[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad8d4f2080c0/ Changeset: ad8d4f2080c0 Branch: next-stable User: greg Date: 2013-05-23 20:57:12 Summary: Fixes for xml handling in the tol shed. Affected #: 12 files diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 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 @@ -14,6 +14,7 @@ from tool_shed.util import repository_dependency_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util +from tool_shed.util import xml_util from galaxy import eggs eggs.require( 'mercurial' ) @@ -131,7 +132,7 @@ # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) @@ -140,7 +141,7 @@ # are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) @@ -268,13 +269,13 @@ # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml': # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) if ok: repo_path = os.path.join( full_path, relative_path ) @@ -330,13 +331,13 @@ # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml': # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) return commit_util.handle_directory_changes( trans, repository, diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -15,6 +15,7 @@ from tool_shed.util import metadata_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util +from tool_shed.util import xml_util from galaxy.util.odict import odict @@ -37,13 +38,13 @@ self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. - tree = util.parse_xml( migrated_tools_config ) + tree = xml_util.parse_xml( migrated_tools_config ) root = tree.getroot() self.tool_path = root.get( 'tool_path' ) print "Repositories will be installed into configured tool_path location ", str( self.tool_path ) # Parse tool_shed_install_config to check each of the tools. self.tool_shed_install_config = tool_shed_install_config - tree = util.parse_xml( tool_shed_install_config ) + tree = xml_util.parse_xml( tool_shed_install_config ) root = tree.getroot() self.tool_shed = suc.clean_tool_shed_url( root.get( 'name' ) ) self.repository_owner = common_util.REPOSITORY_OWNER @@ -107,7 +108,7 @@ tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs. migrated_tool_configs = [] - tree = util.parse_xml( tools_xml_file_path ) + tree = xml_util.parse_xml( tools_xml_file_path ) root = tree.getroot() for elem in root: if elem.tag == 'repository': @@ -116,7 +117,7 @@ # Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them. tool_panel_elems = [] for proprietary_tool_conf in self.proprietary_tool_confs: - tree = util.parse_xml( proprietary_tool_conf ) + tree = xml_util.parse_xml( proprietary_tool_conf ) root = tree.getroot() for elem in root: if elem.tag == 'tool': diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -10,6 +10,7 @@ import tool_shed.util.common_util as cu from tool_shed.util import encoding_util from tool_shed.util import tool_dependency_util +from tool_shed.util import xml_util from galaxy.model.orm import and_ from galaxy.web import url_for @@ -478,7 +479,7 @@ tool_dependency = None action_dict = {} if tool_dependencies_config: - required_td_tree = parse_xml( tool_dependencies_config ) + required_td_tree = xml_util.parse_xml( tool_dependencies_config ) if required_td_tree: required_td_root = required_td_tree.getroot() for required_td_elem in required_td_root: @@ -623,17 +624,6 @@ file_name = fpath return file_name -def parse_xml( file_name ): - """Returns a parsed xml tree.""" - try: - tree = ElementTree.parse( file_name ) - except Exception, e: - print "Exception attempting to parse ", file_name, ": ", str( e ) - return None - root = tree.getroot() - ElementInclude.include( root ) - return tree - def url_join( *args ): parts = [] for arg in args: diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/tool_shed_registry.py --- a/lib/tool_shed/tool_shed_registry.py +++ b/lib/tool_shed/tool_shed_registry.py @@ -1,9 +1,8 @@ import logging import sys import urllib2 -from galaxy.util import parse_xml from galaxy.util.odict import odict -from xml.etree import ElementTree +from tool_shed.util import xml_util log = logging.getLogger( __name__ ) @@ -15,7 +14,7 @@ self.tool_sheds_auth = odict() if root_dir and config: # Parse tool_sheds_conf.xml - tree = parse_xml( config ) + tree = xml_util.parse_xml( config ) root = tree.getroot() log.debug( 'Loading references to tool sheds from %s' % config ) for elem in root.findall( 'tool_shed' ): diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -9,7 +9,7 @@ from galaxy.web import url_for import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_util -import xml.etree.ElementTree +from tool_shed.util import xml_util from galaxy import eggs eggs.require( 'mercurial' ) @@ -60,17 +60,6 @@ message = 'The file "%s" contains image content.