[galaxy-commits] commit/galaxy-central: greg: Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively.

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/fdaad2cad392/ Changeset: fdaad2cad392 User: greg Date: 2014-06-24 19:11:24 Summary: Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively. Affected #: 10 files

diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -10,14 +10,14 @@ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest from galaxy.web.framework.helpers import time_ago +from tool_shed.capsule import capsule_manager import tool_shed.repository_types.util as rt_util -import tool_shed.util.shed_util_common as suc from tool_shed.util import basic_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util

log = logging.getLogger( __name__ ) @@ -248,10 +248,14 @@ except tarfile.ReadError, e: log.debug( 'Error opening capsule file %s: %s' % ( str( capsule_file_name ), str( e ) ) ) return {} + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) capsule_dict[ 'tar_archive' ] = tar_archive capsule_dict[ 'capsule_file_name' ] = capsule_file_name - capsule_dict = import_util.extract_capsule_files( **capsule_dict ) - capsule_dict = import_util.validate_capsule( **capsule_dict ) + capsule_dict = irm.extract_capsule_files( **capsule_dict ) + capsule_dict = irm.validate_capsule( **capsule_dict ) status = capsule_dict.get( 'status', 'error' ) if status == 'error': log.debug( 'The capsule contents are invalid and cannot be imported:<br/>%s' % \ @@ -263,15 +267,12 @@ return {} file_path = encoding_util.tool_shed_decode( encoded_file_path ) export_info_file_path = os.path.join( file_path, 'export_info.xml' ) - export_info_dict = import_util.get_export_info_dict( export_info_file_path ) + export_info_dict = irm.get_export_info_dict( export_info_file_path ) manifest_file_path = os.path.join( file_path, 'manifest.xml' ) # The manifest.xml file has already been validated, so no error_message should be returned here. - repository_info_dicts, error_message = import_util.get_repository_info_from_manifest( manifest_file_path ) + repository_info_dicts, error_message = irm.get_repository_info_from_manifest( manifest_file_path ) # Determine the status for each exported repository archive contained within the capsule. - repository_status_info_dicts = import_util.get_repository_status_from_tool_shed( trans.app, - trans.user, - trans.user_is_admin(), - repository_info_dicts ) + repository_status_info_dicts = irm.get_repository_status_from_tool_shed( repository_info_dicts ) # Generate a list of repository name / import results message tuples for display after the capsule is imported. import_results_tups = [] # Only create repositories that do not yet exist and that the current user is authorized to create. The @@ -280,12 +281,9 @@ # Add the capsule_file_name and encoded_file_path to the repository_status_info_dict. repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path - import_results_tups = import_util.create_repository_and_import_archive( trans.app, - trans.request.host, - trans.user, - repository_status_info_dict, - import_results_tups ) - import_util.check_status_and_reset_downloadable( trans.app, import_results_tups ) + import_results_tups = irm.create_repository_and_import_archive( repository_status_info_dict, + import_results_tups ) + irm.check_status_and_reset_downloadable( import_results_tups ) basic_util.remove_dir( file_path ) # NOTE: the order of installation is defined in import_results_tups, but order will be lost # when transferred to return_dict.

diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -5,7 +5,7 @@ from galaxy import util from galaxy.model.orm import and_, not_, select from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest -from tool_shed.util import export_util +from tool_shed.capsule import capsule_manager from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc

@@ -53,15 +53,14 @@ log.debug( error_message ) return None, error_message repository_id = trans.security.encode_id( repository.id ) - return export_util.export_repository( trans.app, - trans.user, - tool_shed_url, - repository_id, - str( repository.name ), - changeset_revision, - file_type, - export_repository_dependencies, - api=True ) + erm = capsule_manager.ExportRepositoryManager( app=trans.app, + user=trans.user, + tool_shed_url=tool_shed_url, + repository=repository, + changeset_revision=changeset_revision, + export_repository_dependencies=export_repository_dependencies, + using_api=True ) + return erm.export_repository()

def __get_value_mapper( self, trans ): value_mapper = { 'id' : trans.security.encode_id,

diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 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 @@ -14,20 +14,19 @@ from galaxy.web.framework.helpers import grids from galaxy.util import json from galaxy.model.orm import and_ -import tool_shed.util.shed_util_common as suc +from tool_shed.capsule import capsule_manager from tool_shed.util import basic_util from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import encoding_util -from tool_shed.util import export_util from tool_shed.util import hg_util -from tool_shed.util import import_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 shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import workflow_util @@ -1149,7 +1148,7 @@ # server account's .hgrc file to include the following setting: # [web] # allow_archive = bz2, gz, zip - file_type_str = export_util.get_file_type_str( changeset_revision, file_type ) + file_type_str = basic_util.get_file_type_str( changeset_revision, file_type ) repository.times_downloaded += 1 trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1172,15 +1171,14 @@ file_type = 'gz' export_repository_dependencies = CheckboxField.is_checked( export_repository_dependencies ) tool_shed_url = web.url_for( '/', qualified=True ) - repositories_archive, error_message = export_util.export_repository( trans.app, - trans.user, - tool_shed_url, - repository_id, - str( repository.name ), - changeset_revision, - file_type, - export_repository_dependencies, - api=False ) + erm = capsule_manager.ExportRepositoryManager( app=trans.app, + user=trans.user, + tool_shed_url=tool_shed_url, + repository=repository, + changeset_revision=changeset_revision, + export_repository_dependencies=export_repository_dependencies, + using_api=False ) + repositories_archive, error_message = erm.export_repository() repositories_archive_filename = os.path.basename( repositories_archive.name ) if error_message: message = error_message @@ -1969,15 +1967,16 @@ encoded_file_path = kwd.get( 'encoded_file_path', None ) file_path = encoding_util.tool_shed_decode( encoded_file_path ) export_info_file_path = os.path.join( file_path, 'export_info.xml' ) - export_info_dict = import_util.get_export_info_dict( export_info_file_path ) + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) + export_info_dict = irm.get_export_info_dict( export_info_file_path ) manifest_file_path = os.path.join( file_path, 'manifest.xml' ) # The manifest.xml file has already been validated, so no error_message should be returned here. - repository_info_dicts, error_message = import_util.get_repository_info_from_manifest( manifest_file_path ) + repository_info_dicts, error_message = irm.get_repository_info_from_manifest( manifest_file_path ) # Determine the status for each exported repository archive contained within the capsule. - repository_status_info_dicts = import_util.get_repository_status_from_tool_shed( trans.app, - trans.user, - trans.user_is_admin(), - repository_info_dicts ) + repository_status_info_dicts = irm.get_repository_status_from_tool_shed( repository_info_dicts ) if 'import_capsule_button' in kwd: # Generate a list of repository name / import results message tuples for display after the capsule is imported. import_results_tups = [] @@ -1987,12 +1986,9 @@ # Add the capsule_file_name and encoded_file_path to the repository_status_info_dict. repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path - import_results_tups = import_util.create_repository_and_import_archive( trans.app, - trans.request.host, - trans.user, - repository_status_info_dict, - import_results_tups ) - import_util.check_status_and_reset_downloadable( trans.app, import_results_tups ) + import_results_tups = irm.create_repository_and_import_archive( repository_status_info_dict, + import_results_tups ) + irm.check_status_and_reset_downloadable( import_results_tups ) basic_util.remove_dir( file_path ) return trans.fill_template( '/webapps/tool_shed/repository/import_capsule_results.mako', export_info_dict=export_info_dict, @@ -3081,13 +3077,17 @@ status = kwd.get( 'status', 'done' ) url = kwd.get( 'url', '' ) if 'upload_capsule_button' in kwd: - capsule_dict = import_util.upload_capsule( **kwd ) + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) + capsule_dict = irm.upload_capsule( **kwd ) status = capsule_dict.get( 'status', 'error' ) if status == 'error': message = capsule_dict.get( 'error_message', '' ) else: - capsule_dict = import_util.extract_capsule_files( **capsule_dict ) - capsule_dict = import_util.validate_capsule( **capsule_dict ) + capsule_dict = irm.extract_capsule_files( **capsule_dict ) + capsule_dict = irm.validate_capsule( **capsule_dict ) status = capsule_dict.get( 'status', 'error' ) if status == 'ok': return trans.response.send_redirect( web.url_for( controller='repository',

diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/capsule/capsule_manager.py --- /dev/null +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -0,0 +1,867 @@ +import logging +import os +import shutil +import tarfile +import tempfile +import threading +import urllib +from time import gmtime +from time import strftime +import tool_shed.repository_types.util as rt_util +from galaxy import web +from galaxy.util import asbool +from galaxy.util import CHUNK_SIZE +from galaxy.util.odict import odict +from tool_shed.dependencies import dependency_manager +from tool_shed.util import basic_util +from tool_shed.util import commit_util +from tool_shed.util import common_util +from tool_shed.util import encoding_util +from tool_shed.util import hg_util +from tool_shed.util import metadata_util +from tool_shed.util import repository_dependency_util +from tool_shed.util import repository_maintenance_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util +from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager + +log = logging.getLogger( __name__ ) + + +class ExportedRepositoryRegistry( object ): + + def __init__( self ): + self.exported_repository_elems = [] + +class ExportRepositoryManager( object ): + + def __init__( self, app, user, tool_shed_url, repository, changeset_revision, export_repository_dependencies, using_api ): + self.app = app + self.capsule_filename = 'capsule' + self.capsule_with_dependencies_filename = 'capsule_with_dependencies' + self.changeset_revision = changeset_revision + self.export_repository_dependencies = asbool( export_repository_dependencies ) + self.file_type = 'gz' + self.repository = repository + self.repository_id = self.app.security.encode_id( repository.id ) + self.tool_shed_url = tool_shed_url + self.user = user + self.using_api = using_api + + def export_repository( self ): + repositories_archive_filename = self.generate_repository_archive_filename( use_tmp_archive_dir=True ) + if self.export_repository_dependencies: + repo_info_dicts = self.get_repo_info_dicts() + repository_ids = self.get_repository_ids( repo_info_dicts ) + ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ + self.order_components_for_import( repository_ids, repo_info_dicts ) + else: + ordered_repository_ids = [] + ordered_repositories = [] + ordered_changeset_revisions = [] + if self.repository: + repository_metadata = \ + suc.get_current_repository_metadata_for_changeset_revision( self.app, + self.repository, + self.changeset_revision ) + if repository_metadata: + ordered_repository_ids = [ self.repository_id ] + ordered_repositories = [ self.repository ] + ordered_changeset_revisions = [ repository_metadata.changeset_revision ] + repositories_archive = None + error_messages = '' + lock = threading.Lock() + lock.acquire( True ) + try: + repositories_archive = tarfile.open( repositories_archive_filename, "w:%s" % self.file_type ) + exported_repository_registry = ExportedRepositoryRegistry() + for index, repository_id in enumerate( ordered_repository_ids ): + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" ) + ordered_repository = ordered_repositories[ index ] + ordered_changeset_revision = ordered_changeset_revisions[ index ] + repository_archive, error_message = self.generate_repository_archive( ordered_repository, + ordered_changeset_revision, + work_dir ) + if error_message: + error_messages = '%s %s' % ( error_messages, error_message ) + else: + archive_name = str( os.path.basename( repository_archive.name ) ) + repositories_archive.add( repository_archive.name, arcname=archive_name ) + attributes, sub_elements = self.get_repository_attributes_and_sub_elements( ordered_repository, + archive_name ) + elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) + exported_repository_registry.exported_repository_elems.append( elem ) + basic_util.remove_dir( work_dir ) + # Keep information about the export in a file named export_info.xml in the archive. + sub_elements = self.generate_export_elem() + export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements ) + tmp_export_info = xml_util.create_and_write_tmp_file( export_elem, use_indent=True ) + repositories_archive.add( tmp_export_info, arcname='export_info.xml' ) + # Write the manifest, which must preserve the order in which the repositories should be imported. + exported_repository_root = xml_util.create_element( 'repositories' ) + for exported_repository_elem in exported_repository_registry.exported_repository_elems: + exported_repository_root.append( exported_repository_elem ) + tmp_manifest = xml_util.create_and_write_tmp_file( exported_repository_root, use_indent=True ) + repositories_archive.add( tmp_manifest, arcname='manifest.xml' ) + except Exception, e: + log.exception( str( e ) ) + finally: + lock.release() + if repositories_archive is not None: + repositories_archive.close() + if self.using_api: + encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename ) + params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name + download_url = common_util.url_join( web.url_for( '/', qualified=True ), + 'repository/export_via_api%s' % params ) + return dict( download_url=download_url, error_messages=error_messages ) + return repositories_archive, error_messages + + def generate_export_elem( self ): + sub_elements = odict() + sub_elements[ 'export_time' ] = strftime( '%a, %d %b %Y %H:%M:%S +0000', gmtime() ) + sub_elements[ 'tool_shed' ] = str( self.tool_shed_url.rstrip( '/' ) ) + sub_elements[ 'repository_name' ] = str( self.repository.name ) + sub_elements[ 'repository_owner' ] = str( self.repository.user.username ) + sub_elements[ 'changeset_revision' ] = str( self.changeset_revision ) + sub_elements[ 'export_repository_dependencies' ] = str( self.export_repository_dependencies ) + sub_elements[ 'exported_via_api' ] = str( self.using_api ) + return sub_elements + + def generate_repository_archive( self, repository, changeset_revision, work_dir ): + rdah = dependency_manager.RepositoryDependencyAttributeHandler( self.app, unpopulate=True ) + tdah = dependency_manager.ToolDependencyAttributeHandler( self.app, unpopulate=True ) + file_type_str = basic_util.get_file_type_str( changeset_revision, self.file_type ) + file_name = '%s-%s' % ( repository.name, file_type_str ) + return_code, error_message = hg_util.archive_repository_revision( self.app, + repository, + work_dir, + changeset_revision ) + if return_code: + return None, error_message + repository_archive_name = os.path.join( work_dir, file_name ) + # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files. + repository_archive = tarfile.open( repository_archive_name, "w:%s" % self.file_type ) + for root, dirs, files in os.walk( work_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + for dir in dirs: + if dir in commit_util.UNDESIRABLE_DIRS: + dirs.remove( dir ) + for name in files: + name = str( name ) + if str( name ) in commit_util.UNDESIRABLE_FILES: + continue + full_path = os.path.join( root, name ) + relative_path = full_path.replace( work_dir, '' ).lstrip( '/' ) + # See if we have a repository dependencies defined. + if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. + altered, root_elem, error_message = rdah.handle_tag_attributes( full_path ) + if error_message: + return None, error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) + shutil.move( tmp_filename, full_path ) + elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. + altered, root_elem, error_message = tdah.handle_tag_attributes( full_path ) + if error_message: + return None, error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) + shutil.move( tmp_filename, full_path ) + repository_archive.add( full_path, arcname=relative_path ) + repository_archive.close() + return repository_archive, error_message + + def generate_repository_archive_filename( self, use_tmp_archive_dir=False ): + tool_shed = self.remove_protocol_from_tool_shed_url() + file_type_str = basic_util.get_file_type_str( self.changeset_revision, self.file_type ) + if self.export_repository_dependencies: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( self.capsule_with_dependencies_filename, + tool_shed, + str( self.repository.name ), + str( self.repository.user.username ), + file_type_str ) + else: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( self.capsule_filename, + tool_shed, + str( self.repository.name ), + str( self.repository.user.username ), + file_type_str ) + if use_tmp_archive_dir: + tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) + repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) + return repositories_archive_filename + + def get_components_from_repo_info_dict( self, repo_info_dict ): + """ + Return the repository and the associated latest installable changeset_revision (including + # updates) for the repository defined by the received repo_info_dict. + """ + for repository_name, repo_info_tup in repo_info_dict.items(): + # There should only be one entry in the received repo_info_dict. + description, \ + repository_clone_url, \ + changeset_revision, \ + ctx_rev, \ + repository_owner, \ + repository_dependencies, \ + tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner ) + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( self.app, + repository, + changeset_revision ) + if repository_metadata: + return repository, repository_metadata.changeset_revision + return None, None + + def get_repo_info_dict_for_import( self, encoded_repository_id, encoded_repository_ids, repo_info_dicts ): + """ + The received encoded_repository_ids and repo_info_dicts are lists that contain associated + elements at each location in the list. This method will return the element from repo_info_dicts + associated with the received encoded_repository_id by determining its location in the received + encoded_repository_ids list. + """ + for index, repository_id in enumerate( encoded_repository_ids ): + if repository_id == encoded_repository_id: + repo_info_dict = repo_info_dicts[ index ] + return repo_info_dict + return None + + def get_repo_info_dicts( self ): + """ + Return a list of dictionaries defining repositories that are required by the repository + associated with self.repository_id. + """ + rdm = RepositoryDependencyManager( self.app ) + repository = suc.get_repository_in_tool_shed( self.app, self.repository_id ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.repository_id, + self.changeset_revision ) + # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=self.app, + repository=self.repository, + repository_metadata=repository_metadata, + toolshed_base_url=toolshed_base_url, + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None ) + repo = hg_util.get_repo_for_repository( self.app, + repository=self.repository, + repo_path=None, + create=False ) + ctx = hg_util.get_changectx_for_changeset( repo, self.changeset_revision ) + repo_info_dict = {} + # Cast unicode to string. + repo_info_dict[ str( repository.name ) ] = ( str( self.repository.description ), + common_util.generate_clone_url_for_repository_in_tool_shed( self.user, + self.repository ), + str( self.changeset_revision ), + str( ctx.rev() ), + str( self.repository.user.username ), + repository_dependencies, + None ) + all_required_repo_info_dict = rdm.get_required_repo_info_dicts( self.tool_shed_url, [ repo_info_dict ] ) + all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] ) + return all_repo_info_dicts + + def get_repository_attributes_and_sub_elements( self, repository, archive_name ): + """ + Get the information about a repository to create and populate an XML tag set. The + generated attributes will be contained within the <repository> tag, while the sub_elements + will be tag sets contained within the <repository> tag set. + """ + attributes = odict() + sub_elements = odict() + attributes[ 'name' ] = str( repository.name ) + attributes[ 'type' ] = str( repository.type ) + # We have to associate the public username since the user_id will be different between tool sheds. + attributes[ 'username' ] = str( repository.user.username ) + # Don't coerce description or long description from unicode to string because the fields are free text. + sub_elements[ 'description' ] = repository.description + sub_elements[ 'long_description' ] = repository.long_description + sub_elements[ 'archive' ] = archive_name + # Keep track of Category associations. + categories = [] + for rca in repository.categories: + category = rca.category + categories.append( ( 'category', str( category.name ) ) ) + sub_elements[ 'categories' ] = categories + return attributes, sub_elements + + def get_repository_ids( self, repo_info_dicts ): + """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" + repository_ids = [] + for repo_info_dict in repo_info_dicts: + for repository_name, repo_info_tup in repo_info_dict.items(): + description, \ + repository_clone_url, \ + changeset_revision, \ + ctx_rev, \ + repository_owner, \ + repository_dependencies, \ + tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner ) + repository_ids.append( self.app.security.encode_id( repository.id ) ) + return repository_ids + + def order_components_for_import( self, repository_ids, repo_info_dicts ): + """ + Some repositories may have repository dependencies that must be imported and have metadata set on + them before the dependent repository is imported. This method will inspect the list of repositories + about to be exported and make sure to order them appropriately for proper import. For each repository + about to be exported, if required repositories are not contained in the list of repositories about to + be exported, then they are not considered. Repository dependency definitions that contain circular + dependencies should not result in an infinite loop, but obviously ordering the list will not be handled + for one or more of the repositories that require prior import. + """ + # The received list of repository_ids are the ids of all of the primary exported repository's + # repository dependencies. The primary repository will always be last in the returned lists. + ordered_repository_ids = [] + ordered_repositories = [] + ordered_changeset_revisions = [] + # Create a dictionary whose keys are the received repository_ids and whose values are a list of + # repository_ids, each of which is contained in the received list of repository_ids and whose associated + # repository must be imported prior to the repository associated with the repository_id key. + prior_import_required_dict = suc.get_prior_import_or_install_required_dict( self.app, + repository_ids, + repo_info_dicts ) + processed_repository_ids = [] + # Process the list of repository dependencies defined for the primary exported repository. + while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ): + repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict, + processed_repository_ids ) + if repository_id == self.repository_id: + # Append self.repository_id without processing it since it must be returned last in the order. + # It will be processed below after all dependencies are processed. + processed_repository_ids.append( self.repository_id ) + continue + processed_repository_ids.append( repository_id ) + if repository_id not in ordered_repository_ids: + prior_import_required_ids = prior_import_required_dict[ repository_id ] + for prior_import_required_id in prior_import_required_ids: + if prior_import_required_id not in ordered_repository_ids: + # Import the associated repository dependency first. + prior_repo_info_dict = \ + self.get_repo_info_dict_for_import( prior_import_required_id, + repository_ids, + repo_info_dicts ) + prior_repository, prior_import_changeset_revision = \ + self.get_components_from_repo_info_dict( prior_repo_info_dict ) + if prior_repository and prior_import_changeset_revision: + ordered_repository_ids.append( prior_import_required_id ) + ordered_repositories.append( prior_repository ) + ordered_changeset_revisions.append( prior_import_changeset_revision ) + repo_info_dict = self.get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts ) + repository, changeset_revision = self.get_components_from_repo_info_dict( repo_info_dict ) + if repository and changeset_revision: + ordered_repository_ids.append( repository_id ) + ordered_repositories.append( repository ) + ordered_changeset_revisions.append( changeset_revision ) + # Process the repository associated with self.repository_id last. + repo_info_dict = self.get_repo_info_dict_for_import( self.repository_id, repository_ids, repo_info_dicts ) + repository, changeset_revision = self.get_components_from_repo_info_dict( repo_info_dict ) + if repository and changeset_revision: + ordered_repository_ids.append( repository_id ) + ordered_repositories.append( repository ) + ordered_changeset_revisions.append( changeset_revision ) + return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions + + def remove_protocol_from_tool_shed_url( self ): + protocol, base = self.tool_shed_url.split( '://' ) + base = base.replace( ':', '_colon_' ) + base = base.rstrip( '/' ) + return base + + +class ImportRepositoryManager( object ): + + def __init__( self, app, host, user, user_is_admin ): + self.app = app + self.host = host + self.user = user + self.user_is_admin = user_is_admin + + def check_status_and_reset_downloadable( self, import_results_tups ): + """Check the status of each imported repository and set downloadable to False if errors.""" + sa_session = self.app.model.context.current + flush = False + for import_results_tup in import_results_tups: + ok, name_owner, message = import_results_tup + name, owner = name_owner + if not ok: + repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) + if repository is not None: + # Do not allow the repository to be automatically installed if population resulted in errors. + tip_changeset_revision = repository.tip( self.app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.app.security.encode_id( repository.id ), + tip_changeset_revision ) + if repository_metadata: + if repository_metadata.downloadable: + repository_metadata.downloadable = False + sa_session.add( repository_metadata ) + if not flush: + flush = True + # Do not allow dependent repository revisions to be automatically installed if population + # resulted in errors. + dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( self.app, repository_metadata ) + for dependent_downloadable_revision in dependent_downloadable_revisions: + if dependent_downloadable_revision.downloadable: + dependent_downloadable_revision.downloadable = False + sa_session.add( dependent_downloadable_revision ) + if not flush: + flush = True + if flush: + sa_session.flush() + + def create_repository_and_import_archive( self, repository_archive_dict, import_results_tups ): + """ + Create a new repository in the tool shed and populate it with the contents of a gzip compressed + tar archive that was exported as part or all of the contents of a capsule. + """ + results_message = '' + name = repository_archive_dict.get( 'name', None ) + username = repository_archive_dict.get( 'owner', None ) + if name is None or username is None: + ok = False + results_message += 'Import failed: required repository name <b>%s</b> or owner <b>%s</b> is missing.' % \ + ( str( name ), str( username )) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + status = repository_archive_dict.get( 'status', None ) + if status is None: + # The repository does not yet exist in this Tool Shed and the current user is authorized to import + # the current archive file. + type = repository_archive_dict.get( 'type', 'unrestricted' ) + description = repository_archive_dict.get( 'description', '' ) + long_description = repository_archive_dict.get( 'long_description', '' ) + # The owner entry in the repository_archive_dict is the public username of the user associated with + # the exported repository archive. + user = suc.get_user_by_username( self.app, username ) + if user is None: + ok = False + results_message += 'Import failed: repository owner <b>%s</b> does not have an account in this Tool Shed.' % \ + str( username ) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + user_id = user.id + # The categories entry in the repository_archive_dict is a list of category names. If a name does not + # exist in the current Tool Shed, the category will not be created, so it will not be associated with + # the repository. + category_ids = [] + category_names = repository_archive_dict.get( 'category_names', [] ) + for category_name in category_names: + category = suc.get_category_by_name( self.app, category_name ) + if category is None: + results_message += 'This Tool Shed does not have the category <b>%s</b> so it ' % str( category_name ) + results_message += 'will not be associated with this repository.' + else: + category_ids.append( self.app.security.encode_id( category.id ) ) + # Create the repository record in the database. + repository, create_message = repository_maintenance_util.create_repository( self.app, + name, + type, + description, + long_description, + user_id=user_id, + category_ids=category_ids ) + if create_message: + results_message += create_message + # Populate the new repository with the contents of exported repository archive. + results_dict = self.import_repository_archive( repository, repository_archive_dict ) + ok = results_dict.get( 'ok', False ) + error_message = results_dict.get( 'error_message', '' ) + if error_message: + results_message += error_message + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + # The repository either already exists in this Tool Shed or the current user is not authorized to create it. + ok = True + results_message += 'Import not necessary: repository status for this Tool Shed is: %s.' % str( status ) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + return import_results_tups + + def extract_capsule_files( self, **kwd ): + """ + Extract the uploaded capsule archive into a temporary location for inspection, validation + and potential import. + """ + return_dict = {} + tar_archive = kwd.get( 'tar_archive', None ) + capsule_file_name = kwd.get( 'capsule_file_name', None ) + if tar_archive is not None and capsule_file_name is not None: + return_dict.update( kwd ) + extract_directory_path = tempfile.mkdtemp( prefix="tmp-capsule-ecf" ) + if capsule_file_name.endswith( '.tar.gz' ): + extract_directory_name = capsule_file_name.replace( '.tar.gz', '' ) + elif capsule_file_name.endswith( '.tar' ): + extract_directory_name = capsule_file_name.replace( '.tar', '' ) + else: + extract_directory_name = capsule_file_name + file_path = os.path.join( extract_directory_path, extract_directory_name ) + return_dict[ 'encoded_file_path' ] = encoding_util.tool_shed_encode( file_path ) + tar_archive.extractall( path=file_path ) + try: + tar_archive.close() + except Exception, e: + log.exception( "Cannot close tar_archive: %s" % str( e ) ) + del return_dict[ 'tar_archive' ] + return return_dict + + def get_archives_from_manifest( self, manifest_file_path ): + """ + Return the list of archive names defined in the capsule manifest. This method will validate + the manifest by ensuring all <repository> tag sets contain a valid <archive> sub-element. + """ + archives = [] + error_message = '' + manifest_tree, error_message = xml_util.parse_xml( manifest_file_path ) + if error_message: + return archives, error_message + manifest_root = manifest_tree.getroot() + for elem in manifest_root: + # <repository name="package_lapack_3_4" type="tool_dependency_definition" username="test"> + if elem.tag != 'repository': + error_message = 'All level one sub-elements in the manifest.xml file must be <repository> tag sets. ' + error_message += 'The tag <b><%s></b> is invalid.' % str( elem.tag ) + return [], error_message + archive_file_name = None + for repository_elem in elem: + if repository_elem.tag == 'archive': + # <archive>package_lapack_3_4-9e7a45ad3522.tar.gz</archive> + archive_file_name = repository_elem.text + break + if archive_file_name is None: + error_message = 'The %s tag set is missing a required <archive> sub-element.' % str( elem.tag ) + return [], error_message + archives.append( archive_file_name ) + return archives, error_message + + def get_export_info_dict( self, export_info_file_path ): + """ + Parse the export_info.xml file contained within the capsule and return a dictionary + containing its entries. + """ + export_info_tree, error_message = xml_util.parse_xml( export_info_file_path ) + export_info_root = export_info_tree.getroot() + export_info_dict = {} + for elem in export_info_root: + if elem.tag == 'export_time': + export_info_dict[ 'export_time' ] = elem.text + elif elem.tag == 'tool_shed': + export_info_dict[ 'tool_shed' ] = elem.text + elif elem.tag == 'repository_name': + export_info_dict[ 'repository_name' ] = elem.text + elif elem.tag == 'repository_owner': + export_info_dict[ 'repository_owner' ] = elem.text + elif elem.tag == 'changeset_revision': + export_info_dict[ 'changeset_revision' ] = elem.text + elif elem.tag == 'export_repository_dependencies': + if asbool( elem.text ): + export_info_dict[ 'export_repository_dependencies' ] = 'Yes' + else: + export_info_dict[ 'export_repository_dependencies' ] = 'No' + return export_info_dict + + def get_repository_info_from_manifest( self, manifest_file_path ): + """ + Parse the capsule manifest and return a list of dictionaries containing information about + each exported repository archive contained within the capsule. + """ + repository_info_dicts = [] + manifest_tree, error_message = xml_util.parse_xml( manifest_file_path ) + if error_message: + return repository_info_dicts, error_message + manifest_root = manifest_tree.getroot() + for elem in manifest_root: + # <repository name="package_lapack_3_4" type="tool_dependency_definition" username="test"> + if elem.tag != 'repository': + error_message = 'All level one sub-elements in the manifest.xml file must be <repository> tag sets. ' + error_message += 'The tag <b><%s></b> is invalid.' % str( elem.tag ) + return [], error_message + name = elem.get( 'name', None ) + owner = elem.get( 'username', None ) + type = elem.get( 'type', None ) + if name is None or owner is None or type is None: + error_message = 'Missing required name, type, owner attributes from the tag %s' % str( elem.tag ) + return [], error_message + repository_info_dict = dict( name=name, owner=owner, type=type ) + for repository_elem in elem: + if repository_elem.tag == 'archive': + # <archive>package_lapack_3_4-9e7a45ad3522.tar.gz</archive> + archive_file_name = repository_elem.text + repository_info_dict[ 'archive_file_name' ] = archive_file_name + items = archive_file_name.split( '-' ) + changeset_revision = items[ 1 ].rstrip( '.tar.gz' ) + repository_info_dict [ 'changeset_revision' ] = changeset_revision + elif repository_elem.tag == 'categories': + category_names = [] + for category_elem in repository_elem: + if category_elem.tag == 'category': + category_names.append( category_elem.text ) + repository_info_dict[ 'category_names' ] = category_names + elif repository_elem.tag == 'description': + repository_info_dict[ 'description' ] = repository_elem.text + elif repository_elem.tag == 'long_description': + repository_info_dict[ 'long_description' ] = repository_elem.text + repository_info_dicts.append( repository_info_dict ) + return repository_info_dicts, error_message + + def get_repository_status_from_tool_shed( self, repository_info_dicts ): + """ + For each exported repository