Don't re-import TRS workflow if it already exists

lib/galaxy/managers/workflows.py

@@ -27,9 +27,12 @@
     and_,
     desc,
     false,
+    func,
     or_,
+    select,
     true,
 )
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.orm import (
     aliased,
     joinedload,
@@ -320,6 +323,31 @@ def attach_stored_workflow(self, trans, workflow):
                 trans.sa_session.commit()
             return stored_workflow
 
+    def get_workflow_by_trs_id_and_version(self, sa_session, trs_id: str, trs_version: str, user_id: int) -> Optional[model.Workflow]:
+        def to_json(column, keys: List[str]):
+            if sa_session.bind.dialect.name == "postgresql":
+                cast = func.cast(func.convert_from(column, "UTF8"), JSONB)
+                for key in keys:
+                    cast = cast.__getitem__(key)
+                return cast.astext
+            else:
+                for key in keys:
+                    column = column.__getitem__(key)
+                return column
+
+        return sa_session.execute(
+            select([model.Workflow])
+            .join(model.StoredWorkflow, model.Workflow.stored_workflow_id == model.StoredWorkflow.id)
+            .filter(
+                and_(
+                    to_json(model.Workflow.source_metadata, ["trs_tool_id"]) == trs_id,
+                    to_json(model.Workflow.source_metadata, ["trs_version_id"]) == trs_version,
+                    model.StoredWorkflow.user_id == user_id,
+                    model.StoredWorkflow.latest_workflow_id == model.Workflow.id,
+                )
+            )
+        ).scalar()
+
     def get_owned_workflow(self, trans, encoded_workflow_id):
         """Get a workflow (non-stored) from a encoded workflow id and
         make sure it accessible to the user.

lib/galaxy/model/custom_types.py

@@ -14,6 +14,7 @@
 from sqlalchemy.inspection import inspect
 from sqlalchemy.types import (
     CHAR,
+    JSON,
     LargeBinary,
     String,
     TypeDecorator,
@@ -94,27 +95,33 @@ class JSONType(TypeDecorator):
     cache_ok = True
 
     def process_bind_param(self, value, dialect):
-        if value is not None:
+        if value is not None and dialect.name in ("postgresql", "mysql"):
             value = json_encoder.encode(value).encode()
         return value
 
     def process_result_value(self, value, dialect):
-        if value is not None:
+        if value is not None and dialect.name == "postgresql":
             value = json_decoder.decode(unicodify(_sniffnfix_pg9_hex(value)))
         return value
 
     def load_dialect_impl(self, dialect):
         if dialect.name == "mysql":
-            return dialect.type_descriptor(sqlalchemy.dialects.mysql.MEDIUMBLOB)
-        else:
-            return self.impl
+            self.impl = dialect.type_descriptor(sqlalchemy.dialects.mysql.MEDIUMBLOB)
+        elif dialect.name == "sqlite":
+            self.impl = dialect.type_descriptor(sqlalchemy.dialects.sqlite.JSON)
+        return self.impl
 
     def copy_value(self, value):
         return copy.deepcopy(value)
 
     def compare_values(self, x, y):
         return x == y
 
+    @property
+    def comparator_factory(self):
+        """express comparison behavior in terms of the base type"""
+        return sqlalchemy.dialects.sqlite.JSON.comparator_factory
+
 
 class MutableJSONType(JSONType):
     """Associated with MutationObj"""

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -289,6 +289,16 @@ def create(self, trans: GalaxyWebTransaction, payload=None, **kwd):
                         trs_tool_id = payload.get("trs_tool_id")
                         trs_version_id = payload.get("trs_version_id")
 
+                    workflow = self.workflow_manager.get_workflow_by_trs_id_and_version(
+                        trans.sa_session, trs_tool_id, trs_version_id, trans.user.id
+                    )
+                    if workflow and workflow.stored_workflow:
+                        return self.__import_response(
+                            trans,
+                            workflow,
+                            workflow.stored_workflow.id,
+                            message=f"Workflow '{escape(workflow.name)}' already imported.",
+                        )
                     archive_data = server.get_version_descriptor(trs_tool_id, trs_version_id)
                 else:
                     try:
@@ -622,6 +632,23 @@ def get_tool_predictions(self, trans: ProvidesUserContext, payload, **kwd):
     #
     # -- Helper methods --
     #
+    def __import_response(self, trans: GalaxyWebTransaction, workflow: model.Workflow, workflow_id: str, message: str):
+        response = {
+            "message": message,
+            "status": "success",
+            "id": trans.security.encode_id(workflow_id),
+        }
+        if workflow.has_errors:
+            response["message"] = "Imported, but some steps in this workflow have validation errors."
+            response["status"] = "error"
+        elif len(workflow.steps) == 0:
+            response["message"] = "Imported, but this workflow has no steps."
+            response["status"] = "error"
+        elif workflow.has_cycles:
+            response["message"] = "Imported, but this workflow contains cycles."
+            response["status"] = "error"
+        return response
+
     def __api_import_from_archive(self, trans: GalaxyWebTransaction, archive_data, source=None, payload=None):
         payload = payload or {}
         try:
@@ -640,22 +667,12 @@ def __api_import_from_archive(self, trans: GalaxyWebTransaction, archive_data, s
         )
         workflow_id = workflow.id
         workflow = workflow.latest_workflow
-
-        response = {
-            "message": f"Workflow '{escape(workflow.name)}' imported successfully.",
-            "status": "success",
-            "id": trans.security.encode_id(workflow_id),
-        }
-        if workflow.has_errors:
-            response["message"] = "Imported, but some steps in this workflow have validation errors."
-            response["status"] = "error"
-        elif len(workflow.steps) == 0:
-            response["message"] = "Imported, but this workflow has no steps."
-            response["status"] = "error"
-        elif workflow.has_cycles:
-            response["message"] = "Imported, but this workflow contains cycles."
-            response["status"] = "error"
-        return response
+        self.__import_response(
+            trans,
+            workflow,
+            workflow_id=workflow_id,
+            message=f"Workflow '{escape(workflow.name)}' imported successfully.",
+        )
 
     def __api_import_new_workflow(self, trans: GalaxyWebTransaction, payload, **kwd):
         data = payload["workflow"]

test/unit/workflows/test_workflows_manager.py

@@ -0,0 +1,22 @@
+from galaxy import model
+
+from .workflow_support import MockApp
+
+TRS_TOOL_ID = "#the_id"
+TRS_TOOL_VERSION = "v1"
+
+
+def test_find_workflow_by_trs_id():
+    app = MockApp()
+    with app.model.session.begin():
+        w = model.Workflow()
+
+        w.stored_workflow = model.StoredWorkflow()
+        w.stored_workflow.latest_workflow = w
+        u = model.User("test@test.com", "test", "test")
+        w.stored_workflow.user = u
+        w.source_metadata = {"trs_server": "dockstore", "trs_tool_id": TRS_TOOL_ID, "trs_version_id": TRS_TOOL_VERSION}
+        app.model.session.add(w)
+        app.model.session.commit()
+        app.model.session.flush()
+    assert app.workflow_manager.get_workflow_by_trs_id_and_version(app.model.session, TRS_TOOL_ID, TRS_TOOL_VERSION, u.id) == w