Add a "maxseconds" attribute to the "test" tag in tool configs. Allows the tool writer to decide how long Galaxy should wait for tool execution to complete. Resolves issue #219.

lib/galaxy/tools/__init__.py

@@ -547,7 +547,8 @@ class Tool:
         self.tests = []
         for i, test_elem in enumerate( tests_elem.findall( 'test' ) ):
             name = test_elem.get( 'name', 'Test-%d' % (i+1) )
-            test = ToolTestBuilder( self, name )
+            maxseconds = int( test_elem.get( 'maxseconds', '120' ) )
+            test = ToolTestBuilder( self, name, maxseconds )
             try:
                 for param_elem in test_elem.findall( "param" ):
                     attrib = dict( param_elem.attrib )

lib/galaxy/tools/test.py

@@ -11,9 +11,10 @@ class ToolTestBuilder( object ):
     dynamic TestCase class (the unittest framework is very class oriented, 
     doing dynamic tests in this was allows better integration)
     """
-    def __init__( self, tool, name ):
+    def __init__( self, tool, name, maxseconds ):
         self.tool = tool
         self.name = name
+        self.maxseconds = maxseconds
         self.required_files = []
         self.inputs = []
         self.outputs = []

test/base/twilltestcase.py

@@ -513,10 +513,10 @@ class TwillTestCase( unittest.TestCase ):
             hid = elem.get('hid')
             hids.append(hid)
         return hids
-    def verify_dataset_correctness( self, filename, hid=None, wait=True ):
+    def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120 ):
         """Verifies that the attributes and contents of a history item meet expectations"""
         if wait:
-            self.wait() #wait for job to finish
+            self.wait( maxseconds=maxseconds ) #wait for job to finish
         data_list = self.get_history_as_data_list()
         self.assertTrue( data_list )
         if hid is None: # take last hid
@@ -906,21 +906,23 @@ class TwillTestCase( unittest.TestCase ):
         tc.fv( "1","hgta_doGalaxyQuery", "Send query to Galaxy" )
         self.submit_form( button="Send query to Galaxy" )#, **output_params ) #AssertionError: Attempting to set field 'fbQual' to value '['whole']' in form 'None' threw exception: no matching forms! control: <RadioControl(fbQual=[whole, upstreamAll, endAll])>
 
-    def wait( self, maxiter=20 ):
+    def wait( self, maxseconds=120 ):
         """Waits for the tools to finish"""
-        count = 0
         sleep_amount = 0.1
+        slept = 0
         self.home()
-        while count < maxiter:
-            count += 1
+        while slept <= maxseconds:
             self.visit_page( "history" )
             page = tc.browser.get_html()
             if page.find( '<!-- running: do not change this comment, used by TwillTestCase.wait -->' ) > -1:
                 time.sleep( sleep_amount )
+                slept += sleep_amount
                 sleep_amount *= 2
+                if slept + sleep_amount > maxseconds:
+                    sleep_amount = maxseconds - slept # don't overshoot maxseconds
             else:
                 break
-        self.assertNotEqual(count, maxiter)
+        assert slept < maxseconds
 
     # Dataset Security stuff
     # Tests associated with users

test/functional/test_toolbox.py

@@ -63,7 +63,7 @@ class ToolTestCase( TwillTestCase ):
         # Check the result
         assert len( testdef.outputs ) == 1, "ToolTestCase does not deal with multiple outputs properly yet."
         for name, file in testdef.outputs:
-            self.verify_dataset_correctness( file )
+            self.verify_dataset_correctness( file, maxseconds=testdef.maxseconds )
         self.delete_history( id=self.security.encode_id( latest_history.id ) )
 
     def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ):