Bug fix - expose proper element_identifier in tool action template expansions. (#5049)

xref https://github.com/galaxyproject/tools-iuc/commit/f57f1bf4816f212b83c08e0e3c3782ebba8b7d9a

lib/galaxy/tools/actions/__init__.py

@@ -257,7 +257,7 @@ class DefaultToolAction(object):
         # Add the dbkey to the incoming parameters
         incoming["dbkey"] = input_dbkey
         # wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed
-        wrapped_params = self._wrapped_params(trans, tool, incoming)
+        wrapped_params = self._wrapped_params(trans, tool, incoming, inp_data)
 
         out_data = odict()
         input_collections = dict((k, v[0][0]) for k, v in inp_dataset_collections.items())
@@ -514,8 +514,8 @@ class DefaultToolAction(object):
             trans.log_event("Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id)
             return job, out_data
 
-    def _wrapped_params(self, trans, tool, incoming):
-        wrapped_params = WrappedParameters(trans, tool, incoming)
+    def _wrapped_params(self, trans, tool, incoming, input_datasets=None):
+        wrapped_params = WrappedParameters(trans, tool, incoming, input_datasets=input_datasets)
         return wrapped_params
 
     def _get_on_text(self, inp_data):

lib/galaxy/tools/evaluation.py

@@ -26,6 +26,7 @@ from galaxy.tools.wrappers import (
     DatasetCollectionWrapper,
     DatasetFilenameWrapper,
     DatasetListWrapper,
+    ElementIdentifierMapper,
     InputValueWrapper,
     RawObjectWrapper,
     SelectToolParameterWrapper,
@@ -234,11 +235,9 @@ class ToolEvaluator(object):
                     real_path = dataset.file_name
                     if real_path in input_dataset_paths:
                         wrapper_kwds["dataset_path"] = input_dataset_paths[real_path]
-                identifier_key = identifier_key_dict.get(dataset, None)
-                if identifier_key:
-                    element_identifier = param_dict.get(identifier_key, None)
-                    if element_identifier:
-                        wrapper_kwds["identifier"] = element_identifier
+                element_identifier = element_identifier_mapper.identifier(dataset, param_dict)
+                if element_identifier:
+                    wrapper_kwds["identifier"] = element_identifier
                 input_values[input.name] = \
                     DatasetFilenameWrapper(dataset, **wrapper_kwds)
             elif isinstance(input, DataCollectionToolParameter):
@@ -266,7 +265,7 @@ class ToolEvaluator(object):
         #       tools where the inputs don't even get passed through. These
         #       tools (e.g. UCSC) should really be handled in a special way.
         if self.tool.check_values:
-            identifier_key_dict = dict((v, "%s|__identifier__" % k) for k, v in input_datasets.items())  # allows lookup of identifier through HDA.
+            element_identifier_mapper = ElementIdentifierMapper(input_datasets)
             self.__walk_inputs(self.tool.inputs, param_dict, wrap_input)
 
     def __populate_input_dataset_wrappers(self, param_dict, input_datasets, input_dataset_paths):

lib/galaxy/tools/parameters/wrapped.py

@@ -12,6 +12,7 @@ from galaxy.tools.wrappers import (
     DatasetCollectionWrapper,
     DatasetFilenameWrapper,
     DatasetListWrapper,
+    ElementIdentifierMapper,
     InputValueWrapper,
     SelectToolParameterWrapper
 )
@@ -21,11 +22,12 @@ PARAMS_UNWRAPPED = object()
 
 class WrappedParameters(object):
 
-    def __init__(self, trans, tool, incoming):
+    def __init__(self, trans, tool, incoming, input_datasets=None):
         self.trans = trans
         self.tool = tool
         self.incoming = incoming
         self._params = PARAMS_UNWRAPPED
+        self._input_datasets = input_datasets
 
     @property
     def params(self):
@@ -40,6 +42,8 @@ class WrappedParameters(object):
         tool = self.tool
         incoming = self.incoming
 
