diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py index e2ff8f83ae6..945fc2d3235 100644 --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -524,16 +524,18 @@ class WorkflowContentsManager(UsesAnnotations): workflow.reports_config = data["report"] workflow.license = data.get("license") workflow.creator_metadata = data.get("creator") - if hasattr(workflow_state_resolution_options, "trs_tool_id") and hasattr( - workflow_state_resolution_options, "trs_version_id" - ): - if workflow_state_resolution_options.trs_tool_id and workflow_state_resolution_options.trs_version_id: - workflow.trs_tool_id = workflow_state_resolution_options.trs_tool_id - workflow.trs_version_id = workflow_state_resolution_options.trs_version_id - workflow_state_resolution_options.trs_tool_id, workflow_state_resolution_options.trs_version_id = ( - None, - None, - ) # so trs_id is not set for subworkflows + + if hasattr(workflow_state_resolution_options, "archive_source"): + if workflow_state_resolution_options.archive_source: + source_metadata = {} + if workflow_state_resolution_options.archive_source == "trs_tool": + source_metadata["trs_tool_id"] = workflow_state_resolution_options.trs_tool_id + source_metadata["trs_version_id"] = workflow_state_resolution_options.trs_version_id + source_metadata["trs_server"] = workflow_state_resolution_options.trs_server + elif not workflow_state_resolution_options.archive_source.startswith("file://"): # URL import + source_metadata["url"] = workflow_state_resolution_options.archive_source + workflow_state_resolution_options.archive_source = None # so trs_id is not set for subworkflows + workflow.source_metadata = source_metadata # Assume no errors until we find a step that has some workflow.has_errors = False @@ -859,8 +861,7 @@ class WorkflowContentsManager(UsesAnnotations): data["report"] = workflow.reports_config or {} data["license"] = workflow.license data["creator"] = workflow.creator_metadata - data["trs_tool_id"] = workflow.trs_tool_id - data["trs_version_id"] = workflow.trs_version_id + data["source_metadata"] = workflow.source_metadata data["annotation"] = self.get_item_annotation_str(trans.sa_session, trans.user, stored) or "" output_label_index = set() @@ -1100,10 +1101,8 @@ class WorkflowContentsManager(UsesAnnotations): data["creator"] = workflow.creator_metadata if workflow.license: data["license"] = workflow.license - if workflow.trs_tool_id: - data["trs_tool_id"] = workflow.trs_tool_id - if workflow.trs_version_id: - data["trs_version_id"] = workflow.trs_version_id + if workflow.source_metadata: + data["source_metadata"] = workflow.source_metadata # For each step, rebuild the form and encode the state for step in workflow.steps: # Load from database representation @@ -1654,9 +1653,11 @@ class WorkflowCreateOptions(WorkflowStateResolutionOptions): tool_panel_section_mapping: Dict = {} shed_tool_conf: Optional[str] = None - # for workflows imported by trs id + # for workflows imported by archive source + archive_source: str = "" trs_tool_id: str = "" trs_version_id: str = "" + trs_server: str = "" @property def is_importable(self): diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 976aa7a570d..c49579d97d9 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -6608,8 +6608,7 @@ class Workflow(Base, Dictifiable, RepresentById): reports_config = Column(MutableJSONType) creator_metadata = Column(MutableJSONType) license = Column(TEXT) - trs_tool_id = Column(TEXT) - trs_version_id = Column(TEXT) + source_metadata = Column(MutableJSONType) uuid = Column(UUIDType, nullable=True) steps = relationship( diff --git a/lib/galaxy/model/migrate/versions/0181_add_trs_id_workflow_table.py b/lib/galaxy/model/migrate/versions/0181_add_source_metadata_workflow_table.py similarity index 50% rename from lib/galaxy/model/migrate/versions/0181_add_trs_id_workflow_table.py rename to lib/galaxy/model/migrate/versions/0181_add_source_metadata_workflow_table.py index b4a1b1c0709..59755972891 100644 --- a/lib/galaxy/model/migrate/versions/0181_add_trs_id_workflow_table.py +++ b/lib/galaxy/model/migrate/versions/0181_add_source_metadata_workflow_table.py @@ -1,5 +1,5 @@ """ -Migration script for adding trs_id column