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EttoreMEttoreM
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Removed MUST/SHOULD/MAY folder structure from provenance-run-crate profile.
1 parent 5133d57 commit 620c5b5

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+439
-511
lines changed

rocrate_validator/profiles/provenance-run-crate/must/0_computational_workflow.ttl renamed to rocrate_validator/profiles/provenance-run-crate/0_computational_workflow.ttl

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@@ -23,6 +23,9 @@
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@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
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@prefix provenance-run-crate: <https://github.com/crs4/rocrate-validator/profiles/provenance-run-crate/> .
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#=== MUST shapes ===#
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provenance-run-crate:ProvRCComputationalWorkflowRequired a sh:NodeShape ;
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sh:name "Provenance Run Crate ComputationalWorkflow MUST" ;
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sh:description "Required properties of the Provenance Run Crate ComputationalWorkflow" ;
@@ -39,6 +42,7 @@ provenance-run-crate:ProvRCComputationalWorkflowRequired a sh:NodeShape ;
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) ;
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sh:minCount 1 ;
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sh:message "ComputationalWorkflow MUST refer to orchestrated tools via hasPart" ;
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sh:severity sh:Violation ;
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] ;
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sh:property [
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a sh:PropertyShape ;
@@ -47,6 +51,7 @@ provenance-run-crate:ProvRCComputationalWorkflowRequired a sh:NodeShape ;
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sh:path wfrun:connection ;
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sh:class wfrun:ParameterConnection ;
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sh:message "If the ComputationalWorkflow has a connection, it must point to a ParameterConnection" ;
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sh:severity sh:Violation ;
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] .
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@@ -73,4 +78,68 @@ provenance-run-crate:ProvRCComputationalWorkflowWithSteps a sh:NodeShape ;
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sh:hasValue schema:HowTo;
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sh:minCount 1 ;
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sh:message "A ComputationalWorkflow that links to steps MUST have the HowTo type" ;
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sh:severity sh:Violation ;
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] .
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#=== SHOULD shapes ===#
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provenance-run-crate:ProvRCComputationalWorkflowRecommended a sh:NodeShape ;
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sh:name "Provenance Run Crate ComputationalWorkflow SHOULD" ;
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sh:description "Recommended properties of the Provenance Run Crate ComputationalWorkflow" ;
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sh:targetClass bioschemas:ComputationalWorkflow ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "ComputationalWorkflow step" ;
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sh:description "ComputationalWorkflow SHOULD refer to HowToStep instances via step" ;
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sh:path schema:step ;
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sh:class schema:HowToStep ;
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sh:minCount 1 ;
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sh:message "ComputationalWorkflow SHOULD refer to HowToStep instances via step" ;
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sh:severity sh:Warning ;
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] .
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#=== MAY shapes ===#
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provenance-run-crate:ProvRCComputationalWorkflowOptional a sh:NodeShape ;
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sh:name "Provenance Run Crate ComputationalWorkflow MAY" ;
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sh:description "Optional properties of the Provenance Run Crate ComputationalWorkflow" ;
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sh:targetClass bioschemas:ComputationalWorkflow ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "ComputationalWorkflow connection" ;
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sh:description "ComputationalWorkflow may have a connection property" ;
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sh:path wfrun:connection ;
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sh:minCount 1 ;
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sh:message "ComputationalWorkflow may have a connection property" ;
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sh:severity sh:Info ;
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] .
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provenance-run-crate:ProvRCComputationalWorkflowHowToOptional a sh:NodeShape ;
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sh:name "Provenance Run Crate ComputationalWorkflow / HowTo MAY" ;
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sh:description "Optional properties of a Provenance Run Crate ComputationalWorkflow that is also a HowTo" ;
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sh:target [
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a sh:SPARQLTarget ;
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sh:prefixes ro-crate:sparqlPrefixes ;
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sh:select """
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SELECT ?this
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WHERE {
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?this a bioschemas:ComputationalWorkflow .
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?this a schema:HowTo .
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}
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"""
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "ComputationalWorkflow buildInstructions" ;
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sh:description "A ComputationalWorkflow / HowTo MAY have a buildInstructions pointing to a File" ;
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sh:path codemeta:buildInstructions ;
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sh:class schema:MediaObject ;
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sh:minCount 1 ;
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sh:message "A ComputationalWorkflow / HowTo MAY have a buildInstructions pointing to a File" ;
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sh:severity sh:Info ;
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] .
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rocrate_validator/profiles/provenance-run-crate/may/0_tool.ttl renamed to rocrate_validator/profiles/provenance-run-crate/0_tool.ttl

