def __init__(self):
"""
"""
module_prefix = self.__module__
self.cli_shells = plugins_dict(f"{module_prefix}.shell", "__name__")
self.cli_job_interfaces = plugins_dict(f"{module_prefix}.job",
"__name__")
self.active_cli_shells = {}
def __init__(self, app):
self.__app = app
import galaxy.auth.providers
self.__plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers, 'plugin_type' )
auth_config_file = app.config.auth_config_file
# parse XML
ct = xml.etree.ElementTree.parse(auth_config_file)
conf_root = ct.getroot()
authenticators = []
# process authenticators
for auth_elem in conf_root.getchildren():
type_elem = auth_elem.find('type')
plugin = self.__plugins_dict.get(type_elem.text)()
# check filterelem
filter_elem = auth_elem.find('filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
options_elem = auth_elem.find('options')
options = {}
if options_elem is not None:
for opt in options_elem:
options[opt.tag] = opt.text
authenticator = Authenticator(
plugin=plugin,
filter_template=filter_template,
options=options,
)
authenticators.append(authenticator)
self.authenticators = authenticators
def get_authenticators(auth_config_file):
__plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers, 'plugin_type')
# parse XML
ct = xml.etree.ElementTree.parse(auth_config_file)
conf_root = ct.getroot()
authenticators = []
# process authenticators
for auth_elem in conf_root:
type_elem = auth_elem.find('type')
plugin = __plugins_dict.get(type_elem.text)()
# check filterelem
filter_elem = auth_elem.find('filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
options_elem = auth_elem.find('options')
options = {}
if options_elem is not None:
for opt in options_elem:
options[opt.tag] = opt.text
authenticator = Authenticator(
plugin=plugin,
filter_template=filter_template,
options=options,
)
authenticators.append(authenticator)
return authenticators
def get_authenticators(auth_config_file):
__plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers,
'plugin_type')
# parse XML
ct = xml.etree.ElementTree.parse(auth_config_file)
conf_root = ct.getroot()
authenticators = []
# process authenticators
for auth_elem in conf_root:
type_elem = auth_elem.find('type')
plugin = __plugins_dict.get(type_elem.text)()
# check filterelem
filter_elem = auth_elem.find('filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
options_elem = auth_elem.find('options')
options = {}
if options_elem is not None:
for opt in options_elem:
options[opt.tag] = opt.text
authenticator = Authenticator(
plugin=plugin,
filter_template=filter_template,
options=options,
)
authenticators.append(authenticator)
return authenticators
def __init__(self, app):
self.__app = app
import galaxy.auth.providers
self.__plugins_dict = plugin_config.plugins_dict(
galaxy.auth.providers, 'plugin_type')
auth_config_file = app.config.auth_config_file
self.__init_authenticators(auth_config_file)
def __init__(self, app):
self.__app = app
import galaxy.auth.providers
self.__plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers, 'plugin_type' )
auth_config_file = app.config.auth_config_file
# parse XML
ct = xml.etree.ElementTree.parse(auth_config_file)
conf_root = ct.getroot()
authenticators = []
# process authenticators
for auth_elem in conf_root.getchildren():
type_elem = auth_elem.find('type')
plugin = self.__plugins_dict.get(type_elem.text)()
# check filterelem
filter_elem = auth_elem.find('filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
options_elem = auth_elem.find('options')
options = {}
if options_elem is not None:
for opt in options_elem:
options[opt.tag] = opt.text
authenticator = Authenticator(
plugin=plugin,
filter_template=filter_template,
options=options,
)
authenticators.append(authenticator)
self.authenticators = authenticators
def generate_report_json(trans,
invocation,
runtime_report_config_json=None,
plugin_type=None):
import galaxy.workflow.reports.generators
plugin_classes = plugin_config.plugins_dict(
galaxy.workflow.reports.generators, 'plugin_type')
plugin_type = plugin_type or DEFAULT_REPORT_GENERATOR_TYPE
plugin = plugin_classes[plugin_type]()
return plugin.generate_report_json(
trans,
invocation,
runtime_report_config_json=runtime_report_config_json)
def get_authenticators(auth_config_file, auth_config_file_set):
__plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers,
'plugin_type')
# parse XML
try:
ct = parse_xml(auth_config_file)
conf_root = ct.getroot()
except (OSError, IOError) as exc:
