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Merge pull request #31 from eScienceLab/30-requested-workflow-run
Requested workflow run
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‎rocrate_validator/profiles/five-safes-crate/must/7_requested_workflow_run.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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five-safes-crate:RootDataEntityMentionsCreateAction
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a sh:NodeShape ;
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sh:name "RootDataEntity" ;
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sh:targetClass ro-crate:RootDataEntity ;
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sh:description "" ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "mentions" ;
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sh:path schema:mentions;
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sh:qualifiedValueShape [
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sh:class schema:CreateAction ;
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] ;
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sh:qualifiedMinCount 1 ;
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sh:severity sh:Violation ;
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sh:message "`RootDataEntity` MUST reference at least one `CreateAction` through `mentions`" ;
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] .
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five-safes-crate:CreateActionInstrumentAndStatus
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a sh:NodeShape ;
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sh:name "CreateAction" ;
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sh:targetClass schema:CreateAction ;
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sh:description "" ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "instrument" ;
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sh:path schema:instrument;
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sh:minCount 1 ;
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sh:severity sh:Violation ;
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sh:message "`CreateAction` MUST have the `schema:instrument` property" ;
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] ;
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sh:sparql [
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a sh:SPARQLConstraint ;
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sh:name "instrument" ;
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sh:prefixes ro-crate:sparqlPrefixes ;
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sh:select """
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SELECT $this ?main ?instrument
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WHERE {
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?root schema:mainEntity ?main .
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$this schema:instrument ?instrument .
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FILTER (?instrument != ?main)
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}
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""" ;
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sh:severity sh:Violation ;
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sh:message "`CreateAction` --> `instrument` MUST reference the same entity as `Root Data Entity` --> `mainEntity`" ;
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] ;
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sh:sparql [
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a sh:SPARQLConstraint ;
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sh:prefixes ro-crate:sparqlPrefixes ;
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sh:name "object" ;
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sh:select """
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SELECT $this ?object
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WHERE {
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$this schema:object ?object .
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FILTER NOT EXISTS { ?object a ?type . }
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}
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""" ;
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sh:severity sh:Violation ;
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sh:message "Each `object` in `CreateAction` MUST reference an existing entity." ;
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] .

‎rocrate_validator/profiles/five-safes-crate/should/7_requested_workflow_run.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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# CreateAction SHOULD have object property with minimum cardinality 1
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five-safes-crate:CreateActionShouldHaveObjectProperty
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a sh:NodeShape ;
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sh:targetClass schema:CreateAction ;
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sh:name "CreateAction" ;
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sh:property [
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sh:path schema:object ;
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sh:minCount 1 ;
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sh:nodeKind sh:IRI ;
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sh:severity sh:Warning ;
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sh:message "`CreateAction` SHOULD have the property `object` with IRI values." ;
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] .

‎tests/data/crates/valid/five-safes-crate-result/ro-crate-metadata.json‎

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"@type": "PropertyValue",
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"name": "tre72",
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"value": "project81"
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},
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},
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{
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"@id": "input1.txt",
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"@type": "File",

‎tests/integration/profiles/five-safes-crate/test_5src_7_requesting_workflow_run.py‎

