Fix problem with cleaning up jobs in local runner.

Fixes galaxyproject#3801 (broken in b78287f as part of galaxyproject#3291).
jmchilton · Mar 22, 2017 · a5a3946 · a5a3946
1 parent c84b3ba
commit a5a3946
Showing 1 changed file with 15 additions and 9 deletions.
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
@@ -404,6 +404,8 @@ def __init__( self, job_wrapper, job_destination ):
         self.job_wrapper = job_wrapper
         self.job_destination = job_destination
 
+        self.cleanup_file_attributes = [ 'job_file', 'output_file', 'error_file', 'exit_code_file' ]
+
     def set_defaults( self, files_dir ):
         if self.job_wrapper is not None:
             id_tag = self.job_wrapper.get_id_tag()
@@ -427,6 +429,19 @@ def default_job_file( files_dir, id_tag ):
     def default_exit_code_file( files_dir, id_tag ):
         return os.path.join( files_dir, 'galaxy_%s.ec' % id_tag )
 
+    def cleanup( self ):
+        for file in [ getattr( self, a ) for a in self.cleanup_file_attributes if hasattr( self, a ) ]:
+            try:
+                os.unlink( file )
+            except Exception as e:
+                # TODO: Move this prefix stuff to a method so we don't have dispatch on attributes we may or may
+                # have.
+                if not hasattr( self, "job_id" ):
+                    prefix = "(%s)" % self.job_wrapper.get_id_tag()
+                else:
+                    prefix = "(%s/%s)" % ( self.job_wrapper.get_id_tag(), self.job_id )
+                log.debug( "%s Unable to cleanup %s: %s" % (prefix, file, str( e ) ) )
+
 
 class AsynchronousJobState( JobState ):
     """
@@ -453,8 +468,6 @@ def __init__( self, files_dir=None, job_wrapper=None, job_id=None, job_file=None
 
         self.set_defaults( files_dir )
 
-        self.cleanup_file_attributes = [ 'job_file', 'output_file', 'error_file', 'exit_code_file' ]
-
     @property
     def running( self ):
         return self._running
@@ -482,13 +495,6 @@ def check_limits( self, runtime=None ):
             return True
         return False
 
-    def cleanup( self ):
-        for file in [ getattr( self, a ) for a in self.cleanup_file_attributes if hasattr( self, a ) ]:
-            try:
-                os.unlink( file )
-            except Exception as e:
-                log.debug( "(%s/%s) Unable to cleanup %s: %s" % ( self.job_wrapper.get_id_tag(), self.job_id, file, str( e ) ) )
-
     def register_cleanup_file_attribute( self, attribute ):
         if attribute not in self.cleanup_file_attributes:
             self.cleanup_file_attributes.append( attribute )