if exc.errno == errno.ENOENT and not auth_config_file_set:
conf_root = parse_xml_string(AUTH_CONF_XML)
else:
raise
authenticators = []
# process authenticators
for auth_elem in conf_root:
type_elem_text = auth_elem.find('type').text
plugin_class = __plugins_dict.get(type_elem_text)
if not plugin_class:
raise Exception(
"Authenticator type '%s' not recognized, should be one of %s" %
(type_elem_text, ', '.join(__plugins_dict)))
plugin = plugin_class()
# check filterelem
filter_elem = auth_elem.find('filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
options_elem = auth_elem.find('options')
options = {}
if options_elem is not None:
for opt in options_elem:
options[opt.tag] = opt.text
authenticator = Authenticator(
plugin=plugin,
filter_template=filter_template,
options=options,
)
authenticators.append(authenticator)
return authenticators
def get_authenticators(auth_config_file, auth_config_file_set):
__plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers,
'plugin_type')
# parse XML
try:
ct = xml.etree.ElementTree.parse(auth_config_file)
conf_root = ct.getroot()
except (OSError, IOError) as exc:
if exc.errno == errno.ENOENT and not auth_config_file_set:
conf_root = xml.etree.ElementTree.fromstring(AUTH_CONF_XML)
else:
raise
authenticators = []
# process authenticators
for auth_elem in conf_root:
type_elem = auth_elem.find('type')
plugin = __plugins_dict.get(type_elem.text)()
# check filterelem
filter_elem = auth_elem.find('filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
options_elem = auth_elem.find('options')
options = {}
if options_elem is not None:
for opt in options_elem:
options[opt.tag] = opt.text
authenticator = Authenticator(
plugin=plugin,
filter_template=filter_template,
options=options,
)
authenticators.append(authenticator)
return authenticators
def generate_report(trans,
invocation,
runtime_report_config_json=None,
plugin_type=None,
target_format="json"):
import galaxy.workflow.reports.generators
plugin_classes = plugin_config.plugins_dict(
galaxy.workflow.reports.generators, 'plugin_type')
plugin_type = plugin_type or DEFAULT_REPORT_GENERATOR_TYPE
plugin = plugin_classes[plugin_type]()
if target_format == "json":
return plugin.generate_report_json(
trans,
invocation,
runtime_report_config_json=runtime_report_config_json)
elif target_format == "pdf":
return plugin.generate_report_pdf(
trans,
invocation,
runtime_report_config_json=runtime_report_config_json)
else:
raise RequestParameterInvalidException(
f"Unknown report format [{target_format}]")
def _file_source_plugins_dict(self):
import galaxy.files.sources
return plugin_config.plugins_dict(galaxy.files.sources, 'plugin_type')
def __resolvers_dict( self ):
import galaxy.tools.deps.container_resolvers
return plugin_config.plugins_dict( galaxy.tools.deps.container_resolvers, 'resolver_type' )
def __init__(self, app):
self.__app = app
import galaxy.auth.providers
self.__plugins_dict = plugin_config.plugins_dict( galaxy.auth.providers, 'plugin_type' )
auth_config_file = app.config.auth_config_file
self.__init_authenticators(auth_config_file)
def __plugins_dict(self):
import galaxy.jobs.metrics.instrumenters
return plugin_config.plugins_dict(galaxy.jobs.metrics.instrumenters, 'plugin_type')
def __resolvers_dict(self):
import galaxy.tool_util.deps.resolvers
return plugin_config.plugins_dict(galaxy.tool_util.deps.resolvers,
'resolver_type')
def __plugins_dict(self):
import galaxy.tools.error_reports.plugins
return plugin_config.plugins_dict(galaxy.tools.error_reports.plugins,
'plugin_type')
def __plugins_dict(self):
import galaxy.job_metrics.instrumenters
return plugin_config.plugins_dict(galaxy.job_metrics.instrumenters,
'plugin_type')
def __plugins_dict(self):
return plugin_config.plugins_dict(galaxy.workflow.schedulers,
'plugin_type')
def __resolvers_dict(self):
import galaxy.tools.deps.resolvers
return plugin_config.plugins_dict(galaxy.tools.deps.resolvers, "resolver_type")
def __resolvers_dict(self):
import galaxy.tool_util.locations
return plugin_config.plugins_dict(galaxy.tool_util.locations, 'scheme')
def __resolvers_dict( self ):
import galaxy.tools.locations
return plugin_config.plugins_dict(galaxy.tools.locations, 'scheme')
def __plugins_dict(self):
import galaxy.tools.error_reports.plugins
return plugin_config.plugins_dict(galaxy.tools.error_reports.plugins, 'plugin_type')
def __plugins_dict( self ):
return plugin_config.plugins_dict( galaxy.workflow.schedulers, 'plugin_type' )
