Implement Metadata File expectations

rocrate_validator/profiles/five-safes-crate/must/15_metadata_file.py

@@ -0,0 +1,64 @@
+# 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.
+
+import re
+
+import rocrate_validator.log as logging
+from rocrate_validator.models import Severity, ValidationContext
+from rocrate_validator.requirements.python import PyFunctionCheck, check, requirement
+
+# set up logging
+logger = logging.getLogger(__name__)
+
+
+@requirement(name="RO-Crate context version")
+class FileDescriptorContextVersion(PyFunctionCheck):
+    """The RO-Crate metadata file MUST include the RO-Crate context version 1.2
+    (or later minor version) in `@context`"""
+
+    @check(name="RO-Crate context version", severity=Severity.REQUIRED)
+    def test_existence(self, context: ValidationContext) -> bool:
+        """
+        The RO-Crate metadata file MUST include the RO-Crate context version 1.2
+        (or later minor version) in `@context`
+        """
+        try:
+            json_dict = context.ro_crate.metadata.as_dict()
+            context_value = json_dict["@context"]
+            pattern = re.compile(
+                r"https://w3id\.org/ro/crate/1\.[2-9](-DRAFT)?/context"
+            )
+            passed = True
+            if isinstance(context_value, list):
+                if not any(
+                    pattern.match(item)
+                    for item in context_value
+                    if isinstance(item, str)
+                ):
+                    passed = False
+            else:
+                if not pattern.match(context_value):
+                    passed = False
+            if not passed:
+                context.result.add_issue(
+                    "The RO-Crate metadata file MUST include the RO-Crate context "
+                    "version 1.2 (or later minor version) in `@context`",
+                    self,
+                )
+            return passed
+
+        except Exception as e:
+            if logger.isEnabledFor(logging.DEBUG):
+                logger.exception(e)
+        return True

rocrate_validator/profiles/five-safes-crate/must/15_metadata_file.ttl

@@ -0,0 +1,41 @@
+# 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-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 purl: <http://purl.org/dc/terms/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix validator: <https://github.com/crs4/rocrate-validator/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix dct: <http://purl.org/dc/terms/> .
+
+five-safes-crate:MetadataFileDescriptorProperties a sh:NodeShape ;
+    sh:name "RO-Crate conforms to 1.2 or later minor version" ;
+    sh:description """The RO-Crate metadata file descriptor MUST have a `conformsTo` property with RO-Crate specification version 1.2 or later minor version""";
+    sh:targetClass ro-crate:ROCrateMetadataFileDescriptor ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "RO-Crate conforms to 1.2 or later minor version" ;
+        sh:description "The RO-Crate metadata file descriptor MUST have a `conformsTo` property with RO-Crate specification version 1.2 or later minor version" ;
+        sh:minCount 1 ;
+        sh:nodeKind sh:IRI ;
+        sh:path dct:conformsTo ;
+        sh:pattern "https://w3id\\.org/ro/crate/(1\\.[2-9](-DRAFT)?)" ;
+        sh:severity sh:Violation;
+        sh:message "The RO-Crate metadata file descriptor MUST have a `conformsTo` property with RO-Crate specification version 1.2 or later minor version" ;
+    ] .
+
+ro-crate:conformsToROCrateSpec sh:deactivated true .

rocrate_validator/profiles/ro-crate/must/1_file-descriptor_metadata.ttl

@@ -89,13 +89,12 @@ ro-crate:ROCrateMetadataFileDescriptorRecommendedProperties a sh:NodeShape ;
         sh:class schema_org:Dataset ;
         sh:message "The RO-Crate metadata file descriptor MUST have an `about` property referencing the Root Data Entity" ;
     ] ;
-    sh:property [
-        a sh:PropertyShape ;
-        sh:name "Metadata File Descriptor entity: `conformsTo` property" ;
-        sh:description """Check if the RO-Crate Metadata File Descriptor has a `conformsTo` property which points to the RO-Crate specification version""" ;
-        sh:minCount 1 ;
-        sh:nodeKind sh:IRI ;
-        sh:path dct:conformsTo ;
-        sh:hasValue <https://w3id.org/ro/crate/1.1> ;
-        sh:message "The RO-Crate metadata file descriptor MUST have a `conformsTo` property with the RO-Crate specification version" ;
-    ] .
+    sh:property ro-crate:conformsToROCrateSpec .
+
+ro-crate:conformsToROCrateSpec sh:name "Metadata File Descriptor entity: `conformsTo` property" ;
+    sh:description """Check if the RO-Crate Metadata File Descriptor has a `conformsTo` property which points to the RO-Crate specification version""" ;
+    sh:minCount 1 ;
+    sh:nodeKind sh:IRI ;
+    sh:path dct:conformsTo ;
+    sh:hasValue <https://w3id.org/ro/crate/1.1> ;
+    sh:message "The RO-Crate metadata file descriptor MUST have a `conformsTo` property with the RO-Crate specification version" .

