1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/fb3a05f1f28e/ changeset: fb3a05f1f28e user: greg date: 2013-02-28 17:06:10 summary: Add blank lines to the tool_shed repository controller per new dev team coding standards. affected #: 1 file

diff -r c494556d21a8c6bde808fccb8d584e8bb9f73662 -r fb3a05f1f28e0b0652065dc3c87155004e65f0b3 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 @@ -27,14 +27,21 @@ VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9_]+$" ) malicious_error = " This changeset cannot be downloaded because it potentially produces malicious behavior or contains inappropriate content." malicious_error_can_push = " Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content." - + + class CategoryGrid( grids.Grid ): + + class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name + + class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description + + class RepositoriesColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): if category.repositories: @@ -44,6 +51,7 @@ viewable_repositories += 1 return viewable_repositories return 0 + title = "Categories" model_class = model.Category template='/webapps/tool_shed/category/grid.mako' @@ -69,7 +77,10 @@ preserve_state = False use_paging = True

+ class ValidCategoryGrid( CategoryGrid ): + + class RepositoriesColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): if category.repositories: @@ -80,6 +91,7 @@ viewable_repositories += 1 return viewable_repositories return 0 + title = "Categories of valid repositories" model_class = model.Category template='/webapps/tool_shed/category/valid_grid.mako' @@ -106,13 +118,20 @@ preserve_state = False use_paging = True

+ class RepositoryGrid( grids.Grid ): + + class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return escape_html( repository.name ) + + class MetadataRevisionColumn( grids.GridColumn ): + def __init__( self, col_name ): grids.GridColumn.__init__( self, col_name ) + def get_value( self, trans, grid, repository ): """Display a SelectField whose options are the changeset_revision strings of all metadata revisions of this repository.""" # A repository's metadata revisions may not all be installable, as some may contain only invalid tools. @@ -122,16 +141,26 @@ elif len( select_field.options ) == 1: return select_field.options[ 0 ][ 0 ] return '' + + class TipRevisionColumn( grids.GridColumn ): + def __init__( self, col_name ): grids.GridColumn.__init__( self, col_name ) + def get_value( self, trans, grid, repository ): """Display the repository tip revision label.""" return escape_html( repository.revision( trans.app ) ) + + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): return escape_html( repository.description ) + + class CategoryColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): rval = '<ul>' if repository.categories: @@ -142,34 +171,49 @@ rval += '<li>not set</li>' rval += '</ul>' return rval + + class RepositoryCategoryColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): """Modify query to filter by category.""" if column_filter == "All": return query return query.filter( model.Category.name == column_filter ) + + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): if repository.user: return escape_html( repository.user.username ) return 'no user' + + class EmailColumn( grids.TextColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query return query.filter( and_( model.Repository.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter ) ) + + class EmailAlertsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): if trans.user and repository.email_alerts and trans.user.email in json.from_json_string( repository.email_alerts ): return 'yes' return '' + + class DeprecatedColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): if repository.deprecated: return 'yes' return '' - # Grid definition + title = "Repositories" model_class = model.Repository template='/webapps/tool_shed/repository/grid.mako' @@ -217,6 +261,7 @@ num_rows_per_page = 50 preserve_state = False use_paging = True + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, @@ -225,6 +270,7 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table )

+ class RepositoriesByUserGrid( RepositoryGrid ): title = "Repositories by user" columns = [ @@ -248,6 +294,7 @@ num_rows_per_page = 50 preserve_state = False use_paging = True + def build_initial_query( self, trans, **kwd ): decoded_user_id = trans.security.decode_id( kwd[ 'user_id' ] ) return trans.sa_session.query( model.Repository ) \ @@ -258,6 +305,7 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table )

+ class RepositoriesIOwnGrid( RepositoryGrid ): title = "Repositories I own" columns = [ @@ -287,6 +335,7 @@ allow_multiple=False, condition=( lambda item: not item.deleted and item.deprecated ), async_compatible=False ) ] + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, @@ -295,6 +344,7 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table )

+ class DeprecatedRepositoriesIOwnGrid( RepositoriesIOwnGrid ): title = "Deprecated repositories I own" columns = [ @@ -314,6 +364,7 @@ key="free-text-search", visible=False, filterable="standard" ) ) + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, @@ -323,6 +374,7 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table )

