Skip to content

Five safes on upstream develop #126

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
EttoreM merged 6 commits into from
Jul 17, 2026
Merged

Five safes on upstream develop #126

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
5fa8068
Add Five Safes Crate profile to upstream RO-Crate 1.2 base
EttoreM Jul 2, 2026
5dec215
Amended formatting
EttoreM Jul 2, 2026
9bddab2
More formatting fixes
EttoreM Jul 2, 2026
ee3ca75
Remove leftover conflict markers after rebase
EttoreM Jul 17, 2026
8aafd74
Addressed Eli's comments
EttoreM Jul 17, 2026
e291b4e
Rileset 15 removed from SHACL shapes and python tests as per Eli' sug…
EttoreM Jul 17, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/0_workflow_run_inference.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
# 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 ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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#> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/10_outputs.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
6 changes: 3 additions & 3 deletions rocrate_validator/profiles/five-safes-crate/11_workflow_execution_phase.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down Expand Up @@ -75,7 +75,7 @@ five-safes-crate:WorkflowexecutionObjectHasEndTimeIfEnded
a sh:SPARQLTarget ;
sh:select """
PREFIX schema: <http://schema.org/>
PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/>
PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/>

SELECT ?this
WHERE {
Expand Down Expand Up @@ -115,7 +115,7 @@ five-safes-crate:WorkflowexecutionObjectHasStartTimeIfBegun
a sh:SPARQLTarget ;
sh:select """
PREFIX schema: <http://schema.org/>
PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/>
PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/>

SELECT ?this
WHERE {
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/12_check_phase.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/13_validation_phase.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/14_workflow_retrieval_phase.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
64 changes: 0 additions & 64 deletions rocrate_validator/profiles/five-safes-crate/15_metadata_file.py
View file
Open in desktop

This file was deleted.

53 changes: 0 additions & 53 deletions rocrate_validator/profiles/five-safes-crate/15_metadata_file.ttl
View file
Open in desktop

This file was deleted.

2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/16_publishing_phase.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/1_requesting_agent.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/1_responsible_project.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/1_root_data_entity.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/2_requesting_agent.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/3_timestamp_format.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
6 changes: 3 additions & 3 deletions rocrate_validator/profiles/five-safes-crate/4_sign_off.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down Expand Up @@ -190,7 +190,7 @@ five-safes-crate:SignOffPhaseProperties
sh:description "Check if the Sign Off phase lists the workflow as an object" ;
sh:select """
PREFIX schema: <http://schema.org/>
PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/>
PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/>
SELECT $this
WHERE {
?root a schema:Dataset ;
Expand All @@ -209,7 +209,7 @@ five-safes-crate:SignOffPhaseProperties
sh:description "Check if the Sign Off phase lists the Responsible Project as an object" ;
sh:select """
PREFIX schema: <http://schema.org/>
PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/>
PREFIX rocrate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/>
SELECT $this
WHERE {
?root a schema:Dataset ;
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/5_profile_conformance.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/6_workflow_reference.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/7_requested_workflow_run.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/8_disclosure_phase.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/9_inputs.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# limitations under the License.

@prefix ro: <./> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@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/> .
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/ontology.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
@prefix schema: <http://schema.org/> .
@prefix rocrate: <https://w3id.org/ro/crate/1.1/> .
@prefix bioschemas: <https://bioschemas.org/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate-1.2/> .
@prefix isa-ro-crate: <https://github.com/crs4/rocrate-validator/profiles/isa-ro-crate/> .

<urn:absolute:.> rdf:type owl:Ontology ;
Expand Down
2 changes: 1 addition & 1 deletion rocrate_validator/profiles/five-safes-crate/profile.ttl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@
# 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> ;
prof:isTransitiveProfileOf <https://w3id.org/ro/crate/1.2> ;
# TODO: resolve failures when these profiles are applied
# <https://w3id.org/ro/wfrun/process/0.5> ,
# <https://w3id.org/workflowhub/workflow-ro-crate/1.0> ;
Expand Down
2 changes: 2 additions & 0 deletions tests/data/crates/valid/five-safes-crate-result/ro-crate-metadata.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -393,6 +393,8 @@
"@id": "https://tre72.example.com/#crate-validator",
"@type": "SoftwareApplication",
"name": "RO-Crate validator at TRE72",
"url": "https://tre72.example.com/#crate-validator",
"version": "1.0",
"provider": {
"@id": "https://tre72.example.com/"
}
Expand Down
6 changes: 2 additions & 4 deletions tests/integration/profiles/five-safes-crate/test_5src_10_outputs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@

from rocrate_validator.models import Severity
from tests.ro_crates import ValidROC
from tests.shared import do_entity_test, SPARQL_PREFIXES
from tests.shared import SPARQL_PREFIXES, do_entity_test

# set up logging
logger = logging.getLogger(__name__)
Expand Down Expand Up @@ -87,9 +87,7 @@ def test_result_output_does_not_have_allowed_type():
requirement_severity=Severity.RECOMMENDED,
expected_validation_result=False,
expected_triggered_requirements=["Output"],
expected_triggered_issues=[
"Result SHOULD have a `@type` among an allowed set of values."
],
expected_triggered_issues=["Result SHOULD have a `@type` among an allowed set of values."],
profile_identifier="five-safes-crate",
rocrate_entity_mod_sparql=sparql,
)
6 changes: 2 additions & 4 deletions tests/integration/profiles/five-safes-crate/test_5src_11_workflow_execution.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@

from rocrate_validator.models import Severity
from tests.ro_crates import ValidROC
from tests.shared import do_entity_test, SPARQL_PREFIXES
from tests.shared import SPARQL_PREFIXES, do_entity_test

# set up logging
logger = logging.getLogger(__name__)
Expand Down Expand Up @@ -267,9 +267,7 @@ def test_5src_workflow_object_has_no_end_time_if_ended():
requirement_severity=Severity.RECOMMENDED,
expected_validation_result=False,
expected_triggered_requirements=["WorkflowExecution"],
expected_triggered_issues=[
"The workflow execution object SHOULD have an endTime property if it has ended."
],
expected_triggered_issues=["The workflow execution object SHOULD have an endTime property if it has ended."],
profile_identifier="five-safes-crate",
rocrate_entity_mod_sparql=sparql,
)
Expand Down
Loading