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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/may/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 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: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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] .

‎rocrate_validator/profiles/five-safes-crate/may/12_check_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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five-safes-crate:CheckValueMayHaveStartTime
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a sh:NodeShape ;
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sh:name "CheckValue" ;
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sh:description "" ;
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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 shp: <https://w3id.org/shp#>
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SELECT ?this
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WHERE {
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?this schema:additionalType shp:CheckValue ;
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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:message "`CheckValue` MAY have the `startTime` property." ;
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] .

‎rocrate_validator/profiles/five-safes-crate/may/13_validation_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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five-safes-crate:DownloadActionMayHaveStartTimeIfBegun
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a sh:NodeShape ;
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sh:name "ValidationCheck" ;
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sh:description "" ;
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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 shp: <https://w3id.org/shp#>
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SELECT ?this
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WHERE {
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?this schema:additionalType shp:ValidationCheck ;
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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 "ValidationCheck MAY have the `startTime` property if `actionStatus` is either ActiveActionStatus, CompletedActionStatus or FailedActionStatus." ;
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sh:message "ValidationCheck MAY have the `startTime` property if `actionStatus` is either ActiveActionStatus, CompletedActionStatus or FailedActionStatus." ;
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] .

‎rocrate_validator/profiles/five-safes-crate/may/14_workflow_retrieval_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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five-safes-crate:DownloadedWorkflowSHOULDExistAndBeReferencedByDownloadActionResult
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a sh:NodeShape ;
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sh:name "DownloadAction" ;
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sh:description "Validates that DownloadAction result references an existing entity" ;
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sh:targetClass schema:DownloadAction ;
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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:description "The result property must reference an existing entity in the RO-Crate" ;
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sh:path schema:result ;
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sh:minCount 1 ;
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sh:nodeKind sh:IRI ;
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sh:sparql [
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a sh:SPARQLConstraint ;
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sh:select """
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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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SELECT $this $value
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WHERE {
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$this schema:result $value .
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# Entity must have BOTH type AND name (proper definition)
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FILTER NOT EXISTS {
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$value rdf:type schema:Dataset .
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}
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}
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""" ;
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] ;
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sh:severity sh:Info ;
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sh:message "The entity representing the downloaded workflow is not defined, OR is not referenced by `DownloadAction` --> `result`, OR is not of type `Dataset`." ;
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] .
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five-safes-crate:DownloadActionMayHaveStartTimeIfBegun
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a sh:NodeShape ;
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sh:name "DownloadAction" ;
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sh:description (
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"`DownloadAction` MAY have the `startTime` property if `actionStatus` "
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"is 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 rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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SELECT ?this
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WHERE {
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?this rdf:type schema:DownloadAction ;
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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:description (
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"`DownloadAction` MAY have the `startTime` property if `actionStatus` "
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"is either ActiveActionStatus, CompletedActionStatus or FailedActionStatus."
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);
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sh:severity sh:Info ;
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sh:message "`DownloadAction` MAY have the `startTime` property if `actionStatus` is either ActiveActionStatus, CompletedActionStatus or FailedActionStatus." ;
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] .

‎rocrate_validator/profiles/five-safes-crate/may/1_responsible_project.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:ResponsibleProject
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a sh:NodeShape ;
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sh:name "Responsible Project" ;
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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 DISTINCT ?this WHERE {
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?action a ro-crate:WorkflowRunAction ;
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schema:agent ?agent .
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?agent schema:memberOf ?this .
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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 "funding" ;
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sh:path schema:funding;
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sh:minCount 1 ;
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sh:severity sh:Info ;
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sh:message """The Responsible Project does not have the property `funding`.""" ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "member" ;
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sh:path schema:member;
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sh:minCount 1 ;
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sh:severity sh:Info ;
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sh:message """The Responsible Project does not have the property `member`.""" ;
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] .

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