1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/477979aa944f/ Changeset: 477979aa944f User: greg Date: 2013-05-16 17:55:41 Summary: Fixes for determining if a new metadata revision is required when inspecting tool shed repository dependency definitions. Affected #: 2 files

diff -r 311cf2ae1623289551b0b568975e9840d46097a2 -r 477979aa944f14ab7189aa51e67168da333f0840 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -1,15 +1,27 @@ -import sys, os, shutil, logging, tarfile, tempfile, urllib +import logging +import os +import shutil +import sys +import tarfile +import tempfile +import urllib from galaxy.web.base.controller import BaseUIController -from galaxy import web, util +from galaxy import util +from galaxy import web from galaxy.datatypes import checkers from galaxy.util import json

import tool_shed.util.shed_util_common as suc -from tool_shed.util import metadata_util, repository_dependency_util, tool_dependency_util, tool_util +from tool_shed.util import metadata_util +from tool_shed.util import repository_dependency_util +from tool_shed.util import tool_dependency_util +from tool_shed.util import tool_util

from galaxy import eggs -eggs.require('mercurial') -from mercurial import hg, ui, commands +eggs.require( 'mercurial' ) +from mercurial import commands +from mercurial import hg +from mercurial import ui

log = logging.getLogger( __name__ )

@@ -17,7 +29,9 @@ undesirable_files = [ '.hg_archival.txt', 'hgrc', '.DS_Store' ] CHUNK_SIZE = 2**20 # 1Mb

+ class UploadController( BaseUIController ): + def check_file_contents_for_email_alerts( self, trans ): """ See if any admin users have chosen to receive email alerts when a repository is updated. If so, the file contents of the update must be @@ -31,6 +45,7 @@ if user_email in admin_users: return True return False + def check_file_content_for_html_and_images( self, file_path ): message = '' if checkers.check_html( file_path ): @@ -38,6 +53,7 @@ elif checkers.check_image( file_path ): message = 'The file "%s" contains image content.\n' % str( file_path ) return message + @web.expose @web.require_login( 'upload', use_panels=True ) def upload( self, trans, **kwd ): @@ -235,6 +251,7 @@ remove_repo_files_not_in_tar=remove_repo_files_not_in_tar, message=message, status=status ) + def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -269,7 +286,9 @@ os.remove(repo_path) shutil.move(os.path.join(uploaded_directory, relative_path), repo_path) filenames_in_archive.append( relative_path ) - return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed) + return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, + undesirable_dirs_removed, undesirable_files_removed) + def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path( trans.app ) @@ -303,8 +322,18 @@ tar.extractall( path=full_path ) tar.close() uploaded_file.close() - return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed) - def __handle_directory_changes( self, trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ): + return self.__handle_directory_changes( trans, + repository, + full_path, + filenames_in_archive, + remove_repo_files_not_in_tar, + new_repo_alert, + commit_message, + undesirable_dirs_removed, + undesirable_files_removed ) + + def __handle_directory_changes( self, trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, + undesirable_dirs_removed, undesirable_files_removed ): repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) content_alert_str = '' @@ -369,6 +398,7 @@ admin_only = len( repository.downloadable_revisions ) != 1 suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed + def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: self.__handle_gzip( repository, uploaded_file_name ) @@ -376,6 +406,7 @@ if isbz2: self.__handle_bz2( repository, uploaded_file_name ) return uploaded_file_filename.rstrip( '.bz2' ) + def __handle_gzip( self, repository, uploaded_file_name ): fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) @@ -393,6 +424,7 @@ os.close( fd ) gzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) + def __handle_bz2( self, repository, uploaded_file_name ): fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_bunzip2_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) bzipped_file = bz2.BZ2File( uploaded_file_name, 'rb' ) @@ -410,6 +442,7 @@ os.close( fd ) bzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) + def __get_upload_point( self, repository, **kwd ): upload_point = kwd.get( 'upload_point', None ) if upload_point is not None: @@ -430,6 +463,7 @@ # Must have been an error selecting something that didn't exist, so default to repository root upload_point = None return upload_point + def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only

diff -r 311cf2ae1623289551b0b568975e9840d46097a2 -r 477979aa944f14ab7189aa51e67168da333f0840 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1088,7 +1088,7 @@ owner = repository_elem.get( 'owner' ) changeset_revision = repository_elem.get( 'changeset_revision' ) prior_installation_required = repository_elem.get( 'prior_installation_required', False ) - repository_dependency_tup = ( toolshed, name, owner, changeset_revision, prior_installation_required ) + repository_dependency_tup = [ toolshed, name, owner, changeset_revision, prior_installation_required ] user = None repository = None if app.name == 'galaxy': @@ -1284,11 +1284,8 @@ if new_repository_dependencies_metadata: new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] # The saved metadata must be a subset of the new metadata. - for new_repository_dependency in new_repository_dependencies: - if new_repository_dependency not in saved_repository_dependencies: - return True - for saved_repository_dependency_metadata in saved_repository_dependencies: - if saved_repository_dependency_metadata not in new_repository_dependencies: + for saved_repository_dependency in saved_repository_dependencies: + if saved_repository_dependency not in new_repository_dependencies: return True return False else: @@ -1318,9 +1315,6 @@ new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) if new_tool_dependencies: # The saved metadata must be a subset of the new metadata. - for new_tool_dependency in new_tool_dependencies: - if new_tool_dependency not in saved_tool_dependencies: - return True for saved_tool_dependency in saved_tool_dependencies: if saved_tool_dependency not in new_tool_dependencies: return True

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

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