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elichadelichad
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Merge branch 'develop' into upstream-develop
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‎pyproject.toml‎

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@@ -133,6 +133,9 @@ extend-ignore-re = ["[0-9a-f]{7,40}"] # Ignore long hexadecimal strings, which a
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[tool.typos.files]
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extend-exclude = ["tests/data", "docs/diagrams", "*.json", "*.html", "*__init__.py"]
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[tool.typos.default.extend-words]
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TRE = "TRE"
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# Pylint configuration.
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# Ruff (see ruff.toml) is the primary linter/formatter; this section keeps
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# pylint consistent with it so the two tools do not disagree on style or on

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

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# Copyright (c) 2025 eScience Lab, The University of Manchester
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix schema: <http://schema.org/> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix validator: <https://github.com/crs4/rocrate-validator/> .
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ro-crate:FindWorkflowRunAction a sh:NodeShape, validator:HiddenShape;
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sh:order 1 ; # load this check after ro-crate:FindRootDataEntity; pySHACL sorts rules by sh:order before execution
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sh:name "Identify the CreateAction Entity that corresponds to the Workflow run" ;
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sh:description """The Workflow Run is the CreateAction entity that refers to Workflow run.
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This is identified by checking that the CreateAction entity has an `instrument` property
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that references the same entity as the `mainEntity` property of the Root Data Entity.""" ;
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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 ;
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schema:instrument ?instrument .
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?root a ro-crate:RootDataEntity ;
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schema:mainEntity ?instrument .
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}
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"""
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] ;
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sh:rule [
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a sh:TripleRule ;
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sh:subject sh:this ;
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sh:predicate rdf:type ;
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sh:object ro-crate:WorkflowRunAction ;
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] .

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

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# Copyright (c) 2025 eScience Lab, The University of Manchester
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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@prefix ro: <./> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix five-safes-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/five-safes-crate/> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix schema: <http://schema.org/> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix validator: <https://github.com/crs4/rocrate-validator/> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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#=== MUST shapes ===#
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# (none)
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#=== SHOULD shapes ===#
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five-safes-crate:CreateActionHasResultIfActionCompleted
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a sh:NodeShape ;
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sh:name "WorkflowRunAction" ;
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sh:description "The `CreateAction` corresponding to the workflow run, with CompletedActionStatus, SHOULD have the `schema:result` property." ;
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sh:target [
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a sh:SPARQLTarget ;
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sh:name "WorkflowRunAction" ;
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sh:description "The `CreateAction` corresponding to the workflow run, with CompletedActionStatus, SHOULD have the `result` property." ;
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sh:prefixes ro-crate:sparqlPrefixes ;
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sh:select """
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SELECT ?this WHERE {
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?this a ro-crate:WorkflowRunAction ;
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schema:actionStatus "http://schema.org/CompletedActionStatus" .
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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 "Result" ;
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sh:path schema:result ;
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sh:minCount 1 ;
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sh:severity sh:Warning ;
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sh:message "The `CreateAction` corresponding to the workflow run, with CompletedActionStatus, SHOULD have the `result` property." ;
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] .
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five-safes-crate:WorkflowRunActionResultOutputsHaveAllowedTypes
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a sh:NodeShape ;
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sh:name "Output" ;
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sh:description "Result SHOULD have a `@type` among an allowed set of values." ;
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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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?workflowRunAction a ro-crate:WorkflowRunAction .
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?workflowRunAction schema:result ?this .
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}
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""" ;
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] ;
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sh:message "Result SHOULD have a `@type` among an allowed set of values." ;
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sh:severity sh:Warning ;
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sh:or (
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[
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sh:class schema:MediaObject;
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]
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[
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sh:class schema:Dataset;
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]
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[
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sh:class schema:Collection;
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]
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[
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sh:class schema:DigitalDocument;
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]
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[
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sh:class schema:PropertyValue;
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]
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) .
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#=== MAY shapes ===#
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# (none)

