1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8059779d2a6c/ Changeset: 8059779d2a6c User: greg Date: 2013-07-25 17:01:18 Summary: A bit of refactoring of the tool shed's repository controller. Affected #: 6 files
diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 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 @@ -1,7 +1,5 @@ -import ConfigParser import logging import os -import re import string import tempfile from time import gmtime @@ -11,22 +9,21 @@ from galaxy import util from galaxy import web from galaxy.util.odict import odict -from galaxy.util.expressions import ExpressionContext from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import CheckboxField -from galaxy.web.form_builder import build_select_field from galaxy.webapps.tool_shed import model from galaxy.webapps.tool_shed.model import directory_hash_id from galaxy.web.framework.helpers import grids from galaxy.util import json from galaxy.model.orm import and_ -from galaxy.model.orm import or_ import tool_shed.util.shed_util_common as suc from tool_shed.util import encoding_util from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_dependency_util +from tool_shed.util import repository_maintenance_util from tool_shed.util import review_util +from tool_shed.util import search_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import workflow_util @@ -48,7 +45,6 @@
log = logging.getLogger( __name__ )
-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."
@@ -142,7 +138,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', **kwd ) ) - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -168,7 +164,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='deprecate', **kwd ) ) - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -390,7 +386,7 @@ kwd[ 'message' ] = 'You must be logged in to set email alerts.' kwd[ 'status' ] = 'error' del kwd[ 'operation' ] - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -421,7 +417,7 @@ kwd[ 'user_id' ] = trans.security.encode_id( repository.user.id ) else: # The user selected a repository revision which results in a refresh_on_change. - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', @@ -449,7 +445,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='deprecate', **kwd ) ) - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -478,7 +474,7 @@ self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username kwd[ 'user_id' ] = user_id return self.repositories_by_user_grid( trans, **kwd ) - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: # The user selected a repository revision which results in a refresh_on_change. return trans.response.send_redirect( web.url_for( controller='repository', @@ -796,7 +792,7 @@ category_id = kwd.get( 'id', None ) category = suc.get_category( trans, category_id ) kwd[ 'f-Category.name' ] = category.name - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', @@ -811,28 +807,6 @@ 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 ): - if user.username not in current_push_list: - options.append( user ) - return build_select_field( trans, - objs=options, - label_attr='username', - select_field_name='allow_push', - 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 ) - config.read( hgrc_file ) - config.set( 'web', 'name', new_name ) - 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.""" @@ -929,24 +903,6 @@ # 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 - # purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll remove unknown files - # and empty directories. This is not currently used because it is not supported in the mercurial API. - repo = hg.repository( suc.get_configured_ui(), path=repository.repo_path( trans.app ) ) - fp = repo.opener( 'hgrc', 'wb' ) - fp.write( '[paths]\n' ) - fp.write( 'default = .\n' ) - fp.write( 'default-push = .\n' ) - fp.write( '[web]\n' ) - fp.write( 'allow_push = %s\n' % repository.user.username ) - fp.write( 'name = %s\n' % repository.name ) - fp.write( 'push_ssl = false\n' ) - fp.write( '[extensions]\n' ) - fp.write( 'hgext.purge=' ) - fp.close() - @web.expose def create_repository( self, trans, **kwd ): message = kwd.get( 'message', '' ) @@ -968,7 +924,7 @@ repository_type = kwd.get( 'repository_type', rt_util.UNRESTRICTED ) if kwd.get( 'create_repository_button', False ): error = False - message = self.__validate_repository_name( name, trans.user ) + message = repository_maintenance_util.validate_repository_name( name, trans.user ) if message: error = True if not description: @@ -1002,7 +958,7 @@ lhs = "repos/%s/%s" % ( repository.user.username, repository.name ) trans.app.hgweb_config_manager.add_entry( lhs, repository_path ) # Create a .hg/hgrc file for the local repository - self.__create_hgrc_file( trans, repository ) + repository_maintenance_util.create_hgrc_file( trans, repository ) flush_needed = False if category_ids: # Create category associations @@ -1061,7 +1017,7 @@ repository, tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) if message: status = 'error' - tool_state = self.__new_state( trans, tool, invalid=False ) + tool_state = tool_util.new_state( trans, tool, invalid=False ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) try: return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", @@ -1176,7 +1132,11 @@ match_tuples = [] ok = True if tool_ids or tool_names or tool_versions: - ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions ) + ok, match_tuples = search_util.search_repository_metadata( trans, + exact_matches_checked, + tool_ids=tool_ids, + tool_names=tool_names, + tool_versions=tool_versions ) if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view @@ -1195,7 +1155,7 @@ return self.install_matched_repository_grid( trans, **kwd ) else: 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>" % \ - ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) ) + ( common_util.stringify( tool_ids ), common_util.stringify( tool_names ), common_util.stringify( tool_versions ), str( exact_matches_checked ) ) self.matched_repository_grid.title = "Repositories with matching tools" return self.matched_repository_grid( trans, **kwd ) else: @@ -1203,9 +1163,9 @@ status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/tool_shed/repository/find_tools.mako', - tool_id=self.