Merge remote-tracking branch 'upstream/develop' into develop-testmerge

Author: douglowe

CHANGELOG.md

@@ -19,6 +19,12 @@ authors:
   - family-names: Bauer
     given-names: Daniel
     orcid: https://orcid.org/0000-0001-9447-460X
+  - family-names: "Wetzels"
+    given-names: "Florian"
+    orcid: https://orcid.org/0000-0002-5526-7138
+  - family-names: "Weil"
+    given-names: "Heinrich Lukas"
+    orcid: https://orcid.org/0000-0003-1945-6342
 repository-code: "https://github.com/crs4/rocrate-validator"
 url: "https://github.com/crs4/rocrate-validator"
 keywords:

CITATION.cff

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "roc-validator"
-version = "0.8.0"
+version = "0.8.1"
 description = "A Python package to validate RO-Crates"
 authors = [
     "Marco Enrico Piras <kikkomep@crs4.it>",
@@ -60,7 +60,7 @@ include = [
 [tool.poetry.dependencies]
 python = ">=3.10,<4.0"
 rdflib = ">=7.1,<8.0"
-pyshacl = ">=0.26,<0.31"
+pyshacl = ">=0.26"
 click = ">=8.2,<9.0"
 rich = ">=13.9,<14.0"
 toml = ">=0.10.2,<1.0"
@@ -106,9 +106,17 @@ skip_dirs = [".git", ".github", ".vscode"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
+filterwarnings = [
+    # Ignore deprecation warnings from rdflib's JSON-LD parser,
+    # used internally by pyshacl. These warnings are unrelated to
+    # our code and currently noisy.
+    # See: https://github.com/RDFLib/rdflib/issues/3064
+    # Fix in progress: https://github.com/RDFLib/rdflib/issues/3302
+    "ignore::DeprecationWarning:rdflib.plugins.parsers.jsonld",
+]
 
 [tool.typos.files]
-extend-exclude = ["tests/data","docs/diagrams","*.json","*.html","*__init__.py"]
+extend-exclude = ["tests/data", "docs/diagrams", "*.json", "*.html", "*__init__.py"]
 
 [tool.typos.default.extend-words]
 TRE = "TRE"

poetry.lock

@@ -17,4 +17,10 @@
 ; log_cli=true
 ; log_level=DEBUG
 addopts = -n auto
-; filterwarnings =
+filterwarnings =
+    # Ignore deprecation warnings from rdflib's JSON-LD parser,
+    # used internally by pyshacl. These warnings are unrelated to
+    # our code and currently noisy.
+    # See: https://github.com/RDFLib/rdflib/issues/3064
+    # Fix in progress: https://github.com/RDFLib/rdflib/issues/3302
+    ignore::DeprecationWarning:rdflib.plugins.parsers.jsonld

pyproject.toml

@@ -16,6 +16,7 @@
 
 import os
 import sys
+from contextlib import nullcontext
 from pathlib import Path
 from typing import Optional
 
@@ -276,7 +277,7 @@ def validate(ctx,
             "profile_identifier": profile_identifier,
             "requirement_severity": requirement_severity,
             "requirement_severity_only": requirement_severity_only,
-            "enable_profile_inheritance": not disable_profile_inheritance,
+            "disable_inherited_profiles_issue_reporting": disable_profile_inheritance,
             "rocrate_uri": rocrate_uri,
             "rocrate_relative_root_path": relative_root_path,
             "abort_on_first": fail_fast,
@@ -472,7 +473,7 @@ def validate(ctx,
                     console.print(f"\n{' '*2}📋 [bold]The validation report in JSON format: [/bold]\n")
 
             # Generate the JSON output and write it to the specified output file or to stdout
-            with open(output_file, "w", encoding="utf-8") if output_file else sys.stdout as f:
+            with open(output_file, "w", encoding="utf-8") if output_file else nullcontext(sys.stdout) as f:
                 out = Console(width=output_line_width, file=f)
                 out.register_formatter(JSONOutputFormatter())
                 out.print(results)

pytest.ini

@@ -29,7 +29,7 @@
 
 
 @click.group(invoke_without_command=True)
-@click.rich_config(help_config=click.RichHelpConfiguration(use_rich_markup=True))
+@click.rich_config(help_config=click.RichHelpConfiguration(text_markup="rich"))
 @click.option(
     '--debug',
     is_flag=True,

rocrate_validator/cli/commands/validate.py

@@ -1007,26 +1007,43 @@ def _do_validate_(self, context: ValidationContext) -> bool:
 
