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Merge pull request crs4#13 from crs4/feat/workflow-run-crate
Workflow Run Crate
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‎rocrate_validator/profiles/ro-crate/prefixes.ttl

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sh:prefix "rocrate" ;
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sh:namespace "https://w3id.org/ro/crate/1.1/"^^xsd:anyURI ;
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] ;
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sh:declare [
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sh:prefix "wfrun" ;
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sh:namespace "https://w3id.org/ro/terms/workflow-run#"^^xsd:anyURI ;
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] ;
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sh:declare [
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sh:prefix "ro" ;
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sh:namespace "./"^^xsd:anyURI ;

‎rocrate_validator/profiles/workflow-run-crate/may/0_computational_workflow.ttl

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# Copyright (c) 2024 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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@prefix ro: <./> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix schema: <http://schema.org/> .
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@prefix bioschemas: <https://bioschemas.org/> .
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@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix workflow-run-crate: <https://github.com/crs4/rocrate-validator/profiles/workflow-run-crate/> .
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@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
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workflow-run-crate:WfRCComputationalWorkflowOptional a sh:NodeShape ;
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sh:name "Workflow Run Crate ComputationalWorkflow MAY" ;
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sh:description "Optional properties of the Workflow 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 input" ;
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sh:description "A ComputationalWorkflow MAY have an input" ;
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sh:path bioschemas-cw:input ;
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sh:minCount 1 ;
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sh:message "A ComputationalWorkflow MAY have an input" ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "ComputationalWorkflow output" ;
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sh:description "A ComputationalWorkflow MAY have an output" ;
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sh:path bioschemas-cw:output ;
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sh:minCount 1 ;
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sh:message "A ComputationalWorkflow MAY have an output" ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "Workflow environment" ;
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sh:description "The Workflow MAY have an environment" ;
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sh:path wfrun:environment ;
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sh:minCount 1 ;
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sh:message "The Workflow MAY have an environment" ;
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] .

‎rocrate_validator/profiles/workflow-run-crate/may/3_formal_parameter.ttl

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# Copyright (c) 2024 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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@prefix ro: <./> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix schema: <http://schema.org/> .
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@prefix bioschemas: <https://bioschemas.org/> .
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@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix workflow-run-crate: <https://github.com/crs4/rocrate-validator/profiles/workflow-run-crate/> .
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workflow-run-crate:WfRCFormalParameterOptional a sh:NodeShape ;
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sh:name "Workflow Run Crate FormalParameter MAY" ;
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sh:description "Optional properties of the Workflow Run Crate FormalParameter" ;
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sh:targetClass bioschemas:FormalParameter ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "FormalParameter workExample" ;
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sh:description "FormalParameter MAY refer to a data entity or PropertyValue via workExample" ;
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sh:path schema:workExample ;
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sh:or (
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[ sh:class schema:MediaObject ; ]
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[ sh:class schema:Dataset ; ]
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[ sh:class schema:Collection ; ]
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[ sh:class schema:PropertyValue ; ]
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) ;
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sh:minCount 1 ;
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sh:message "FormalParameter MAY refer to a data entity or PropertyValue via workExample" ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "FormalParameter description" ;
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sh:description "FormalParameter MAY have a description" ;
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sh:path schema:description ;
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sh:minCount 1 ;
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sh:message "FormalParameter MAY have a description" ;
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] .

‎rocrate_validator/profiles/workflow-run-crate/must/0_computational_workflow.ttl

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# Copyright (c) 2024 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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@prefix ro: <./> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix schema: <http://schema.org/> .
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@prefix bioschemas: <https://bioschemas.org/> .
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@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix workflow-run-crate: <https://github.com/crs4/rocrate-validator/profiles/workflow-run-crate/> .
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workflow-run-crate:WfRCComputationalWorkflowRequired a sh:NodeShape ;
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sh:name "Workflow Run Crate ComputationalWorkflow MUST" ;
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sh:description "Required properties of the Workflow 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 input and output" ;
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sh:description "ComputationalWorkflow 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 "ComputationalWorkflow input and output MUST point to FormalParameter entities" ;
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] .

‎rocrate_validator/profiles/workflow-run-crate/must/2_root_data_entity_metadata.ttl

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# Copyright (c) 2024 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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@prefix ro: <./> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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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 workflow-run-crate: <https://github.com/crs4/rocrate-validator/profiles/workflow-run-crate/> .
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workflow-run-crate:WfRCRootDataEntityMetadata a sh:NodeShape ;
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sh:name "Root Data Entity Metadata" ;
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sh:description "Properties of the 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 Workflow 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/workflow/.*" ;
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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 Workflow Run Crate profile" ;
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] .

‎rocrate_validator/profiles/workflow-run-crate/must/3_formal_parameter.ttl

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# Copyright (c) 2024 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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@prefix ro: <./> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix schema: <http://schema.org/> .
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@prefix bioschemas: <https://bioschemas.org/> .
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@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix workflow-run-crate: <https://github.com/crs4/rocrate-validator/profiles/workflow-run-crate/> .
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workflow-run-crate:WfRCFormalParameterRequired a sh:NodeShape ;
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sh:name "Workflow Run Crate FormalParameter MUST" ;
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sh:description "Required properties of the Workflow Run Crate FormalParameter" ;
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sh:targetClass bioschemas:FormalParameter ;
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sh:property [
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a sh:PropertyShape ;
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sh:name "FormalParameter additionalType" ;
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sh:description "FormalParameter MUST have an additionalType" ;
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sh:path schema:additionalType ;
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sh:minCount 1 ;
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sh:message "FormalParameter MUST have an additionalType" ;
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] .

