generalize to source_metadata column and set for url uploads;

add new column to test_model_mapping

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):

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(

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)

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():

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):