1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/c7c8316a1d13/ changeset: c7c8316a1d13 user: greg date: 2013-03-01 22:08:25 summary: Implement more granular grids for valid Galaxy utilities in the tool shed - custom datatypes, tools, tool dependencies and repository dependencies are now accessible. affected #: 2 files

diff -r 513adadb31a2a4b014b3f03c5af2817919ea1760 -r c7c8316a1d134a19e929a2257a701ec1ebc3a33a lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -646,13 +646,15 @@ class RepositoryNameColumn( grids.TextColumn ):

def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.repository.name ) + repository = repository_metadata.repository + return escape_html( repository.name )

class RepositoryOwnerColumn( grids.TextColumn ):

def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.user.username ) + repository = repository_metadata.repository + return escape_html( repository.user.username )

class ChangesetRevisionColumn( grids.TextColumn ): @@ -763,18 +765,53 @@

class RepositoryDependenciesGrid( RepositoryMetadataGrid ): - - title = "Repository dependencies available in this Tool Shed" + + + class RequiredRepositoryColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + rd_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + rd_dict = metadata.get( 'repository_dependencies', {} ) + if rd_dict: + rd_tups = rd_dict[ 'repository_dependencies' ] + # "repository_dependencies": [["http://localhost:9009", "bwa059", "test", "a07baa797d53"]] + # Sort rd_tups by by required repository name. + sorted_rd_tups = sorted( rd_tups, key=lambda rd_tup: rd_tup[ 1 ] ) + num_tups = len( sorted_rd_tups ) + for index, rd_tup in enumerate( sorted_rd_tups ): + name = rd_tup[ 1 ] + owner = rd_tup[ 2 ] + required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + if required_repository: + required_repository_id = trans.security.encode_id( required_repository.id ) + rd_str += '<a href="browse_repository_dependencies?operation=browse_repository&id=%s">' % required_repository_id + rd_str += '<b>name:</b> %s | <b>owner:</b> %s | <b>revision:</b> %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) ) + if required_repository: + rd_str += '</a>' + if index < num_tups - 1: + rd_str += '<br/>' + return rd_str + + title = "Repository dependency definitions in this tool shed" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), + model_class=model.Repository, + link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", model_class=model.User, attach_popup=False, - key="User.username" ) + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + RequiredRepositoryColumn( "Repository dependency", + attach_popup=False ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, @@ -790,9 +827,190 @@ .order_by( model.Repository.name )

+class ToolDependenciesGrid( RepositoryMetadataGrid ): + + + class ToolDependencyColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + td_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tds_dict = metadata.get( 'tool_dependencies', {} ) + if tds_dict: + # Example: {"bwa/0.5.9": {"name": "bwa", "type": "package", "version": "0.5.9"}} + sorted_keys = sorted( [ k for k in tds_dict.keys() ] ) + num_keys = len( sorted_keys ) + # Handle environment settings first. + if 'set_environment' in sorted_keys: + # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}] + env_dicts = tds_dict[ 'set_environment' ] + num_env_dicts = len( env_dicts ) + td_str += '<b>environment:</b> ' + for index, env_dict in enumerate( env_dicts ): + td_str += '%s' % escape_html( env_dict[ 'name' ] ) + if index < num_env_dicts - 1: + td_str += ', ' + td_str += '<br/>' + for index, key in enumerate( sorted_keys ): + if key == 'set_environment': + continue + td_dict = tds_dict[ key ] + # Example: {"name": "bwa", "type": "package", "version": "0.5.9"} + name = td_dict[ 'name' ] + type = td_dict[ 'type' ] + version = td_dict[ 'version' ] + td_str += '<b>%s</b> version <b>%s</b>' % ( escape_html( name ), escape_html( version ) ) + if index < num_keys - 1: + td_str += '<br/>' + return td_str + + title = "Tool dependency definitions in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + ToolDependencyColumn( "Tool dependency", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + + +class ToolsGrid( RepositoryMetadataGrid ): + + + class ToolsColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + tool_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tool_dicts = metadata.get( 'tools', [] ) + if tool_dicts: + num_tool_dicts = len( tool_dicts ) + for index, tool_dict in enumerate( tool_dicts ): + tool_id = tool_dict[ 'id' ] + name = tool_dict[ 'name' ] + version = tool_dict[ 'version' ] + tool_str += '<b>%s</b> | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) ) + if index < num_tool_dicts - 1: + tool_str += '<br/>' + return tool_str + + title = "Valid tools in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + ToolsColumn( "Tool id | name | version", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + + +class DatatypesGrid( RepositoryMetadataGrid ): + + + class DatatypesColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + datatype_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + datatype_dicts = metadata.get( 'datatypes', [] ) + if datatype_dicts: + num_datatype_dicts = len( datatype_dicts ) + for index, datatype_dict in enumerate( datatype_dicts ): + # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} + extension = datatype_dict[ 'extension' ] + dtype = datatype_dict[ 'dtype' ] + mimetype = datatype_dict[ 'mimetype' ] + display_in_upload = datatype_dict.get( 'display_in_upload', False ) + datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) + if index < num_datatype_dicts - 1: + datatype_str += '<br/>' + return datatype_str + + title = "Custom datatypes in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + DatatypesColumn( "Datatype extension | Type | Mimetype", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + class RepositoryController( BaseUIController, common_util.ItemRatings ):

