2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a91b182a433/ Changeset: 0a91b182a433 User: Dave Bouvier Date: 2013-09-25 19:38:24 Summary: Correction to the fix in 10677:448487d92454 for the tool migration install manager. Affected #: 1 file diff -r e23dda978523ac4368aeb617e0ef209c24cac59e -r 0a91b182a433f3cdec901c258e953d22802c0639 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -6,6 +6,7 @@ import shutil import tempfile import threading +import logging from galaxy import util from galaxy.tools import ToolSection from galaxy.util.json import from_json_string @@ -20,6 +21,8 @@ from tool_shed.util import xml_util from galaxy.util.odict import odict +log = logging.getLogger( __name__ ) + class InstallManager( object ): @@ -160,15 +163,8 @@ if rd_key in [ 'root_key', 'description' ]: continue for rd_tup in rd_tups: - if len( rd_tup ) == 4: - rd_tool_shed, rd_name, rd_owner, rd_changeset_revision = \ - common_util.parse_repository_dependency_tuple( rd_tup ) - elif len( rd_tup ) == 5: - rd_tool_shed, rd_name, rd_owner, rd_changeset_revision, rd_prior_installation_required = \ - common_util.parse_repository_dependency_tuple( rd_tup ) - elif len( rd_tup ) == 6: - rd_tool_shed, rd_name, rd_owner, rd_changeset_revision, rd_prior_installation_required, only_if_compiling_contained_td = \ - common_util.parse_repository_dependency_tuple( rd_tup ) + parsed_rd_tup = common_util.parse_repository_dependency_tuple( rd_tup ) + rd_tool_shed, rd_name, rd_owner, rd_changeset_revision = parsed_rd_tup[ 0:4 ] # TODO: Make sure the repository description is applied to the new repository record during installation. tool_shed_repository = self.create_or_update_tool_shed_repository_record( rd_name, rd_owner, rd_changeset_revision, description=None ) if tool_shed_repository: https://bitbucket.org/galaxy/galaxy-central/commits/3640bed9d3a9/ Changeset: 3640bed9d3a9 User: Dave Bouvier Date: 2013-09-25 19:39:59 Summary: Correctly display tool dependency information in the exception raised when a new tool migration is available. Affected #: 1 file diff -r 0a91b182a433f3cdec901c258e953d22802c0639 -r 3640bed9d3a98e286b2c3d65125868be3d6473c1 lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -113,7 +113,7 @@ msg += "setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).\n" processed_tool_dependencies = [] for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): - for tool_dependencies_tup in tool_dependencies: + for tool_dependencies_tup in missing_tool_configs_dict[ missing_tool_config ][ 'tool_dependencies' ]: if tool_dependencies_tup not in processed_tool_dependencies: msg += "------------------------------------\n" msg += "Tool Dependency\n" @@ -121,7 +121,7 @@ msg += "Name: %s, Version: %s, Type: %s\n" % ( tool_dependencies_tup[ 0 ], tool_dependencies_tup[ 1 ], tool_dependencies_tup[ 2 ] ) - if tool_dependencies_tup[ 3 ]: + if len( tool_dependencies_tup ) >= 4: msg += "Requirements and installation information:\n" msg += "%s\n" % tool_dependencies_tup[ 3 ] else: 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.