tests/data/crates/invalid/five_safes_crate/context_multiple_wrong_version/ro-crate-metadata.json

@@ -0,0 +1,169 @@
+{
+    "@context": ["https://w3id.org/ro/crate/1.1/context", "http://schema.org", {"test": "http://schema.org/test"}],
+    "@graph": [
+        {
+            "@type": "CreativeWork",
+            "@id": "ro-crate-metadata.json",
+            "about": {
+                "@id": "./"
+            },
+            "conformsTo": {
+                "@id": "https://w3id.org/ro/crate/1.2"
+            }
+        },
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "name": "5-Safe RO-Crate Request",
+            "description": "example 5-Safe RO-Crate request metadata for testing",
+            "license": "Apache-2.0",
+            "datePublished": "2025-09-20T14:38:00+00:00",
+            "conformsTo": {
+                "@id": "https://w3id.org/5s-crate/0.4"
+            },
+            "hasPart": [
+                {
+                    "@id": "https://workflowhub.eu/workflows/289?version=1"
+                },
+                {
+                    "@id": "input1.txt"
+                }
+            ],
+            "mainEntity": {
+                "@id": "https://workflowhub.eu/workflows/289?version=1"
+            },
+            "mentions": {
+                "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538"
+            },
+            "sourceOrganization": {
+                "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70"
+            }
+        },
+        {
+            "@id": "https://w3id.org/5s-crate/0.4",
+            "@type": "Profile",
+            "name": "Five Safes RO-Crate profile"
+        },
+        {
+            "@id": "https://workflowhub.eu/workflows/289?version=1",
+            "@type": "Dataset",
+            "name": "CWL Protein MD Setup tutorial with mutations",
+            "conformsTo": {
+                "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+            },
+            "distribution": {
+                "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1"
+            }
+        },
+        {
+            "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1",
+            "@type": "DataDownload",
+            "conformsTo": {
+                "@id": "https://w3id.org/ro/crate"
+            },
+            "encodingFormat": "application/zip"
+        },
+        {
+            "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538",
+            "@type": "CreateAction",
+            "actionStatus": "http://schema.org/PotentialActionStatus",
+            "agent": {
+                "@id": "https://orcid.org/0000-0001-9842-9718"
+            },
+            "instrument": {
+                "@id": "https://workflowhub.eu/workflows/289?version=1"
+            },
+            "name": "Execute query 12389 on workflow ",
+            "object": [
+                {
+                    "@id": "input1.txt"
+                },
+                {
+                    "@id": "#enableFastMode"
+                }
+            ]
+        },
+        {
+            "@id": "https://orcid.org/0000-0001-9842-9718",
+            "@type": "Person",
+            "name": "Stian Soiland-Reyes",
+            "affiliation": {
+                "@id": "https://ror.org/027m9bs27"
+            },
+            "memberOf": [
+                {
+                    "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70"
+                }
+            ]
+        },
+        {
+            "@id": "https://ror.org/027m9bs27",
+            "@type": "Organization",
+            "name": "The University of Manchester"
+        },
+        {
+            "@id": "https://ror.org/01ee9ar58",
+            "@type": "Organization",
+            "name": "University of Nottingham"
+        },
+        {
+            "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70",
+            "@type": "Project",
+            "name": "Investigation of cancer (TRE72 project 81)",
+            "identifier": [
+                {
+                    "@id": "_:localid:tre72:project81"
+                }
+            ],
+            "funding": {
+                "@id": "https://gtr.ukri.org/projects?ref=10038961"
+            },
+            "member": [
+                {
+                    "@id": "https://ror.org/027m9bs27"
+                },
+                {
+                    "@id": "https://ror.org/01ee9ar58"
+                }
+            ]
+        },
+        {
+            "@id": "_:localid:tre72:project81",
+            "@type": "PropertyValue",
+            "name": "tre72",
+            "value": "project81"
+        },
+        {
+            "@id": "https://gtr.ukri.org/projects?ref=10038961",
+            "@type": "Grant",
+            "name": "EOSC4Cancer"
+        },
+        {
+            "@id": "input1.txt",
+            "@type": "File",
+            "name": "input1",
+            "exampleOfWork": {
+                "@id": "#sequence"
+            }
+        },
+        {
+            "@id": "#enableFastMode",
+            "@type": "PropertyValue",
+            "name": "--fast-mode",
+            "value": "True",
+            "exampleOfWork": {
+                "@id": "#fast"
+            }
+        },
+        {
+            "@id": "#sequence",
+            "@type": "FormalParameter",
+            "name": "input-sequence"
+        },
+        {
+            "@id": "#fast",
+            "@type": "FormalParameter",
+            "name": "fast-mode"
+        }
+    ]
+}