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Tool functional tests - refactor reusable function for verifing output
... from verify_dataset_correctness. Introduce simple, extensible abstraction for fetching outputs for verification in twilltestcase.py. Will want to reuse the core verification of the displayed dataset in the API driven case and will not need or be able to use the extra cruft related to checking UI, job state, etc... Also small twilltestcase code structure updates for Python 2.6+.
This commit is contained in:
John Chilton
+113
-102
@@ -833,113 +833,45 @@ class TwillTestCase( unittest.TestCase ):
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if ext != test_ext:
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raise AssertionError( errmsg )
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else:
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hda_id = self.security.encode_id( elem.get( 'id' ) )
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self.home()
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# See not in controllers/root.py about encoded_id.
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self.visit_page( "display?encoded_id=%s" % hda_id )
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data = self.last_page()
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if attributes is not None and attributes.get( "assert_list", None ) is not None:
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hda_id = self.security.encode_id( elem.get( 'id' ) )
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self.verify_hid( filename, hid=hid, hda_id=hda_id, attributes=attributes, shed_tool_id=shed_tool_id)
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def verify_hid( self, filename, hda_id, attributes, shed_tool_id, hid="", dataset_fetcher=None):
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dataset_fetcher = dataset_fetcher or self.__default_dataset_fetcher()
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data = dataset_fetcher( hda_id )
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if attributes is not None and attributes.get( "assert_list", None ) is not None:
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try:
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verify_assertions(data, attributes["assert_list"])
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except AssertionError, err:
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errmsg = 'History item %s different than expected\n' % (hid)
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errmsg += str( err )
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raise AssertionError( errmsg )
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if filename is not None:
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local_name = self.get_filename( filename, shed_tool_id=shed_tool_id )
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temp_name = self.makeTfname(fname=filename)
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file( temp_name, 'wb' ).write( data )
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# if the server's env has GALAXY_TEST_SAVE, save the output file to that dir
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if self.keepOutdir:
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ofn = os.path.join( self.keepOutdir, os.path.basename( local_name ) )
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log.debug( 'keepoutdir: %s, ofn: %s', self.keepOutdir, ofn )
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try:
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verify_assertions(data, attributes["assert_list"])
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except AssertionError, err:
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errmsg = 'History item %s different than expected\n' % (hid)
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errmsg += str( err )
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raise AssertionError( errmsg )
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if filename is not None:
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local_name = self.get_filename( filename, shed_tool_id=shed_tool_id )
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temp_name = self.makeTfname(fname=filename)
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file( temp_name, 'wb' ).write( data )
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# if the server's env has GALAXY_TEST_SAVE, save the output file to that dir
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if self.keepOutdir:
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ofn = os.path.join( self.keepOutdir, os.path.basename( local_name ) )
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log.debug( 'keepoutdir: %s, ofn: %s', self.keepOutdir, ofn )
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try:
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shutil.copy( temp_name, ofn )
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except Exception, exc:
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error_log_msg = ( 'TwillTestCase could not save output file %s to %s: ' % ( temp_name, ofn ) )
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error_log_msg += str( exc )
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log.error( error_log_msg, exc_info=True )
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else:
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log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % ( self.keepOutdir, ofn ) )
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try:
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# have to nest try-except in try-finally to handle 2.4
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try:
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if attributes is None:
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attributes = {}
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compare = attributes.get( 'compare', 'diff' )
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if attributes.get( 'ftype', None ) == 'bam':
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local_fh, temp_name = self._bam_to_sam( local_name, temp_name )
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local_name = local_fh.name
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extra_files = attributes.get( 'extra_files', None )
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if compare == 'diff':
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self.files_diff( local_name, temp_name, attributes=attributes )
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elif compare == 're_match':
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self.files_re_match( local_name, temp_name, attributes=attributes )
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elif compare == 're_match_multiline':
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self.files_re_match_multiline( local_name, temp_name, attributes=attributes )
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elif compare == 'sim_size':
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delta = attributes.get('delta', '100')
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s1 = len(data)
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s2 = os.path.getsize(local_name)
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if abs(s1 - s2) > int(delta):
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raise Exception( 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name, s1, local_name, s2, delta) )
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elif compare == "contains":
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self.files_contains( local_name, temp_name, attributes=attributes )
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else:
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raise Exception( 'Unimplemented Compare type: %s' % compare )
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if extra_files:
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self.verify_extra_files_content( extra_files, elem.get( 'id' ), shed_tool_id=shed_tool_id )
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except AssertionError, err:
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errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare )
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errmsg += "( %s v. %s )\n" % ( local_name, temp_name )
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errmsg += str( err )
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raise AssertionError( errmsg )
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finally:
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os.remove( temp_name )
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def _bam_to_sam( self, local_name, temp_name ):
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temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' )
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fd, temp_temp = tempfile.mkstemp( suffix='.sam', prefix='history_bam_converted_to_sam_' )
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os.close( fd )
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p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name ), shell=True )
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assert not p.wait(), 'Converting local (test-data) bam to sam failed'
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p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_temp, temp_name ), shell=True )
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assert not p.wait(), 'Converting history bam to sam failed'
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os.remove( temp_name )
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return temp_local, temp_temp
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def verify_extra_files_content( self, extra_files, hda_id, shed_tool_id=None ):
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files_list = []
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for extra_type, extra_value, extra_name, extra_attributes in extra_files:
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if extra_type == 'file':
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files_list.append( ( extra_name, extra_value, extra_attributes ) )
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elif extra_type == 'directory':
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for filename in os.listdir( self.get_filename( extra_value, shed_tool_id=shed_tool_id ) ):
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files_list.append( ( filename, os.path.join( extra_value, filename ), extra_attributes ) )
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else:
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raise ValueError( 'unknown extra_files type: %s' % extra_type )
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for filename, filepath, attributes in files_list:
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self.verify_composite_datatype_file_content( filepath, hda_id, base_name=filename, attributes=attributes, shed_tool_id=shed_tool_id )
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def verify_composite_datatype_file_content( self, file_name, hda_id, base_name=None, attributes=None, shed_tool_id=None ):
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local_name = self.get_filename( file_name, shed_tool_id=shed_tool_id )
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if base_name is None:
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base_name = os.path.split(file_name)[-1]
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temp_name = self.makeTfname(fname=base_name)
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self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, hda_id, base_name ) )
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data = self.last_page()
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file( temp_name, 'wb' ).write( data )
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if self.keepOutdir > '':
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ofn = os.path.join(self.keepOutdir, base_name)
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shutil.copy(temp_name, ofn)
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log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % (self.keepOutdir, ofn))
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try:
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# have to nest try-except in try-finally to handle 2.4
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shutil.copy( temp_name, ofn )
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except Exception, exc:
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error_log_msg = ( 'TwillTestCase could not save output file %s to %s: ' % ( temp_name, ofn ) )
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error_log_msg += str( exc )
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log.error( error_log_msg, exc_info=True )
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else:
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log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % ( self.keepOutdir, ofn ) )
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try:
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if attributes is None:
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attributes = {}
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compare = attributes.get( 'compare', 'diff' )
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if attributes.get( 'ftype', None ) == 'bam':
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local_fh, temp_name = self._bam_to_sam( local_name, temp_name )
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local_name = local_fh.name
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extra_files = attributes.get( 'extra_files', None )
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if compare == 'diff':
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self.files_diff( local_name, temp_name, attributes=attributes )
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elif compare == 're_match':
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@@ -952,12 +884,91 @@ class TwillTestCase( unittest.TestCase ):
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s2 = os.path.getsize(local_name)
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if abs(s1 - s2) > int(delta):
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raise Exception( 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name, s1, local_name, s2, delta) )
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elif compare == "contains":
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self.files_contains( local_name, temp_name, attributes=attributes )
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else:
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raise Exception( 'Unimplemented Compare type: %s' % compare )
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if extra_files:
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self.verify_extra_files_content( extra_files, hda_id, shed_tool_id=shed_tool_id, dataset_fetcher=dataset_fetcher )
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except AssertionError, err:
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errmsg = 'Composite file (%s) of History item %s different than expected, difference (using %s):\n' % ( base_name, hda_id, compare )
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errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare )
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errmsg += "( %s v. %s )\n" % ( local_name, temp_name )
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errmsg += str( err )
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raise AssertionError( errmsg )
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finally:
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os.remove( temp_name )
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def __default_dataset_fetcher( self ):
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def fetcher( hda_id, filename=None ):
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if filename is None:
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page_url = "display?encoded_id=%s" % hda_id
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self.home() # I assume this is not needed.