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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
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#=== MUST shapes ===#
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provenance-run-crate:ProvRCToolRequired a sh:NodeShape ;
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sh:name "ProvRC tool MUST" ;
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sh:description "Required properties of a Provenance Run Crate tool" ;
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sh:target [
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a sh:SPARQLTarget ;
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sh:prefixes ro-crate:sparqlPrefixes ;
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sh:select """
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SELECT ?this
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WHERE {
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{ ?this a schema:SoftwareApplication } UNION
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{ ?this a schema:SoftwareSourceCode } UNION
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{ ?this a bioschemas:ComputationalWorkflow } .
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?workflow schema:hasPart ?this .
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?workflow a bioschemas:ComputationalWorkflow .
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}
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"""
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "tool input and output" ;
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sh:description "Tool input and output MUST point to FormalParameter entities" ;
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sh:path [
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sh:alternativePath (bioschemas-cw:input bioschemas-cw:output) ;
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] ;
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sh:class bioschemas:FormalParameter ;
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sh:message "Tool input and output MUST point to FormalParameter entities" ;
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sh:severity sh:Violation ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "Tool inverse instrument" ;
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sh:description "A tool must be referred to from an action via instrument" ;
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sh:path [ sh:inversePath schema:instrument ] ;
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sh:or (
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[ sh:class schema:CreateAction ; ]
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[ sh:class schema:ActivateAction ; ]
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[ sh:class schema:UpdateAction ; ]
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) ;
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sh:minCount 1 ;
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sh:message "A tool must be referred to from an action via instrument" ;
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sh:severity sh:Violation ;
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] .
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#=== SHOULD shapes ===#
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provenance-run-crate:ProvRCToolRecommended a sh:NodeShape ;
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sh:name "ProvRC tool SHOULD" ;
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sh:description "Recommended properties of a Provenance Run Crate tool" ;
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sh:target [
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a sh:SPARQLTarget ;
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sh:prefixes ro-crate:sparqlPrefixes ;
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sh:select """
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SELECT ?this
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WHERE {
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{ ?this a schema:SoftwareApplication } UNION
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{ ?this a schema:SoftwareSourceCode } UNION
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{ ?this a bioschemas:ComputationalWorkflow } .
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?workflow schema:hasPart ?this .
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?workflow a bioschemas:ComputationalWorkflow .
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}
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"""
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "tool environment" ;
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sh:description "If the tool has an environment, it SHOULD point to entities of type FormalParameter" ;
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sh:path wfrun:environment ;
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sh:class bioschemas:FormalParameter ;
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sh:message "If the tool has an environment, it SHOULD point to entities of type FormalParameter" ;
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sh:severity sh:Warning ;
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] .
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#=== MAY shapes ===#
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provenance-run-crate:ProvRCToolOptional a sh:NodeShape ;
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sh:name "ProvRC tool MAY" ;
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sh:description "Optional properties of a Provenance Run Crate tool" ;
@@ -46,6 +125,7 @@ provenance-run-crate:ProvRCToolOptional a sh:NodeShape ;
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sh:path bioschemas-cw:input ;
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sh:minCount 1 ;
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sh:message "A tool MAY have an input" ;
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sh:severity sh:Info ;
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] ;
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sh:property [
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a sh:PropertyShape ;
@@ -54,6 +134,7 @@ provenance-run-crate:ProvRCToolOptional a sh:NodeShape ;
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sh:path bioschemas-cw:output ;
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sh:minCount 1 ;
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sh:message "A tool MAY have an output" ;
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sh:severity sh:Info ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:path wfrun:environment ;
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sh:minCount 1 ;
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sh:message "A tool MAY have an environment" ;
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sh:severity sh:Info ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:softwareRequirements ;
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sh:class schema:SoftwareApplication ;
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sh:minCount 1 ;
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sh:severity sh:Info ;
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] ;
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sh:property [
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a sh:PropertyShape ;
@@ -80,4 +163,6 @@ provenance-run-crate:ProvRCToolOptional a sh:NodeShape ;
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sh:path schema:mainEntity ;
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sh:class schema:SoftwareApplication ;
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sh:minCount 1 ;
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sh:severity sh:Info ;
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] .
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rocrate_validator/profiles/provenance-run-crate/must/1_howtostep.ttl renamed to rocrate_validator/profiles/provenance-run-crate/1_howtostep.ttl

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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
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#=== MUST shapes ===#
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provenance-run-crate:ProvRCHowToStepRequired a sh:NodeShape ;
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sh:name "ProvRC HowToStep MUST" ;
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sh:description "Required properties of a Provenance Run Crate HowToStep" ;
@@ -48,6 +51,7 @@ provenance-run-crate:ProvRCHowToStepRequired a sh:NodeShape ;
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) ;
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sh:minCount 1 ;
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sh:message "A HowToStep must refer to its corresponding tool via workExample" ;
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sh:severity sh:Violation ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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) ;
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sh:pattern "\\d+" ;
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sh:message "If specified, position must be a string representing an integer" ;
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sh:severity sh:Violation ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:path wfrun:connection ;
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sh:class wfrun:ParameterConnection ;
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sh:message "If the HowToStep has a connection, it must point to a ParameterConnection" ;
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sh:severity sh:Violation ;
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] .
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#=== SHOULD shapes ===#
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# (none)
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#=== MAY shapes ===#
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provenance-run-crate:ProvRCHowToStepOptional a sh:NodeShape ;
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sh:name "ProvRC HowToStep MAY" ;
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sh:description "Optional properties of a Provenance Run Crate HowToStep" ;
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sh:targetClass schema:HowToStep ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "HowToStep position" ;
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sh:description "A HowToStep may indicate its position in the execution order via position" ;
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sh:path schema:position ;
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sh:minCount 1 ;
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sh:message "A HowToStep may indicate its position in the execution order via position" ;
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sh:severity sh:Info ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "HowToStep connection" ;
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sh:description "HowToStep may have a connection property" ;
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sh:path wfrun:connection ;
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sh:minCount 1 ;
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sh:message "HowToStep may have a connection property" ;
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sh:severity sh:Info ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "HowToStep buildInstructions" ;
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sh:description "A HowToStep MAY have a buildInstructions pointing to a File" ;
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sh:path codemeta:buildInstructions ;
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sh:class schema:MediaObject ;
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sh:minCount 1 ;
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sh:message "A HowToStep MAY have a buildInstructions pointing to a File" ;
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sh:severity sh:Info ;
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] .
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rocrate_validator/profiles/provenance-run-crate/must/1_tool_action.ttl renamed to rocrate_validator/profiles/provenance-run-crate/1_tool_action.ttl