+        element_identifier_mapper = ElementIdentifierMapper(self._input_datasets)
+
         # Wrap tool inputs as necessary
         for input in inputs.values():
             if input.name not in input_values and skip_missing_values:
@@ -64,11 +68,16 @@ class WrappedParameters(object):
                                        tool=tool,
                                        name=input.name)
             elif isinstance(input, DataToolParameter):
-                input_values[input.name] = \
-                    DatasetFilenameWrapper(value,
-                                           datatypes_registry=trans.app.datatypes_registry,
-                                           tool=tool,
-                                           name=input.name)
+                wrapper_kwds = dict(
+                    datatypes_registry=trans.app.datatypes_registry,
+                    tool=tool,
+                    name=input.name
+                )
+                element_identifier = element_identifier_mapper.identifier(value, input_values)
+                if element_identifier:
+                    wrapper_kwds["identifier"] = element_identifier
+
+                input_values[input.name] = DatasetFilenameWrapper(value, **wrapper_kwds)
             elif isinstance(input, SelectToolParameter):
                 input_values[input.name] = SelectToolParameterWrapper(input, input_values[input.name], other_values=incoming)
             elif isinstance(input, DataCollectionToolParameter):

lib/galaxy/tools/wrappers.py

@@ -430,3 +430,21 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         # not specified or if resulting collection is empty.
         return self.__input_supplied and bool(self.__element_instance_list)
     __nonzero__ = __bool__
+
+
+class ElementIdentifierMapper(object):
+    """Track mapping of dataset collection elements datasets to element identifiers."""
+
+    def __init__(self, input_datasets=None):
+        if input_datasets is not None:
+            self.identifier_key_dict = dict((v, "%s|__identifier__" % k) for k, v in input_datasets.items())
+        else:
+            self.identifier_key_dict = {}
+
+    def identifier(self, dataset_value, input_values):
+        identifier_key = self.identifier_key_dict.get(dataset_value, None)
+        element_identifier = None
+        if identifier_key:
+            element_identifier = input_values.get(identifier_key, None)
+
+        return element_identifier

test/api/test_tools.py

@@ -978,6 +978,36 @@ class ToolsTestCase(api.ApiTestCase):
         output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
         self.assertEquals(output1_content.strip(), '\n'.join([d['name'] for d in element_identifiers]))
 
+    @skip_without_tool("identifier_in_actions")
+    def test_identifier_in_actions(self):
+        history_id = self.dataset_populator.new_history()
+
+        element_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents=["1\t2"])
+
+        payload = dict(
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=json.dumps(element_identifiers),
+            collection_type="list",
+        )
+
+        create_response = self._post("dataset_collections", payload)
+        dataset_collection = create_response.json()
+
+        inputs = {
+            "input": {'batch': True, 'values': [{'src': 'hdca', 'id': dataset_collection['id']}]},
+        }
+
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        create_response = self._run("identifier_in_actions", history_id, inputs)
+        self._assert_status_code_is(create_response, 200)
+        create = create_response.json()
+        outputs = create['outputs']
+        output1 = outputs[0]
+
+        output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output1)
+        assert output_details["metadata_column_names"][1] == "data1", output_details
+
     @skip_without_tool("cat1")
     def test_map_over_nested_collections(self):
         history_id = self.dataset_populator.new_history()

test/functional/tools/identifier_in_actions.xml

@@ -0,0 +1,23 @@
+<tool id="identifier_in_actions" name="identifier_in_actions" version="1.0.0">
+    <command><![CDATA[
+        cp '$input' '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" multiple="false" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output">
+            <actions>
+                <action name="column_names" type="metadata" default="First,${input.element_identifier}" />
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="2.tabular" />
+            <output name="output">
+                <metadata name="column_names" value="First,2.tabular"/>
+            </output>
+        </test>
+    </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -91,6 +91,7 @@
   <tool file="identifier_multiple_in_conditional.xml" />
   <tool file="identifier_multiple_in_repeat.xml" />
   <tool file="identifier_collection.xml" />
+  <tool file="identifier_in_actions.xml" />
   <tool file="tool_directory.xml" />
   <tool file="output_action_change_format.xml" />
   <tool file="collection_paired_test.xml" />