Merge pull request #10087 from mvdbeek/fix_pja_dataset_new

Fix change_datatype PJA when dataset is not yet in object store

lib/galaxy/datatypes/registry.py

@@ -587,7 +587,7 @@ class Registry:
         # initialization.
         if data.has_data():
             data.set_size()
-            data.init_meta(copy_from=data)
+        data.init_meta(copy_from=data)
         return data
 
     def load_datatype_converters(self, toolbox, installed_repository_dict=None, deactivate=False, use_cached=False):

lib/galaxy/model/__init__.py

@@ -2324,6 +2324,10 @@ class Dataset(StorableObject, RepresentById):
         self.sources = []
         self.hashes = []
 
+    @property
+    def is_new(self):
+        return self.state == self.states.NEW
+
     def in_ready_state(self):
         return self.state in self.ready_states
 
@@ -2447,7 +2451,7 @@ class Dataset(StorableObject, RepresentById):
 
     def has_data(self):
         """Detects whether there is any data"""
-        return self.get_size() > 0
+        return not self.is_new and self.get_size() > 0
 
     def mark_deleted(self):
         self.deleted = True

lib/galaxy_test/api/test_workflows.py

@@ -201,12 +201,43 @@ class BaseWorkflowsApiTestCase(ApiTestCase):
         assert tool_state_value["__class__"] == "RuntimeValue"
 
 
+class ChangeDatatypeTestCase(object):
+
+    def test_assign_column_pja(self):
+        with self.dataset_populator.test_history() as history_id:
+            self.workflow_populator.run_workflow("""
+class: GalaxyWorkflow
+inputs:
+  input1: data
+steps:
+  first_cat:
+    tool_id: cat
+    in:
+      input1: input1
+    outputs:
+      out_file1:
+        change_datatype: bed
+        set_columns:
+          chromCol: 1
+          endCol: 2
+          startCol: 3
+""", test_data="""
+input1:
+  value: 1.bed
+  type: File
+""", history_id=history_id)
+            details_dataset_new_col = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=True)
+            assert details_dataset_new_col["history_content_type"] == "dataset", details_dataset_new_col
+            assert details_dataset_new_col['metadata_endCol'] == 2
+            assert details_dataset_new_col['metadata_startCol'] == 3
+
+
 # Workflow API TODO:
 # - Allow history_id as param to workflow run action. (hist_id)
 # - Allow post to workflows/<workflow_id>/run in addition to posting to
 #    /workflows with id in payload.
 # - Much more testing obviously, always more testing.
-class WorkflowsApiTestCase(BaseWorkflowsApiTestCase):
+class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
 
     def test_show_valid(self):
         workflow_id = self.workflow_populator.simple_workflow("dummy")
@@ -3196,35 +3227,6 @@ input1:
             assert details1["history_content_type"] == "dataset_collection"
             assert details1["tags"][0] == "name:foo", details1
 
-    @skip_without_tool("cat")
-    def test_assign_column_pja(self):
-        with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
-class: GalaxyWorkflow
-inputs:
-  input1: data
-steps:
-  first_cat:
-    tool_id: cat
-    in:
-      input1: input1
-    outputs:
-      out_file1:
-        change_datatype: bed
-        set_columns:
-          chromCol: 1
-          endCol: 2
-          startCol: 3
-""", test_data="""
-input1:
-  value: 1.bed
-  type: File
-""", history_id=history_id)
-            details_dataset_new_col = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=True)
-            assert details_dataset_new_col["history_content_type"] == "dataset", details_dataset_new_col
-            assert details_dataset_new_col['metadata_endCol'] == 2
-            assert details_dataset_new_col['metadata_startCol'] == 3
-
     @skip_without_tool("collection_creates_pair")
     @skip_without_tool("cat")
     def test_run_remove_tag_on_collection_output(self):

test/integration/test_change_datatype_with_store_by_id.py

@@ -0,0 +1,22 @@
+from galaxy_test.api.test_workflows import ChangeDatatypeTestCase
+from galaxy_test.base.populators import (
+    DatasetPopulator,
+    WorkflowPopulator,
+)
+from galaxy_test.driver import integration_util
+
+
+class ChangeDatatypeStoreByIdIntegrationTestCase(integration_util.IntegrationTestCase, ChangeDatatypeTestCase):
+    """Test changing datatype with object_store_store_by: id."""
+
+    framework_tool_and_types = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["object_store_store_by"] = "id"
+        config["retry_metadata_internally"] = False
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)