Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.dependencies

"""
Determine what optional dependencies are needed.
"""
from __future__ import print_function

import sys
from os.path import dirname, join
from xml.etree import ElementTree

import pkg_resources

from galaxy.containers import parse_containers_config
from galaxy.util import asbool
from galaxy.util.properties import (
    find_config_file,
    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.container_interface_types = [] 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 # Parse containers config containers_conf_yml = self.config.get( "containers_config_file", join(dirname(self.config_file), 'containers_conf.yml')) containers_conf = parse_containers_config(containers_conf_yml) self.container_interface_types = [c.get('type', None) for c in containers_conf.values()]
[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 Exception: return False
[docs] def check_psycopg2_binary(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 or "galaxy.jobs.runners.drmaauniva:DRMAAUnivaJobRunner" 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_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_python_pam(self): return 'PAM' in self.authenticators
[docs] def check_azure_storage(self): return 'azure_blob' in self.object_stores
[docs] def check_cloudbridge(self): return 'cloud' 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 check_docker(self): return (self.config.get("enable_beta_containers_interface", False) and ('docker' in self.container_interface_types or 'docker_swarm' in self.container_interface_types))
[docs]def optional(config_file=None): if not config_file: config_file = find_config_file(['galaxy', 'universe_wsgi']) if not config_file: print("galaxy.dependencies.optional: no config file found", file=sys.stderr) return [] rval = [] conditional = ConditionalDependencies(config_file) for opt in conditional.conditional_reqs: if conditional.check(opt.key): rval.append(str(opt)) return rval