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Source code for galaxy.dependencies

"""
Determine what optional dependencies are needed.
"""
from os.path import dirname, join
from xml.etree import ElementTree

import pkg_resources

from galaxy.util import asbool
from galaxy.util.properties import load_app_properties


[docs]class ConditionalDependencies(object):
[docs] def __init__(self, config_file): self.config_file = config_file self.config = None self.job_runners = [] self.authenticators = [] self.object_stores = [] self.conditional_reqs = [] self.parse_configs() self.get_conditional_requirements()
[docs] def parse_configs(self): self.config = load_app_properties(config_file=self.config_file) job_conf_xml = self.config.get( "job_config_file", join(dirname(self.config_file), 'job_conf.xml')) try: for plugin in ElementTree.parse(job_conf_xml).find('plugins').findall('plugin'): if 'load' in plugin.attrib: self.job_runners.append(plugin.attrib['load']) except (OSError, IOError): pass object_store_conf_xml = self.config.get( "object_store_config_file", join(dirname(self.config_file), 'object_store_conf.xml')) try: for store in ElementTree.parse(object_store_conf_xml).iter('object_store'): if 'type' in store.attrib: self.object_stores.append(store.attrib['type']) except (OSError, IOError): pass # Parse auth conf auth_conf_xml = self.config.get( "auth_config_file", join(dirname(self.config_file), 'auth_conf.xml')) try: for auth in ElementTree.parse(auth_conf_xml).findall('authenticator'): auth_type = auth.find('type') if auth_type is not None: self.authenticators.append(auth_type.text) except (OSError, IOError): pass
[docs] def get_conditional_requirements(self): crfile = join(dirname(__file__), 'conditional-requirements.txt') for req in pkg_resources.parse_requirements(open(crfile).readlines()): self.conditional_reqs.append(req)
[docs] def check(self, name): try: name = name.replace('-', '_').replace('.', '_') return getattr(self, 'check_' + name)() except: return False
[docs] def check_psycopg2(self): return self.config["database_connection"].startswith("postgres")
[docs] def check_mysql_python(self): return self.config["database_connection"].startswith("mysql")
[docs] def check_drmaa(self): return ("galaxy.jobs.runners.drmaa:DRMAAJobRunner" in self.job_runners or "galaxy.jobs.runners.slurm:SlurmJobRunner" in self.job_runners)
[docs] def check_pbs_python(self): return "galaxy.jobs.runners.pbs:PBSJobRunner" in self.job_runners
[docs] def check_python_openid(self): return asbool(self.config["enable_openid"])
[docs] def check_chronos_python(self): return "galaxy.jobs.runners.chronos:ChronosJobRunner" in self.job_runners
[docs] def check_fluent_logger(self): return asbool(self.config["fluent_log"])
[docs] def check_raven(self): return self.config.get("sentry_dsn", None) is not None
[docs] def check_statsd(self): return self.config.get("statsd_host", None) is not None
[docs] def check_graphite(self): return self.config.get("graphite_host", None) is not None
[docs] def check_weberror(self): return (asbool(self.config["debug"]) and asbool(self.config["use_interactive"]))
[docs] def check_pygments(self): # pygments is a dependency of weberror and only weberror return self.check_weberror()
[docs] def check_python_ldap(self): return ('ldap' in self.authenticators or 'activedirectory' in self.authenticators)
[docs] def check_azure_storage(self): return 'azure_blob' in self.object_stores
[docs] def check_kamaki(self): return 'pithos' in self.object_stores
[docs] def check_watchdog(self): install_set = {'auto', 'True', 'true', 'polling'} return (self.config['watch_tools'] in install_set or self.config['watch_tool_data_dir'] in install_set)
[docs]def optional(config_file): rval = [] conditional = ConditionalDependencies(config_file) for opt in conditional.conditional_reqs: if conditional.check(opt.key): rval.append(str(opt)) return rval