Unverified Commit 133b0a5b authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #16193 from mvdbeek/support_ro_crate_0_8_0_and_0_7_0 

[23.0] Support ro crate 0.8.0 and 0.7.0
parents 2a5b442f 7cb93b3d

lib/galaxy/model/store/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -2450,7 +2450,7 @@ class WriteCrates: 
                    "encodingFormat": encoding_format,

                }

                ro_crate.add_file(

                    file_name,

                    os.path.join(self.export_directory, file_name),

                    dest_path=file_name,

                    properties=properties,

                )

lib/galaxy/model/store/ro_crate_utils.py

+12 −2
Original line number Diff line number Diff line
@@ -6,6 +6,8 @@ from typing import ( 
    Optional,

)



from packaging.version import parse

from rocrate import __version__ as rocrate_version

from rocrate.model.computationalworkflow import (

    ComputationalWorkflow,

    WorkflowDescription,
@@ -102,13 +104,21 @@ class WorkflowRunCrateProfileBuilder: 
        if dataset.dataset.id in self.model_store.dataset_id_to_path:

            filename, _ = self.model_store.dataset_id_to_path[dataset.dataset.id]

            if not filename:

                # dataset was not serialized

                filename = f"datasets/dataset_{dataset.dataset.uuid}"

                if parse(rocrate_version) >= parse("0.8.0"):

                    source = None

                else:

                    # Drop in 23.1

                    source = filename

            else:

                source = os.path.join(self.model_store.export_directory, filename)

            name = dataset.name

            encoding_format = dataset.datatype.get_mime()

            properties["name"] = name

            properties["encodingFormat"] = encoding_format

            file_entity = crate.add_file(

                filename,

                source,

                dest_path=filename,

                properties=properties,

            )
@@ -272,7 +282,7 @@ class WorkflowRunCrateProfileBuilder: 
                    "encodingFormat": "application/json",

                }

                crate.add_file(

                    attrs,

                    attrs_path,

                    dest_path=attrs,

                    properties=properties,

                )

test/unit/data/model/test_model_store.py

+0 −1
Original line number Diff line number Diff line
@@ -347,7 +347,6 @@ def validate_has_pl_galaxy(ro_crate: ROCrate): 
    assert programming_language.id == "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"

    assert programming_language.name == "Galaxy"

    assert programming_language.url == "https://galaxyproject.org/"

    assert programming_language.version





def validate_organize_action(ro_crate: ROCrate):