+ class EmailAlertsRepositoryGrid( RepositoryGrid ): columns = [ RepositoryGrid.NameColumn( "Name", @@ -352,6 +404,7 @@ grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) ) ]

+ class MyWritableRepositoriesGrid( RepositoryGrid ): # This grid filters out repositories that have been marked as either deprecated or deleted. columns = [ @@ -386,6 +439,7 @@ allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ) ] + def build_initial_query( self, trans, **kwd ): # TODO: improve performance by adding a db table associating users with repositories for which they have write access. username = trans.user.username @@ -408,8 +462,11 @@ return trans.sa_session.query( model.Repository ) \ .filter( model.Repository.table.c.id < 0 )

+ class ValidRepositoryGrid( RepositoryGrid ): # This grid filters out repositories that have been marked as either deleted or deprecated. + + class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): rval = '<ul>' @@ -421,15 +478,21 @@ rval += '<li>not set</li>' rval += '</ul>' return rval + + class RepositoryCategoryColumn( grids.GridColumn ): def filter( self, trans, user, query, column_filter ): """Modify query to filter by category.""" if column_filter == "All": return query return query.filter( model.Category.name == column_filter ) + + class RevisionColumn( grids.GridColumn ): + def __init__( self, col_name ): grids.GridColumn.__init__( self, col_name ) + def get_value( self, trans, grid, repository ): """Display a SelectField whose options are the changeset_revision strings of all download-able revisions of this repository.""" select_field = build_changeset_revision_select_field( trans, repository, downloadable=True ) @@ -462,6 +525,7 @@ visible=False, filterable="standard" ) ) operations = [] + def build_initial_query( self, trans, **kwd ): if 'id' in kwd: # The user is browsing categories of valid repositories, so filter the request by the received id, which is a category id. @@ -484,22 +548,36 @@ .outerjoin( model.Category.table ) \ .filter( model.RepositoryMetadata.table.c.downloadable == True )

+ class MatchedRepositoryGrid( grids.Grid ): # This grid filters out repositories that have been marked as deprecated. + + 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 = "Matching repositories" model_class = model.RepositoryMetadata @@ -524,6 +602,7 @@ 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 = [] @@ -545,6 +624,7 @@ return trans.sa_session.query( model.RepositoryMetadata ) \ .filter( model.RepositoryMetadata.id < 0 )

+ class InstallMatchedRepositoryGrid( MatchedRepositoryGrid ): columns = [ col for col in MatchedRepositoryGrid.columns ] # Override the NameColumn @@ -552,6 +632,7 @@ link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False )

+ class RepositoryController( BaseUIController, common_util.ItemRatings ):

