Refactor collection test def objects out of galaxy.tools.

Part of ongoing effort to isolate the galaxy.tools.parser and not have it depend on things in galaxy.tools outside that module.

lib/galaxy/tools/__init__.py

@@ -2989,42 +2989,6 @@ class BadValue( object ):
         self.value = value
 
 
-class TestCollectionDef( object ):
-
-    def __init__( self, elem, parse_param_elem ):
-        self.elements = []
-        attrib = dict( elem.attrib )
-        self.collection_type = attrib[ "type" ]
-        self.name = attrib.get( "name", "Unnamed Collection" )
-        for element in elem.findall( "element" ):
-            element_attrib = dict( element.attrib )
-            element_identifier = element_attrib[ "name" ]
-            nested_collection_elem = element.find( "collection" )
-            if nested_collection_elem is not None:
-                self.elements.append( ( element_identifier, TestCollectionDef( nested_collection_elem, parse_param_elem ) ) )
-            else:
-                self.elements.append( ( element_identifier, parse_param_elem( element ) ) )
-
-    def collect_inputs( self ):
-        inputs = []
-        for element in self.elements:
-            value = element[ 1 ]
-            if isinstance( value, TestCollectionDef ):
-                inputs.extend( value.collect_inputs() )
-            else:
-                inputs.append( value )
-        return inputs
-
-
-class TestCollectionOutputDef( object ):
-
-    def __init__( self, name, attrib, element_tests ):
-        self.name = name
-        self.collection_type = attrib.get( "type", None )
-        self.attrib = attrib
-        self.element_tests = element_tests
-
-
 def json_fix( val ):
     if isinstance( val, list ):
         return [ json_fix( v ) for v in val ]

lib/galaxy/tools/parser/interface.py

@@ -280,3 +280,41 @@ class ToolStdioExitCode( object ):
         # TODO: Define a common class or constant for error level:
         self.error_level = "fatal"
         self.desc = ""
+
+
+class TestCollectionDef( object ):
+    # TODO: do not require XML directly here.
+
+    def __init__( self, elem, parse_param_elem ):
+        self.elements = []
+        attrib = dict( elem.attrib )
+        self.collection_type = attrib[ "type" ]
+        self.name = attrib.get( "name", "Unnamed Collection" )
+        for element in elem.findall( "element" ):
+            element_attrib = dict( element.attrib )
+            element_identifier = element_attrib[ "name" ]
+            nested_collection_elem = element.find( "collection" )
+            if nested_collection_elem is not None:
+                self.elements.append( ( element_identifier, TestCollectionDef( nested_collection_elem, parse_param_elem ) ) )
+            else:
+                self.elements.append( ( element_identifier, parse_param_elem( element ) ) )
+
+    def collect_inputs( self ):
+        inputs = []
+        for element in self.elements:
+            value = element[ 1 ]
+            if isinstance( value, TestCollectionDef ):
+                inputs.extend( value.collect_inputs() )
+            else:
+                inputs.append( value )
+        return inputs
+
+
+class TestCollectionOutputDef( object ):
+    # TODO: do not require XML directly here.
+
+    def __init__( self, name, attrib, element_tests ):
+        self.name = name
+        self.collection_type = attrib.get( "type", None )
+        self.attrib = attrib
+        self.element_tests = element_tests

lib/galaxy/tools/parser/xml.py

@@ -12,6 +12,8 @@ from .interface import (
     InputSource,
     ToolStdioExitCode,
     ToolStdioRegex,
+    TestCollectionDef,
+    TestCollectionOutputDef,
 )
 from galaxy.util import string_as_bool, xml_text, xml_to_string
 from galaxy.util.odict import odict
@@ -321,7 +323,7 @@ def __parse_output_collection_elem( output_collection_elem ):
         if identifier is None:
             raise Exception( "Test primary dataset does not have a 'identifier'" )
         element_tests[ identifier ] = __parse_test_attributes( element, element_attrib )
-    return galaxy.tools.TestCollectionOutputDef( name, attrib, element_tests )
+    return TestCollectionOutputDef( name, attrib, element_tests )
 
 
 def __parse_test_attributes( output_elem, attrib ):
@@ -486,7 +488,7 @@ def __parse_param_elem( param_elem, i=0 ):
             elif child.tag == 'edit_attributes':
                 attrib['edit_attributes'].append( child )
             elif child.tag == 'collection':
-                attrib[ 'collection' ] = galaxy.tools.TestCollectionDef( child, __parse_param_elem )
+                attrib[ 'collection' ] = TestCollectionDef( child, __parse_param_elem )
         if composite_data_name:
             # Composite datasets need implicit renaming;
             # inserted at front of list so explicit declarations

lib/tool_shed/metadata/metadata_generator.py

@@ -7,7 +7,7 @@ from galaxy import util
 from galaxy.datatypes import checkers
 from galaxy.model.orm import and_
 from galaxy.tools.data_manager.manager import DataManager
-from galaxy.tools import TestCollectionDef
+from galaxy.tools.parser.interface import TestCollectionDef
 from galaxy.web import url_for
 
 from tool_shed.repository_types import util as rt_util

test/base/interactor.py

@@ -1,7 +1,7 @@
 import os
 import re
 from StringIO import StringIO
-from galaxy.tools import TestCollectionDef
+from galaxy.tools.parser.interface import TestCollectionDef
 from galaxy import eggs
 eggs.require( "requests" )
 from galaxy import util