1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/7d9bb95caaa7/ changeset: 7d9bb95caaa7 user: greg date: 2011-10-14 21:20:12 summary: Enhance tool searching in tool shed repositories to enable multiple values in any of tool_id, tool_name, tool_version. In the tool shed search form, taking advantage of this feature requires comma-separated lists to be entered in the form fields. affected #: 3 files (-1 bytes)

--- a/lib/galaxy/web/controllers/workflow.py Fri Oct 14 15:12:45 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Fri Oct 14 15:20:12 2011 -0400 @@ -1157,14 +1157,15 @@ galaxy_url = trans.request.host message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" - for missing_tool_tup in missing_tool_tups: - missing_tool_id = missing_tool_tup[0] - for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): - if tool_shed_url.endswith( '/' ): - tool_shed_url = tool_shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?tool_id=%s&galaxy_url=%s&webapp=community' % ( tool_shed_url, missing_tool_id, galaxy_url ) - message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name ) - status = 'error' + for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if tool_shed_url.endswith( '/' ): + tool_shed_url = tool_shed_url.rstrip( '/' ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) + for missing_tool_tup in missing_tool_tups: + missing_tool_id = missing_tool_tup[0] + url += '&tool_id=%s' % missing_tool_id + message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name ) + status = 'error' return trans.response.send_redirect( web.url_for( controller='admin', action='index', webapp='galaxy',

--- a/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 15:12:45 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 15:20:12 2011 -0400 @@ -280,8 +280,18 @@ .join( model.User.table ) \ .filter( self.model_class.table.c.repository_id == 0 )

+class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ): + # Grid definition + title = "Repositories with required tools" + operations = [ grids.GridOperation( "Preview and install tools", + url_args = dict( action='find_tools', + operation='install_tools' ), + allow_multiple=True, + async_compatible=False ) ] + class RepositoryController( BaseUIController, ItemRatings ):

+ install_matched_repository_list_grid = InstallMatchedRepositoryListGrid() matched_repository_list_grid = MatchedRepositoryListGrid() downloadable_repository_list_grid = DownloadableRepositoryListGrid() repository_list_grid = RepositoryListGrid() @@ -366,11 +376,18 @@ url_args=url_args, allow_multiple=False, async_compatible=False ) ] - # Render the list view return self.downloadable_repository_list_grid( trans, **kwd ) @web.expose def find_tools( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # Set the toolshedgalaxyurl cookie so we can get back + # to the calling local Galaxy instance. + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "view_or_manage_repository": @@ -389,61 +406,98 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', **kwd ) ) - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # Set the toolshedgalaxyurl cookie so we can get back - # to the calling local Galaxy instance. - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) - tool_id = kwd.get( 'tool_id', '' ).lower() - tool_name = kwd.get( 'tool_name', '' ).lower() - tool_version = kwd.get( 'tool_version', '' ).lower() + if operation == "preview and install tools": + pass + tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ] + tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ] + tool_versions = [ tv.lower() for tv in util.listify( kwd.get( 'tool_version', '' ) ) ] exact_matches = params.get( 'exact_matches', '' ) exact_matches_checked = CheckboxField.is_checked( exact_matches ) match_tuples = [] - if tool_id or tool_name or tool_version: + ok = True + if tool_ids or tool_names or tool_versions: for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): metadata = repository_metadata.metadata tools = metadata[ 'tools' ] - found = False for tool_dict in tools: - if tool_id and not tool_name and not tool_version: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - found = ( tool_id == tool_dict_tool_id ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 ) - elif tool_name and not tool_id and not tool_version: - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 ) - elif tool_version and not tool_id and not tool_name: - tool_dict_tool_version = tool_dict[ 'version' ].lower() - found = ( tool_version == tool_dict_tool_version ) or \ - ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 ) - elif tool_id and tool_name and not tool_version: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) - elif tool_id and tool_version and not tool_name: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - tool_dict_tool_version = tool_dict[ 'version' ].lower() - found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 ) - elif tool_version and tool_name and not tool_id: - tool_dict_tool_version = tool_dict[ 'version' ].lower() - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) - if found: - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - kwd[ 'match_tuples' ] = match_tuples - kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( tool_id, tool_name, tool_version, str( exact_matches_checked ) ) - # Render the list view - return self.matched_repository_list_grid( trans, **kwd ) + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + for i, tool_id in enumerate( tool_ids ): + tool_name = tool_names[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + for i, tool_id in enumerate( tool_ids ): + tool_version = tool_versions[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + ok = False + if ok: + kwd[ 'match_tuples' ] = match_tuples + # Render the list view + if galaxy_url: + # Our request originated from a Galaxy instance, so we're listing tools + # that have been found for a workflow in Galaxy. + return self.install_matched_repository_list_grid( trans, **kwd ) + else: + if tool_ids: + tool_id_str = ','.join( tool_ids ) + else: + tool_id_str = '' + if tool_names: + tool_name_str = ','.join( tool_names ) + else: + tool_name_str = '' + if tool_versions: + tool_version_str = ','.join( tool_versions ) + else: + tool_version_str = '' + kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ + ( tool_id_str, tool_name_str, tool_version_str, str( exact_matches_checked ) ) + return self.matched_repository_list_grid( trans, **kwd ) exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + if tool_ids: + tool_id = ','.join( tool_ids ) + else: + tool_id = '' + if tool_names: + tool_name = ','.join( tool_names ) + else: + tool_name = '' + if tool_versions: + tool_version = ','.join( tool_versions ) + else: + tool_version = '' return trans.fill_template( '/webapps/community/repository/find_tools.mako', tool_id=tool_id, tool_name=tool_name, @@ -451,6 +505,36 @@ exact_matches_check_box=exact_matches_check_box, message=message, status=status ) + def _in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): + found = False + if tool_id and not tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 ) + elif tool_name and not tool_id and not tool_version: + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_version and not tool_id and not tool_name: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_id and tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_id and tool_version and not tool_name: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_version and tool_name and not tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + return found @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd )

--- a/templates/webapps/community/repository/find_tools.mako Fri Oct 14 15:12:45 2011 -0400 +++ b/templates/webapps/community/repository/find_tools.mako Fri Oct 14 15:20:12 2011 -0400 @@ -19,6 +19,8 @@ <div class="toolFormBody"><div class="form-row"> Valid tools are those that properly load in Galaxy. Enter any combination of the following tool attributes to locate matching valid tools. + Comma-separated strings may be entered in each field to expand search criteria. Each field must contain the same number of comma-separated + strings if these types of strings are entered in more than one field. </div><div style="clear: both"></div><form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" >

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

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