‎rocrate_validator/profiles/workflow-run-crate/profile.ttl

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# Copyright (c) 2024 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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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix prof: <http://www.w3.org/ns/dx/prof/> .
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@prefix role: <http://www.w3.org/ns/dx/prof/role/> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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<https://w3id.org/ro/wfrun/workflow/0.5>
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a prof:Profile ;
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# the Profile's label
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rdfs:label "Workflow Run Crate 0.5" ;
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# regular metadata, a basic description of the Profile
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rdfs:comment """Workflow Run Crate Metadata Specification 0.5"""@en ;
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# URI of the publisher of the Metadata Specification
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dct:publisher <https://w3id.org/ro/wfrun> ;
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# This profile is an extension of Process Run Crate and Workflow RO-Crate
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prof:isProfileOf <https://w3id.org/ro/wfrun/process/0.5> ,
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<https://w3id.org/workflowhub/workflow-ro-crate/1.0> ;
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# This profile is a transitive profile of Process Run Crate, Workflow RO-Crate and the RO-Crate Metadata Specification
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prof:isTransitiveProfileOf <https://w3id.org/ro/crate/1.1> ,
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<https://w3id.org/ro/wfrun/process/0.5> ,
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<https://w3id.org/workflowhub/workflow-ro-crate/1.0>;
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# this profile has a JSON-LD context resource
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prof:hasResource [
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a prof:ResourceDescriptor ;
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# it's in JSON-LD format
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dct:format <https://w3id.org/mediatype/application/ld+json> ;
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# it conforms to JSON-LD, here refered to by its namespace URI as a Profile
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dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
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# this profile resource plays the role of "Vocabulary"
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# described in this ontology's accompanying Roles vocabulary
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prof:hasRole role:Vocabulary ;
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# this profile resource's actual file
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prof:hasArtifact <https://w3id.org/ro/terms/workflow-run/context> ;
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] ;
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# this profile has a human-readable documentation resource
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prof:hasResource [
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a prof:ResourceDescriptor ;
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# it's in HTML format
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dct:format <https://w3id.org/mediatype/text/html> ;
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# it conforms to HTML, here refered to by its namespace URI as a Profile
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dct:conformsTo <https://www.w3.org/TR/html/> ;
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# this profile resource plays the role of "Specification"
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# described in this ontology's accompanying Roles vocabulary
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prof:hasRole role:Specification ;
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# this profile resource's actual file
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prof:hasArtifact <https://www.researchobject.org/workflow-run-crate/profiles/0.5/workflow_run_crate/> ;
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# this profile is inherited from Process Run Crate and Workflow RO-Crate
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prof:isInheritedFrom <https://w3id.org/ro/wfrun/process/0.5> ,
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<https://w3id.org/workflowhub/workflow-ro-crate/1.0> ;
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] ;
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# a short code to refer to the Profile with when a URI can't be used
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prof:hasToken "workflow-run-crate" ;
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.

‎rocrate_validator/profiles/workflow-run-crate/should/0_computational_workflow.ttl

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# Copyright (c) 2024 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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@prefix ro: <./> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix schema: <http://schema.org/> .
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@prefix bioschemas: <https://bioschemas.org/> .
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@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix workflow-run-crate: <https://github.com/crs4/rocrate-validator/profiles/workflow-run-crate/> .
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@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
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workflow-run-crate:WfRCComputationalWorkflowRecommended a sh:NodeShape ;
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sh:name "Workflow Run Crate ComputationalWorkflow SHOULD" ;
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sh:description "Recommended properties of the Workflow 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 "Workflow environment" ;
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sh:description "If the Workflow 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 Workflow has an environment, it SHOULD point to entities of type FormalParameter" ;
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] .

‎rocrate_validator/profiles/workflow-run-crate/should/2_root_data_entity_metadata.ttl

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# Copyright (c) 2024 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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@prefix ro: <./> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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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 workflow-run-crate: <https://github.com/crs4/rocrate-validator/profiles/workflow-run-crate/> .
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workflow-run-crate:WfRCRootDataEntityMetadataRecommended a sh:NodeShape ;
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sh:name "Root Data Entity Metadata SHOULD" ;
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sh:description "Recommended Properties of the 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 SHOULD reference CreativeWork entities corresponding to the Process Run Crate and Workflow RO-Crate profiles" ;
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sh:path dct:conformsTo ;
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sh:class schema:CreativeWork;
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sh:qualifiedValueShape [
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sh:pattern "^https://w3id.org/(ro/wfrun/process|workflowhub/workflow-ro-crate)/.*" ;
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] ;
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# At least two values of conformsTo must match the pattern
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sh:qualifiedMinCount 2 ;
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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 and Workflow RO-Crate profiles" ;
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] .

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