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

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# Copyright (c) 2025 eScience Lab, The University of Manchester
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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@prefix ro: <./> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix five-safes-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/five-safes-crate/> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix schema: <http://schema.org/> .
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@prefix purl: <http://purl.org/dc/terms/> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix validator: <https://github.com/crs4/rocrate-validator/> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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#=== MUST shapes ===#
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five-safes-crate:WorkflowMustHaveDescriptiveName
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a sh:NodeShape ;
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sh:name "WorkflowExecution" ;
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sh:targetClass ro-crate:WorkflowRunAction ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "name" ;
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sh:minCount 1 ;
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sh:description "The `CreateAction` corresponding to the workflow run MUST have a name string of at least 10 characters." ;
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sh:path schema:name ;
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sh:datatype xsd:string ;
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sh:minLength 10 ;
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sh:severity sh:Violation ;
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sh:message "The `CreateAction` corresponding to the workflow run MUST have a name string of at least 10 characters." ;
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] .
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five-safes-crate:WorkflowMustHaveActionStatusWithAllowedValues
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a sh:NodeShape ;
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sh:name "WorkflowExecution" ;
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sh:targetClass ro-crate:WorkflowRunAction ;
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sh:property [
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a sh:PropertyShape ;
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sh:minCount 1 ;
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sh:name "actionStatus" ;
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sh:description "`CreateAction` MUST have an actionStatus with an allowed value (see https://schema.org/ActionStatusType)." ;
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sh:path schema:actionStatus ;
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sh:in (
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"http://schema.org/PotentialActionStatus"
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"http://schema.org/ActiveActionStatus"
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"http://schema.org/CompletedActionStatus"
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"http://schema.org/FailedActionStatus"
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) ;
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sh:severity sh:Violation ;
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sh:message "`CreateAction` MUST have an actionStatus with an allowed value (see https://schema.org/ActionStatusType)." ;
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] .
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#=== SHOULD shapes ===#
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five-safes-crate:WorkflowexecutionObjectHasEndTimeIfEnded
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a sh:NodeShape ;
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sh:name "WorkflowExecution" ;
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sh:description "The workflow run object SHOULD have an endTime property if it has ended." ;
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sh:target [
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a sh:SPARQLTarget ;
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sh:select """
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PREFIX schema: <http://schema.org/>
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PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/>
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SELECT ?this
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WHERE {
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?this a rocrate:WorkflowRunAction ;
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schema:actionStatus ?status .
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FILTER(?status IN (
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"http://schema.org/CompletedActionStatus",
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"http://schema.org/FailedActionStatus"
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))
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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 "EndTime" ;
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sh:path schema:endTime ;
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sh:minCount 1 ;
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sh:maxCount 1 ;
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sh:severity sh:Warning ;
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sh:description "The workflow execution object SHOULD have an endTime property if it has ended." ;
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sh:message "The workflow execution object SHOULD have an endTime property if it has ended." ;
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] .
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#=== MAY shapes ===#
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five-safes-crate:WorkflowexecutionObjectHasStartTimeIfBegun
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a sh:NodeShape ;
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sh:name "WorkflowExecution" ;
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sh:description (
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"The workflow execution object MAY have a startTime if actionStatus is "
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"either ActiveActionStatus, CompletedActionStatus or FailedActionStatus."
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) ;
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sh:target [
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a sh:SPARQLTarget ;
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sh:select """
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PREFIX schema: <http://schema.org/>
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PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/>
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SELECT ?this
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WHERE {
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?this a rocrate:WorkflowRunAction ;
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schema:actionStatus ?status .
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FILTER(?status IN (
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"http://schema.org/CompletedActionStatus",
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"http://schema.org/FailedActionStatus",
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"http://schema.org/ActiveActionStatus"
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))
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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 "StartTime" ;
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sh:path schema:startTime ;
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sh:minCount 1 ;
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sh:maxCount 1 ;
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sh:severity sh:Info ;
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sh:description (
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"The workflow execution object MAY have a startTime if actionStatus is "
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"either ActiveActionStatus, CompletedActionStatus or FailedActionStatus."
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) ;
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sh:message "The workflow execution object MAY have a startTime if actionStatus is either ActiveActionStatus, CompletedActionStatus or FailedActionStatus." ;
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] .

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