From d7b4b367565efc5ea18077c13d4753a8f8690fe7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 15 May 2014 13:01:36 -0500
Subject: [PATCH] Change paired collections terminology from left/right to
 forward/reverse. If you have paired datasets in your database they will no
 longer work - send me an e-mail and I can give you an SQL update statement.

---
 .../dataset_collections/types/paired.py       | 22 ++++++++++---------
 test/api/helpers.py                           |  4 ++--
 test/api/test_tools.py                        |  4 ++--
 .../tools/collection_mixed_param.xml          |  4 ++--
 .../tools/collection_paired_test.xml          |  6 ++---
 5 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/lib/galaxy/dataset_collections/types/paired.py b/lib/galaxy/dataset_collections/types/paired.py
index 7b3310fcc36..32037ee4db9 100644
--- a/lib/galaxy/dataset_collections/types/paired.py
+++ b/lib/galaxy/dataset_collections/types/paired.py
@@ -2,8 +2,10 @@ from ..types import BaseDatasetCollectionType
 
 from galaxy.model import DatasetCollectionElement
 
-LEFT_IDENTIFIER = "left"
-RIGHT_IDENTIFIER = "right"
+FORWARD_IDENTIFIER = "forward"
+REVERSE_IDENTIFIER = "reverse"
+
+INVALID_IDENTIFIERS_MESSAGE = "Paired instance must define '%s' and '%s' datasets ." % ( FORWARD_IDENTIFIER, REVERSE_IDENTIFIER )
 
 
 class PairedDatasetCollectionType( BaseDatasetCollectionType ):
@@ -16,16 +18,16 @@ class PairedDatasetCollectionType( BaseDatasetCollectionType ):
         pass
 
     def build_collection( self, elements ):
-        left_dataset = elements.get("left", None)
-        right_dataset = elements.get("right", None)
-        if not left_dataset or not right_dataset:
-            self._validation_failed("Paired instance must define 'left' and 'right' datasets .")
+        forward_dataset = elements.get( FORWARD_IDENTIFIER, None )
+        reverse_dataset = elements.get( REVERSE_IDENTIFIER, None )
+        if not forward_dataset or not reverse_dataset:
+            self._validation_failed( INVALID_IDENTIFIERS_MESSAGE )
         left_association = DatasetCollectionElement(
-            element=left_dataset,
-            element_identifier=LEFT_IDENTIFIER,
+            element=forward_dataset,
+            element_identifier=FORWARD_IDENTIFIER,
         )
         right_association = DatasetCollectionElement(
-            element=right_dataset,
-            element_identifier=RIGHT_IDENTIFIER,
+            element=reverse_dataset,
+            element_identifier=REVERSE_IDENTIFIER,
         )
         return self._new_collection_for_elements([left_association, right_association])
diff --git a/test/api/helpers.py b/test/api/helpers.py
index fef666b142a..12eb2bd09ca 100644
--- a/test/api/helpers.py
+++ b/test/api/helpers.py
@@ -292,8 +292,8 @@ class DatasetCollectionPopulator( object ):
         hda1, hda2 = self.__datasets( history_id, count=2, contents=contents )
 
         element_identifiers = [
-            dict( name="left", src="hda", id=hda1[ "id" ] ),
-            dict( name="right", src="hda", id=hda2[ "id" ] ),
+            dict( name="forward", src="hda", id=hda1[ "id" ] ),
+            dict( name="reverse", src="hda", id=hda2[ "id" ] ),
         ]
         return element_identifiers
 
diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index d0b4c87facc..9d645dde10a 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -204,8 +204,8 @@ class ToolsTestCase( api.ApiTestCase ):
         first_object = first_element[ "object" ]
         assert first_object[ "collection_type" ] == "paired"
         assert len( first_object[ "elements" ] ) == 2
-        first_object_left_element = first_object[ "elements" ][ 0 ]
-        self.assertEquals( outputs[ 0 ][ "id" ], first_object_left_element[ "object" ][ "id" ] )
+        first_object_forward_element = first_object[ "elements" ][ 0 ]
+        self.assertEquals( outputs[ 0 ][ "id" ], first_object_forward_element[ "object" ][ "id" ] )
 
     @skip_without_tool( "cat1" )
     def test_map_over_two_collections( self ):
diff --git a/test/functional/tools/collection_mixed_param.xml b/test/functional/tools/collection_mixed_param.xml
index 8fa6e73c881..98d435be3a3 100644
--- a/test/functional/tools/collection_mixed_param.xml
+++ b/test/functional/tools/collection_mixed_param.xml
@@ -13,8 +13,8 @@
     <test>
       <param name="f1">
         <collection type="paired">
-          <element name="left" value="simple_line.txt" />
-          <element name="right" value="simple_line_alternative.txt" />
+          <element name="forward" value="simple_line.txt" />
+          <element name="reverse" value="simple_line_alternative.txt" />
         </collection>
       </param>
       <param name="f2" value="simple_lines_both.txt" />
diff --git a/test/functional/tools/collection_paired_test.xml b/test/functional/tools/collection_paired_test.xml
index 21f5b2fe29e..f82e77c2225 100644
--- a/test/functional/tools/collection_paired_test.xml
+++ b/test/functional/tools/collection_paired_test.xml
@@ -1,6 +1,6 @@
 <tool id="collection_paired_test" name="paired_test" version="0.1.0">
   <command>
-    cat #for $f in $f1# ${f} #end for# >> $out1;
+    cat $f1.forward $f1.reverse >> $out1;
   </command>
   <inputs>
     <param name="f1" type="data_collection" collection_type="paired" />
@@ -12,8 +12,8 @@
     <test>
       <param name="f1">
         <collection type="paired">
-          <element name="left" value="simple_line.txt" />
-          <element name="right" value="simple_line_alternative.txt" />
+          <element name="forward" value="simple_line.txt" />
+          <element name="reverse" value="simple_line_alternative.txt" />
         </collection>
       </param>
       <output name="out1">