validator/profiles/five-safes-crate/ontology.ttl
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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.

@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 WorkflowRun class
ro-crate:WorkflowRun rdf:type owl:Class ;
rdfs:subClassOf schema:CreateAction ;
rdfs:label "WorkflowRun"@en .
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