         logger.debug("Running %s checks for Requirement '%s'", len(self._checks), self.name)
         all_passed = True
-        for check in [_ for _ in self._checks
-                      if not context.settings.skip_checks
-                      or _.identifier not in context.settings.skip_checks]:
-
+        checks_to_perform = [
+            _ for _ in self._checks
+            if not context.settings.skip_checks
+            or _.identifier not in context.settings.skip_checks
+        ]
+        for check in checks_to_perform:
             try:
                 if check.overridden and not check.requirement.profile.identifier == context.profile_identifier:
                     logger.debug("Skipping check '%s' because overridden by '%r'",
                                  check.identifier, [_.identifier for _ in check.overridden_by])
                     continue
-                context.validator.notify(RequirementCheckValidationEvent(
-                    EventType.REQUIREMENT_CHECK_VALIDATION_START, check))
+                # Determine whether to skip event notification for inherited profiles
+                skip_event_notify = False
+                if check.requirement.profile.identifier != context.profile_identifier and \
+                        context.settings.disable_inherited_profiles_issue_reporting:
+                    logger.debug("Inherited profiles reporting disabled. "
+                                 "Skipping requirement %s as it belongs to an inherited profile %s",
+                                 check.requirement.identifier, check.requirement.profile.identifier)
+                    skip_event_notify = True
+                # Notify the start of the check execution if not skip_event_notify is set to True
+                if not skip_event_notify:
+                    context.validator.notify(RequirementCheckValidationEvent(
+                        EventType.REQUIREMENT_CHECK_VALIDATION_START, check))
+                # Execute the check
                 check_result = check.execute_check(context)
                 logger.debug("Result of check %s: %s", check.identifier, check_result)
                 context.result._add_executed_check(check, check_result)
-                context.validator.notify(RequirementCheckValidationEvent(
-                    EventType.REQUIREMENT_CHECK_VALIDATION_END, check, validation_result=check_result))
+                # Notify the end of the check execution if not skip_event_notify is set to True
+                if not skip_event_notify:
+                    context.validator.notify(RequirementCheckValidationEvent(
+                        EventType.REQUIREMENT_CHECK_VALIDATION_END, check, validation_result=check_result))
                 logger.debug("Ran check '%s'. Got result %s", check.identifier, check_result)
+                # Ensure the check result is a boolean
                 if not isinstance(check_result, bool):
                     logger.warning("Ignoring the check %s as it returned the value %r instead of a boolean", check.name)
                     raise RuntimeError(f"Ignoring invalid result from check {check.name}")
+                # Aggregate the check result
                 all_passed = all_passed and check_result
                 if not all_passed and context.fail_fast:
                     break
@@ -1040,7 +1057,8 @@ def _do_validate_(self, context: ValidationContext) -> bool:
                 logger.warning("Consider reporting this as a bug.")
                 if logger.isEnabledFor(logging.DEBUG):
                     logger.exception(e)
-
+        skipped_checks = set(self._checks) - set(checks_to_perform)
+        context.result.skipped_checks.update(skipped_checks)
         logger.debug("Checks for Requirement '%s' completed. Checks passed? %s", self.name, all_passed)
         return all_passed
 
@@ -1625,7 +1643,7 @@ def __initialise__(cls, validation_settings: ValidationSettings):
         profiles = [profile]
 
         # add inherited profiles if enabled
-        if validation_settings.enable_profile_inheritance:
+        if not validation_settings.disable_inherited_profiles_issue_reporting:
             profiles.extend(profile.inherited_profiles)
         logger.debug("Inherited profiles: %r", profile.inherited_profiles)
 
@@ -1656,9 +1674,20 @@ def __initialise__(cls, validation_settings: ValidationSettings):
                     if severity < severity_validation:
                         continue
                     # count the checks
-                    requirement_checks = [_ for _ in requirement.get_checks_by_level(LevelCollection.get(severity.name))
-                                          if not _.overridden or
-                                          _.requirement.profile.identifier == target_profile_identifier]
+                    requirement_checks = [
+                        _
+                        for _ in requirement.get_checks_by_level(
+                            LevelCollection.get(severity.name)
+                        )
+                        if (
+                            not validation_settings.skip_checks
+                            or _.identifier not in validation_settings.skip_checks
+                        )
+                        and (
+                            not _.overridden
+                            or _.requirement.profile.identifier == target_profile_identifier
+                        )
+                    ]
                     num_checks = len(requirement_checks)
                     requirement_checks_count += num_checks
                     if num_checks > 0:
@@ -2325,12 +2354,20 @@ class ValidationSettings:
     #: The profile identifier to validate against
     profile_identifier: str = DEFAULT_PROFILE_IDENTIFIER
     #: Flag to enable profile inheritance
+    # Use the `enable_profile_inheritance` flag with caution: disable inheritance only if the
+    # target validation profile is fully self-contained and does not rely on definitions
+    # from inherited profiles (e.g., entities defined upstream). For modularization
+    # purposes, some base entities and properties are defined in the base RO-Crate
+    # profile and are intentionally not redefined in specialized profiles; they are
+    # required for validations targeting those specializations and therefore cannot be skipped.
+    # Nevertheless, the validator can still suppress issue reporting for checks defined
+    # in inherited profiles by setting disable_inherited_profiles_issue_reporting to `True`.
     enable_profile_inheritance: bool = True
     # Validation settings
     #: Flag to abort on first error
     abort_on_first: Optional[bool] = False
-    #: Flag to disable inherited profiles reporting
-    disable_inherited_profiles_reporting: bool = False
+    #: Flag to disable reporting of issues related to inherited profiles
+    disable_inherited_profiles_issue_reporting: bool = False
     #: Flag to disable remote crate download
     disable_remote_crate_download: bool = True
     # Requirement settings