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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
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#=== MUST shapes ===#
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provenance-run-crate:ProvRCToolActionRequired a sh:NodeShape ;
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sh:name "Provenance Run Crate tool action MUST" ;
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sh:description "Required properties of a Provenance Run Crate action that represents a tool execution" ;
@@ -48,4 +51,43 @@ provenance-run-crate:ProvRCToolActionRequired a sh:NodeShape ;
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sh:path wfrun:resourceUsage ;
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sh:class schema:PropertyValue ;
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sh:message "If present, resourceUsage MUST point to PropertyValue" ;
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sh:severity sh:Violation ;
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] .
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#=== SHOULD shapes ===#
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# (none)
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#=== MAY shapes ===#
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provenance-run-crate:ProvRCToolActionOptional a sh:NodeShape ;
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sh:name "Provenance Run Crate tool action MAY" ;
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sh:description "Optional properties of a Provenance Run Crate action that represents a tool execution" ;
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sh:target [
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a sh:SPARQLTarget ;
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sh:prefixes ro-crate:sparqlPrefixes ;
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sh:select """
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SELECT ?this
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WHERE {
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{ ?this a schema:CreateAction } UNION
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{ ?this a schema:ActivateAction } UNION
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{ ?this a schema:UpdateAction } .
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?this schema:instrument ?tool .
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{ ?tool a schema:SoftwareApplication } UNION
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{ ?tool a schema:SoftwareSourceCode } UNION
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{ ?tool a bioschemas:ComputationalWorkflow } .
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?workflow schema:hasPart ?tool .
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?workflow a bioschemas:ComputationalWorkflow .
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}
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"""
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "Tool action resourceUsage" ;
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sh:description "A tool action MAY have a resourceUsage" ;
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sh:path wfrun:resourceUsage ;
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sh:minCount 1 ;
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sh:message "A tool action MAY have a resourceUsage" ;
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sh:severity sh:Info ;
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] .

rocrate_validator/profiles/provenance-run-crate/should/2_root_data_entity_metadata.ttl renamed to rocrate_validator/profiles/provenance-run-crate/2_root_data_entity_metadata.ttl

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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix provenance-run-crate: <https://github.com/crs4/rocrate-validator/profiles/provenance-run-crate/> .
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#=== MUST shapes ===#
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provenance-run-crate:ProvRCRootDataEntityMetadata a sh:NodeShape ;
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sh:name "Provenance Run Crate Root Data Entity" ;
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sh:description "Properties of the Provenance Run Crate Root Data Entity" ;
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sh:targetClass ro-crate:RootDataEntity ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "Root Data Entity conformsTo" ;
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sh:description "The Root Data Entity MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned permalink of the Provenance Run Crate profile" ;
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sh:path dct:conformsTo ;
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sh:class schema:CreativeWork;
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# At least one value of conformsTo must match the pattern
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sh:qualifiedValueShape [
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sh:pattern "^https://w3id.org/ro/wfrun/provenance/.*" ;
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] ;
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sh:qualifiedMinCount 1 ;
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sh:minCount 1 ;
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sh:message "The Root Data Entity MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned permalink of the Provenance Run Crate profile" ;
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sh:severity sh:Violation ;
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] .
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#=== SHOULD shapes ===#
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provenance-run-crate:ProvRCRootDataEntityRecommended a sh:NodeShape ;
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sh:name "Provenance Run Crate Root Data Entity SHOULD" ;
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sh:description "Recommended Properties of the Provenance Run Crate Root Data Entity" ;
@@ -36,4 +62,8 @@ provenance-run-crate:ProvRCRootDataEntityRecommended a sh:NodeShape ;
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sh:qualifiedMinCount 3 ;
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sh:minCount 1 ;
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sh:message "The Root Data Entity SHOULD reference CreativeWork entities corresponding to the Process Run Crate, Workflow Run Crate and Workflow RO-Crate profiles" ;
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sh:severity sh:Warning ;
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] .
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#=== MAY shapes ===#
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# (none)

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