category_grid = CategoryGrid() + datatypes_grid = DatatypesGrid() deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid() email_alerts_repository_grid = EmailAlertsRepositoryGrid() install_matched_repository_grid = InstallMatchedRepositoryGrid() @@ -800,9 +1018,12 @@ my_writable_repositories_grid = MyWritableRepositoriesGrid() repositories_by_user_grid = RepositoriesByUserGrid() repositories_i_own_grid = RepositoriesIOwnGrid() + repository_dependencies_grid = RepositoryDependenciesGrid() repository_grid = RepositoryGrid() # The repository_metadata_grid is not currently displayed, but is sub-classed by several grids. repository_metadata_grid = RepositoryMetadataGrid() + tool_dependencies_grid = ToolDependenciesGrid() + tools_grid = ToolsGrid() valid_category_grid = ValidCategoryGrid() valid_repository_grid = ValidRepositoryGrid()

@@ -824,7 +1045,7 @@ pass return self.browse_repositories( trans, **kwd ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation in [ "repositories_by_category", "repositories_by_user" ]: # Eliminate the current filters if any exist. for k, v in kwd.items(): @@ -836,6 +1057,16 @@ return self.category_grid( trans, **kwd )

@web.expose + def browse_datatypes( 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='view_or_manage_repository', + **kwd ) ) + return self.datatypes_grid( trans, **kwd ) + + @web.expose def browse_invalid_tools( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -881,7 +1112,7 @@ # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search # link. We have to take this approach because the "-" character is illegal in HTTP requests. if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', @@ -1000,6 +1231,40 @@ status=status )

@web.expose + def browse_repository_dependencies( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "browse_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + **kwd ) ) + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + return self.repository_dependencies_grid( trans, **kwd ) + + @web.expose + def browse_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='view_or_manage_repository', + **kwd ) ) + return self.tools_grid( trans, **kwd ) + + @web.expose + def browse_tool_dependencies( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "browse_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + **kwd ) ) + return self.tool_dependencies_grid( trans, **kwd ) + + @web.expose def browse_valid_categories( self, trans, **kwd ): # The request came from Galaxy, so restrict category links to display only valid repository changeset revisions. galaxy_url = kwd.get( 'galaxy_url', None ) @@ -1022,7 +1287,7 @@ pass return self.browse_valid_repositories( trans, **kwd ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation in [ "valid_repositories_by_category", "valid_repositories_by_user" ]: # Eliminate the current filters if any exist. for k, v in kwd.items(): @@ -2420,7 +2685,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation == "receive email alerts": if trans.user: if kwd[ 'id' ]:

diff -r 513adadb31a2a4b014b3f03c5af2817919ea1760 -r c7c8316a1d134a19e929a2257a701ec1ebc3a33a templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -67,6 +67,22 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + Valid Galaxy Utilities + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_tools' )}">Tools</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_datatypes' )}">Custom datatypes</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repository_dependencies' )}">Repository dependency definitions</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_tool_dependencies' )}">Tool dependency definitions</a> + </div> %endif <div class="toolSectionPad"></div><div class="toolSectionTitle">

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

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