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.

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])

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
 

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 ):

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" />

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">