install_matched_repository_grid = InstallMatchedRepositoryGrid() @@ -594,6 +675,7 @@ action='browse_repositories', **kwd ) ) return self.category_grid( trans, **kwd ) + @web.expose def browse_invalid_tools( self, trans, **kwd ): params = util.Params( kwd ) @@ -634,6 +716,7 @@ invalid_tools_dict=invalid_tools_dict, message=message, status=status ) + @web.expose def browse_repositories( self, trans, **kwd ): # 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 @@ -705,6 +788,7 @@ id=trans.security.encode_id( repository.id ), changeset_revision=selected_changeset_revision ) ) return self.repository_grid( trans, **kwd ) + @web.expose def browse_repositories_by_user( self, trans, **kwd ): """Display the list of repositories owned by a specified user.""" @@ -735,6 +819,7 @@ user = suc.get_user( trans, kwd[ 'user_id' ] ) self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username return self.repositories_by_user_grid( trans, **kwd ) + @web.expose def browse_repository( self, trans, id, **kwd ): params = util.Params( kwd ) @@ -754,6 +839,7 @@ is_malicious=is_malicious, message=message, status=status ) + @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. @@ -787,6 +873,7 @@ action='browse_valid_repositories', **kwd ) ) return self.valid_category_grid( trans, **kwd ) + @web.expose def browse_valid_repositories( self, trans, **kwd ): galaxy_url = kwd.get( 'galaxy_url', None ) @@ -832,6 +919,7 @@ allow_multiple=False, async_compatible=False ) ] return self.valid_repository_grid( trans, **kwd ) + def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): options = [] for user in trans.sa_session.query( trans.model.User ): @@ -844,6 +932,7 @@ selected_value=selected_value, refresh_on_change=False, multiple=True ) + def __change_repository_name_in_hgrc_file( self, hgrc_file, new_name ): config = ConfigParser.ConfigParser() config.read( hgrc_file ) @@ -852,6 +941,7 @@ new_file = open( hgrc_file, 'wb' ) config.write( new_file ) new_file.close() + @web.expose def check_for_updates( self, trans, **kwd ): """Handle a request from a local Galaxy instance.""" @@ -929,6 +1019,7 @@ url += str( latest_changeset_revision ) url += '&latest_ctx_rev=%s' % str( update_to_ctx.rev() ) return trans.response.send_redirect( url ) + @web.expose def contact_owner( self, trans, id, **kwd ): params = util.Params( kwd ) @@ -945,6 +1036,7 @@ else: # Do all we can to eliminate spam. return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) + def __create_hgrc_file( self, trans, repository ): # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path( trans.app ). # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. The hg @@ -962,6 +1054,7 @@ fp.write( '[extensions]\n' ) fp.write( 'hgext.purge=' ) fp.close() + @web.expose def create_repository( self, trans, **kwd ): params = util.Params( kwd ) @@ -1040,6 +1133,7 @@ categories=categories, message=message, status=status ) + @web.expose @web.require_login( "deprecate repository" ) def deprecate( self, trans, **kwd ): @@ -1061,6 +1155,7 @@ operation='repositories_i_own', message=message, status=status ) ) + @web.expose def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): params = util.Params( kwd ) @@ -1098,6 +1193,7 @@ changeset_revision=changeset_revision, message=message, status='error' ) ) + @web.expose def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. @@ -1118,6 +1214,7 @@ trans.sa_session.flush() download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str ) return trans.response.send_redirect( download_url ) + @web.expose def find_tools( self, trans, **kwd ): params = util.Params( kwd ) @@ -1204,6 +1301,7 @@ exact_matches_check_box=exact_matches_check_box, message=message, status=status ) + @web.expose def find_workflows( self, trans, **kwd ): params = util.Params( kwd ) @@ -1291,10 +1389,12 @@ exact_matches_check_box=exact_matches_check_box, message=message, status=status ) + @web.expose def generate_workflow_image( self, trans, workflow_name, repository_metadata_id=None ): """Return an svg image representation of a workflow dictionary created when the workflow was exported.""" return workflow_util.generate_workflow_image( trans, workflow_name, repository_metadata_id=repository_metadata_id, repository_id=None ) + @web.expose def get_changeset_revision_and_ctx_rev( self, trans, **kwd ): """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated.""" @@ -1392,6 +1492,7 @@ update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) return encoding_util.tool_shed_encode( update_dict ) + @web.expose def get_ctx_rev( self, trans, **kwd ): """Given a repository and changeset_revision, return the correct ctx.rev() value.""" @@ -1405,12 +1506,14 @@ if ctx: return str( ctx.rev() ) return '' + @web.json def get_file_contents( self, trans, file_path ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' return suc.get_repository_file_contents( file_path ) + def get_file_from_changeset_revision( self, repo_files_dir, changeset_revision, file_name, dir ): """Return file_name from the received changeset_revision of the repository manifest.""" stripped_file_name = suc.strip_path( file_name ) @@ -1418,11 +1521,13 @@ ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) named_tmp_file = suc.get_named_tmpfile_from_ctx( ctx, file_name, dir ) return named_tmp_file + def get_metadata( self, trans, repository_id, changeset_revision ): repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata and repository_metadata.metadata: return repository_metadata.metadata return None + @web.json def get_readme_files( self, trans, **kwd ): """ @@ -1435,6 +1540,7 @@ repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) return suc.build_readme_files_dict( repository_metadata.metadata ) + @web.json def get_repository_dependencies( self, trans, **kwd ): """Return an encoded dictionary of all repositories upon which the contents of the received repository depends.""" @@ -1459,6 +1565,7 @@ if repository_dependencies: return encoding_util.tool_shed_encode( repository_dependencies ) return '' + def __get_repository_from_refresh_on_change( self, trans, **kwd ): # The changeset_revision_select_field in several grids performs a refresh_on_change which sends in request parameters like # changeset_revison_1, changeset_revision_2, etc. One of the many select fields on the grid performed the refresh_on_change, @@ -1474,6 +1581,7 @@ return v, repository # This should never be reached - raise an exception? return v, None + @web.json def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ): """ @@ -1517,6 +1625,7 @@ has_repository_dependencies=has_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts ) + @web.json def get_required_repo_info_dict( self, trans, encoded_str ): """ @@ -1540,6 +1649,7 @@ else: repo_info_dict = {} return repo_info_dict + @web.expose def get_tool_dependencies( self, trans, **kwd ): """Handle a request from a Galaxy instance to get the tool_dependencies entry from the metadata for a specified changeset revision.""" @@ -1556,6 +1666,7 @@ if tool_dependencies: return encoding_util.tool_shed_encode( tool_dependencies ) return '' + @web.expose def get_tool_dependencies_config_contents( self, trans, **kwd ): """Handle a request from a Galaxy instance to get the tool_dependencies.xml file contents for a specified changeset revision.""" @@ -1576,6 +1687,7 @@ tool_dependencies_config_file.close() return contents return '' + @web.expose def get_tool_versions( self, trans, **kwd ): """ @@ -1599,6 +1711,7 @@ if tool_version_dicts: return json.to_json_string( tool_version_dicts ) return '' + @web.json def get_updated_repository_information( self, trans, name, owner, changeset_revision, **kwd ): """Generate a dictionary that contains the information about a repository that is necessary for installing it into a local Galaxy instance.""" @@ -1655,6 +1768,7 @@ includes_workflows=includes_workflows, readme_files_dict=readme_files_dict, repo_info_dict=repo_info_dict ) + def get_versions_of_tool( self, trans, repository, repository_metadata, guid ): """Return the tool lineage in descendant order for the received guid contained in the received repsitory_metadata.tool_versions.""" encoded_id = trans.security.encode_id( repository.id ) @@ -1685,12 +1799,14 @@ current_parent_guid = child_guid break return tool_guid_lineage + @web.expose def help( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd ) + 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: @@ -1732,10 +1848,12 @@ tool_dict_tool_name.find( tool_name ) >= 0 and \ tool_dict_tool_id.find( tool_id ) >= 0 ) return found + def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ): workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() return ( workflow_name == workflow_dict_workflow_name ) or \ ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) + @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) @@ -1771,6 +1889,7 @@ changeset_revision=changeset_revision, message=message, status=status ) + @web.expose def install_repositories_by_revision( self, trans, **kwd ): """ @@ -1793,6 +1912,7 @@ 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) return trans.response.send_redirect( url ) + @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): params = util.Params( kwd ) @@ -1837,6 +1957,7 @@ changeset_revision=changeset_revision, message=message, status='error' ) ) + def __make_same_length( self, list1, list2 ): # If either list is 1 item, we'll append to it until its length is the same as the other. if len( list1 ) == 1: @@ -1846,6 +1967,7 @@ for i in range( 1, len( list1 ) ): list2.append( list2[ 0 ] ) return list1, list2 + @web.expose @web.require_login( "manage email alerts" ) def manage_email_alerts( self, trans, **kwd ): @@ -1877,6 +1999,7 @@ email_alert_repositories=email_alert_repositories, message=message, status=status ) + @web.expose @web.require_login( "manage repository" ) def manage_repository( self, trans, id, **kwd ): @@ -2083,12 +2206,14 @@ can_browse_repository_reviews=can_browse_repository_reviews, message=message, status=status ) + @web.expose @web.require_login( "review repository revision" ) def manage_repository_reviews_of_revision( self, trans, **kwd ): return trans.response.send_redirect( web.url_for( controller='repository_review', action='manage_repository_reviews_of_revision', **kwd ) ) + @web.expose @web.require_login( "multi select email alerts" ) def multi_select_email_alerts( self, trans, **kwd ): @@ -2110,6 +2235,7 @@ del kwd[ 'operation' ] self.email_alerts_repository_grid.title = "Set email alerts for repository changes" return self.email_alerts_repository_grid( trans, **kwd ) + def __new_state( self, trans, all_pages=False ): """ Create a new `DefaultToolState` for this tool. It will not be initialized @@ -2121,12 +2247,14 @@ state = galaxy.tools.DefaultToolState() state.inputs = {} return state + @web.json def