__stringify( tool_ids ), - tool_name=self.__stringify( tool_names ), - tool_version=self.__stringify( tool_versions ), + tool_id=common_util.stringify( tool_ids ), + tool_name=common_util.stringify( tool_names ), + tool_version=common_util.stringify( tool_versions ), exact_matches_check_box=exact_matches_check_box, message=message, status=status ) @@ -1259,9 +1219,9 @@ match_tuples = [] ok = True if workflow_names: - ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) + ok, match_tuples = search_util.search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) else: - ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) + ok, match_tuples = search_util.search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) if ok: kwd[ 'match_tuples' ] = match_tuples if trans.webapp.name == 'galaxy': @@ -1279,7 +1239,7 @@ return self.install_matched_repository_grid( trans, **kwd ) else: kwd[ 'message' ] = "workflow name: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( self.__stringify( workflow_names ), str( exact_matches_checked ) ) + ( common_util.stringify( workflow_names ), str( exact_matches_checked ) ) self.matched_repository_grid.title = "Repositories with matching workflows" return self.matched_repository_grid( trans, **kwd ) else: @@ -1290,7 +1250,7 @@ workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/tool_shed/repository/find_workflows.mako', - workflow_name=self.__stringify( workflow_names ), + workflow_name=common_util.stringify( workflow_names ), exact_matches_check_box=exact_matches_check_box, message=message, status=status ) @@ -1559,23 +1519,6 @@ 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, - # so we loop through all of the received values to see which value is not the repository tip. If we find it, we know the - # refresh_on_change occurred and we have the necessary repository id and change set revision to pass on. - repository_id = None - v = None - for k, v in kwd.items(): - changeset_revision_str = 'changeset_revision_' - if k.startswith( changeset_revision_str ): - repository_id = trans.security.encode_id( int( k.lstrip( changeset_revision_str ) ) ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) - if repository.tip( trans.app ) != v: - 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 ): """ @@ -1792,53 +1735,6 @@ status = kwd.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: - 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 ) - elif tool_version and tool_name and tool_id: - tool_dict_tool_version = tool_dict[ 'version' ].lower() - tool_dict_tool_name = tool_dict[ 'name' ].lower() - tool_dict_tool_id = tool_dict[ 'id' ].lower() - found = ( tool_version == tool_dict_tool_version and \ - tool_name == tool_dict_tool_name and \ - tool_id == tool_dict_tool_id ) or \ - ( not exact_matches_checked and \ - tool_dict_tool_version.find( tool_version ) >= 0 and \ - 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 ): message = kwd.get( 'message', '' ) @@ -1908,7 +1804,7 @@ status = kwd.get( 'status', 'error' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) - tool_state = self.__new_state( trans, tool, invalid=True ) + tool_state = tool_util.new_state( trans, tool, invalid=True ) invalid_file_tups = [] if tool: invalid_file_tups = tool_util.check_tool_input_params( trans.app, @@ -1946,16 +1842,6 @@ 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: - for i in range( 1, len( list2 ) ): - list1.append( list1[ 0 ] ) - elif len( list2 ) == 1: - 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 ): @@ -2035,7 +1921,7 @@ repository.long_description = long_description flush_needed = True if repository.times_downloaded == 0 and repo_name != repository.name: - message = self.__validate_repository_name( repo_name, user ) + message = repository_maintenance_util.validate_repository_name( repo_name, user ) if message: error = True else: @@ -2045,7 +1931,7 @@ trans.app.hgweb_config_manager.change_entry( old_lhs, new_lhs, repo_dir ) # Change the entry in the repository's hgrc file. hgrc_file = os.path.join( repo_dir, '.hg', 'hgrc' ) - self.__change_repository_name_in_hgrc_file( hgrc_file, repo_name ) + repository_maintenance_util.change_repository_name_in_hgrc_file( hgrc_file, repo_name ) repository.name = repo_name flush_needed = True elif repository.times_downloaded != 0 and repo_name != repository.name: @@ -2130,7 +2016,7 @@ current_allow_push_list = current_allow_push.split( ',' ) else: current_allow_push_list = [] - allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) + allow_push_select_field = repository_maintenance_util.build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, @@ -2248,28 +2134,6 @@ 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, tool, invalid=False ): - """ - Create a new `DefaultToolState` for this tool. It will not be initialized - with default values for inputs. - - Only inputs on the first page will be initialized unless `all_pages` is - True, in which case all inputs regardless of page are initialized. - """ - state = galaxy.tools.DefaultToolState() - state.inputs = {} - if invalid: - # We're attempting to display a tool in the tool shed that has been determined to have errors of some kind. - return state - inputs = tool.inputs_by_page[ 0 ] - context = ExpressionContext( state.inputs, parent=None ) - for input in inputs.itervalues(): - try: - state.inputs[ input.name ] = input.get_initial_value( trans, context ) - except: - state.inputs[ input.name ] = [] - return state - @web.json def