5 profile conformance

rocrate_validator/profiles/five-safes-crate/must/1_funder.ttl

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+# Copyright (c) 2024-2025 CRS4
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix five-safes-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/five-safes-crate/> .
+@prefix schema_org: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix bioschemas: <https://bioschemas.org/> .
+
+five-safes-crate:FundingBody a sh:NodeShape ;
+    sh:name "Funding body Project" ;
+    sh:description "Project which is funding this work" ;
+    sh:targetClass schema_org:Project ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "Project Name" ;
+        sh:description """Check if the Project Entity `name` (as specified by schema.org) 
+        to clearly identify the dataset and distinguish it from other projects.""" ;
+        sh:minCount 1 ;
+        sh:nodeKind sh:Literal ;
+        sh:path schema_org:name;
+        sh:message "The Project Entity MUST have a `name` property (as specified by schema.org)" ;
+    ] .

rocrate_validator/profiles/five-safes-crate/must/1_root_data_entity_metadata.ttl

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+# Copyright (c) 2024-2025 CRS4
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix five-safes-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/five-safes-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema_org: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix validator: <https://github.com/crs4/rocrate-validator/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+
+five-safes-crate:RootDataEntityRequiredProperties
+    a sh:NodeShape ;
+    sh:name "Five Safes Crate Root Data Entity REQUIRED properties" ;
+    sh:description "The Root Data Entity MUST have a `sourceOrganisation`" ;
+    sh:targetClass ro-crate:RootDataEntity ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "Root Data Entity: `sourceOrganization` property" ;
+        sh:description """Check if the Root Data Entity includes a `sourceOrganization` (as specified by schema.org).""" ;
+        sh:path schema_org:sourceOrganization;
+        sh:minCount 1 ;
+        sh:class ro-crate:ContextualEntity ;
+        sh:message """The Root Data Entity MUST have a `sourceOrganization` property  (as specified by schema.org).
+                   SHOULD link to a Contextual Entity in the RO-Crate Metadata File with a name.""" ;
+    ] .

rocrate_validator/profiles/five-safes-crate/must/2_requesting_agent.ttl

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+# Copyright (c) 2025 eScience Lab, The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix five-safes-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/five-safes-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix validator: <https://github.com/crs4/rocrate-validator/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+
+
+five-safes-crate:CreateActionHasAgent
+  a sh:NodeShape ;
+  sh:name "CreateAction" ;
+  sh:targetClass schema:CreateAction ;
+  sh:description "Checks that a CreateAction has an agent and that each agent is a schema:Person." ;
+
+  # CreateAction entity MUST have an agent (IRI)
+  sh:property [
+    a sh:PropertyShape ;
+    sh:name "Has Agent" ;
+    sh:path schema:agent ;
+    sh:minCount 1 ;
+    sh:nodeKind sh:IRI ;
+    sh:severity sh:Violation ;
+    sh:message "CreateAction MUST have at least one schema:agent that is an IRI." ;
+  ] ;
+
+  # The agent of a CreateAction entity MUST be a Person
+  sh:property [
+    a sh:PropertyShape ;
+    sh:name "Agent is a Person" ;
+    sh:path schema:agent ;
+    sh:nodeKind sh:IRI ;
+    sh:class schema:Person ;
+    sh:severity sh:Violation ;
+    sh:message "Each CreateAction agent MUST be typed as schema:Person and be an IRI." ;
+  ] ;
+
+  # If any agent affiliation exists, it MUST be an Organization (IRI)
+  sh:property [
+    a sh:PropertyShape ;
+    sh:name "Affiliation is an Organization" ;
+    sh:path ( schema:agent schema:affiliation ) ;
+    sh:class schema:Organization ;
+    sh:nodeKind sh:IRI ;
+    sh:severity sh:Violation ;
+    sh:message "The affiliation (if any) of a CreateAction's agent MUST be a schema:Organization and be an IRI." ;
+  ] .

rocrate_validator/profiles/five-safes-crate/profile.ttl

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+# Copyright (c) 2024-2025 CRS4, University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix dct: <http://purl.org/dc/terms/> .
+@prefix prof: <http://www.w3.org/ns/dx/prof/> .
+@prefix role: <http://www.w3.org/ns/dx/prof/role/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+<https://w3id.org/5s-crate/0.4>
+    a prof:Profile ;
+
+    # the Profile's label
+    rdfs:label "Five Safes RO-Crate 0.4" ;
+
+    # regular metadata, a basic description of the Profile
+    rdfs:comment """Five Safes RO-Crate Metadata Specification 0.4"""@en ;
+
+    # URI of the publisher of the Metadata Specification
+    dct:publisher <https://w3id.org/5s-crate> ;
+
+    # This profile is an extension of Workflow Run Crate for use in Trusted Research Environments (TRE)
+    prof:isProfileOf <https://w3id.org/ro/wfrun/workflow/0.5> ;
+
+    # This profile is a transitive profile of the RO-Crate Metadata Specification
+    prof:isTransitiveProfileOf <https://w3id.org/ro/crate/1.1> ,
+                               <https://w3id.org/ro/wfrun/process/0.5> ,
+                               <https://w3id.org/workflowhub/workflow-ro-crate/1.0> ;
+
+    # this profile has a JSON-LD context resource
+    prof:hasResource [
+        a prof:ResourceDescriptor ;
+
+        # it's in JSON-LD format
+        dct:format <https://w3id.org/mediatype/application/ld+json> ;
+
+        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
+
+        # this profile resource plays the role of "Vocabulary"
+        # described in this ontology's accompanying Roles vocabulary
+        prof:hasRole role:Vocabulary ;
+
+        # this profile resource's actual file
+        prof:hasArtifact <https://w3id.org/ro/terms/workflow-run/context> ;
+    ] ;
+
+    # this profile has a human-readable documentation resource
+    prof:hasResource [
+        a prof:ResourceDescriptor ;
+
+        # it's in HTML format
+        dct:format <https://w3id.org/mediatype/text/html> ;
+
+        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        dct:conformsTo <https://www.w3.org/TR/html/> ;
+
+        # this profile resource plays the role of "Specification"
+        # described in this ontology's accompanying Roles vocabulary
+        prof:hasRole role:Specification ;
+
+        # this profile resource's actual file
+        prof:hasArtifact <https://trefx.uk/5s-crate/0.4/> ;
+
+        # this profile is inherited from Workflow Run profile
+        prof:isInheritedFrom <https://www.researchobject.org/workflow-run-crate/profiles/0.5/workflow_run_crate/> ;
+    ] ;
+
+    # a short code to refer to the Profile with when a URI can't be used
+    prof:hasToken "five-safes-crate" ;
+.

