1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/7fe346183e46/ changeset: 7fe346183e46 user: greg date: 2011-10-13 20:47:13 summary: Add the ability to search for tools within tool shed repositories by any combination of tool id, name and version (exact or partial matches). affected #: 4 files (-1 bytes)

--- a/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 10:59:14 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 14:47:13 2011 -0400 @@ -189,7 +189,7 @@ def get_value( self, trans, grid, repository ): """ Display a SelectField whose options are the changeset_revision - strings of all downloadable_revisions of this repository. + strings of all download-able revisions of this repository. """ select_field = build_changeset_revision_select_field( trans, repository ) if len( select_field.options ) > 1: @@ -220,8 +220,75 @@ .join( model.RepositoryMetadata.table ) \ .join( model.User.table )

+class MatchedRepositoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.description + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.changeset_revision + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.user: + return repository_metadata.repository.user.username + return 'no user' + # Grid definition + title = "Matched repositories" + model_class = model.RepositoryMetadata + template='/webapps/community/repository/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.repository.id, + webapp="community" ) ), + attach_popup=True ), + DescriptionColumn( "Synopsis", + key="description", + attach_popup=False ), + RevisionColumn( "Revision" ), + UserColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ) + ] + operations = [] + standard_filters = [] + default_filter = {} + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + match_tuples = kwd.get( 'match_tuples', [] ) + clause_list = [] + if match_tuples: + for match_tuple in match_tuples: + repository_id, changeset_revision = match_tuple + clause_list.append( "%s=%d and %s='%s'" % ( self.model_class.table.c.repository_id, + int( repository_id ), + self.model_class.table.c.changeset_revision, + changeset_revision ) ) + q = trans.sa_session.query( self.model_class ) \ + .join( model.Repository ) \ + .join( model.User.table ) \ + .filter( or_( *clause_list ) ) + return trans.sa_session.query( self.model_class ) \ + .join( model.Repository ) \ + .join( model.User.table ) \ + .filter( or_( *clause_list ) ) + # Return an empty query + return trans.sa_session.query( self.model_class ) \ + .join( model.Repository ) \ + .join( model.User.table ) \ + .filter( self.model_class.table.c.repository_id == 0 ) + class RepositoryController( BaseUIController, ItemRatings ):

+ matched_repository_list_grid = MatchedRepositoryListGrid() downloadable_repository_list_grid = DownloadableRepositoryListGrid() repository_list_grid = RepositoryListGrid() category_list_grid = CategoryListGrid() @@ -304,6 +371,76 @@ # Render the list view return self.downloadable_repository_list_grid( trans, **kwd ) @web.expose + def find_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + **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() + 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: + for repository_metadata in trans.sa_session.query( model.RepositoryMetadata.table ).all(): + 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 ) + exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + return trans.fill_template( '/webapps/community/repository/find_tools.mako', + tool_id=tool_id, + tool_name=tool_name, + tool_version=tool_version, + exact_matches_check_box=exact_matches_check_box, + message=message, + status=status ) + @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) )

--- a/templates/webapps/community/admin/center.mako Thu Oct 13 10:59:14 2011 -0400 +++ b/templates/webapps/community/admin/center.mako Thu Oct 13 14:47:13 2011 -0400 @@ -1,7 +1,13 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +

<%def name="title()">Galaxy Administration</%def>

+%if message: + ${render_msg( message, status )} +%endif + <h2>Administration</h2><p>The menu on the left provides the following features</p>

--- a/templates/webapps/community/index.mako Thu Oct 13 10:59:14 2011 -0400 +++ b/templates/webapps/community/index.mako Thu Oct 13 14:47:13 2011 -0400 @@ -61,6 +61,9 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a></div> %endif + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for tools</a> + </div></div></div><div class="toolSectionBody">

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

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