rocrate_validator/cli/main.py

@@ -0,0 +1,136 @@
+# Copyright (c) 2026 DataPLANT
+# Copyright (c) 2026 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 isa-ro-crate: <https://github.com/crs4/rocrate-validator/profiles/isa-ro-crate/> .
+@prefix bioschemas: <https://bioschemas.org/> .
+@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#> .
+
+isa-ro-crate:RootDataEntityMustBeInvestigation a sh:NodeShape ;
+    sh:name "Root Data Entity must be Investigation" ;
+    sh:description "The root data entity must follow the investigation profile" ;
+    sh:targetClass ro-crate:RootDataEntity ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:path schema:additionalType ;
+        sh:minCount 1 ;
+        sh:hasValue "Investigation";
+        sh:description "Check if the root data entity is specified as an investigation through additionalType" ;
+        sh:message "The root data entity must have additionalType of `Investigation`" ;
+        sh:severity sh:Violation ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:path schema:identifier ;
+        sh:minCount 1 ;
+        sh:datatype xsd:string ;
+        sh:not [
+            sh:hasValue ""
+        ] ;
+        sh:description "Check if the root data entity (investigation) has an identifier" ;
+        sh:message "The root data entity must have a non-empty identifier" ;
+        sh:severity sh:Violation ;
+    ] ;
+    # sh:property [
+    #     a sh:PropertyShape ;
+    #     sh:path schema:name ;
+    #     sh:minCount 1 ;
+    #     sh:not [
+    #         sh:hasValue ""
+    #     ] ;
+    #     sh:description "Check if the root data entity (investigation) has a name" ;
+    #     sh:message "The root data entity must have a non-empty name" ;
+    #     sh:severity sh:Violation ;
+    # ] ;
+    # sh:property [
+    #     a sh:PropertyShape ;
+    #     sh:path schema:description ;
+    #     sh:minCount 1 ;
+    #     sh:not [
+    #         sh:hasValue ""
+    #     ] ;
+    #     sh:description "Check if the root data entity (investigation) has a description" ;
+    #     sh:message "The root data entity must have a non-empty description" ;
+    #     sh:severity sh:Violation ;
+    # ] ;
+    # sh:property [
+    #     a sh:PropertyShape ;
+    #     sh:path schema:license ;
+    #     sh:minCount 1 ;
+    #     sh:description "Check if the root data entity (investigation) specifies a license" ;
+    #     sh:message "The root data entity must specify a license" ;
+    #     sh:severity sh:Violation ;
+    # ] ;
+    # sh:property [
+    #     a sh:PropertyShape ;
+    #     sh:path schema:datePublished ;
+    #     sh:minCount 1 ;
+    #     sh:nodeKind sh:Literal ;
+    #     sh:pattern "^([\\+-]?\\d{4})((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))|W([0-4]\\d|5[0-2])(-?[1-7])|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)?[0-5]\\d)?|24:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)$" ;
+    #     sh:description "Check if the root data entity (investigation) has a datePublished" ;
+    #     sh:message "The root data entity must have a datePublished" ;
+    #     sh:severity sh:Violation ;
+    # ] ;
+.
+
+isa-ro-crate:InvestigationShouldHaveCreator a sh:NodeShape ;
+    sh:name "Investigation SHOULD have creator" ;
+    sh:description "An Investigation SHOULD have a creator" ;
+    sh:targetClass ro-crate:RootDataEntity ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:path schema:creator ;
+        sh:minCount 1 ;
+        sh:description "Check that investigation does have at least one creator" ;
+        sh:message "Investigation entity SHOULD have a creator" ;
+        sh:severity sh:Warning ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:path schema:creator ;
+        sh:class schema:Person ;
+        sh:description "Check that if investigation does have at least one creator, it MUST be of type Person" ;
+        sh:message "Investigation creator MUST be of type Person" ;
+        sh:severity sh:Violation ;
+    ]
+.
+
+isa-ro-crate:InvestigationShouldHaveDateCreated a sh:NodeShape ;
+    sh:name "Investigation SHOULD have dateCreated" ;
+    sh:description "An Investigation SHOULD have a dateCreated" ;
+    sh:targetClass ro-crate:RootDataEntity ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:path schema:dateCreated ;
+        sh:minCount 1 ;
+        sh:description "Check that investigation does have at least one dateCreated" ;
+        sh:message "Investigation entity SHOULD have a dateCreated" ;
+        sh:severity sh:Warning ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:path schema:dateCreated ;
+        sh:nodeKind sh:Literal ;
+        sh:pattern "^([\\+-]?\\d{4})((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))|W([0-4]\\d|5[0-2])(-?[1-7])|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)?[0-5]\\d)?|24:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)$" ;
+        sh:description "Check that if investigation does have at least one dateCreated, it MUST be a valid ISO 8601 date." ;
+        sh:message "Investigation dateCreated MUST be a valid ISO 8601 date" ;
+        sh:severity sh:Violation ;
+    ]
+.