2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7be69524cfaa/ Changeset: 7be69524cfaa Branch: next-stable User: Dave Bouvier Date: 2013-05-30 16:36:40 Summary: Fix error reporting in the tool dependency installation process. Affected #: 2 files diff -r 7b2c4fff40c0682bdb64a5fe8049df15cf836541 -r 7be69524cfaae9c56f1eb9cd77a857a9b912108c lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -1,7 +1,9 @@ import logging import os import shutil +import sys import tarfile +import traceback import urllib2 import zipfile import tool_shed.util.shed_util_common as suc @@ -78,6 +80,10 @@ tar.extractall( path=file_path ) tar.close() +def format_traceback(): + ex_type, ex, tb = sys.exc_info() + return ''.join( traceback.format_tb( tb ) ) + def extract_zip( archive_path, extraction_path ): # TODO: change this method to use zipfile.Zipfile.extractall() when we stop supporting Python 2.5. if not zipfile_ok( archive_path ): @@ -220,6 +226,8 @@ dst = open( file_path,'wb' ) dst.write( data ) except: + raise + finally: if src: src.close() if dst: diff -r 7b2c4fff40c0682bdb64a5fe8049df15cf836541 -r 7be69524cfaae9c56f1eb9cd77a857a9b912108c lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -165,8 +165,9 @@ # There is currently only one fabric method. fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) except Exception, e: + log.exception( 'Error installing tool dependency %s version %s.', str( tool_dependency.name ), str( tool_dependency.version ) ) tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = str( e ) + tool_dependency.error_message = '%s\n%s' % ( common_util.format_traceback(), str( e ) ) sa_session.add( tool_dependency ) sa_session.flush() if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: https://bitbucket.org/galaxy/galaxy-central/commits/b37711ed16fe/ Changeset: b37711ed16fe User: Dave Bouvier Date: 2013-05-30 16:37:11 Summary: Merge in next-stable. Affected #: 2 files diff -r e47d4ab261370d174641e0db1f5b7dd2adc96365 -r b37711ed16fe64bc96ec8eacc6e6ce7026643bab lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -1,7 +1,9 @@ import logging import os import shutil +import sys import tarfile +import traceback import urllib2 import zipfile import tool_shed.util.shed_util_common as suc @@ -78,6 +80,10 @@ tar.extractall( path=file_path ) tar.close() +def format_traceback(): + ex_type, ex, tb = sys.exc_info() + return ''.join( traceback.format_tb( tb ) ) + def extract_zip( archive_path, extraction_path ): # TODO: change this method to use zipfile.Zipfile.extractall() when we stop supporting Python 2.5. if not zipfile_ok( archive_path ): @@ -220,6 +226,8 @@ dst = open( file_path,'wb' ) dst.write( data ) except: + raise + finally: if src: src.close() if dst: diff -r e47d4ab261370d174641e0db1f5b7dd2adc96365 -r b37711ed16fe64bc96ec8eacc6e6ce7026643bab lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -165,8 +165,9 @@ # There is currently only one fabric method. fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) except Exception, e: + log.exception( 'Error installing tool dependency %s version %s.', str( tool_dependency.name ), str( tool_dependency.version ) ) tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = str( e ) + tool_dependency.error_message = '%s\n%s' % ( common_util.format_traceback(), str( e ) ) sa_session.add( tool_dependency ) sa_session.flush() if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.