archive contained in the capsule, inspect the Tool Shed to + see if that repository already exists or if the current user is authorized to create the + repository and set a status appropriately. If repository dependencies are included in the + capsule, repositories may have various owners. We will keep repositories associated with + owners, so we need to restrict created repositories to those the current user can create. + If the current user is an admin or a member of the IUC, all repositories will be created + no matter the owner. Otherwise only repositories whose associated owner is the current + user will be created. + """ + repository_status_info_dicts = [] + for repository_info_dict in repository_info_dicts: + repository = suc.get_repository_by_name_and_owner( self.app, + repository_info_dict[ 'name' ], + repository_info_dict[ 'owner' ] ) + if repository: + if repository.deleted: + repository_info_dict[ 'status' ] = 'Exists, deleted' + elif repository.deprecated: + repository_info_dict[ 'status' ] = 'Exists, deprecated' + else: + repository_info_dict[ 'status' ] = 'Exists' + else: + # No repository with the specified name and owner currently exists, so make sure + # the current user can create one. + if self.user_is_admin: + repository_info_dict[ 'status' ] = None + elif self.app.security_agent.user_can_import_repository_archive( self.user, + repository_info_dict[ 'owner' ] ): + repository_info_dict[ 'status' ] = None + else: + repository_info_dict[ 'status' ] = 'Not authorized to import' + repository_status_info_dicts.append( repository_info_dict ) + return repository_status_info_dicts + + def import_repository_archive( self, repository, repository_archive_dict ): + """Import a repository archive contained within a repository capsule.""" + rdah = dependency_manager.RepositoryDependencyAttributeHandler( self.app, unpopulate=False ) + tdah = dependency_manager.ToolDependencyAttributeHandler( self.app, unpopulate=False ) + archive_file_name = repository_archive_dict.get( 'archive_file_name', None ) + capsule_file_name = repository_archive_dict[ 'capsule_file_name' ] + encoded_file_path = repository_archive_dict[ 'encoded_file_path' ] + file_path = encoding_util.tool_shed_decode( encoded_file_path ) + results_dict = dict( ok=True, error_message='' ) + archive_file_path = os.path.join( file_path, archive_file_name ) + archive = tarfile.open( archive_file_path, 'r:*' ) + repo_dir = repository.repo_path( self.app ) + repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 + ok, error_message = commit_util.check_archive( repository, archive ) + if ok: + full_path = os.path.abspath( repo_dir ) + filenames_in_archive = [] + for tarinfo_obj in archive.getmembers(): + # Check files and directories in the archive. + ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES + if ok: + for file_path_item in tarinfo_obj.name.split( '/' ): + if file_path_item in commit_util.UNDESIRABLE_DIRS: + undesirable_dirs_removed += 1 + error_message = 'Import failed: invalid file path <b>%s</b> in archive <b>%s</b>' % \ + ( str( file_path_item ), str( archive_file_name ) ) + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + return results_dict + filenames_in_archive.append( tarinfo_obj.name ) + else: + undesirable_files_removed += 1 + # Extract the uploaded archive to the repository root. + archive.extractall( path=full_path ) + archive.close() + for filename in filenames_in_archive: + uploaded_file_name = os.path.join( full_path, filename ) + if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + if altered: + 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 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + commit_message = 'Imported from capsule %s' % str( capsule_file_name ) + # Send email notification to those that have registered to receive alerts for new repositories in this Tool Shed. + new_repo_alert = True + # Since the repository is new, the following must be False. + remove_repo_files_not_in_tar = False + ok, error_message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ + commit_util.handle_directory_changes( self.app, + self.host, + self.user.username, + repository, + full_path, + filenames_in_archive, + remove_repo_files_not_in_tar, + new_repo_alert, + commit_message, + undesirable_dirs_removed, + undesirable_files_removed ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + try: + status, error_message = metadata_util.set_repository_metadata_due_to_new_tip( self.app, + self.host, + self.user, + repository, + content_alert_str=content_alert_str ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + except Exception, e: + log.debug( "Error setting metadata on repository %s created from imported archive %s: %s" % \ + ( str( repository.name ), str( archive_file_name ), str( e ) ) ) + else: + archive.close() + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + return results_dict + + def upload_capsule( self, **kwd ): + """Upload and prepare an exported repository capsule for validation.""" + file_data = kwd.get( 'file_data', '' ) + url = kwd.get( 'url', '' ) + uploaded_file = None + return_dict = dict( error_message='', + encoded_file_path=None, + status='ok', + tar_archive=None, + uploaded_file=None, + capsule_file_name=None ) + if file_data == '' and url == '': + message = 'No files were entered on the import form.' + status = 'error' + elif url: + valid_url = True + try: + stream = urllib.urlopen( url ) + except Exception, e: + valid_url = False + message = 'Error importing file via http: %s' % str( e ) + status = 'error' + if valid_url: + fd, uploaded_file_name = tempfile.mkstemp() + uploaded_file = open( uploaded_file_name, 'wb' ) + while 1: + chunk = stream.read( CHUNK_SIZE ) + if not chunk: + break + uploaded_file.write( chunk ) + uploaded_file.flush() + uploaded_file_filename = url.split( '/' )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + elif file_data not in ( '', None ): + uploaded_file = file_data.file + uploaded_file_name = uploaded_file.name + uploaded_file_filename = os.path.split( file_data.filename )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + if uploaded_file is not None: + if isempty: + uploaded_file.close() + return_dict[ 'error_message' ] = 'Your uploaded capsule file is empty.' + return_dict[ 'status' ] = 'error' + return return_dict + try: + # Open for reading with transparent compression. + tar_archive = tarfile.open( uploaded_file_name, 'r:*' ) + except tarfile.ReadError, e: + error_message = 'Error opening file %s: %s' % ( str( uploaded_file_name ), str( e ) ) + log.exception( error_message ) + return_dict[ 'error_message' ] = error_message + return_dict[ 'status' ] = 'error' + uploaded_file.close() + return return_dict + return_dict[ 'tar_archive' ] = tar_archive + return_dict[ 'capsule_file_name' ] = uploaded_file_filename + uploaded_file.close() + else: + return_dict[ 'error_message' ] = 'No files were entered on the import form.' + return_dict[ 'status' ] = 'error' + return return_dict + return return_dict + + def validate_capsule( self, **kwd ): + """ + Inspect the uploaded capsule's manifest and its contained files to ensure it is a valid + repository capsule. + """ + capsule_dict = {} + capsule_dict.update( kwd ) + encoded_file_path = capsule_dict.get( 'encoded_file_path', '' ) + file_path = encoding_util.tool_shed_decode( encoded_file_path ) + # The capsule must contain a valid XML file named export_info.xml. + export_info_file_path = os.path.join( file_path, 'export_info.xml' ) + export_info_tree, error_message = xml_util.parse_xml( export_info_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # The capsule must contain a valid XML file named manifest.xml. + manifest_file_path = os.path.join( file_path, 'manifest.xml' ) + # Validate the capsule manifest by inspecting name, owner, changeset_revision and type + # information contained within each <repository> tag set. + repository_info_dicts, error_message = self.get_repository_info_from_manifest( manifest_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # Validate the capsule manifest by ensuring all <repository> tag sets contain a valid + # <archive> sub-element. + archives, error_message = self.get_archives_from_manifest( manifest_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # Validate the capsule manifest by ensuring each defined archive file name exists within + # the capsule. + error_message = self.verify_archives_in_capsule( file_path, archives ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + capsule_dict[ 'status' ] = 'ok' + return capsule_dict + + def verify_archives_in_capsule( self, file_path, archives ): + """ + Inspect the files contained within the capsule and make sure each is defined correctly + in the capsule manifest. + """ + error_message = '' + for archive_file_name in archives: + full_path = os.path.join( file_path, archive_file_name ) + if not os.path.exists( full_path ): + error_message = 'The uploaded capsule is invalid because the contained manifest.xml ' + error_message += 'file defines an archive file named <b>%s</b> which ' % str( archive_file_name ) + error_message += 'is not contained within the capsule.' + break + return error_message

diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/scripts/api/export.py --- a/lib/tool_shed/scripts/api/export.py +++ b/lib/tool_shed/scripts/api/export.py @@ -1,6 +1,7 @@ #!/usr/bin/env python """ -Export a specified repository revision and optionally all of its defined repository dependencies from the tool shed into a compressed archive. +Export a specified repository revision and optionally all of its defined repository +dependencies from the tool shed into a compressed archive.

Here is a working example of how to use this script to export a repository from the tool shed. ./export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp @@ -8,15 +9,45 @@

import os import sys +import tempfile import argparse import urllib2 sys.path.insert( 0, os.path.dirname( __file__ ) ) from common import display from common import submit -from tool_shed.util import export_util +from tool_shed.util import basic_util

+CAPSULE_FILENAME = 'capsule' +CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies' CHUNK_SIZE = 2**20 # 1Mb

+def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type, + export_repository_dependencies, use_tmp_archive_dir=False ): + tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url ) + file_type_str = basic_util.get_file_type_str( changeset_revision, file_type ) + if self.export_repository_dependencies: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME, + tool_shed, + name, + owner, + file_type_str ) + else: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_FILENAME, + tool_shed, + name, + owner, + file_type_str ) + if use_tmp_archive_dir: + tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) + repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) + return repositories_archive_filename + +def remove_protocol_from_tool_shed_url( tool_shed_url ): + protocol, base = tool_shed_url.split( '://' ) + base = base.replace( ':', '_colon_' ) + base = base.rstrip( '/' ) + return base + def string_as_bool( string ): if str( string ).lower() in ( 'true', 'yes', 'on' ): return True @@ -50,14 +81,15 @@ if error_messages: print "Error attempting to export revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner, ":\n", error_messages else: + export_repository_dependencies = string_as_bool( options.export_repository_dependencies ) repositories_archive_filename = \ - export_util.generate_repository_archive_filename( base_tool_shed_url, - options.name, - options.owner, - options.changeset_revision, - file_type, - export_repository_dependencies=string_as_bool( options.export_repository_dependencies ), - use_tmp_archive_dir=False ) + generate_repository_archive_filename( base_tool_shed_url, + options.name, + options.owner, + options.changeset_revision, + file_type, + export_repository_dependencies=export_repository_dependencies, + use_tmp_archive_dir=False ) download_url = export_dict[ 'download_url' ] download_dir = os.path.abspath( options.download_dir ) file_path = os.path.join( download_dir, repositories_archive_filename )

diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -45,6 +45,17 @@ env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32 return env_var_dict

+def get_file_type_str( changeset_revision, file_type ): + if file_type == 'zip': + file_type_str = '%s.zip' % changeset_revision + elif file_type == 'bz2': + file_type_str = '%s.tar.bz2' % changeset_revision + elif file_type == 'gz': + file_type_str = '%s.tar.gz' % changeset_revision + else: + file_type_str = '' + return file_type_str + def move_file( current_dir, source, destination, rename_to=None ): source_path = os.path.abspath( os.path.join( current_dir, source ) ) source_file = os.path.basename( source_path )

diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ /dev/null @@ -1,355 +0,0 @@ -import logging -import os -import shutil -import tarfile -import tempfile -import threading -from time import gmtime -from time import strftime -import tool_shed.repository_types.util as rt_util -from galaxy import web -from galaxy.util.odict import odict -from tool_shed.dependencies import dependency_manager -from tool_shed.util import basic_util -from tool_shed.util import commit_util -from tool_shed.util import common_util -from tool_shed.util import encoding_util -from tool_shed.util import hg_util -from tool_shed.util import repository_dependency_util -from tool_shed.util import shed_util_common as suc -from tool_shed.util import xml_util -from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager - -log = logging.getLogger( __name__ ) - -CAPSULE_FILENAME = 'capsule' -CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies' - -class ExportedRepositoryRegistry( object ): - - def __init__( self ): - self.exported_repository_elems = [] - -def export_repository( app, user, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, - export_repository_dependencies, api=False ): - repository = suc.get_repository_in_tool_shed( app, repository_id ) - repositories_archive_filename = generate_repository_archive_filename( tool_shed_url, - str( repository.name ), - str( repository.user.username ), - changeset_revision, - file_type, - export_repository_dependencies=export_repository_dependencies, - use_tmp_archive_dir=True ) - if export_repository_dependencies: - repo_info_dicts = get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ) - repository_ids = get_repository_ids( app, repo_info_dicts ) - ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ - order_components_for_import( app, repository_id, repository_ids, repo_info_dicts ) - else: - ordered_repository_ids = [] - ordered_repositories = [] - ordered_changeset_revisions = [] - if repository: - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, - repository, - changeset_revision ) - if repository_metadata: - ordered_repository_ids = [ repository_id ] - ordered_repositories = [ repository ] - ordered_changeset_revisions = [ repository_metadata.changeset_revision ] - repositories_archive = None - error_messages = '' - lock = threading.Lock() - lock.acquire( True ) - try: - repositories_archive = tarfile.open( repositories_archive_filename, "w:%s" % file_type ) - exported_repository_registry = ExportedRepositoryRegistry() - for index, repository_id in enumerate( ordered_repository_ids ): - work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" ) - ordered_repository = ordered_repositories[ index ] - ordered_changeset_revision = ordered_changeset_revisions[ index ] - repository_archive, error_message = generate_repository_archive( app, - work_dir, - tool_shed_url, - ordered_repository, - ordered_changeset_revision, - file_type ) - if error_message: - error_messages = '%s %s' % ( error_messages, error_message ) - else: - archive_name = str( os.path.basename( repository_archive.name ) ) - repositories_archive.add( repository_archive.name, arcname=archive_name ) - attributes, sub_elements = get_repository_attributes_and_sub_elements( ordered_repository, archive_name ) - elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) - exported_repository_registry.exported_repository_elems.append( elem ) - basic_util.remove_dir( work_dir ) - # Keep information about the export in a file name export_info.xml in the archive. - sub_elements = generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api ) - export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements ) - tmp_export_info = xml_util.create_and_write_tmp_file( export_elem, use_indent=True ) - repositories_archive.add( tmp_export_info, arcname='export_info.xml' ) - # Write the manifest, which must preserve the order in which the repositories should be imported. - exported_repository_root = xml_util.create_element( 'repositories' ) - for exported_repository_elem in exported_repository_registry.exported_repository_elems: - exported_repository_root.append( exported_repository_elem ) - tmp_manifest = xml_util.create_and_write_tmp_file( exported_repository_root, use_indent=True ) - repositories_archive.add( tmp_manifest, arcname='manifest.xml' ) - except Exception, e: - log.exception( str( e ) ) - finally: - lock.release() - repositories_archive.close() - if api: - encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename ) - params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name - download_url = common_util.url_join( web.url_for( '/', qualified=True ), - 'repository/export_via_api%s' % params ) - return dict( download_url=download_url, error_messages=error_messages ) - return repositories_archive, error_messages - -def generate_repository_archive( app, work_dir, tool_shed_url, repository, changeset_revision, file_type ): - rdah = dependency_manager.RepositoryDependencyAttributeHandler( app, unpopulate=True ) - tdah = dependency_manager.ToolDependencyAttributeHandler( app, unpopulate=True ) - file_type_str = get_file_type_str( changeset_revision, file_type ) - file_name = '%s-%s' % ( repository.name, file_type_str ) - return_code, error_message = hg_util.archive_repository_revision( app, - repository, - work_dir, - changeset_revision ) - if return_code: - return None, error_message - repository_archive_name = os.path.join( work_dir, file_name ) - # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files. - repository_archive = tarfile.open( repository_archive_name, "w:%s" % file_type ) - for root, dirs, files in os.walk( work_dir ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - for dir in dirs: - if dir in commit_util.UNDESIRABLE_DIRS: - dirs.remove( dir ) - for name in files: - name = str( name ) - if str( name ) in commit_util.UNDESIRABLE_FILES: - continue - full_path = os.path.join( root, name ) - relative_path = full_path.replace( work_dir, '' ).lstrip( '/' ) - # See if we have a repository dependencies defined. - if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = rdah.handle_tag_attributes( full_path ) - if error_message: - return None, error_message - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) - shutil.move( tmp_filename, full_path ) - elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = tdah.handle_tag_attributes( full_path ) - if error_message: - return None, error_message - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) - shutil.move( tmp_filename, full_path ) - repository_archive.add( full_path, arcname=relative_path ) - repository_archive.close() - return repository_archive, error_message - -def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type, - export_repository_dependencies=False, use_tmp_archive_dir=False ): - tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url ) - file_type_str = get_file_type_str( changeset_revision, file_type ) - if export_repository_dependencies: - repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME, tool_shed, name, owner, file_type_str ) - else: - repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_FILENAME, tool_shed, name, owner, file_type_str ) - if use_tmp_archive_dir: - tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) - repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) - return repositories_archive_filename - -def generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api ): - sub_elements = odict() - sub_elements[ 'export_time' ] = strftime( '%a, %d %b %Y %H:%M:%S +0000', gmtime() ) - sub_elements[ 'tool_shed' ] = str( tool_shed_url.rstrip( '/' ) ) - sub_elements[ 'repository_name' ] = str( repository.name ) - sub_elements[ 'repository_owner' ] = str( repository.user.username ) - sub_elements[ 'changeset_revision' ] = str( changeset_revision ) - sub_elements[ 'export_repository_dependencies' ] = str( export_repository_dependencies ) - sub_elements[ 'exported_via_api' ] = str( api ) - return sub_elements - -def get_components_from_repo_info_dict( app, repo_info_dict ): - """ - Return the repository and the associated latest installable changeset_revision (including updates) for the - repository defined by the received repo_info_dict. - """ - for repository_name, repo_info_tup in repo_info_dict.items(): - # There should only be one entry in the received repo_info_dict. - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, - repository, - changeset_revision ) - if repository_metadata: - return repository, repository_metadata.changeset_revision - return None, None - -def get_file_type_str( changeset_revision, file_type ): - if file_type == 'zip': - file_type_str = '%s.zip' % changeset_revision - elif file_type == 'bz2': - file_type_str = '%s.tar.bz2' % changeset_revision - elif file_type == 'gz': - file_type_str = '%s.tar.gz' % changeset_revision - else: - file_type_str = '' - return file_type_str - -def get_repo_info_dict_for_import( encoded_repository_id, encoded_repository_ids, repo_info_dicts ): - """ - The received encoded_repository_ids and repo_info_dicts are lists that contain associated elements at each - location in the list. This method will return the element from repo_info_dicts associated with the received - encoded_repository_id by determining its location in the received encoded_repository_ids list. - """ - for index, repository_id in enumerate( encoded_repository_ids ): - if repository_id == encoded_repository_id: - repo_info_dict = repo_info_dicts[ index ] - return repo_info_dict - return None - -def get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ): - """ - Return a list of dictionaries defining repositories that are required by the repository associated with the - received repository_id. - """ - rdm = RepositoryDependencyManager( app ) - repository = suc.get_repository_in_tool_shed( app, repository_id ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, repository_id, changeset_revision ) - # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) - repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=toolshed_base_url, - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None ) - repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) - ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = {} - # Cast unicode to string. - repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), - common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ), - str( changeset_revision ), - str( ctx.rev() ), - str( repository.user.username ), - repository_dependencies, - None ) - all_required_repo_info_dict = rdm.get_required_repo_info_dicts( tool_shed_url, [ repo_info_dict ] ) - all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] ) - return all_repo_info_dicts - -def get_repository_attributes_and_sub_elements( repository, archive_name ): - """ - Get the information about a repository to create and populate an XML tag set. The generated attributes will - be contained within the <repository> tag, while the sub_elements will be tag sets contained within the <repository> - tag set. - """ - attributes = odict() - sub_elements = odict() - attributes[ 'name' ] = str( repository.name ) - attributes[ 'type' ] = str( repository.type ) - # We have to associate the public username since the user_id will be different between tool sheds. - attributes[ 'username' ] = str( repository.user.username ) - # Don't coerce description or long description from unicode to string because the fields are free text. - sub_elements[ 'description' ] = repository.description - sub_elements[ 'long_description' ] = repository.long_description - sub_elements[ 'archive' ] = archive_name - # Keep track of Category associations. - categories = [] - for rca in repository.categories: - category = rca.category - categories.append( ( 'category', str( category.name ) ) ) - sub_elements[ 'categories' ] = categories - return attributes, sub_elements - -def get_repository_ids( app, repo_info_dicts ): - """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" - repository_ids = [] - for repo_info_dict in repo_info_dicts: - for repository_name, repo_info_tup in repo_info_dict.items(): - description, \ - repository_clone_url, \ - changeset_revision, \ - ctx_rev, \ - repository_owner, \ - repository_dependencies, \ - tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) - repository_ids.append( app.security.encode_id( repository.id ) ) - return repository_ids - -def order_components_for_import( app, primary_repository_id, repository_ids, repo_info_dicts ): - """ - Some repositories may have repository dependencies that must be imported and have metadata set on - them before the dependent repository is imported. This method will inspect the list of repositories - about to be exported and make sure to order them appropriately for proper import. For each repository - about to be exported, if required repositories are not contained in the list of repositories about to - be exported, then they are not considered. Repository dependency definitions that contain circular - dependencies should not result in an infinite loop, but obviously ordering the list will not be handled - for one or more of the repositories that require prior import. - """ - # The received primary_repository_id is the id of the repository being exported, with the received list - # of repository_ids being only the ids of all of its repository dependencies. The primary repository will - # always be last in the returned lists. - ordered_repository_ids = [] - ordered_repositories = [] - ordered_changeset_revisions = [] - # Create a dictionary whose keys are the received repository_ids and whose values are a list of - # repository_ids, each of which is contained in the received list of repository_ids and whose associated - # repository must be imported prior to the repository associated with the repository_id key. - prior_import_required_dict = suc.get_prior_import_or_install_required_dict( app, repository_ids, repo_info_dicts ) - processed_repository_ids = [] - # Process the list of repository dependencies defined for the repository associated with the received - # primary_repository_id. - while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ): - repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict, processed_repository_ids ) - if repository_id == primary_repository_id: - # Append the primary_repository_id without processing it since it must be returned last in the order. - # It will be processed below after all dependencies are processed. - processed_repository_ids.append( primary_repository_id ) - continue - processed_repository_ids.append( repository_id ) - if repository_id not in ordered_repository_ids: - prior_import_required_ids = prior_import_required_dict[ repository_id ] - for prior_import_required_id in prior_import_required_ids: - if prior_import_required_id not in ordered_repository_ids: - # Import the associated repository dependency first. - prior_repo_info_dict = get_repo_info_dict_for_import( prior_import_required_id, repository_ids, repo_info_dicts ) - prior_repository, prior_import_changeset_revision = get_components_from_repo_info_dict( app, prior_repo_info_dict ) - if prior_repository and prior_import_changeset_revision: - ordered_repository_ids.append( prior_import_required_id ) - ordered_repositories.append( prior_repository ) - ordered_changeset_revisions.append( prior_import_changeset_revision ) - repo_info_dict = get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) - if repository and changeset_revision: - ordered_repository_ids.append( repository_id ) - ordered_repositories.append( repository ) - ordered_changeset_revisions.append( changeset_revision ) - # Process the repository associated with the received primary_repository_id last. - repo_info_dict = get_repo_info_dict_for_import( primary_repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) - if repository and changeset_revision: - ordered_repository_ids.append( repository_id ) - ordered_repositories.append( repository ) - ordered_changeset_revisions.append( changeset_revision ) - return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions - -def remove_protocol_from_tool_shed_url( base_url ): - protocol, base = base_url.split( '://' ) - base = base.replace( ':', '_colon_' ) - base = base.rstrip( '/' ) - return base

This diff is so big that we needed to truncate the remainder.

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