1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/9c80a2995cc9/ changeset: 9c80a2995cc9 user: greg date: 2012-04-04 21:01:09 summary: Only include invalid tools in the metadata for the repository tip - supporting this in older revisions is a bit more complex and will be supported at a later time. affected #: 3 files

diff -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 -r 9c80a2995cc9ca4248d4673d553461d739142371 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -427,8 +427,13 @@ metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) + """ + FIXME: Handling invalid tools in change sets that are not the repository tip are a bit complex, so this is currently not + supported. One example is the Emboss tools that have a <code file> tag set, which requires the file to exist in a location + that can be found. if invalid_tool_configs: metadata_dict[ 'invalid_tools' ] = invalid_tool_configs + """ return metadata_dict, invalid_files def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """Set repository metadata"""

diff -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 -r 9c80a2995cc9ca4248d4673d553461d739142371 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -428,6 +428,7 @@ for invalid_tool_config in invalid_tools: invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision ) return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', + cntrller=cntrller, invalid_tools_dict=invalid_tools_dict, webapp=webapp, message=message, @@ -1867,6 +1868,7 @@ break if found: break + metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, repository_id, ctx, changeset_revision, repo_dir ) else: for filename in ctx: if filename == tool_config: @@ -1879,7 +1881,7 @@ fh.write( fctx.data() ) fh.close() break - metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, repository_id, ctx, changeset_revision, repo_dir ) + metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, repository_id, ctx, changeset_revision, repo_dir ) for invalid_file_tup in invalid_files: invalid_tool_config, invalid_msg = invalid_file_tup if tool_config == invalid_tool_config:

diff -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 -r 9c80a2995cc9ca4248d4673d553461d739142371 templates/webapps/community/repository/browse_invalid_tools.mako --- a/templates/webapps/community/repository/browse_invalid_tools.mako +++ b/templates/webapps/community/repository/browse_invalid_tools.mako @@ -32,7 +32,11 @@ </div> %else: <div class="form-row"> - You do not own any repositories that contain invalid tools. + %if cntrller == 'admin' and trans.user_is_admin(): + No repositories in this tool shed contain invalid tools. + %else: + None of your repositories contain invalid tools. + %endif </div> %endif </div>

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.