includes_tools_for_display_in_tool_panel = repository_revision_dict[ 'includes_tools_for_display_in_tool_panel' ]
except:
raise HTTPBadRequest( detail="Missing required parameter 'includes_tools_for_display_in_tool_panel'." )
# Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain the repository information.
install_repository_dependencies = payload.get( 'install_repository_dependencies', False )
install_tool_dependencies = payload.get( 'install_tool_dependencies', False )
if install_tool_dependencies:
if trans.app.config.tool_dependency_dir is None:
no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set the value of your 'tool_dependency_dir' "
no_tool_dependency_dir_message += "setting in your Galaxy configuration file (universe_wsgi.ini) and restart your Galaxy server."
raise HTTPBadRequest( detail=no_tool_dependency_dir_message )
new_tool_panel_section = payload.get( 'new_tool_panel_section_label', '' )
shed_tool_conf = payload.get( 'shed_tool_conf', None )
if shed_tool_conf:
# Get the tool_path setting.
index, shed_conf_dict = suc.get_shed_tool_conf_dict( trans.app, shed_tool_conf )
# BUG, FIXME: Shed config dict does not exist in this context
tool_path = shed_config_dict[ 'tool_path' ]
else:
# Pick a semi-random shed-related tool panel configuration file and get the tool_path setting.
for shed_config_dict in trans.app.toolbox.shed_tool_confs:
# Don't use migrated_tools_conf.xml.
if shed_config_dict[ 'config_filename' ] != trans.app.config.migrated_tools_config:
break
shed_tool_conf = shed_config_dict[ 'config_filename' ]
tool_path = shed_config_dict[ 'tool_path' ]
if not shed_tool_conf:
raise HTTPBadRequest( detail="Missing required parameter 'shed_tool_conf'." )
tool_panel_section_id = payload.get( 'tool_panel_section_id', '' )
if tool_panel_section_id not in [ None, '' ]:
tool_panel_section = trans.app.toolbox.tool_panel[ tool_panel_section_id ]
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 __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 = suc.clean_tool_shed_url( root.get( 'name' ) )
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 repository_elem in root:
self.install_repository( repository_elem, install_dependencies )
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
