Merge pull request #15892 from mvdbeek/fewer_pending_not_ok_operation_tools

Allow pending inputs in some collection operation tools

lib/galaxy/tools/__init__.py

@@ -3272,6 +3272,7 @@ class DataManagerTool(OutputParameterJSONTool):
 
 class DatabaseOperationTool(Tool):
     default_tool_action = ModelOperationToolAction
+    require_terminal_states = True
     require_dataset_ok = True
     tool_type_local = True
 
@@ -3279,8 +3280,10 @@ class DatabaseOperationTool(Tool):
     def valid_input_states(self):
         if self.require_dataset_ok:
             return (model.Dataset.states.OK,)
-        else:
+        elif self.require_terminal_states:
             return model.Dataset.terminal_states
+        else:
+            return model.Dataset.valid_input_states
 
     @property
     def allow_errored_inputs(self):
@@ -3288,7 +3291,7 @@ class DatabaseOperationTool(Tool):
 
     def check_inputs_ready(self, input_datasets, input_dataset_collections):
         def check_dataset_state(state):
-            if state in model.Dataset.non_ready_states:
+            if self.require_terminal_states and state in model.Dataset.non_ready_states:
                 raise ToolInputsNotReadyException("An input dataset is pending.")
 
             if self.require_dataset_ok:
@@ -3324,6 +3327,8 @@ class DatabaseOperationTool(Tool):
 
 class UnzipCollectionTool(DatabaseOperationTool):
     tool_type = "unzip_collection"
+    require_terminal_states = False
+    require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         has_collection = incoming["input"]
@@ -3345,6 +3350,8 @@ class UnzipCollectionTool(DatabaseOperationTool):
 
 class ZipCollectionTool(DatabaseOperationTool):
     tool_type = "zip_collection"
+    require_terminal_states = False
+    require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         forward_o = incoming["input_forward"]
@@ -3362,6 +3369,8 @@ class ZipCollectionTool(DatabaseOperationTool):
 
 class BuildListCollectionTool(DatabaseOperationTool):
     tool_type = "build_list"
+    require_terminal_states = False
+    require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         new_elements = {}
@@ -3389,6 +3398,8 @@ class BuildListCollectionTool(DatabaseOperationTool):
 
 class ExtractDatasetCollectionTool(DatabaseOperationTool):
     tool_type = "extract_dataset"
+    require_terminal_states = False
+    require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, tags=None, **kwds):
         has_collection = incoming["input"]
@@ -3419,6 +3430,8 @@ class ExtractDatasetCollectionTool(DatabaseOperationTool):
 
 class MergeCollectionTool(DatabaseOperationTool):
     tool_type = "merge_collection"
+    require_terminal_states = False
+    require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         input_lists = []
@@ -3502,6 +3515,9 @@ class MergeCollectionTool(DatabaseOperationTool):
 
 
 class FilterDatasetsTool(DatabaseOperationTool):
+    require_terminal_states = True
+    require_dataset_ok = False
+
     def _get_new_elements(self, history, elements_to_copy):
         new_elements = {}
         for dce in elements_to_copy:
@@ -3574,6 +3590,8 @@ class FilterEmptyDatasetsTool(FilterDatasetsTool):
 
 class FlattenTool(DatabaseOperationTool):
     tool_type = "flatten_collection"
+    require_terminal_states = False
+    require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
@@ -3602,6 +3620,8 @@ class FlattenTool(DatabaseOperationTool):
 
 class SortTool(DatabaseOperationTool):
     tool_type = "sort_collection"
+    require_terminal_states = False
+    require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
@@ -3733,6 +3753,11 @@ class ApplyRulesTool(DatabaseOperationTool):
 
 class TagFromFileTool(DatabaseOperationTool):
     tool_type = "tag_from_file"
+    # We don't currently discriminate which input has to be in which state
+    # so we do need all inputs to be "ok", when in fact only the file input
+    # needs to be ok.
+    # require_terminal_states = True
+    # require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, tag_handler, **kwds):
         hdca = incoming["input"]
@@ -3841,6 +3866,8 @@ class FilterFromFileTool(DatabaseOperationTool):
 
 class DuplicateFileToCollectionTool(DatabaseOperationTool):
     tool_type = "duplicate_file_to_collection"
+    require_terminal_states = False
+    require_dataset_ok = False
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hda = incoming["input"]

lib/galaxy_test/api/test_tools.py

@@ -694,6 +694,30 @@ class TestToolsApi(ApiTestCase, TestsTools):
             )
             assert zipped_hdca["collection_type"] == "list:paired"
 
+    @skip_without_tool("__EXTRACT_DATASET__")
+    @skip_without_tool("cat_data_and_sleep")
+    def test_database_operation_tool_with_pending_inputs(self):
+        with self.dataset_populator.test_history(require_new=False) as history_id:
+            hdca1_id = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"], wait=True
+            ).json()["outputs"][0]["id"]
+            self.dataset_populator.run_tool(
+                tool_id="cat_data_and_sleep",
+                inputs={
+                    "sleep_time": 15,
+                    "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca1_id}]},
+                },
+                history_id=history_id,
+            )
+            run_response = self.dataset_populator.run_tool(
+                tool_id="__EXTRACT_DATASET__",
+                inputs={
+                    "data_collection": {"src": "hdca", "id": hdca1_id},
+                },
+                history_id=history_id,
+            )
+            assert run_response["outputs"][0]["state"] != "ok"
+
     @skip_without_tool("__FILTER_FAILED_DATASETS__")
     def test_filter_failed_list(self):
         with self.dataset_populator.test_history(require_new=False) as history_id: