Merge remote-tracking branch 'upstream/release_15.05' into dev

lib/galaxy/jobs/runners/pulsar.py

@@ -349,7 +349,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
 
         encoded_job_id = self.app.security.encode_id(job_id)
         job_key = self.app.security.encode_id( job_id, kind="jobs_files" )
-        endpoint_base = "%s/api/jobs/%s?job_key=%s"
+        endpoint_base = "%s/api/jobs/%s/files?job_key=%s"
         if self.app.config.nginx_upload_job_files_path:
             endpoint_base = "%s" + \
                             self.app.config.nginx_upload_job_files_path + \

lib/galaxy/tools/parameters/basic.py

@@ -671,41 +671,19 @@ class ColorToolParameter( ToolParameter ):
     def get_initial_value( self, trans, context, history=None ):
         return self.value.lower();
 
-## This is clearly a HACK, parameters should only be used for things the user
-## can change, there needs to be a different way to specify this. I'm leaving
-## it for now to avoid breaking any tools.
 
-
-class BaseURLToolParameter( ToolParameter ):
+class BaseURLToolParameter( HiddenToolParameter ):
     """
-    Returns a parameter the contains its value prepended by the
+    Returns a parameter that contains its value prepended by the
     current server base url. Used in all redirects.
     """
-
     def __init__( self, tool, input_source ):
         input_source = ensure_input_source( input_source )
-        ToolParameter.__init__( self, tool, input_source )
+        super( BaseURLToolParameter, self ).__init__( tool, input_source )
         self.value = input_source.get( 'value', '' )
 
-    def get_value( self, trans ):
-        # url = trans.request.base + self.value
-        url = url_for( self.value, qualified=True )
-        return url
-
-    def get_html_field( self, trans=None, value=None, other_values={} ):
-        return form_builder.HiddenField( self.name, self.get_value( trans ) )
-
-    def get_initial_value( self, trans, context, history=None ):
-        return self.get_value( trans )
-
-    def get_label( self ):
-        # BaseURLToolParameters are ultimately "hidden" parameters
-        return None
-
-    def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
-        d = super( BaseURLToolParameter, self ).to_dict( trans )
-        d['value'] = self.get_value( trans )
-        return d
+    def from_html( self, value=None, trans=None, context={} ):
+        return url_for( self.value, qualified=True )
 
 
 DEFAULT_VALUE_MAP = lambda x: x
@@ -1656,7 +1634,7 @@ class BaseDataToolParameter( ToolParameter ):
         class_name = self.__class__.__name__
         assert trans is not None, "%s requires a trans" % class_name
         if history is None:
-            history = trans.get_history()
+            history = trans.get_history( create=True )
         assert history is not None, "%s requires a history" % class_name
         return history
 

test/unit/tools/test_data_parameters.py

@@ -150,7 +150,7 @@ class DataToolParameterTestCase( BaseParameterTestCase ):
         self.app.model.context.flush()
         self.trans = bunch.Bunch(
             app=self.app,
-            get_history=lambda: self.test_history,
+            get_history=lambda **k: self.test_history,
             get_current_user_roles=lambda: [],
             workflow_building_mode=False,
             webapp=bunch.Bunch( name="galaxy" ),

test/unit/tools/test_execution.py

@@ -478,7 +478,7 @@ class MockTrans( object ):
         self.webapp = Bunch( name="galaxy" )
         self.sa_session = self.app.model.context
 
-    def get_history( self ):
+    def get_history( self, **kwargs ):
         return self.history
 
 

test/unit/unittest_utils/galaxy_mock.py

@@ -91,7 +91,7 @@ class MockTrans( object ):
 
     user = property( get_user, set_user )
 
-    def get_history( self ):
+    def get_history( self, **kwargs ):
         return self.history
 
     def set_history( self, history ):