1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d7580315fa20/ changeset: d7580315fa20 user: greg date: 2012-06-05 18:51:54 summary: Fixes for handling tool shed repository files that have been renamed or deleted. affected #: 3 files
diff -r f551610b687003fc09cd6ff7bbc506d237c67a75 -r d7580315fa206bcc64bc7607ee52bccfbf95e42f lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -856,14 +856,26 @@ response.close() return ctx_rev def get_named_tmpfile_from_ctx( ctx, filename, dir ): - fctx = ctx[ filename ] - fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return tmp_filename + filename = strip_path( filename ) + for ctx_file in ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if filename == ctx_file_name: + try: + # If the file was moved, its destination file contents will be returned here. + fctx = ctx[ ctx_file ] + except LookupError, e: + # Continue looking in case the file was moved. + fctx = None + continue + if fctx: + fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return tmp_filename + return None def get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): sa_session = app.model.context.current if tool_shed.find( '//' ) > 0:
diff -r f551610b687003fc09cd6ff7bbc506d237c67a75 -r d7580315fa206bcc64bc7607ee52bccfbf95e42f lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -529,17 +529,22 @@ def get_file_context_from_ctx( ctx, filename ): # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to - # the latter: - # ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample'] + # the latter: ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']. Another scenario + # is that the file has been deleted. + deleted = False filename = strip_path( filename ) for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) if filename == ctx_file_name: try: + # If the file was moved, its destination will be returned here. fctx = ctx[ ctx_file ] return fctx except LookupError, e: - return 'DELETED' + # Set deleted for now, and continue looking in case the file was moved instead of deleted. + deleted = True + if deleted: + return 'DELETED' return None def get_latest_repository_metadata( trans, id ): """Get last metadata defined for a specified repository from the database""" @@ -772,37 +777,37 @@ def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): """ Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision - is a valid (downloadable) changset revision. If changeset_revision is the repository tip, then the tool will be loaded from it's file on disk. - Otherwise, the tool config will be located in the repository manifest between the received valid changeset revision and the previous valid - changeset revision (if one exists) or the first changeset revision in the repository (if one doesn't). + is a valid (downloadable) changset revision. The tool config will be located in the repository manifest between the received valid changeset + revision and the first changeset revision in the repository, searching backwards. """ def load_from_tmp_config( ctx, ctx_file, work_dir ): tool = None message = '' tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) - element_tree = util.parse_xml( tmp_tool_config ) - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. - tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) - if tmp_code_file_name: - tmp_code_files.append( tmp_code_file_name ) - try: - tool = load_tool( trans, tmp_tool_config ) - except Exception, e: - tool = None - message = "Error loading tool: %s. " % str( e ) - for tmp_code_file in tmp_code_files: + if tmp_tool_config: + element_tree = util.parse_xml( tmp_tool_config ) + element_tree_root = element_tree.getroot() + # Look for code files required by the tool config. + tmp_code_files = [] + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + if tmp_code_file_name: + tmp_code_files.append( tmp_code_file_name ) try: - os.unlink( tmp_code_file ) + tool = load_tool( trans, tmp_tool_config ) + except Exception, e: + tool = None + message = "Error loading tool: %s. " % str( e ) + for tmp_code_file in tmp_code_files: + try: + os.unlink( tmp_code_file ) + except: + pass + try: + os.unlink( tmp_tool_config ) except: pass - try: - os.unlink( tmp_tool_config ) - except: - pass return tool, message tool_config_filename = strip_path( tool_config_filename ) repository = get_repository( trans, repository_id ) @@ -842,41 +847,42 @@ valid = False error_message = '' tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir ) - if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] - or check_bz2( tmp_config )[ 0 ] or check_zip( tmp_config ) ): - try: - # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( tmp_config ) - element_tree_root = element_tree.getroot() - is_tool_config = element_tree_root.tag == 'tool' - except Exception, e: - log.debug( "Error parsing %s, exception: %s" % ( tmp_config, str( e ) ) ) - is_tool_config = False - if is_tool_config: - # Load entries into the tool_data_tables if the tool requires them. - tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', dir ) - if tool_data_table_config: - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - # Look for code files required by the tool config. The directory to which dir refers should be removed by the caller. - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - if not os.path.exists( os.path.join( dir, code_file_name ) ): - tmp_code_file_name = copy_file_from_disk( code_file_name, repo_dir, dir ) - if tmp_code_file_name is None: - tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, dir ) + if tmp_config: + if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] + or check_bz2( tmp_config )[ 0 ] or check_zip( tmp_config ) ): try: - tool = load_tool( trans, tmp_config ) - valid = True - except KeyError, e: - valid = False - error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) - error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' - error_message += 'this error. ' + # Make sure we're looking at a tool config and not a display application config or something else. + element_tree = util.parse_xml( tmp_config ) + element_tree_root = element_tree.getroot() + is_tool_config = element_tree_root.tag == 'tool' except Exception, e: - valid = False - error_message = str( e ) - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( trans.app ) + log.debug( "Error parsing %s, exception: %s" % ( tmp_config, str( e ) ) ) + is_tool_config = False + if is_tool_config: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', dir ) + if tool_data_table_config: + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) + # Look for code files required by the tool config. The directory to which dir refers should be removed by the caller. + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + if not os.path.exists( os.path.join( dir, code_file_name ) ): + tmp_code_file_name = copy_file_from_disk( code_file_name, repo_dir, dir ) + if tmp_code_file_name is None: + tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, dir ) + try: + tool = load_tool( trans, tmp_config ) + valid = True + except KeyError, e: + valid = False + error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) + error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' + error_message += 'this error. ' + except Exception, e: + valid = False + error_message = str( e ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) return is_tool_config, valid, tool, error_message def new_tool_metadata_required( trans, id, metadata_dict ): """
diff -r f551610b687003fc09cd6ff7bbc506d237c67a75 -r d7580315fa206bcc64bc7607ee52bccfbf95e42f lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -10,7 +10,7 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_named_tmpfile_from_ctx, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path +from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path from galaxy.tool_shed.encoding_util import * from common import *
@@ -1257,12 +1257,6 @@ repo = hg.repository( get_configured_ui(), repo_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) invalid_message = '' - work_dir = make_tmp_directory() - for filename in ctx: - ctx_file_name = strip_path( filename ) - if ctx_file_name == tool_config: - tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, work_dir ) - break metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, repo, repository_id, @@ -1275,17 +1269,11 @@ invalid_tool_config_name = strip_path( invalid_tool_config ) if tool_config == invalid_tool_config_name: invalid_message = invalid_msg - break + break tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) - #if error_message: - # message += error_message tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) try: - shutil.rmtree( work_dir ) - except: - pass - try: if invalid_message: message = invalid_message return trans.fill_template( "/webapps/community/repository/tool_form.mako",
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.