Apply suggested fixes, fix test cases

lib/galaxy/jobs/runners/__init__.py

@@ -169,7 +169,7 @@ class BaseJobRunner( object ):
                 include_metadata=include_metadata,
                 include_work_dir_outputs=include_work_dir_outputs,
             )
-        except Exception, e:
+        except Exception as e:
             log.exception("(%s) Failure preparing job" % job_id)
             job_wrapper.fail( e.message if hasattr( e, 'message' ) else "Job preparation failed", exception=True )
             return False

lib/galaxy/tools/parameters/basic.py

@@ -198,7 +198,7 @@ class ToolParameter( object, Dictifiable ):
                 value = sanitize_param( value )
         return value
 
-    def validate( self, value, trans ):
+    def validate( self, value, trans=None ):
         if value == "" and self.optional:
             return
         for validator in self.validators:
@@ -274,9 +274,9 @@ class TextToolParameter( ToolParameter ):
             rval = util.smart_str( value )
         return rval
 
-    def validate( self, value, trans ):
+    def validate( self, value, trans=None ):
         search = self.type == "text"
-        if not ( trans.workflow_building_mode and contains_workflow_parameter(value, search=search) ):
+        if not ( trans and trans.workflow_building_mode and contains_workflow_parameter(value, search=search) ):
             return super( TextToolParameter, self ).validate( value, trans )
 
     def get_initial_value( self, trans, other_values ):
@@ -292,15 +292,16 @@ class TextToolParameter( ToolParameter ):
 class IntegerToolParameter( TextToolParameter ):
     """
     Parameter that takes an integer value.
-
+    >>> from galaxy.util.bunch import Bunch
+    >>> trans = Bunch( history=Bunch(), workflow_building_mode=True )
     >>> p = IntegerToolParameter( None, XML( '<param name="blah" type="integer" size="4" value="10" />' ) )
     >>> print p.name
     blah
     >>> print p.get_html()
     <input type="text" name="blah" size="4" value="10">
-    >>> type( p.from_html( "10" ) )
+    >>> type( p.from_html( "10", trans ) )
     <type 'int'>
-    >>> type( p.from_html( "bleh" ) )
+    >>> type( p.from_html( "bleh", trans ) )
     Traceback (most recent call last):
         ...
     ValueError: An integer or workflow parameter e.g. ${name} is required
@@ -371,15 +372,16 @@ class IntegerToolParameter( TextToolParameter ):
 class FloatToolParameter( TextToolParameter ):
     """
     Parameter that takes a real number value.
-
+    >>> from galaxy.util.bunch import Bunch
+    >>> trans = Bunch( history=Bunch(), workflow_building_mode=True )
     >>> p = FloatToolParameter( None, XML( '<param name="blah" type="float" size="4" value="3.141592" />' ) )
     >>> print p.name
     blah
     >>> print p.get_html()
     <input type="text" name="blah" size="4" value="3.141592">
-    >>> type( p.from_html( "36.1" ) )
+    >>> type( p.from_html( "36.1", trans ) )
     <type 'float'>
-    >>> type( p.from_html( "bleh" ) )
+    >>> type( p.from_html( "bleh", trans ) )
     Traceback (most recent call last):
         ...
     ValueError: A real number or workflow parameter e.g. ${name} is required
@@ -1832,7 +1834,7 @@ class DataToolParameter( BaseDataToolParameter ):
             name = history_dataset_collection.name
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
-            id = value_modifier( trans.app.security.encode_id( history_dataset_collection.id ) )
+            id = value_modifier( trans.security.encode_id( history_dataset_collection.id ) )
             selected = value and history_dataset_collection in value
             text = "%s:%s %s" % ( hid, hidden_text, name )
             field.add_option( text, id, selected )
@@ -1944,10 +1946,10 @@ class DataToolParameter( BaseDataToolParameter ):
             for single_value in value:
                 if isinstance( single_value, dict ) and 'src' in single_value and 'id' in single_value:
                     if single_value['src'] == 'hda':
-                        rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(single_value['id']) ))
+                        rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id(single_value['id']) ))
                     elif single_value['src'] == 'hdca':
                         found_hdca = True
-                        decoded_id = trans.app.security.decode_id( single_value[ 'id' ] )
+                        decoded_id = trans.security.decode_id( single_value[ 'id' ] )
                         rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id ) )
                     else:
                         raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
@@ -1965,15 +1967,15 @@ class DataToolParameter( BaseDataToolParameter ):
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hda':
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(value['id']) )
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id(value['id']) )
             elif value['src'] == 'hdca':
-                decoded_id = trans.app.security.decode_id( value[ 'id' ] )
+                decoded_id = trans.security.decode_id( value[ 'id' ] )
                 rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
             else:
                 raise ValueError("Unknown input source %s passed to job submission API." % value['src'])
         elif str( value ).startswith( "__collection_reduce__|" ):
             encoded_ids = [ v[ len( "__collection_reduce__|" ): ] for v in str( value ).split(",") ]
-            decoded_ids = map( trans.app.security.decode_id, encoded_ids )
+            decoded_ids = map( trans.security.decode_id, encoded_ids )
             rval = []
             for decoded_id in decoded_ids:
                 hdca = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
@@ -2162,7 +2164,7 @@ class DataToolParameter( BaseDataToolParameter ):
 
         # build and append a new select option
         def append( list, id, hid, name, src ):
-            return list.append( { 'id' : trans.app.security.encode_id( id ), 'hid' : hid, 'name' : name, 'src' : src } )
+            return list.append( { 'id' : trans.security.encode_id( id ), 'hid' : hid, 'name' : name, 'src' : src } )
 
         # add datasets
         visible_hda = other_values.get( self.name )
@@ -2278,8 +2280,8 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
             name = history_dataset_collection.name
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
-            subcollection_type = self._history_query( trans ).collection_type_description.collection_type
-            id = "%s|%s" % ( trans.app.security.encode_id( history_dataset_collection.id ), subcollection_type )
+            subcollection_type = self._history_query( trans ).can_map_over( history_dataset_collection ).collection_type
+            id = "%s|%s" % ( trans.security.encode_id( history_dataset_collection.id ), subcollection_type )
             text = "%s:%s %s" % ( hid, hidden_text, name )
 
             field.add_option( text, id, False )
@@ -2302,13 +2304,13 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hdca':
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.app.security.decode_id(value['id']) )
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.security.decode_id(value['id']) )
         elif isinstance( value, list ):
             if len( value ) > 0:
                 value = value[0]
                 if isinstance( value, dict ) and 'src' in value and 'id' in value:
                     if value['src'] == 'hdca':
-                        rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.app.security.decode_id(value['id']) )
+                        rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.security.decode_id(value['id']) )
         elif isinstance( value, basestring ):
             if value.startswith( "dce:" ):
                 rval = trans.sa_session.query( trans.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] )
@@ -2364,7 +2366,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
             display_text = "No dataset collection."
         return display_text
 
-    def validate( self, value, trans ):
+    def validate( self, value, trans=None ):
         return True  # TODO
 
     def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ):
@@ -2385,7 +2387,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
         # append directly matched collections
         for hdca in self.match_collections( trans, history, dataset_matcher ):
             d['options']['hdca'].append({
-                'id': trans.app.security.encode_id( hdca.id ),
+                'id': trans.security.encode_id( hdca.id ),
                 'hid': hdca.hid,
                 'name': hdca.name,
                 'src': 'hdca'
@@ -2395,7 +2397,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
         for hdca in self.match_multirun_collections( trans, history, dataset_matcher ):
             subcollection_type = self._history_query( trans ).can_map_over( hdca ).collection_type
             d['options']['hdca'].append({
-                'id': trans.app.security.encode_id( hdca.id ),
+                'id': trans.security.encode_id( hdca.id ),
                 'hid': hdca.hid,
                 'name': hdca.name,
                 'src': 'hdca',

test/unit/tools/test_data_parameters.py

@@ -154,6 +154,7 @@ class DataToolParameterTestCase( BaseParameterTestCase ):
             get_current_user_roles=lambda: [],
             workflow_building_mode=False,
             webapp=bunch.Bunch( name="galaxy" ),
+            history=self.test_history,
         )
         self.multiple = False
         self.optional = False

test/unit/tools/test_evaluation.py

@@ -149,7 +149,10 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
             assert name == "path"
             return ["/old/path/human"]
 
-        parameter.options = Bunch(get_field_by_name_for_value=get_field_by_name_for_value)
+        def get_options( trans, other_values ):
+            return [ [ "", "/old/path/human", "" ] ]
+
+        parameter.options = Bunch(get_field_by_name_for_value=get_field_by_name_for_value, get_options=get_options)
         self.tool.set_params( {
             "index_path": parameter
         } )

test/unit/tools/test_execution.py

@@ -268,6 +268,7 @@ class MockTrans( object ):
     def __init__( self, app, history ):
         self.app = app
         self.history = history
+        self.user = None
         self.history._active_datasets_children_and_roles = filter( lambda hda: hda.active and hda.history == history, self.app.model.context.model_objects[ galaxy.model.HistoryDatasetAssociation ] )
         self.workflow_building_mode = False
         self.webapp = Bunch( name="galaxy" )

test/unit/tools/test_select_parameters.py

@@ -28,7 +28,7 @@ class SelectToolParameterTestCase( BaseParameterTestCase ):
     def test_unvalidated_values( self ):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
         self.trans.workflow_building_mode = True
-        assert self.param.from_html("42", self.trans).value == "42"
+        assert self.param.from_html("42", self.trans) == "42"
 
     def test_validated_datasets( self ):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
@@ -42,7 +42,7 @@ class SelectToolParameterTestCase( BaseParameterTestCase ):
     def test_unvalidated_datasets( self ):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
         self.trans.workflow_building_mode = True
-        assert isinstance( self.param.from_html( model.HistoryDatasetAssociation(), self.trans, { "input_bam": basic.RuntimeValue() } ).value, model.HistoryDatasetAssociation )
+        assert isinstance( self.param.from_html( model.HistoryDatasetAssociation(), self.trans, { "input_bam": basic.RuntimeValue() } ), model.HistoryDatasetAssociation )
 
     def test_filter_param_value( self ):
         self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>'''

test/unit/tools_support.py

@@ -154,6 +154,7 @@ class MockContext(object):
         self.flushed = False
         self.model_objects = model_objects or defaultdict( lambda: {} )
         self.created_objects = []
+        self.current = self
 
     def expunge_all(self):
         self.expunged_all = True