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# Copyright (c) 2024-2025 CRS4
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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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import logging
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from rocrate_validator.models import Severity
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from tests.ro_crates import ValidROC
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from tests.shared import do_entity_test, SPARQL_PREFIXES
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# set up logging
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logger = logging.getLogger(__name__)
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# ----- MUST fails tests
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def test_rocrate_does_not_have_createaction():
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"""
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Test a Five Safes Crate where no `CreateAction` entity exists.
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(We remove the entire CreateAction entity from the RO-Crate)
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"""
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sparql = (
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SPARQL_PREFIXES
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+ """
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DELETE {
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?action ?p ?o .
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?s ?p2 ?action .
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}
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WHERE {
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?action a schema:CreateAction .
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?action ?p ?o .
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OPTIONAL { ?s ?p2 ?action . }
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}
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"""
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)
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do_entity_test(
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rocrate_path=ValidROC().five_safes_crate_request,
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requirement_severity=Severity.REQUIRED,
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expected_validation_result=False,
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expected_triggered_requirements=["RootDataEntity"],
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expected_triggered_issues=[
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"`RootDataEntity` MUST reference at least one `CreateAction` through `mentions`"
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],
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profile_identifier="five-safes-crate",
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rocrate_entity_mod_sparql=sparql,
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)
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def test_rootdataentity_does_not_have_mentions_property():
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"""
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Test a Five Safes Crate where RootDataEntity does not have the property mentions.
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(We remove the property mentions from the RootDataEntity entity)
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"""
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sparql = (
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SPARQL_PREFIXES
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+ """
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DELETE {
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<./> schema:mentions ?o .
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}
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WHERE {
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<./> schema:mentions ?o .
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}
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"""
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)
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do_entity_test(
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rocrate_path=ValidROC().five_safes_crate_request,
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requirement_severity=Severity.REQUIRED,
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expected_validation_result=False,
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expected_triggered_requirements=["RootDataEntity"],
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expected_triggered_issues=[
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"`RootDataEntity` MUST reference at least one `CreateAction` through `mentions`"
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],
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profile_identifier="five-safes-crate",
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rocrate_entity_mod_sparql=sparql,
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)
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def test_rootdataentity_does_not_mention_create_action():
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"""
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Test a Five Safes Crate where `RootDataEntity` does not `mention` a `CreateAction` entity.
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(We replace the object of RooDataEntity --> mentions with a string literal).
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"""
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sparql = (
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SPARQL_PREFIXES
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+ """
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DELETE {
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<./> schema:mentions ?o .
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}
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INSERT {
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<./> schema:mentions "This is not a CreateAction entity" .
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}
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WHERE {
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<./> schema:mentions ?o .
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}
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"""
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)
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do_entity_test(
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rocrate_path=ValidROC().five_safes_crate_request,
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requirement_severity=Severity.REQUIRED,
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expected_validation_result=False,
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expected_triggered_requirements=["RootDataEntity"],
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expected_triggered_issues=[
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"`RootDataEntity` MUST reference at least one `CreateAction` through `mentions`"
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],
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profile_identifier="five-safes-crate",
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rocrate_entity_mod_sparql=sparql,
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)
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def test_createaction_does_not_have_instrument_property():
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"""
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Test a Five Safes Crate where `CreateAction` does not have the property `instrument`.
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(We remove the property `instrument` from the `CreateAction` entity)
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"""
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sparql = (
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SPARQL_PREFIXES
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+ """
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DELETE {
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?action schema:instrument ?o .
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}
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WHERE {
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?action schema:instrument ?o ;
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a schema:CreateAction .
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}
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"""
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)
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do_entity_test(
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rocrate_path=ValidROC().five_safes_crate_request,
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requirement_severity=Severity.REQUIRED,
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expected_validation_result=False,
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expected_triggered_requirements=["CreateAction"],
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expected_triggered_issues=[
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"`CreateAction` MUST have the `schema:instrument` property"
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],
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profile_identifier="five-safes-crate",
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rocrate_entity_mod_sparql=sparql,
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)
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def test_createaction_does_not_reference_mainentity_via_instrument():
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"""
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Test a Five Safes Crate where `CreateAction` --> `instrument` does not
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reference `mainEntity`.
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(We replace `mainEntity` with a literal as the object of `CreateAction` --> `instrument`)
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"""
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sparql = (
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SPARQL_PREFIXES
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+ """
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DELETE {
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?action schema:instrument ?o .
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}
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INSERT {
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?action schema:instrument "This is not the mainEntity" .
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}
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WHERE {
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?action schema:instrument ?o ;
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a schema:CreateAction .
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}
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"""
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)
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do_entity_test(
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rocrate_path=ValidROC().five_safes_crate_request,
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requirement_severity=Severity.REQUIRED,
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expected_validation_result=False,
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expected_triggered_requirements=["CreateAction"],
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expected_triggered_issues=[
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"`CreateAction` --> `instrument` MUST reference the same entity as `Root Data Entity` --> `mainEntity`"
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],
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profile_identifier="five-safes-crate",
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rocrate_entity_mod_sparql=sparql,
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)
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def test_createaction_object_does_not_reference_existing_entities():
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"""
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Test a Five Safes Crate where `CreateAction` --> `object` does not
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reference an existing entity in the RO-Crate.
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(We replace the objects of `CreateAction` --> `object` with a literal.`)
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"""
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sparql = (
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SPARQL_PREFIXES
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+ """
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DELETE {
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?action schema:object ?o .
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}
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INSERT {
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?action schema:object "This is not an entity in the RO-Crate" .
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}
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WHERE {
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?action schema:object ?o ;
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a schema:CreateAction .
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}
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"""
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)
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do_entity_test(
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rocrate_path=ValidROC().five_safes_crate_request,
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requirement_severity=Severity.REQUIRED,
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expected_validation_result=False,
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expected_triggered_requirements=["CreateAction"],
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expected_triggered_issues=[
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"Each `object` in `CreateAction` MUST reference an existing entity."
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],
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profile_identifier="five-safes-crate",
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rocrate_entity_mod_sparql=sparql,
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)
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# ----- SHOULD fails tests
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def test_createaction_does_not_have_object_property():
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"""
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Test a Five Safes Crate where `CreateAction` does not have the property `object`.
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(We remove the property `object` from `CreateAction`)
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"""
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sparql = (
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SPARQL_PREFIXES
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+ """
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DELETE {
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?action schema:object ?o .
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}
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WHERE {
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?action schema:object ?o ;
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a schema:CreateAction .
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}
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"""
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)
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do_entity_test(
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rocrate_path=ValidROC().five_safes_crate_request,
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requirement_severity=Severity.RECOMMENDED,
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expected_validation_result=False,
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expected_triggered_requirements=["CreateAction"],
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expected_triggered_issues=[
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"`CreateAction` SHOULD have the property `object` with IRI values."
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],
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profile_identifier="five-safes-crate",
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rocrate_entity_mod_sparql=sparql,
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)

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