1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/24f4f507fdec/ Changeset: 24f4f507fdec User: Dave Bouvier Date: 2013-08-22 20:44:56 Summary: Fix for running a tool migration script that specifies one or more repositories with complex tool dependencies. Affected #: 2 files

diff -r 185232cef732d9b79aad686ca0aa556bb7c63614 -r 24f4f507fdecf214e9090f215fe309249a29252d lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -19,6 +19,7 @@ from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util +import tool_shed.galaxy_install.tool_dependencies.common_util as cu

import pkg_resources

@@ -1123,6 +1124,7 @@ if not toolshed: # Default to the current tool shed. toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + cleaned_toolshed = cu.clean_tool_shed_url( toolshed ) name = repository_elem.get( 'name' ) owner = repository_elem.get( 'owner' ) changeset_revision = repository_elem.get( 'changeset_revision' ) @@ -1135,7 +1137,7 @@ # generating metadata for an installed repository. See if we can locate the installed repository via the changeset_revision defined in the # repository_elem (it may be outdated). If we're successful in locating an installed repository with the attributes defined in the # repository_elem, we know it is valid. - repository = suc.get_repository_for_dependency_relationship( app, toolshed, name, owner, changeset_revision ) + repository = suc.get_repository_for_dependency_relationship( app, cleaned_toolshed, name, owner, changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message else: @@ -1144,7 +1146,7 @@ if text: updated_changeset_revisions = util.listify( text ) for updated_changeset_revision in updated_changeset_revisions: - repository = suc.get_repository_for_dependency_relationship( app, toolshed, name, owner, updated_changeset_revision ) + repository = suc.get_repository_for_dependency_relationship( app, cleaned_toolshed, name, owner, updated_changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message # We'll currently default to setting the repository dependency definition as invalid if an installed repository cannot be found.

diff -r 185232cef732d9b79aad686ca0aa556bb7c63614 -r 24f4f507fdecf214e9090f215fe309249a29252d lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -872,8 +872,8 @@ # tool shed that is associated with repository_metadata. tool_shed_url = get_url_from_tool_shed( app, tool_shed ) url = url_join( tool_shed_url, - 'repository/next_installable_changeset_revision?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ - ( url_for( '/', qualified=True ), name, owner, changeset_revision ) ) + 'repository/next_installable_changeset_revision?name=%s&owner=%s&changeset_revision=%s' % \ + ( name, owner, changeset_revision ) ) text = common_util.tool_shed_get( app, tool_shed_url, url ) if text: repository = get_tool_shed_repository_by_shed_name_owner_changeset_revision( app=app,

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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