1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/2531e085f262/ changeset: 2531e085f262 user: greg date: 2012-08-15 20:50:38 summary: Improve error message handling when setting metadata on tool shed repositories. Display the repository owner in the table grid when displaying invalid tools in the tool shed. affected #: 4 files

diff -r b99cd3b7670169d6b2723aff95c458b5448af34d -r 2531e085f2625b60135a6b4972f125e22a4fd354 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -696,9 +696,14 @@ owner = repository_name_owner_list[ 1 ] repository = get_repository_by_name_and_owner( trans, name, owner ) try: - reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) - log.debug( "Successfully reset metadata on repository %s" % repository.name ) - successful_count += 1 + invalid_file_tups = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) + if invalid_file_tups: + message = generate_message_for_invalid_tools( invalid_file_tups, repository, None, as_html=False ) + log.debug( message ) + unsuccessful_count += 1 + else: + log.debug( "Successfully reset metadata on repository %s" % repository.name ) + successful_count += 1 except Exception, e: log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) ) unsuccessful_count += 1

diff -r b99cd3b7670169d6b2723aff95c458b5448af34d -r 2531e085f2625b60135a6b4972f125e22a4fd354 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -277,6 +277,41 @@ return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) else: return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) +def generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict, as_html=True ): + if as_html: + new_line = '<br/>' + bold_start = '<b>' + bold_end = '</b>' + else: + new_line = '\n' + bold_start = '' + bold_end = '' + message = '' + if metadata_dict: + message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip ) + message += "Correct the following problems if necessary and reset metadata.%s" % new_line + else: + message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip ) + message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.%s" % new_line + for itc_tup in invalid_file_tups: + tool_file, exception_msg = itc_tup + if exception_msg.find( 'No such file or directory' ) >= 0: + exception_items = exception_msg.split() + missing_file_items = exception_items[ 7 ].split( '/' ) + missing_file = missing_file_items[ -1 ].rstrip( ''' ) + if missing_file.endswith( '.loc' ): + sample_ext = '%s.sample' % missing_file + else: + sample_ext = missing_file + correction_msg = "This file refers to a missing file %s%s%s. " % ( bold_start, str( missing_file ), bold_end ) + correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % ( bold_start, sample_ext, bold_end ) + else: + if as_html: + correction_msg = exception_msg + else: + correction_msg = exception_msg.replace( '<br/>', new_line ).replace( '<b>', bold_start ).replace( '</b>', bold_end ) + message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line ) + return message def generate_tool_guid( trans, repository, tool ): """ Generate a guid for the received tool. The form of the guid is @@ -854,6 +889,7 @@ clean_repository_metadata( trans, id, changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset revisions from the changelog. reset_all_tool_versions( trans, id, repo ) + return invalid_file_tups def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset @@ -931,27 +967,7 @@ message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" if invalid_file_tups: - if metadata_dict: - message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip ) - message += "Correct the following problems if necessary and reset metadata.<br/>" - else: - message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip ) - message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.<br/>" - for itc_tup in invalid_file_tups: - tool_file, exception_msg = itc_tup - if exception_msg.find( 'No such file or directory' ) >= 0: - exception_items = exception_msg.split() - missing_file_items = exception_items[ 7 ].split( '/' ) - missing_file = missing_file_items[ -1 ].rstrip( ''' ) - if missing_file.endswith( '.loc' ): - sample_ext = '%s.sample' % missing_file - else: - sample_ext = missing_file - correction_msg = "This file refers to a missing file <b>%s</b>. " % str( missing_file ) - correction_msg += "Upload a file named <b>%s</b> to the repository to correct this error." % sample_ext - else: - correction_msg = exception_msg - message += "<b>%s</b> - %s<br/>" % ( tool_file, correction_msg ) + message = generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict ) status = 'error' return message, status def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ):

diff -r b99cd3b7670169d6b2723aff95c458b5448af34d -r 2531e085f2625b60135a6b4972f125e22a4fd354 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -458,7 +458,10 @@ metadata = downloadable_revision.metadata invalid_tools = metadata.get( 'invalid_tools', [] ) for invalid_tool_config in invalid_tools: - invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision ) + invalid_tools_dict[ invalid_tool_config ] = ( repository.id, + repository.name, + repository.user.username, + downloadable_revision.changeset_revision ) else: for repository in trans.sa_session.query( trans.model.Repository ) \ .filter( and_( trans.model.Repository.table.c.deleted == False, @@ -468,7 +471,10 @@ metadata = downloadable_revision.metadata invalid_tools = metadata.get( 'invalid_tools', [] ) for invalid_tool_config in invalid_tools: - invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision ) + invalid_tools_dict[ invalid_tool_config ] = ( repository.id, + repository.name, + repository.user.username, + downloadable_revision.changeset_revision ) return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', cntrller=cntrller, invalid_tools_dict=invalid_tools_dict, @@ -1373,6 +1379,7 @@ return trans.response.send_redirect( url ) @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): + # FIXME: loading an invalid tool should display an appropriate message as to why the tool is invalid. This worked until recently. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) @@ -1752,9 +1759,14 @@ status=status ) @web.expose def reset_all_metadata( self, trans, id, **kwd ): - reset_all_metadata_on_repository( trans, id, **kwd ) - message = "All repository metadata has been reset." - status = 'done' + invalid_file_tups = reset_all_metadata_on_repository( trans, id, **kwd ) + if invalid_file_tups: + repository = get_repository( trans, id ) + message = generate_message_for_invalid_tools( invalid_file_tups, repository, None ) + status = 'error' + else: + message = "All repository metadata has been reset." + status = 'done' return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id,

diff -r b99cd3b7670169d6b2723aff95c458b5448af34d -r 2531e085f2625b60135a6b4972f125e22a4fd354 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 @@ -13,10 +13,11 @@ <tr><th>Tool config</th><th>Repository name</th> + <th>Repository owner</th><th>Changeset revision</th></tr> %for invalid_tool_config, repository_tup in invalid_tools_dict.items(): - <% repository_id, repository_name, changeset_revision = repository_tup %> + <% repository_id, repository_name, repository_owner, changeset_revision = repository_tup %><tr><td><a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> @@ -24,6 +25,7 @@ </a></td><td>${repository_name}</td> + <td>${repository_owner}</td><td>${changeset_revision}</td></tr> %endfor

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.