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else:
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page_url = "datasets/%s/display/%s" % ( hda_id, filename )
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self.visit_page( page_url )
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data = self.last_page()
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return data
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return fetcher
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def _bam_to_sam( self, local_name, temp_name ):
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temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' )
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fd, temp_temp = tempfile.mkstemp( suffix='.sam', prefix='history_bam_converted_to_sam_' )
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os.close( fd )
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p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name ), shell=True )
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assert not p.wait(), 'Converting local (test-data) bam to sam failed'
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p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_temp, temp_name ), shell=True )
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assert not p.wait(), 'Converting history bam to sam failed'
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os.remove( temp_name )
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return temp_local, temp_temp
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def verify_extra_files_content( self, extra_files, hda_id, dataset_fetcher, shed_tool_id=None ):
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files_list = []
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for extra_type, extra_value, extra_name, extra_attributes in extra_files:
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if extra_type == 'file':
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files_list.append( ( extra_name, extra_value, extra_attributes ) )
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elif extra_type == 'directory':
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for filename in os.listdir( self.get_filename( extra_value, shed_tool_id=shed_tool_id ) ):
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files_list.append( ( filename, os.path.join( extra_value, filename ), extra_attributes ) )
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else:
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raise ValueError( 'unknown extra_files type: %s' % extra_type )
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for filename, filepath, attributes in files_list:
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self.verify_composite_datatype_file_content( filepath, hda_id, base_name=filename, attributes=attributes, dataset_fetcher=dataset_fetcher, shed_tool_id=shed_tool_id )
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def verify_composite_datatype_file_content( self, file_name, hda_id, base_name=None, attributes=None, dataset_fetcher=None, shed_tool_id=None ):
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dataset_fetcher = dataset_fetcher or self.__default_dataset_fetcher()
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local_name = self.get_filename( file_name, shed_tool_id=shed_tool_id )
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if base_name is None:
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base_name = os.path.split(file_name)[-1]
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temp_name = self.makeTfname(fname=base_name)
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data = dataset_fetcher( hda_id, base_name )
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file( temp_name, 'wb' ).write( data )
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if self.keepOutdir > '':
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ofn = os.path.join(self.keepOutdir, base_name)
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shutil.copy(temp_name, ofn)
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log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % (self.keepOutdir, ofn))
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try:
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if attributes is None:
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attributes = {}
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compare = attributes.get( 'compare', 'diff' )
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if compare == 'diff':
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self.files_diff( local_name, temp_name, attributes=attributes )
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elif compare == 're_match':
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self.files_re_match( local_name, temp_name, attributes=attributes )
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elif compare == 're_match_multiline':
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self.files_re_match_multiline( local_name, temp_name, attributes=attributes )
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elif compare == 'sim_size':
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delta = attributes.get('delta', '100')
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s1 = len(data)
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s2 = os.path.getsize(local_name)
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if abs(s1 - s2) > int(delta):
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raise Exception( 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name, s1, local_name, s2, delta) )
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else:
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raise Exception( 'Unimplemented Compare type: %s' % compare )
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except AssertionError, err:
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errmsg = 'Composite file (%s) of History item %s different than expected, difference (using %s):\n' % ( base_name, hda_id, compare )
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errmsg += str( err )
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raise AssertionError( errmsg )
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finally:
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os.remove( temp_name )
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