\n' % str( file_path ) return message -def create_and_write_tmp_file( root ): - tmp_str = '%s\n' % xml.etree.ElementTree.tostring( root, encoding='utf-8' ) - fh = tempfile.NamedTemporaryFile( 'wb' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'wb' ) - fh.write( '<?xml version="1.0"?>\n' ) - fh.write( tmp_str ) - fh.close() - return tmp_filename - def get_upload_point( repository, **kwd ): upload_point = kwd.get( 'upload_point', None ) if upload_point is not None: @@ -198,7 +187,7 @@ altered = False try: # Make sure we're looking at a valid repository_dependencies.xml file. - tree = suc.parse_xml( repository_dependencies_config ) + tree = xml_util.parse_xml( repository_dependencies_config ) root = tree.getroot() except Exception, e: error_message = "Error parsing %s in handle_repository_dependencies_definition: " % str( repository_dependencies_config ) @@ -245,7 +234,7 @@ altered = False try: # Make sure we're looking at a valid tool_dependencies.xml file. - tree = suc.parse_xml( tool_dependencies_config ) + tree = xml_util.parse_xml( tool_dependencies_config ) root = tree.getroot() except Exception, e: error_message = "Error parsing %s in handle_tool_dependencies_definition: " % str( tool_dependencies_config ) diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -1,8 +1,8 @@ import os import urllib2 -from galaxy import util from galaxy.util.odict import odict from tool_shed.util import encoding_util +from tool_shed.util import xml_util REPOSITORY_OWNER = 'devteam' @@ -11,7 +11,7 @@ tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. migrated_tool_configs_dict = odict() - tree = util.parse_xml( tools_xml_file_path ) + tree = xml_util.parse_xml( tools_xml_file_path ) root = tree.getroot() tool_shed = root.get( 'name' ) tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ) @@ -48,7 +48,7 @@ # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. missing_tool_configs_dict = odict() for tool_panel_config in tool_panel_configs: - tree = util.parse_xml( tool_panel_config ) + tree = xml_util.parse_xml( tool_panel_config ) root = tree.getroot() for elem in root: if elem.tag == 'tool': @@ -78,7 +78,7 @@ for config_filename in app.config.tool_configs: # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. # <toolbox tool_path="../shed_tools"> - tree = util.parse_xml( config_filename ) + tree = xml_util.parse_xml( config_filename ) root = tree.getroot() tool_path = root.get( 'tool_path', None ) if tool_path is None: diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/util/data_manager_util.py --- a/lib/tool_shed/util/data_manager_util.py +++ b/lib/tool_shed/util/data_manager_util.py @@ -1,6 +1,6 @@ import logging import os -from galaxy import util +from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc log = logging.getLogger( __name__ ) @@ -10,7 +10,7 @@ fh = open( config_filename, 'wb' ) fh.write( '<?xml version="1.0"?>\n<data_managers>\n' )#% ( shed_tool_conf_filename )) for elem in config_elems: - fh.write( util.xml_to_string( elem, pretty=True ) ) + fh.write( xml_util.xml_to_string( elem ) ) fh.write( '</data_managers>\n' ) fh.close() @@ -21,7 +21,7 @@ for tool_tup in repository_tools_tups: repository_tools_by_guid[ tool_tup[ 1 ] ] = dict( tool_config_filename=tool_tup[ 0 ], tool=tool_tup[ 2 ] ) # Load existing data managers. - config_elems = [ elem for elem in util.parse_xml( shed_data_manager_conf_filename ).getroot() ] + config_elems = [ elem for elem in xml_util.parse_xml( shed_data_manager_conf_filename ).getroot() ] repo_data_manager_conf_filename = metadata_dict['data_manager'].get( 'config_filename', None ) if repo_data_manager_conf_filename is None: log.debug( "No data_manager_conf.xml file has been defined." ) @@ -29,13 +29,13 @@ data_manager_config_has_changes = False relative_repo_data_manager_dir = os.path.join( shed_config_dict.get( 'tool_path', '' ), relative_install_dir ) repo_data_manager_conf_filename = os.path.join( relative_repo_data_manager_dir, repo_data_manager_conf_filename ) - tree = util.parse_xml( repo_data_manager_conf_filename ) + tree = xml_util.parse_xml( repo_data_manager_conf_filename ) root = tree.getroot() for elem in root: if elem.tag == 'data_manager': data_manager_id = elem.get( 'id', None ) if data_manager_id is None: - log.error( "A data manager was defined that does not have