open_folder( self, trans, folder_path ): # Avoid caching @@ -2420,106 +2284,6 @@ 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 - if tool_ids or tool_names or tool_versions: - for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.includes_tools == True ) \ - .join( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.deprecated == False ) ): - metadata = repository_metadata.metadata - if metadata: - tools = metadata.get( 'tools', [] ) - for tool_dict in tools: - 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 ): - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - elif len( tool_ids ) == 1 or len( tool_names ) == 1: - tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - else: - ok = False - elif tool_ids and tool_versions and not tool_names: - if len( tool_ids ) == len( tool_versions ): - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - elif len( tool_ids ) == 1 or len( tool_versions ) == 1: - tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and not tool_ids: - if len( tool_versions ) == len( tool_names ): - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - elif len( tool_versions ) == 1 or len( tool_names ) == 1: - tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and tool_ids: - if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): - for i, tool_version in enumerate( tool_versions ): - tool_name = tool_names[ i ] - tool_id = tool_ids[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - ok = False - elif workflow_names or all_workflows: - for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.includes_workflows == True ) \ - .join( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.deprecated == False ) ): - metadata = repository_metadata.metadata - if metadata: - # metadata[ 'workflows' ] is a list of tuples where each contained tuple is - # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - if workflow_names: - workflow_tups = metadata.get( 'workflows', [] ) - workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] - for workflow_dict in workflows: - for workflow_name in workflow_names: - if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif all_workflows: - 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 ): message = kwd.get( 'message', '' ) @@ -2772,11 +2536,6 @@ action='sharable_owner', owner=owner ) )
- def __stringify( self, list ): - if list: - return ','.join( list ) - return '' - @web.expose def updated_changeset_revisions( self, trans, **kwd ): """ @@ -2806,24 +2565,6 @@ 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. - if name in [ 'None', None, '' ]: - return 'Enter the required repository name.' - if name in [ 'repos' ]: - return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name - for repository in user.active_repositories: - if repository.name == name: - return "You already have a repository named <b>%s</b>, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." - if len( name ) > 80: - return "Repository names cannot be more than 80 characters in length." - 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 ): message = kwd.get( 'message', '' )
diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/galaxy/webapps/tool_shed/util/common_util.py --- a/lib/galaxy/webapps/tool_shed/util/common_util.py +++ b/lib/galaxy/webapps/tool_shed/util/common_util.py @@ -25,3 +25,8 @@ trans.sa_session.add( item_rating ) trans.sa_session.flush() return item_rating + +def stringify( list ): + if list: + return ','.join( list ) + return ''
diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/tool_shed/util/repository_maintenance_util.py --- /dev/null +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -0,0 +1,75 @@ +import ConfigParser +import logging +import re +import tool_shed.util.shed_util_common as suc +from galaxy.web.form_builder import build_select_field + +from galaxy import eggs +eggs.require('mercurial') + +from mercurial import commands +from mercurial import hg +from mercurial import patch +from mercurial import ui + +log = logging.getLogger( __name__ ) + +VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9_]+$" ) + +def build_allow_push_select_field( trans, current_push_list, selected_value='none' ): + options = [] + for user in trans.sa_session.query( trans.model.User ): + if user.username not in current_push_list: + options.append( user ) + return build_select_field( trans, + objs=options, + label_attr='username', + select_field_name='allow_push', + selected_value=selected_value, + refresh_on_change=False, + multiple=True ) + +def change_repository_name_in_hgrc_file( hgrc_file, new_name ): + config = ConfigParser.ConfigParser() + config.read( hgrc_file ) + config.read( hgrc_file ) + config.set( 'web', 'name', new_name ) + new_file = open( hgrc_file, 'wb' ) + config.write( new_file ) + new_file.close() + +def create_hgrc_file( 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 + # purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll remove unknown files + # and empty directories. This is not currently used because it is not supported in the mercurial API. + repo = hg.repository( suc.get_configured_ui(), path=repository.repo_path( trans.app ) ) + fp = repo.opener( 'hgrc', 'wb' ) + fp.write( '[paths]\n' ) + fp.write( 'default = .\n' ) + fp.write( 'default-push = .\n' ) + fp.write( '[web]\n' ) + fp.write( 'allow_push = %s\n' % repository.user.username ) + fp.write( 'name = %s\n' % repository.name ) + fp.write( 'push_ssl = false\n' ) + fp.write( '[extensions]\n' ) + fp.write( 'hgext.purge=' ) + fp.close() + +def validate_repository_name( 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. + if name in [ 'None', None, '' ]: + return 'Enter the required repository name.' + if name in [ 'repos' ]: + return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name + for repository in user.active_repositories: + if repository.name == name: + return "You already have a repository named <b>%s</b>, so choose a different name." % name + if len( name ) < 4: + return "Repository names must be at least 4 characters in length." + if len( name ) > 80: + return "Repository names cannot be more than 80 characters in length." + if not( VALID_REPOSITORYNAME_RE.match( name ) ): + return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>." + return ''
diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/tool_shed/util/search_util.py --- /dev/null +++ b/lib/tool_shed/util/search_util.py @@ -0,0 +1,161 @@ +import logging +from galaxy.model.orm import and_ + +log = logging.getLogger( __name__ ) + +def in_tool_dict( 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 ) + elif tool_version and tool_name and tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_version == tool_dict_tool_version and \ + tool_name == tool_dict_tool_name and \ + tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and \ + tool_dict_tool_version.find( tool_version ) >= 0 and \ + tool_dict_tool_name.find( tool_name ) >= 0 and \ + tool_dict_tool_id.find( tool_id ) >= 0 ) + return found + +def in_workflow_dict( 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 ) + +def make_same_length( 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: + for i in range( 1, len( list2 ) ): + list1.append( list1[ 0 ] ) + elif len( list2 ) == 1: + for i in range( 1, len( list1 ) ): + list2.append( list2[ 0 ] ) + return list1, list2 + +def search_ids_names( 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 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( 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 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( 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 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( trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): + match_tuples = [] + ok = True + if tool_ids or tool_names or tool_versions: + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.includes_tools == True ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): + metadata = repository_metadata.metadata + if metadata: + tools = metadata.get( 'tools', [] ) + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if 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 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 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 ): + match_tuples = search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = make_same_length( tool_ids, tool_names ) + match_tuples = search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = make_same_length( tool_ids, tool_versions ) + match_tuples = search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = make_same_length( tool_versions, tool_names ) + match_tuples = search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + elif workflow_names or all_workflows: + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.includes_workflows == True ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): + metadata = repository_metadata.metadata + if metadata: + # metadata[ 'workflows' ] is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + if workflow_names: + workflow_tups = metadata.get( 'workflows', [] ) + workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] + for workflow_dict in workflows: + for workflow_name in workflow_names: + if in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif all_workflows: + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return ok, match_tuples
diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -804,6 +804,23 @@ contents.sort() return contents
+def get_repository_from_refresh_on_change( 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, + # so we loop through all of the received values to see which value is not the repository tip. If we find it, we know the + # refresh_on_change occurred and we have the necessary repository id and change set revision to pass on. + repository_id = None + v = None + for k, v in kwd.items(): + changeset_revision_str = 'changeset_revision_' + if k.startswith( changeset_revision_str ): + repository_id = trans.security.encode_id( int( k.lstrip( changeset_revision_str ) ) ) + repository = suc.get_repository_in_tool_shed( trans, repository_id ) + if repository.tip( trans.app ) != v: + return v, repository + # This should never be reached - raise an exception? + return v, None + def get_repository_in_tool_shed( trans, id ): """Get a repository on the tool shed side from the database via id.""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) )
diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -11,6 +11,7 @@ from galaxy.tools import parameters from galaxy.tools.parameters import dynamic_options from galaxy.tools.search import ToolBoxSearch +from galaxy.util.expressions import ExpressionContext from galaxy.web.form_builder import SelectField from tool_shed.util import xml_util from galaxy.tools.actions.upload import UploadToolAction @@ -890,6 +891,22 @@ pass return tool, message
+def new_state( trans, tool, invalid=False ): + """Create a new `DefaultToolState` for the received tool. Only inputs on the first page will be initialized.""" + state = galaxy.tools.DefaultToolState() + state.inputs = {} + if invalid: + # We're attempting to display a tool in the tool shed that has been determined to have errors, so is invalid. + return state + inputs = tool.inputs_by_page[ 0 ] + context = ExpressionContext( state.inputs, parent=None ) + for input in inputs.itervalues(): + try: + state.inputs[ input.name ] = input.get_initial_value( trans, context ) + except: + state.inputs[ input.name ] = [] + return state + def panel_entry_per_tool( tool_section_dict ): # Return True if tool_section_dict looks like this. # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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