to workflow table. +Migration script for adding source_metadata column to workflow table. """ import logging @@ -7,9 +7,9 @@ import logging from sqlalchemy import ( Column, MetaData, - Text, ) +from galaxy.model.custom_types import JSONType from galaxy.model.migrate.versions.util import ( add_column, drop_column, @@ -24,16 +24,12 @@ def upgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() - trs_tool_id_column = Column("trs_tool_id", Text) - add_column(trs_tool_id_column, "workflow", metadata) - - trs_version_id_column = Column("trs_version_id", Text) - add_column(trs_version_id_column, "workflow", metadata) + source_metadata_column = Column("source_metadata", JSONType) + add_column(source_metadata_column, "workflow", metadata) def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() - drop_column("trs_tool_id", "workflow", metadata) - drop_column("trs_version_id", "workflow", metadata) + drop_column("source_metadata", "workflow", metadata) diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py index c4a815353aa..d6865f9e70d 100644 --- a/lib/galaxy_test/api/test_workflows.py +++ b/lib/galaxy_test/api/test_workflows.py @@ -645,6 +645,15 @@ steps: other_import_response = self.__import_workflow(workflow_id) self._assert_status_code_is(other_import_response, 403) + def test_url_import(self): + url = "https://raw.githubusercontent.com/galaxyproject/galaxy/release_19.09/test/base/data/test_workflow_1.ga" + workflow_id = self._post("workflows", data={"archive_source": url}).json()["id"] + workflow = self._download_workflow(workflow_id) + assert "TestWorkflow1" in workflow["name"] + assert ( + workflow.get("source_metadata").get("url") == url + ) # disappearance of source_metadata on modification is tested in test_trs_import + def test_trs_import(self): trs_payload = { "archive_source": "trs_tool", @@ -655,8 +664,8 @@ steps: workflow_id = self._post("workflows", data=trs_payload).json()["id"] original_workflow = self._download_workflow(workflow_id) assert "Test Workflow" in original_workflow["name"] - assert original_workflow.get("trs_tool_id") == trs_payload["trs_tool_id"] - assert original_workflow.get("trs_version_id") == trs_payload["trs_version_id"] + assert original_workflow.get("source_metadata").get("trs_tool_id") == trs_payload["trs_tool_id"] + assert original_workflow.get("source_metadata").get("trs_version_id") == trs_payload["trs_version_id"] # refactor workflow and check that the trs id is removed actions = [ @@ -664,12 +673,12 @@ steps: ] self.workflow_populator.refactor_workflow(workflow_id, actions) refactored_workflow = self._download_workflow(workflow_id) - assert refactored_workflow.get("trs_tool_id") is None + assert refactored_workflow.get("source_metadata") is None # reupload original_workflow and check that the trs id is removed reuploaded_workflow_id = self.workflow_populator.create_workflow(original_workflow) reuploaded_workflow = self._download_workflow(reuploaded_workflow_id) - assert reuploaded_workflow.get("trs_tool_id") is None + assert reuploaded_workflow.get("source_metadata") is None def test_anonymous_published(self): def anonymous_published_workflows(): diff --git a/test/unit/data/model/mapping/test_model_mapping.py b/test/unit/data/model/mapping/test_model_mapping.py index 8db4c8eae9e..402e19a1001 100644 --- a/test/unit/data/model/mapping/test_model_mapping.py +++ b/test/unit/data/model/mapping/test_model_mapping.py @@ -5356,6 +5356,7 @@ class TestWorkflow(BaseTest): reports_config = "b" creator_metadata = "c" license = "d" + source_metadata = "e" uuid = uuid4() obj = cls_() @@ -5369,6 +5370,7 @@ class TestWorkflow(BaseTest): obj.reports_config = reports_config obj.creator_metadata = creator_metadata obj.license = license + obj.source_metadata = source_metadata obj.uuid = uuid with dbcleanup(session, obj) as obj_id: @@ -5384,6 +5386,7 @@ class TestWorkflow(BaseTest): assert stored_obj.reports_config == reports_config assert stored_obj.creator_metadata == creator_metadata assert stored_obj.license == license + assert stored_obj.source_metadata == source_metadata assert stored_obj.uuid == uuid def test_relationships(self, session, cls_, stored_workflow, workflow, workflow_step_factory):