mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Removed unneeded log data from functional test error reports, use url_join to generate api URLs.
This commit is contained in:
Dave Bouvier
@@ -37,6 +37,9 @@ eggs.require( "simplejson" )
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# This should not be required, but it is under certain conditions, thanks to this bug: http://code.google.com/p/python-nose/issues/detail?id=284
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eggs.require( "pysqlite" )
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import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories
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import functional.test_toolbox as test_toolbox
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import atexit, logging, os, os.path, sys, tempfile, simplejson
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import twill, unittest, time
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import sys, threading, random
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@@ -151,7 +154,11 @@ def get_repositories_to_install( location, source='file', format='json' ):
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listing = file( location, 'r' ).read()
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elif source == 'url':
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assert tool_shed_api_key is not None, 'Cannot proceed without tool shed API key.'
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params = urllib.urlencode( dict( tools_functionally_correct='false', do_not_test='false', downloadable='true', malicious='false' ) )
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params = urllib.urlencode( dict( tools_functionally_correct='false',
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do_not_test='false',
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downloadable='true',
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malicious='false',
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must_include_tools='true' ) )
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api_url = get_api_url( base=location, parts=[ 'repository_revisions' ], params=params )
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if format == 'json':
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return json_from_url( api_url )
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@@ -177,11 +184,11 @@ def json_from_url( url ):
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def register_test_failure( url, metadata_id, test_errors ):
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params = dict( tools_functionally_correct='false', do_not_test='true', tool_test_errors=test_errors )
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return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params )
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return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False )
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def register_test_success( url, metadata_id ):
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params = dict( tools_functionally_correct='true', do_not_test='false' )
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return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params )
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return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False )
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def run_tests( test_config ):
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loader = nose.loader.TestLoader( config=test_config )
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@@ -354,9 +361,6 @@ def main():
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else:
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raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" )
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log.info( "Embedded galaxy web server started" )
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# ---- Load the modules to generate installation, testing, and uninstallation methods -------------------
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import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories
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import functional.test_toolbox as test_toolbox
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if galaxy_test_proxy_port:
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log.info( "The embedded Galaxy application is running on %s:%s" % ( galaxy_test_host, galaxy_test_proxy_port ) )
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else:
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@@ -365,7 +369,7 @@ def main():
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success = False
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repository_status = {}
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try:
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# Iterate through a list of repository info dicts
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# Iterate through a list of repository info dicts.
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log.info( "Retrieving repositories to install from the URL:\n%s\n" % str( galaxy_tool_shed_url ) )
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repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, source='url' )
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log.info( "Retrieved %d repositories to install..." % len( repositories_to_install ) )
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@@ -381,15 +385,15 @@ def main():
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"""
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repository_id = repository_to_install_dict.get( 'repository_id', None )
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changeset_revision = repository_to_install_dict.get( 'changeset_revision', None )
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metadata_revision_id = repository_to_install_dict[ 'id' ]
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metadata_revision_id = repository_to_install_dict.get( 'id', None )
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repository_to_install_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url
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repository_info = get_repository_info_from_api( galaxy_tool_shed_url, repository_to_install_dict )
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repository_info_dict = get_repository_info_from_api( galaxy_tool_shed_url, repository_to_install_dict )
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# If a repository is deleted or malicious, we don't need to test it.
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if repository_info[ 'deleted' ] or repository_info[ 'deprecated' ]:
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if repository_info_dict[ 'deleted' ] or repository_info_dict[ 'deprecated' ]:
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log.info( "Skipping revision %s of repository id %s since it is either deleted or deprecated..." % ( str( changeset_revision ), str( repository_id ) ) )
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continue
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log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) )
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repository_dict = dict( repository_info.items() + repository_to_install_dict.items() )
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repository_dict = dict( repository_info_dict.items() + repository_to_install_dict.items() )
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"""
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Each repository_dict looks something like:
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{'repository_id': '175812cd7caaf439',
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@@ -412,12 +416,11 @@ def main():
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# If the installation succeeds, set up and run functional tests for this repository. This is equivalent to
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# sh run_functional_tests.sh -installed
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if success:
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log.debug( 'Installation of %s succeeded, running any defined functional tests.' % repository_dict[ 'name' ] )
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log.debug( 'Installation of %s succeeded, running all defined functional tests.' % repository_dict[ 'name' ] )
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# Parse the tool panel config to get the test-data path for this repository.
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if not os.path.exists( galaxy_shed_tools_dict ):
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file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) )
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shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) )
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log.debug( shed_tools_dict )
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# Write this to a file, so the functional test framework can find it.
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file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) )
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# Set up the environment so that test.functional.test_toolbox can find the Galaxy server we configured in this framework.
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@@ -444,7 +447,7 @@ def main():
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else:
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# If the functional tests fail, log the output and submit it to the tool shed whence the repository was installed.
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for failure in result.failures:
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label = str( failure[0] )
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test_status = dict( test=str( failure[0] ) )
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log_output = failure[1].replace( '\\n', '\n' )
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log_output = re.sub( r'control \d+:.+', r'', log_output )
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log_output = re.sub( r'\n+', r'\n', log_output )
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@@ -454,6 +457,8 @@ def main():
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for line in log_output.split( '\n' ):
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if line.startswith( 'Traceback' ):
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appending_to = 'traceback'
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elif '>> end captured' in line:
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continue
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elif 'request returned None from get_history' in line:
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continue
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elif '>> begin captured logging <<' in line:
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@@ -468,9 +473,10 @@ def main():
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if appending_to not in tmp_output:
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tmp_output[ appending_to ] = []
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tmp_output[ appending_to ].append( line )
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for output_type in tmp_output:
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output[ output_type ] = '\n'.join( tmp_output[ output_type ] )
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test_errors.append( dict( test=label, output=output ) )
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for output_type in [ 'stderr', 'stdout', 'traceback' ]:
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if output_type in tmp_output:
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test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] )
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test_errors.append( test_status )
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if test_errors:
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repository_status[ 'test_environment' ] = get_test_environment()
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repository_status[ 'test_errors' ] = test_errors
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