Merging heads

lib/galaxy/web/controllers/root.py

@@ -327,6 +327,7 @@ class RootController( BaseController ):
                     # Are *all* of the job's other output datasets deleted?
                     if job.check_if_output_datasets_deleted():
                         job.mark_deleted()                
+                        self.app.job_manager.job_stop_queue.put( job )
             self.app.model.flush()
 
     @web.expose

test/base/twilltestcase.py

@@ -7,6 +7,7 @@ from itertools import *
 import twill
 import twill.commands as tc
 from twill.other_packages._mechanize_dist import ClientForm
+pkg_resources.require( "elementtree" )
 from elementtree import ElementTree
   
 buffer = StringIO.StringIO()
@@ -255,7 +256,7 @@ class TwillTestCase( unittest.TestCase ):
         self.assertTrue( data_list )
         if hid is None: # take last hid
             elem = data_list[-1]
-            hid = elem.get('hid')
+            hid = int( elem.get('hid') )
         self.assertTrue( hid )
         self.visit_page( 'edit?hid=%d' % hid )
         if form_no == 0:
@@ -511,6 +512,21 @@ class TwillTestCase( unittest.TestCase ):
         tc.find( 'runtool_btn' )
         self.submit_form( **kwd )
 
+    def run_ucsc_main( self, track_params, output_params ):
+        """Gets Data From UCSC"""
+        tool_id = "ucsc_table_direct1"
+        track_string = urllib.urlencode( track_params )
+        galaxy_url = urllib.quote_plus( "%s/tool_runner/index?" % self.url )
+        
+        self.visit_url( "http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=%s&hgta_compressType=none&tool_id=%s&%s" % ( galaxy_url, tool_id, track_string ) )
+        tc.fv( "1","hgta_doTopSubmit", "get output" )
+        self.submit_form( button="get output" )#, **track_params )
+        
+        
+        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 ):
         """Waits for the tools to finish"""
         count = 0

test/functional/__init__.py

@@ -16,6 +16,7 @@ from galaxy.app import UniverseApplication
 from galaxy.web import buildapp
 import test_toolbox
 from galaxy import tools
+from galaxy.util import bunch
 
 log = logging.getLogger( __name__ )
 
@@ -93,7 +94,8 @@ def setup():
     else:
         # FIXME: This doesn't work at all now that toolbox requires an 'app' instance
         #        (to get at datatypes, might just pass a datatype registry directly)
-        test_toolbox.toolbox = tools.ToolBox( 'tool_conf.xml.test', 'tools' )
+        my_app = bunch.Bunch( datatypes_registry = galaxy.datatypes.registry.Registry() )
+        test_toolbox.toolbox = tools.ToolBox( 'tool_conf.xml.test', 'tools', my_app )
         
     # Test if the server is up
     conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port )

test/functional/test_DNAse_flanked_genes.py

@@ -0,0 +1,79 @@
+from base.twilltestcase import TwillTestCase
+
+""" A sample analysis"""
+
+
+
+class AnalysisDNAseHSSFlankedGenes( TwillTestCase ):
+    
+    def test_get_DNAseHSS_flanked_genes( self ):
+        self.login()
+        
+        self.new_history()
+    
+        track_params = dict(
+            db="hg17",
+            hgta_group="regulation",
+            hgta_table="dukeDnaseCd4Sites",
+            hgta_track="dukeDnaseCd4Sites",
+            hgta_regionType="range",
+            position="chr22",
+            hgta_outputType="bed",
+            sendToGalaxy="1"
+        )
+        output_params = dict(
+            fbQual="whole",
+        )
+        
+        self.run_ucsc_main( track_params, output_params )
+        self.wait()
+        self.verify_dataset_correctness('DNAseHSS.dat')
+        
+        self.edit_metadata( name="DNAse HS" )
+        self.check_metadata_for_string( "DNAse HS" )
+        
+        track_params = dict(
+            db="hg17",
+            hgta_group="genes",
+            hgta_table="knownGene",
+            hgta_track="knownGene",
+            hgta_regionType="range",
+            position="chr22",
+            hgta_outputType="bed",
+            sendToGalaxy="1"
+        )
+        output_params = dict(
+            fbQual="whole",
+        )
+        
+        self.run_ucsc_main( track_params, output_params )
+        self.wait()
+        self.verify_dataset_correctness('hg17chr22KnownGenes.dat')
+        
+        self.edit_metadata( name="Genes" )
+        self.check_metadata_for_string( "Genes" )
+        
+        
+        self.run_tool( 'get_flanks1', input="2", region="whole", direction="Upstream", offset="0", size="500" )
+        self.wait()
+        self.verify_dataset_correctness( 'knownGeneUpstream500Flanks.dat' )
+        
+        self.edit_metadata( name="Flanks" )
+        self.check_metadata_for_string( "Flanks" )
+        
+        
+        self.run_tool( 'gops_join_1', input1="3", input2="1", min="1", fill="none"  )
+        self.wait()
+        #self.verify_dataset_correctness( 'joinFlanksDNAse.dat' ) #we cannot verify this dataset, because this tool spits out data in a non-deterministic order
+        
+        
+        self.run_tool( 'Filter1', input="4", cond="c17==1000"  )
+        self.wait()
+        self.verify_dataset_correctness( 'filteredJoinedFlanksDNAse.dat' )
+        
+        
+        self.delete_history()
+        self.logout()
+        
+        
+