def check_for_update( self, repository ):
tool_shed_url = suc.get_url_from_tool_shed( self.app, repository.tool_shed )
url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \
( tool_shed_url, repository.name, repository.owner, repository.changeset_revision )
try:
text = common_util.tool_shed_get( self.app, tool_shed_url, url )
except Exception, e:
# The required tool shed may be unavailable.
text = 'False'
def check_for_update(self, repository):
tool_shed_url = suc.get_url_from_tool_shed(self.app,
repository.tool_shed)
url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \
( tool_shed_url, repository.name, repository.owner, repository.changeset_revision )
try:
text = common_util.tool_shed_get(self.app, tool_shed_url, url)
except Exception, e:
# The required tool shed may be unavailable.
text = 'False'
def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ):
"""
Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool
panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml.
"""
self.app = app
self.toolbox = self.app.toolbox
self.migrated_tools_config = migrated_tools_config
# If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message.
if install_dependencies and app.config.tool_dependency_dir is None:
message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini '
message += 'file. Set this location value to the path where you want tool dependencies installed and rerun the migration script.'
raise Exception( message )
# Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml).
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, error_message = xml_util.parse_xml( migrated_tools_config )
if tree is None:
print error_message
else:
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, error_message = xml_util.parse_xml( tool_shed_install_config )
if tree is None:
print error_message
else:
root = tree.getroot()
self.tool_shed_url = suc.get_url_from_tool_shed( self.app, root.get( 'name' ) )
self.tool_shed = suc.clean_tool_shed_url( self.tool_shed_url )
self.repository_owner = common_util.REPOSITORY_OWNER
index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config )
# Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in
# tool_conf.xml. If no tools associated with the migration stage are defined, no repositories will be installed on disk.
# The default behavior is that the tool shed is down.
tool_shed_accessible = False
tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app )
if tool_panel_configs:
# The missing_tool_configs_dict contents are something like:
# {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]}
tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app,
tool_panel_configs,
latest_migration_script_number )
else:
# It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but
# we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in
# the database.
tool_shed_accessible = True
missing_tool_configs_dict = odict()
if tool_shed_accessible:
if len( self.proprietary_tool_confs ) == 1:
plural = ''
file_names = self.proprietary_tool_confs[ 0 ]
else:
plural = 's'
file_names = ', '.join( self.proprietary_tool_confs )
if missing_tool_configs_dict:
for proprietary_tool_conf in self.proprietary_tool_confs:
# Create a backup of the tool configuration in the un-migrated state.
shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, latest_migration_script_number ) )
for repository_elem in root:
# Make sure we have a valid repository tag.
if self.__is_valid_repository_tag( repository_elem ):
# Get all repository dependencies for the repository defined by the current repository_elem. Repository dependency
# definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository
# dependency that contains a tool. The repository dependency can only contain items that are not loaded into the Galaxy
# tool panel (e.g., tool dependency definitions, custom datatypes, etc). This restriction must be followed down the
# entire dependency hierarchy.
name = repository_elem.get( 'name' )
changeset_revision = repository_elem.get( 'changeset_revision' )
tool_shed_accessible, repository_dependencies_dict = \
common_util.get_repository_dependencies( app, self.tool_shed_url, name, self.repository_owner, changeset_revision )
# Make sure all repository dependency records exist (as tool_shed_repository table rows) in the Galaxy database.
created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name,
changeset_revision,
repository_dependencies_dict )
# Order the repositories for proper installation. This process is similar to the process used when installing tool
# shed repositories (i.e., the order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/
# repository_util), but does not handle managing tool panel sections and other components since repository dependency
# definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository
# dependency that contains a tool.
ordered_tool_shed_repositories = self.order_repositories_for_installation( created_tool_shed_repositories,
repository_dependencies_dict )
for tool_shed_repository in ordered_tool_shed_repositories:
is_repository_dependency = self.__is_repository_dependency( name, changeset_revision, tool_shed_repository )
self.install_repository( repository_elem,
tool_shed_repository,
install_dependencies,
is_repository_dependency=is_repository_dependency )
else:
message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number )
message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names )
print message
else:
message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str( latest_migration_script_number )
message += "Try again later.\n"
print message
def install_repository( self, repository_elem, install_dependencies ):
# Install a single repository, loading contained tools into the tool panel.
name = repository_elem.get( 'name' )
description = repository_elem.get( 'description' )
installed_changeset_revision = repository_elem.get( 'changeset_revision' )
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join( self.tool_shed, 'repos', self.repository_owner, name, installed_changeset_revision )
clone_dir = os.path.join( self.tool_path, relative_clone_dir )
if self.__isinstalled( clone_dir ):
print "Skipping automatic install of repository '", name, "' because it has already been installed in location ", clone_dir
else:
tool_shed_url = suc.get_url_from_tool_shed( self.app, self.tool_shed )
repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name )
relative_install_dir = os.path.join( relative_clone_dir, name )
install_dir = os.path.join( clone_dir, name )
ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, self.repository_owner, installed_changeset_revision )
tool_shed_repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=installed_changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=self.app.model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=self.repository_owner,
dist_to_shed=True )
suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING )
cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
if cloned_ok:
self.handle_repository_contents( tool_shed_repository=tool_shed_repository,
repository_clone_url=repository_clone_url,
relative_install_dir=relative_install_dir,
repository_elem=repository_elem,
install_dependencies=install_dependencies )
self.app.sa_session.refresh( tool_shed_repository )
metadata_dict = tool_shed_repository.metadata
if 'tools' in metadata_dict:
suc.update_tool_shed_repository_status( self.app,
tool_shed_repository,
self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
# Get the tool_versions from the tool shed for each tool in the installed change set.
url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision )
text = common_util.tool_shed_get( self.app, tool_shed_url, url )
if text:
tool_version_dicts = from_json_string( text )
tool_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository )
else:
# Set the tool versions since they seem to be missing for this repository in the tool shed.
# CRITICAL NOTE: These default settings may not properly handle all parent/child associations.
for tool_dict in metadata_dict[ 'tools' ]:
flush_needed = False
tool_id = tool_dict[ 'guid' ]
old_tool_id = tool_dict[ 'id' ]
tool_version = tool_dict[ 'version' ]
tool_version_using_old_id = tool_util.get_tool_version( self.app, old_tool_id )
tool_version_using_guid = tool_util.get_tool_version( self.app, tool_id )
if not tool_version_using_old_id:
tool_version_using_old_id = self.app.model.ToolVersion( tool_id=old_tool_id,
tool_shed_repository=tool_shed_repository )
self.app.sa_session.add( tool_version_using_old_id )
self.app.sa_session.flush()
if not tool_version_using_guid:
tool_version_using_guid = self.app.model.ToolVersion( tool_id=tool_id,
tool_shed_repository=tool_shed_repository )
self.app.sa_session.add( tool_version_using_guid )
self.app.sa_session.flush()
# Associate the two versions as parent / child.
tool_version_association = tool_util.get_tool_version_association( self.app,
tool_version_using_old_id,
tool_version_using_guid )
if not tool_version_association:
tool_version_association = self.app.model.ToolVersionAssociation( tool_id=tool_version_using_guid.id,
parent_id=tool_version_using_old_id.id )
self.app.sa_session.add( tool_version_association )
self.app.sa_session.flush()
suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED )
