From a1b72d5bf02501cc764257f630bc64fd22d40092 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Sep 2014 11:57:48 -0400
Subject: [PATCH] Redo API for subcollection mapping steps in tools. Like the
 reductions - was previously constrained by sequeezing these values into
 simple strings - now the tool form will target the API I think this expanded
 version is a little more straight-forward (though verbose). Adds consistency
 with rest of the tool form API changes.

---
 lib/galaxy/tools/parameters/meta.py |  3 ++-
 test/api/test_tools.py              | 40 +++++++++++++++++++++++++++--
 2 files changed, 40 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/parameters/meta.py b/lib/galaxy/tools/parameters/meta.py
index c8790bfbcd3..3c320820105 100644
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -106,9 +106,10 @@ def __expand_collection_parameter( trans, input_key, incoming_val, collections_t
             if src != "hdca":
                 raise exceptions.ToolMetaParameterException( "Invalid dataset collection source type %s" % src )
             encoded_hdc_id = incoming_val[ "id" ]
+            subcollection_type = incoming_val.get( 'map_over_type', None )
         except TypeError:
             encoded_hdc_id = incoming_val
-        subcollection_type = None
+            subcollection_type = None
     hdc_id = trans.app.security.decode_id( encoded_hdc_id )
     hdc = trans.sa_session.query( model.HistoryDatasetCollectionAssociation ).get( hdc_id )
     collections_to_match.add( input_key, hdc, subcollection_type=subcollection_type )
diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index 99b52996f62..64800c9e45c 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -492,12 +492,27 @@ class ToolsTestCase( api.ApiTestCase ):
         assert len( output2_content.strip().split("\n") ) == 3, output2_content
 
     @skip_without_tool( "collection_paired_test" )
-    def test_subcollection_mapping( self ):
+    def test_subcollection_mapping_legacy( self ):
         history_id = self.dataset_populator.new_history()
         hdca_list_id = self.__build_nested_list( history_id )
         inputs = {
             "f1|__collection_multirun__": "%s|paired" % hdca_list_id
         }
+        self._check_simple_subcollection_mapping( history_id, inputs )
+
+    @skip_without_tool( "collection_paired_test" )
+    def test_subcollection_mapping( self ):
+        history_id = self.dataset_populator.new_history()
+        hdca_list_id = self.__build_nested_list( history_id )
+        inputs = {
+            "f1": {
+                'batch': True,
+                'values': [ { 'src': 'hdca', 'map_over_type': 'paired', 'id': hdca_list_id }],
+            }
+        }
+        self._check_simple_subcollection_mapping( history_id, inputs )
+
+    def _check_simple_subcollection_mapping( self, history_id, inputs ):
         # Following wait not really needed - just getting so many database
         # locked errors with sqlite.
         self.dataset_populator.wait_for_history( history_id, assert_ok=True )
@@ -511,7 +526,7 @@ class ToolsTestCase( api.ApiTestCase ):
         assert output2_content.strip() == "789\n0ab", output2_content
 
     @skip_without_tool( "collection_mixed_param" )
-    def test_combined_mapping_and_subcollection_mapping( self ):
+    def test_combined_mapping_and_subcollection_mapping_legacy( self ):
         history_id = self.dataset_populator.new_history()
         nested_list_id = self.__build_nested_list( history_id )
         create_response = self.dataset_collection_populator.create_list_in_history( history_id, contents=["xxx", "yyy"] )
@@ -520,6 +535,27 @@ class ToolsTestCase( api.ApiTestCase ):
             "f1|__collection_multirun__": "%s|paired" % nested_list_id,
             "f2|__collection_multirun__": list_id,
         }
+        self._check_combined_mapping_and_subcollection_mapping( history_id, inputs )
+
+    @skip_without_tool( "collection_mixed_param" )
+    def test_combined_mapping_and_subcollection_mapping( self ):
+        history_id = self.dataset_populator.new_history()
+        nested_list_id = self.__build_nested_list( history_id )
+        create_response = self.dataset_collection_populator.create_list_in_history( history_id, contents=["xxx", "yyy"] )
+        list_id = create_response.json()[ "id" ]
+        inputs = {
+            "f1": {
+                'batch': True,
+                'values': [ { 'src': 'hdca', 'map_over_type': 'paired', 'id': nested_list_id }],
+            },
+            "f2": {
+                'batch': True,
+                'values': [ { 'src': 'hdca', 'id': list_id }],
+            },
+        }
+        self._check_combined_mapping_and_subcollection_mapping( history_id, inputs )
+
+    def _check_combined_mapping_and_subcollection_mapping( self, history_id, inputs ):
         self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         outputs = self._run_and_get_outputs( "collection_mixed_param", history_id, inputs )
         assert len( outputs ), 2