an id and will not be installed:\n%s" % ( util.xml_to_string( elem ) ) ) + log.error( "A data manager was defined that does not have an id and will not be installed:\n%s" % ( xml_util.xml_to_string( elem ) ) ) continue data_manager_dict = metadata_dict['data_manager'].get( 'data_managers', {} ).get( data_manager_id, None ) if data_manager_dict is None: @@ -77,7 +77,7 @@ if data_manager: rval.append( data_manager ) else: - log.warning( "Encountered unexpected element '%s':\n%s" % ( elem.tag, util.xml_to_string( elem ) ) ) + log.warning( "Encountered unexpected element '%s':\n%s" % ( elem.tag, xml_util.xml_to_string( elem ) ) ) config_elems.append( elem ) data_manager_config_has_changes = True # Persist the altered shed_data_manager_config file. @@ -89,7 +89,7 @@ metadata_dict = repository.metadata if metadata_dict and 'data_manager' in metadata_dict: shed_data_manager_conf_filename = app.config.shed_data_manager_config_file - tree = util.parse_xml( shed_data_manager_conf_filename ) + tree = xml_util.parse_xml( shed_data_manager_conf_filename ) root = tree.getroot() assert root.tag == 'data_managers', 'The file provided (%s) for removing data managers from is not a valid data manager xml file.' % ( shed_data_manager_conf_filename ) guids = [ data_manager_dict.get( 'guid' ) for data_manager_dict in metadata_dict.get( 'data_manager', {} ).get( 'data_managers', {} ).itervalues() if 'guid' in data_manager_dict ] diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/util/datatype_util.py --- a/lib/tool_shed/util/datatype_util.py +++ b/lib/tool_shed/util/datatype_util.py @@ -2,7 +2,7 @@ import os import tempfile from galaxy import eggs -from galaxy import util +from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc import pkg_resources @@ -24,7 +24,7 @@ has been initialized, the registry's contents cannot be overridden by conflicting data types. """ try: - tree = util.parse_xml( datatypes_config ) + tree = xml_util.parse_xml( datatypes_config ) except Exception, e: log.debug( "Error parsing %s, exception: %s" % ( datatypes_config, str( e ) ) ) return None, None @@ -83,9 +83,9 @@ fd, proprietary_datatypes_config = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<datatypes>\n' ) - os.write( fd, '%s' % util.xml_to_string( registration ) ) + os.write( fd, '%s' % xml_util.xml_to_string( registration ) ) if sniffers: - os.write( fd, '%s' % util.xml_to_string( sniffers ) ) + os.write( fd, '%s' % xml_util.xml_to_string( sniffers ) ) os.write( fd, '</datatypes>\n' ) os.close( fd ) os.chmod( proprietary_datatypes_config, 0644 ) diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -17,6 +17,7 @@ from tool_shed.util import readme_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util +from tool_shed.util import xml_util import pkg_resources @@ -363,7 +364,7 @@ 'error_messages': [] } metadata_dict[ 'data_manager' ] = data_manager_metadata try: - tree = util.parse_xml( data_manager_config_filename ) + tree = xml_util.parse_xml( data_manager_config_filename ) except Exception, e: # We are not able to load any data managers. error_message = 'There was an error parsing your Data Manager config file "%s": %s' % ( data_manager_config_filename, e ) @@ -638,7 +639,7 @@ or checkers.check_bz2( full_path )[ 0 ] or checkers.check_zip( full_path ) ): try: # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( full_path ) + element_tree = xml_util.parse_xml( full_path ) element_tree_root = element_tree.getroot() is_tool = element_tree_root.tag == 'tool' except Exception, e: @@ -751,7 +752,7 @@ error_message = '' try: # Make sure we're looking at a valid repository_dependencies.xml file. - tree = util.parse_xml( repository_dependencies_config ) + tree = xml_util.parse_xml( repository_dependencies_config ) root = tree.getroot() xml_is_valid = root.tag == 'repositories' except Exception, e: diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 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 @@ -14,7 +14,7 @@ from galaxy.model.orm import and_ import sqlalchemy.orm.exc from tool_shed.util import common_util -from xml.etree import ElementTree as XmlET +from tool_shed.util import xml_util from galaxy import eggs import pkg_resources @@ -37,17 +37,6 @@ MAX_DISPLAY_SIZE = 32768 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) - -class CommentedTreeBuilder ( XmlET.XMLTreeBuilder ): - def __init__ ( self, html=0, target=None ): - XmlET.XMLTreeBuilder.__init__( self, html, target ) - self._parser.CommentHandler = self.handle_comment - - def handle_comment ( self, data ): - self._target.start( XmlET.Comment, {} ) - self._target.data( data ) - self._target.end( XmlET.Comment ) - new_repo_email_alert_template = """ Sharable link: ${sharable_link} Repository name: ${repository_name} @@ -188,7 +177,7 @@ os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<toolbox tool_path="%s">\n' % str( tool_path ) ) for elem in config_elems: - os.write( fd, '%s' % util.xml_to_string( elem, pretty=True ) ) + os.write( fd, '%s' % xml_util.xml_to_string( elem ) ) os.write( fd, '</toolbox>\n' ) os.close( fd ) shutil.move( filename, os.path.abspath( config_filename ) ) @@ -346,7 +335,7 @@ file_name = strip_path( tool_config ) guids_and_configs[ guid ] = file_name # Parse the shed_tool_conf file in which all of this repository's tools are defined and generate the tool_panel_dict. - tree = util.parse_xml( shed_tool_conf ) + tree = xml_util.parse_xml( shed_tool_conf ) root = tree.getroot() for elem in root: if elem.tag == 'tool': @@ -1084,13 +1073,6 @@ prior_installation_required = util.asbool( str( prior_installation_required ) ) return tool_shed, name, owner, changeset_revision, prior_installation_required -def parse_xml( fname ): - """Returns a parsed xml tree with comments in tact.""" - fobj = open( fname, 'r' ) - tree = XmlET.parse( fobj, parser=CommentedTreeBuilder() ) - fobj.close() - return tree - def pretty_print( dict=None ): if dict: return json.to_json_string( dict, sort_keys=True, indent=4 * ' ' ) @@ -1271,7 +1253,7 @@ for tool_config_filename, guid, tool in repository_tools_tups: guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) config_elems = [] - tree = util.parse_xml( shed_tool_conf ) + tree = xml_util.parse_xml( shed_tool_conf ) root = tree.getroot() for elem in root: if elem.tag == 'section': diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -12,6 +12,7 @@ from galaxy.tools.parameters import dynamic_options from galaxy.tools.search import ToolBoxSearch from galaxy.web.form_builder import SelectField +from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc import pkg_resources @@ -36,7 +37,7 @@ shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] tool_path = shed_tool_conf_dict[ 'tool_path' ] config_elems = [] - tree = util.parse_xml( shed_tool_conf ) + tree = xml_util.parse_xml( shed_tool_conf ) root = tree.getroot() for elem in root: config_elems.append( elem ) @@ -803,7 +804,7 @@ message = '' tmp_tool_config = suc.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) if tmp_tool_config: - element_tree = util.parse_xml( tmp_tool_config ) + element_tree = xml_util.parse_xml( tmp_tool_config ) element_tree_root = element_tree.getroot() # Look for code files required by the tool config. tmp_code_files = [] @@ -845,7 +846,7 @@ shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] tool_path = shed_tool_conf_dict[ 'tool_path' ] config_elems = [] - tree = util.parse_xml( shed_tool_conf ) + tree = xml_util.parse_xml( shed_tool_conf ) root = tree.getroot() for elem in root: config_elems.append( elem ) diff -r 3370974992f38c9f1de1527982adb362ba644fd9 -r ad8d4f2080c062f7c01bfc6f2f86dd0f5431f106 lib/tool_shed/util/xml_util.py --- /dev/null +++ b/lib/tool_shed/util/xml_util.py @@ -0,0 +1,43 @@ +import logging +import os +import tempfile +from xml.etree import ElementTree as XmlET +import xml.etree.ElementTree + +log = logging.getLogger( __name__ ) + + +class CommentedTreeBuilder ( XmlET.XMLTreeBuilder ): + def __init__ ( self, html=0, target=None ): + XmlET.XMLTreeBuilder.__init__( self, html, target ) + self._parser.CommentHandler = self.handle_comment + + def handle_comment ( self, data ): + self._target.start( XmlET.Comment, {} ) + self._target.data( data ) + self._target.end( XmlET.Comment ) + +def create_and_write_tmp_file( elem ): + tmp_str = xml_to_string( elem ) + fh = tempfile.NamedTemporaryFile( 'wb' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + fh.write( '<?xml version="1.0"?>\n' ) + fh.write( tmp_str ) + fh.close() + return tmp_filename + +def parse_xml( file_name ): + """Returns a parsed xml tree with comments intact.""" + try: + fobj = open( file_name, 'r' ) + tree = XmlET.parse( fobj, parser=CommentedTreeBuilder() ) + fobj.close() + except Exception, e: + log.exception( "Exception attempting to parse %s: %s" % ( str( file_name ), str( e ) ) ) + return None + return tree + +def xml_to_string( elem, encoding='utf-8' ): + return '%s\n' % xml.etree.ElementTree.tostring( elem, encoding=encoding ) https://bitbucket.org/galaxy/galaxy-central/commits/7ee9bfda98e5/ Changeset: 7ee9bfda98e5 User: greg Date: 2013-05-23 20:58:00 Summary: Merged from next-stable Affected #: 12 files diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 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 @@ -14,6 +14,7 @@ from tool_shed.util import repository_dependency_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util +from tool_shed.util import xml_util from galaxy import eggs eggs.require( 'mercurial' ) @@ -131,7 +132,7 @@ # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) @@ -140,7 +141,7 @@ # are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) @@ -268,13 +269,13 @@ # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml': # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) if ok: repo_path = os.path.join( full_path, relative_path ) @@ -330,13 +331,13 @@ # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml': # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) return commit_util.handle_directory_changes( trans, repository, diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -15,6 +15,7 @@ from tool_shed.util import metadata_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util +from tool_shed.util import xml_util from galaxy.util.odict import odict @@ -37,13 +38,13 @@ self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. - tree = util.parse_xml( migrated_tools_config ) + tree = xml_util.parse_xml( migrated_tools_config ) root = tree.getroot() self.tool_path = root.get( 'tool_path' ) print "Repositories will be installed into configured tool_path location ", str( self.tool_path ) # Parse tool_shed_install_config to check each of the tools. self.tool_shed_install_config = tool_shed_install_config - tree = util.parse_xml( tool_shed_install_config ) + tree = xml_util.parse_xml( tool_shed_install_config ) root = tree.getroot() self.tool_shed = suc.clean_tool_shed_url( root.get( 'name' ) ) self.repository_owner = common_util.REPOSITORY_OWNER @@ -107,7 +108,7 @@ tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs. migrated_tool_configs = [] - tree = util.parse_xml( tools_xml_file_path ) + tree = xml_util.parse_xml( tools_xml_file_path ) root = tree.getroot() for elem in root: if elem.tag == 'repository': @@ -116,7 +117,7 @@ # Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them. tool_panel_elems = [] for proprietary_tool_conf in self.proprietary_tool_confs: - tree = util.parse_xml( proprietary_tool_conf ) + tree = xml_util.parse_xml( proprietary_tool_conf ) root = tree.getroot() for elem in root: if elem.tag == 'tool': diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -10,6 +10,7 @@ import tool_shed.util.common_util as cu from tool_shed.util import encoding_util from tool_shed.util import tool_dependency_util +from tool_shed.util import xml_util from galaxy.model.orm import and_ from galaxy.web import url_for @@ -478,7 +479,7 @@ tool_dependency = None action_dict = {} if tool_dependencies_config: - required_td_tree = parse_xml( tool_dependencies_config ) + required_td_tree = xml_util.parse_xml( tool_dependencies_config ) if required_td_tree: required_td_root = required_td_tree.getroot() for required_td_elem in required_td_root: @@ -623,17 +624,6 @@ file_name = fpath return file_name -def parse_xml( file_name ): - """Returns a parsed xml tree.""" - try: - tree = ElementTree.parse( file_name ) - except Exception, e: - print "Exception attempting to parse ", file_name, ": ", str( e ) - return None - root = tree.getroot() - ElementInclude.include( root ) - return tree - def url_join( *args ): parts = [] for arg in args: diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/tool_shed_registry.py --- a/lib/tool_shed/tool_shed_registry.py +++ b/lib/tool_shed/tool_shed_registry.py @@ -1,9 +1,8 @@ import logging import sys import urllib2 -from galaxy.util import parse_xml from galaxy.util.odict import odict -from xml.etree import ElementTree +from tool_shed.util import xml_util log = logging.getLogger( __name__ ) @@ -15,7 +14,7 @@ self.tool_sheds_auth = odict() if root_dir and config: # Parse tool_sheds_conf.xml - tree = parse_xml( config ) + tree = xml_util.parse_xml( config ) root = tree.getroot() log.debug( 'Loading references to tool sheds from %s' % config ) for elem in root.findall( 'tool_shed' ): diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -9,7 +9,7 @@ from galaxy.web import url_for import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_util -import xml.etree.ElementTree +from tool_shed.util import xml_util from galaxy import eggs eggs.require( 'mercurial' ) @@ -60,17 +60,6 @@ message = 'The file "%s" contains image content.\n' % str( file_path ) return message -def create_and_write_tmp_file( root ): - tmp_str = '%s\n' % xml.etree.ElementTree.tostring( root, encoding='utf-8' ) - fh = tempfile.NamedTemporaryFile( 'wb' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'wb' ) - fh.write( '<?xml version="1.0"?>\n' ) - fh.write( tmp_str ) - fh.close() - return tmp_filename - def get_upload_point( repository, **kwd ): upload_point = kwd.get( 'upload_point', None ) if upload_point is not None: @@ -198,7 +187,7 @@ altered = False try: # Make sure we're looking at a valid repository_dependencies.xml file. - tree = suc.parse_xml( repository_dependencies_config ) + tree = xml_util.parse_xml( repository_dependencies_config ) root = tree.getroot() except Exception, e: error_message = "Error parsing %s in handle_repository_dependencies_definition: " % str( repository_dependencies_config ) @@ -245,7 +234,7 @@ altered = False try: # Make sure we're looking at a valid tool_dependencies.xml file. - tree = suc.parse_xml( tool_dependencies_config ) + tree = xml_util.parse_xml( tool_dependencies_config ) root = tree.getroot() except Exception, e: error_message = "Error parsing %s in handle_tool_dependencies_definition: " % str( tool_dependencies_config ) diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -1,8 +1,8 @@ import os import urllib2 -from galaxy import util from galaxy.util.odict import odict from tool_shed.util import encoding_util +from tool_shed.util import xml_util REPOSITORY_OWNER = 'devteam' @@ -11,7 +11,7 @@ tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. migrated_tool_configs_dict = odict() - tree = util.parse_xml( tools_xml_file_path ) + tree = xml_util.parse_xml( tools_xml_file_path ) root = tree.getroot() tool_shed = root.get( 'name' ) tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ) @@ -48,7 +48,7 @@ # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. missing_tool_configs_dict = odict() for tool_panel_config in tool_panel_configs: - tree = util.parse_xml( tool_panel_config ) + tree = xml_util.parse_xml( tool_panel_config ) root = tree.getroot() for elem in root: if elem.tag == 'tool': @@ -78,7 +78,7 @@ for config_filename in app.config.tool_configs: # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. # <toolbox tool_path="../shed_tools"> - tree = util.parse_xml( config_filename ) + tree = xml_util.parse_xml( config_filename ) root = tree.getroot() tool_path = root.get( 'tool_path', None ) if tool_path is None: diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/util/data_manager_util.py --- a/lib/tool_shed/util/data_manager_util.py +++ b/lib/tool_shed/util/data_manager_util.py @@ -1,6 +1,6 @@ import logging import os -from galaxy import util +from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc log = logging.getLogger( __name__ ) @@ -10,7 +10,7 @@ fh = open( config_filename, 'wb' ) fh.write( '<?xml version="1.0"?>\n<data_managers>\n' )#% ( shed_tool_conf_filename )) for elem in config_elems: - fh.write( util.xml_to_string( elem, pretty=True ) ) + fh.write( xml_util.xml_to_string( elem ) ) fh.write( '</data_managers>\n' ) fh.close() @@ -21,7 +21,7 @@ for tool_tup in repository_tools_tups: repository_tools_by_guid[ tool_tup[ 1 ] ] = dict( tool_config_filename=tool_tup[ 0 ], tool=tool_tup[ 2 ] ) # Load existing data managers. - config_elems = [ elem for elem in util.parse_xml( shed_data_manager_conf_filename ).getroot() ] + config_elems = [ elem for elem in xml_util.parse_xml( shed_data_manager_conf_filename ).getroot() ] repo_data_manager_conf_filename = metadata_dict['data_manager'].get( 'config_filename', None ) if repo_data_manager_conf_filename is None: log.debug( "No data_manager_conf.xml file has been defined." ) @@ -29,13 +29,13 @@ data_manager_config_has_changes = False relative_repo_data_manager_dir = os.path.join( shed_config_dict.get( 'tool_path', '' ), relative_install_dir ) repo_data_manager_conf_filename = os.path.join( relative_repo_data_manager_dir, repo_data_manager_conf_filename ) - tree = util.parse_xml( repo_data_manager_conf_filename ) + tree = xml_util.parse_xml( repo_data_manager_conf_filename ) root = tree.getroot() for elem in root: if elem.tag == 'data_manager': data_manager_id = elem.get( 'id', None ) if data_manager_id is None: - log.error( "A data manager was defined that does not have an id and will not be installed:\n%s" % ( util.xml_to_string( elem ) ) ) + log.error( "A data manager was defined that does not have an id and will not be installed:\n%s" % ( xml_util.xml_to_string( elem ) ) ) continue data_manager_dict = metadata_dict['data_manager'].get( 'data_managers', {} ).get( data_manager_id, None ) if data_manager_dict is None: @@ -77,7 +77,7 @@ if data_manager: rval.append( data_manager ) else: - log.warning( "Encountered unexpected element '%s':\n%s" % ( elem.tag, util.xml_to_string( elem ) ) ) + log.warning( "Encountered unexpected element '%s':\n%s" % ( elem.tag, xml_util.xml_to_string( elem ) ) ) config_elems.append( elem ) data_manager_config_has_changes = True # Persist the altered shed_data_manager_config file. @@ -89,7 +89,7 @@ metadata_dict = repository.metadata if metadata_dict and 'data_manager' in metadata_dict: shed_data_manager_conf_filename = app.config.shed_data_manager_config_file - tree = util.parse_xml( shed_data_manager_conf_filename ) + tree = xml_util.parse_xml( shed_data_manager_conf_filename ) root = tree.getroot() assert root.tag == 'data_managers', 'The file provided (%s) for removing data managers from is not a valid data manager xml file.' % ( shed_data_manager_conf_filename ) guids = [ data_manager_dict.get( 'guid' ) for data_manager_dict in metadata_dict.get( 'data_manager', {} ).get( 'data_managers', {} ).itervalues() if 'guid' in data_manager_dict ] diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/util/datatype_util.py --- a/lib/tool_shed/util/datatype_util.py +++ b/lib/tool_shed/util/datatype_util.py @@ -2,7 +2,7 @@ import os import tempfile from galaxy import eggs -from galaxy import util +from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc import pkg_resources @@ -24,7 +24,7 @@ has been initialized, the registry's contents cannot be overridden by conflicting data types. """ try: - tree = util.parse_xml( datatypes_config ) + tree = xml_util.parse_xml( datatypes_config ) except Exception, e: log.debug( "Error parsing %s, exception: %s" % ( datatypes_config, str( e ) ) ) return None, None @@ -83,9 +83,9 @@ fd, proprietary_datatypes_config = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<datatypes>\n' ) - os.write( fd, '%s' % util.xml_to_string( registration ) ) + os.write( fd, '%s' % xml_util.xml_to_string( registration ) ) if sniffers: - os.write( fd, '%s' % util.xml_to_string( sniffers ) ) + os.write( fd, '%s' % xml_util.xml_to_string( sniffers ) ) os.write( fd, '</datatypes>\n' ) os.close( fd ) os.chmod( proprietary_datatypes_config, 0644 ) diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -17,6 +17,7 @@ from tool_shed.util import readme_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util +from tool_shed.util import xml_util import pkg_resources @@ -363,7 +364,7 @@ 'error_messages': [] } metadata_dict[ 'data_manager' ] = data_manager_metadata try: - tree = util.parse_xml( data_manager_config_filename ) + tree = xml_util.parse_xml( data_manager_config_filename ) except Exception, e: # We are not able to load any data managers. error_message = 'There was an error parsing your Data Manager config file "%s": %s' % ( data_manager_config_filename, e ) @@ -638,7 +639,7 @@ or checkers.check_bz2( full_path )[ 0 ] or checkers.check_zip( full_path ) ): try: # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( full_path ) + element_tree = xml_util.parse_xml( full_path ) element_tree_root = element_tree.getroot() is_tool = element_tree_root.tag == 'tool' except Exception, e: @@ -751,7 +752,7 @@ error_message = '' try: # Make sure we're looking at a valid repository_dependencies.xml file. - tree = util.parse_xml( repository_dependencies_config ) + tree = xml_util.parse_xml( repository_dependencies_config ) root = tree.getroot() xml_is_valid = root.tag == 'repositories' except Exception, e: diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 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 @@ -14,7 +14,7 @@ from galaxy.model.orm import and_ import sqlalchemy.orm.exc from tool_shed.util import common_util -from xml.etree import ElementTree as XmlET +from tool_shed.util import xml_util from galaxy import eggs import pkg_resources @@ -37,17 +37,6 @@ MAX_DISPLAY_SIZE = 32768 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) - -class CommentedTreeBuilder ( XmlET.XMLTreeBuilder ): - def __init__ ( self, html=0, target=None ): - XmlET.XMLTreeBuilder.__init__( self, html, target ) - self._parser.CommentHandler = self.handle_comment - - def handle_comment ( self, data ): - self._target.start( XmlET.Comment, {} ) - self._target.data( data ) - self._target.end( XmlET.Comment ) - new_repo_email_alert_template = """ Sharable link: ${sharable_link} Repository name: ${repository_name} @@ -188,7 +177,7 @@ os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<toolbox tool_path="%s">\n' % str( tool_path ) ) for elem in config_elems: - os.write( fd, '%s' % util.xml_to_string( elem, pretty=True ) ) + os.write( fd, '%s' % xml_util.xml_to_string( elem ) ) os.write( fd, '</toolbox>\n' ) os.close( fd ) shutil.move( filename, os.path.abspath( config_filename ) ) @@ -346,7 +335,7 @@ file_name = strip_path( tool_config ) guids_and_configs[ guid ] = file_name # Parse the shed_tool_conf file in which all of this repository's tools are defined and generate the tool_panel_dict. - tree = util.parse_xml( shed_tool_conf ) + tree = xml_util.parse_xml( shed_tool_conf ) root = tree.getroot() for elem in root: if elem.tag == 'tool': @@ -1084,13 +1073,6 @@ prior_installation_required = util.asbool( str( prior_installation_required ) ) return tool_shed, name, owner, changeset_revision, prior_installation_required -def parse_xml( fname ): - """Returns a parsed xml tree with comments in tact.""" - fobj = open( fname, 'r' ) - tree = XmlET.parse( fobj, parser=CommentedTreeBuilder() ) - fobj.close() - return tree - def pretty_print( dict=None ): if dict: return json.to_json_string( dict, sort_keys=True, indent=4 * ' ' ) @@ -1271,7 +1253,7 @@ for tool_config_filename, guid, tool in repository_tools_tups: guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) config_elems = [] - tree = util.parse_xml( shed_tool_conf ) + tree = xml_util.parse_xml( shed_tool_conf ) root = tree.getroot() for elem in root: if elem.tag == 'section': diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -12,6 +12,7 @@ from galaxy.tools.parameters import dynamic_options from galaxy.tools.search import ToolBoxSearch from galaxy.web.form_builder import SelectField +from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc import pkg_resources @@ -36,7 +37,7 @@ shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] tool_path = shed_tool_conf_dict[ 'tool_path' ] config_elems = [] - tree = util.parse_xml( shed_tool_conf ) + tree = xml_util.parse_xml( shed_tool_conf ) root = tree.getroot() for elem in root: config_elems.append( elem ) @@ -803,7 +804,7 @@ message = '' tmp_tool_config = suc.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) if tmp_tool_config: - element_tree = util.parse_xml( tmp_tool_config ) + element_tree = xml_util.parse_xml( tmp_tool_config ) element_tree_root = element_tree.getroot() # Look for code files required by the tool config. tmp_code_files = [] @@ -845,7 +846,7 @@ shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] tool_path = shed_tool_conf_dict[ 'tool_path' ] config_elems = [] - tree = util.parse_xml( shed_tool_conf ) + tree = xml_util.parse_xml( shed_tool_conf ) root = tree.getroot() for elem in root: config_elems.append( elem ) diff -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c -r 7ee9bfda98e5bb8b0ee348309037ad2ba309cef6 lib/tool_shed/util/xml_util.py --- /dev/null +++ b/lib/tool_shed/util/xml_util.py @@ -0,0 +1,43 @@ +import logging +import os +import tempfile +from xml.etree import ElementTree as XmlET +import xml.etree.ElementTree + +log = logging.getLogger( __name__ ) + + +class CommentedTreeBuilder ( XmlET.XMLTreeBuilder ): + def __init__ ( self, html=0, target=None ): + XmlET.XMLTreeBuilder.__init__( self, html, target ) + self._parser.CommentHandler = self.handle_comment + + def handle_comment ( self, data ): + self._target.start( XmlET.Comment, {} ) + self._target.data( data ) + self._target.end( XmlET.Comment ) + +def create_and_write_tmp_file( elem ): + tmp_str = xml_to_string( elem ) + fh = tempfile.NamedTemporaryFile( 'wb' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + fh.write( '<?xml version="1.0"?>\n' ) + fh.write( tmp_str ) + fh.close() + return tmp_filename + +def parse_xml( file_name ): + """Returns a parsed xml tree with comments intact.""" + try: + fobj = open( file_name, 'r' ) + tree = XmlET.parse( fobj, parser=CommentedTreeBuilder() ) + fobj.close() + except Exception, e: + log.exception( "Exception attempting to parse %s: %s" % ( str( file_name ), str( e ) ) ) + return None + return tree + +def xml_to_string( elem, encoding='utf-8' ): + return '%s\n' % xml.etree.ElementTree.tostring( elem, encoding=encoding ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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