open_folder( self, trans, folder_path ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' return suc.open_repository_files_folder( trans, folder_path ) + @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) @@ -2173,6 +2301,7 @@ metadata=metadata, message=message, status=status ) + @web.expose def previous_changeset_revisions( self, trans, **kwd ): """ @@ -2201,6 +2330,7 @@ changeset_hashes_str = ','.join( changeset_hashes ) return changeset_hashes_str return '' + @web.expose @web.require_login( "rate repositories" ) def rate_repository( self, trans, **kwd ): @@ -2240,6 +2370,7 @@ is_malicious=is_malicious, message=message, status=status ) + @web.expose def reset_all_metadata( self, trans, id, **kwd ): # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. @@ -2257,24 +2388,28 @@ id=id, message=message, status=status ) ) + def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, 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 ) ) return match_tuples + def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, 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 ) ) return match_tuples + def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): for i, tool_name in enumerate( tool_names ): tool_version = tool_versions[ i ] if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return match_tuples + def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): match_tuples = [] ok = True @@ -2346,6 +2481,7 @@ elif all_workflows and 'workflows' in metadata: match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return ok, match_tuples + @web.expose def select_files_to_delete( self, trans, id, **kwd ): params = util.Params( kwd ) @@ -2412,6 +2548,7 @@ is_malicious=is_malicious, message=message, status=status ) + @web.expose def send_to_owner( self, trans, id, message='' ): repository = suc.get_repository_in_tool_shed( trans, id ) @@ -2450,6 +2587,7 @@ id=id, message=message, status=status ) ) + @web.expose @web.require_login( "set email alerts" ) def set_email_alerts( self, trans, **kwd ): @@ -2490,6 +2628,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action=caller, **kwd ) ) + @web.expose @web.require_login( "set repository as malicious" ) def set_malicious( self, trans, id, ctx_str, **kwd ): @@ -2512,6 +2651,7 @@ malicious=malicious, message=message, status=status ) ) + @web.expose def sharable_owner( self, trans, owner ): """Support for sharable URL for each repository owner's tools, e.g. http://example.org/view/owner.""" @@ -2527,6 +2667,7 @@ else: return trans.show_error_message( "The tool shed <b>%s</b> contains no repositories owned by <b>%s</b>." % \ ( web.url_for( '/', qualified=True ).rstrip( '/' ), str( owner ) ) ) + @web.expose def sharable_repository( self, trans, owner, name ): """Support for sharable URL for a specified repository, e.g. http://example.org/view/owner/name.""" @@ -2556,6 +2697,7 @@ else: return trans.show_error_message( "The tool shed <b>%s</b> contains no repositories named <b>%s</b> with owner <b>%s</b>." % \ ( web.url_for( '/', qualified=True ).rstrip( '/' ), str( name ), str( owner ) ) ) + @web.expose def sharable_repository_revision( self, trans, owner, name, changeset_revision ): """Support for sharable URL for a specified repository revision, e.g. http://example.org/view/owner/name/changeset_revision.""" @@ -2592,10 +2734,12 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='sharable_owner', owner=owner ) ) + def __stringify( self, list ): if list: return ','.join( list ) return '' + @web.expose def updated_changeset_revisions( self, trans, **kwd ): """ @@ -2625,6 +2769,7 @@ changeset_hashes_str = ','.join( changeset_hashes ) return changeset_hashes_str return '' + def __validate_repository_name( self, name, user ): # Repository names must be unique for each user, must be at least four characters # in length and must contain only lower-case letters, numbers, and the '_' character. @@ -2642,6 +2787,7 @@ if not( VALID_REPOSITORYNAME_RE.match( name ) ): return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>." return '' + @web.expose def view_changelog( self, trans, id, **kwd ): params = util.Params( kwd ) @@ -2679,6 +2825,7 @@ is_malicious=is_malicious, message=message, status=status ) + @web.expose def view_changeset( self, trans, id, ctx_str, **kwd ): params = util.Params( kwd ) @@ -2719,6 +2866,7 @@ is_malicious=is_malicious, message=message, status=status ) + @web.expose def view_or_manage_repository( self, trans, **kwd ): repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) @@ -2730,6 +2878,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', **kwd ) ) + @web.expose def view_repository( self, trans, id, **kwd ): params = util.Params( kwd ) @@ -2829,6 +2978,7 @@ can_browse_repository_reviews=can_browse_repository_reviews, message=message, status=status ) + @web.expose def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ): params = util.Params( kwd ) @@ -2907,6 +3057,7 @@ review_id=review_id, message=message, status=status ) + @web.expose def view_workflow( self, trans, workflow_name, repository_metadata_id, **kwd ): """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image.""" @@ -2927,6 +3078,7 @@ metadata=metadata, message=message, status=status ) + # ----- Utility methods -----

def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True,

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

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