rocrate_validator/profiles/five-safes-crate/should/2_requesting_agent.ttl

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+# Copyright (c) 2025 eScience Lab, The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix five-safes-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/five-safes-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix validator: <https://github.com/crs4/rocrate-validator/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+
+# Person who is the agent of a CreateAction SHOULD have an affiliation
+five-safes-crate:PersonAgentHasAffiliation
+    a sh:NodeShape ;
+    sh:name "Agent of CreateAction" ;
+    sh:description "The agent of a CreateAction entity" ;
+    sh:target [
+        a sh:SPARQLTarget ;
+        sh:prefixes ro-crate:sparqlPrefixes ;
+        sh:select """
+            SELECT DISTINCT ?this WHERE {
+              ?action a schema:CreateAction ;
+                      schema:agent ?this .
+            }
+        """
+    ] ;
+
+    # The agent of a CreateAction entity SHOULD have an affiliation
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "Presence of affiliations" ;
+        sh:path schema:affiliation ;
+        sh:minCount 1 ;
+        sh:severity sh:Warning ;
+        sh:message "The agent of a CreateAction entity SHOULD have an affiliation" ;
+    ] ;
+
+    # If the agent has an affiliation, validate the affiliation node's IRI
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "Affiliation IRI" ;
+        sh:path schema:affiliation ;
+        sh:nodeKind sh:IRI ;
+        sh:or (
+            [ sh:pattern "^https://ror\\.org/0[0-9a-hjkmnp-tv-z]{6}[0-9]{2}$" ; sh:flags "i"]
+            [ sh:pattern "^https://isni\\.org/isni/\\d{15}[\\dX]$" ; sh:flags "i"]
+            [ sh:pattern "^https://(?:www\\.)?wikidata\\.org/entity/Q\\d+$" ; sh:flags "i"]
+        ) ;
+        sh:severity sh:Warning ;
+        sh:message "Affiliation Organization @id SHOULD be a permalink (ROR/ISNI/Wikidata)." ;
+    ] .

rocrate_validator/profiles/five-safes-crate/should/5_profile_conformance.ttl

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+# Copyright (c) 2025 eScience Lab, The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix five-safes-crate: <https://github.com/eScienceLab/rocrate-validator/profiles/five-safes-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix validator: <https://github.com/crs4/rocrate-validator/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+# Root Dataset SHOULD declare conformsTo Five Safes profile
+five-safes-crate:RootDatasetConformsToFiveSafes
+    a sh:NodeShape ;
+    sh:name "Root Dataset Five Safes RO-Crate profile conformance" ;
+    sh:description "The Root Data Entity (./) SHOULD declare conformsTo the Five Safes RO-Crate profile." ; 
+    sh:targetNode ro: ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "conformsTo Five Safes profile" ;
+        sh:description "Root Dataset SHOULD include schema:conformsTo https://w3id.org/5s-crate/0.4" ;
+        sh:path schema:conformsTo ;
+        sh:qualifiedValueShape [
+            sh:hasValue <https://w3id.org/5s-crate/0.4>
+        ] ;
+        sh:qualifiedMinCount 1 ;
+        sh:severity sh:Warning ;
+        sh:message "Profile Conformance: Root Dataset SHOULD include schema:conformsTo with @id https://w3id.org/5s-crate/0.4" ;
+    ] .
+
+five-safes-crate:RootDatasetDatePublishedWhenPublished
+    a sh:NodeShape ;
+    sh:name "datePublished present on published crates" ;
+    sh:description "If the root dataset is published (has schema:publisher), it SHOULD have schema:datePublished." ;
+    sh:targetNode ro: ;
+    sh:severity sh:Warning ;
+    sh:message "Published crates SHOULD include schema:datePublished." ;
+    sh:or (
+        # datePublished not required if no publisher:
+        [ sh:not [ sh:property [
+            sh:path schema:publisher ;
+            sh:minCount 1 ;
+        ]]]
+        # datePublished required if publisher present:
+        [ sh:property [
+            sh:path schema:datePublished ;
+            sh:minCount 1 ;
+        ]]
+    ) .
+
+five-safes-crate:RootDatasetLicenseWhenPublished
+    a sh:NodeShape ;
+    sh:name "License present on published crates" ;
+    sh:description "If the root dataset is published (has schema:publisher), it SHOULD declare a license." ;
+    sh:targetNode ro: ;
+    sh:severity sh:Warning ;
+    sh:message "Profile Conformance: Published crates SHOULD include a license." ;
+    sh:or (
+        # license not required if no publisher:
+        [ sh:not [ sh:property [
+            sh:path schema:publisher ;
+            sh:minCount 1 ;
+        ]]]
+        # license required if publisher present:
+        [ sh:property [
+            sh:path schema:license ;
+            sh:minCount 1 ;
+        ]]
+    ) .