From fb116f5715d9cd291d2fdf956b5a3a91b3e84296 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 29 Jun 2016 14:04:43 +0200
Subject: [PATCH] fix missing element_identifier with data_collection input
 parama

---
 lib/galaxy/tools/wrappers.py                  |  4 +--
 test/api/test_tools.py                        |  9 +++---
 .../tools/identifier_conditional.xml          | 15 ++++++++++
 .../identifier_multiple_in_conditional.xml    | 28 -------------------
 test/functional/tools/samples_tool_conf.xml   |  2 +-
 5 files changed, 22 insertions(+), 36 deletions(-)
 create mode 100644 test/functional/tools/identifier_conditional.xml
 delete mode 100644 test/functional/tools/identifier_multiple_in_conditional.xml

diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index 0acf136163a..885702d04b3 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -307,7 +307,7 @@ class DatasetListWrapper( list, ToolParameterValueWrapper, HasDatasets ):
                 element = dataset
                 dataset = element.dataset_instance
                 kwargs["identifier"] = element.element_identifier
-            return self._dataset_wrapper( dataset, dataset_paths, **kwargs )
+            return self._dataset_wrapper( dataset, dataset_paths, identifier = element_identifier, **kwargs )
 
         list.__init__( self, map( to_wrapper, datasets ) )
         self.job_working_directory = job_working_directory
@@ -365,7 +365,7 @@ class DatasetCollectionWrapper( ToolParameterValueWrapper, HasDatasets ):
             if dataset_collection_element.is_collection:
                 element_wrapper = DatasetCollectionWrapper(job_working_directory, dataset_collection_element, dataset_paths, **kwargs )
             else:
-                element_wrapper = self._dataset_wrapper( element_object, dataset_paths, **kwargs)
+                element_wrapper = self._dataset_wrapper( element_object, dataset_paths, identifier=element_identifier, **kwargs)
 
             element_instances[element_identifier] = element_wrapper
             element_instance_list.append( element_wrapper )
diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index 535dc56f182..7c0f68b1d2c 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -806,8 +806,8 @@ class ToolsTestCase( api.ApiTestCase ):
         output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
         self.assertEquals( output1_content.strip(), "Pasted Entry\nPasted Entry" )
 
-    @skip_without_tool( "identifier_multiple_in_conditional" )
-    def test_identifier_with_multiple_normal_datasets_in_conditional( self ):
+    @skip_without_tool( "identifier_collection" )
+    def test_identifier_with_data_collection( self ):
         history_id = self.dataset_populator.new_history()
 
         element_identifiers = self.dataset_collection_populator.list_identifiers( history_id )
@@ -823,12 +823,11 @@ class ToolsTestCase( api.ApiTestCase ):
         dataset_collection = create_response.json()
 
         inputs = {
-            "options|choice": "one",
-            "options|input1": {'src': 'hdca', 'id': dataset_collection['id']},
+            "input1": {'src': 'hdca', 'id': dataset_collection['id']},
         }
 
         self.dataset_populator.wait_for_history( history_id, assert_ok=True )
-        create_response = self._run( "identifier_multiple_in_conditional", history_id, inputs )
+        create_response = self._run( "identifier_conditional", history_id, inputs )
         self._assert_status_code_is( create_response, 200 )
         create = create_response.json()
         outputs = create[ 'outputs' ]
diff --git a/test/functional/tools/identifier_conditional.xml b/test/functional/tools/identifier_conditional.xml
new file mode 100644
index 00000000000..ff548d679f6
--- /dev/null
+++ b/test/functional/tools/identifier_conditional.xml
@@ -0,0 +1,15 @@
+<tool id="identifier_conditional" name="identifier_conditional">
+  <command>
+    #for $input in $input1:
+      echo '$input.element_identifier' >> 'output1';
+    #end for
+  </command>
+  <inputs>
+    <param type="data_collection" collection_type="list" name="input1" label="Input 1" multiple="true" />
+  </inputs>
+  <outputs>
+    <data name="output1" type="tabular" from_work_dir="output1" />
+  </outputs>
+  <tests>
+  </tests>
+</tool>
diff --git a/test/functional/tools/identifier_multiple_in_conditional.xml b/test/functional/tools/identifier_multiple_in_conditional.xml
deleted file mode 100644
index ff02e284055..00000000000
--- a/test/functional/tools/identifier_multiple_in_conditional.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<tool id="identifier_multiple_in_conditional" name="identifier_multiple_in_conditional">
-  <command>
-    #if $options.choice == "one":
-        #for $input in $options.input1:
-          echo '$input.element_identifier' >> 'output1';
-        #end for
-    #end if
-  </command>
-  <inputs>
-    <conditional name="options">
-        <param name="choice" type="select" label="choice1">
-            <option value="one" selected="true">One</option>
-            <option value="two">Two</option>
-        </param>
-        <when value="one">
-            <param type="data_collection" collection_type="list" name="input1" label="Input 1" multiple="true" />
-        </when>
-        <when value="two">
-            <param type="data_collection" collection_type="list" name="input2" label="Input 2" multiple="true" />
-        </when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data name="output1" type="tabular" from_work_dir="output1" />
-  </outputs>
-  <tests>
-  </tests>
-</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 16ed1fecf64..112aa9da8c8 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -64,7 +64,7 @@
   <tool file="validation_empty_dataset.xml" />
   <tool file="identifier_single.xml" />
   <tool file="identifier_multiple.xml" />
-  <tool file="identifier_multiple_in_conditional.xml" />
+  <tool file="identifier_conditional.xml" />
   <tool file="tool_directory.xml" />
   <tool file="output_action_change_format.xml" />
   <tool file="collection_paired_test.xml" />