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Source code for galaxy.dependencies

"""
Determine what optional dependencies are needed.
"""

import sys
from os.path import dirname, exists, join

import pkg_resources
import yaml

from galaxy.containers import parse_containers_config
from galaxy.util import (
    asbool,
    etree,
    parse_xml,
    which,
)
from galaxy.util.properties import (
    find_config_file,
    load_app_properties
)


[docs]class ConditionalDependencies:
[docs] def __init__(self, config_file, config=None): self.config_file = config_file self.job_runners = [] self.authenticators = [] self.object_stores = [] self.file_sources = [] self.conditional_reqs = [] self.container_interface_types = [] self.job_rule_modules = [] self.error_report_modules = [] if config is None: self.config = load_app_properties(config_file=self.config_file) else: self.config = config self.parse_configs() self.get_conditional_requirements()
[docs] def parse_configs(self): def load_job_config_dict(job_conf_dict): for runner in job_conf_dict.get("runners"): if "load" in runner: self.job_runners.append(runner.get("load")) if "rules_module" in runner: self.job_rule_modules.append(plugin.text) if "params" in runner: runner_params = runner["params"] if "rules_module" in runner_params: self.job_rule_modules.append(plugin.text) if "job_config" in self.config: load_job_config_dict(self.config.get("job_config")) else: job_conf_path = self.config.get( "job_config_file", join(dirname(self.config_file), 'job_conf.xml')) if '.xml' in job_conf_path: try: try: for plugin in parse_xml(job_conf_path).find('plugins').findall('plugin'): if 'load' in plugin.attrib: self.job_runners.append(plugin.attrib['load']) except OSError: pass try: for plugin in parse_xml(job_conf_path).findall('.//destination/param[@id="rules_module"]'): self.job_rule_modules.append(plugin.text) except OSError: pass except etree.ParseError: pass else: try: with open("job_conf_path") as f: job_conf_dict = yaml.safe_load(f) load_job_config_dict(job_conf_dict) except OSError: pass object_store_conf_path = self.config.get( "object_store_config_file", join(dirname(self.config_file), 'object_store_conf.xml')) try: if '.xml' in object_store_conf_path: for store in parse_xml(object_store_conf_path).iter('object_store'): if 'type' in store.attrib: self.object_stores.append(store.attrib['type']) else: with open(object_store_conf_path) as f: job_conf_dict = yaml.safe_load(f) def collect_types(from_dict): if not isinstance(from_dict, dict): return if 'type' in from_dict: self.object_stores.append(from_dict['type']) for value in from_dict.values(): if isinstance(value, list): for val in value: collect_types(val) else: collect_types(value) collect_types(job_conf_dict) except OSError: 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 parse_xml(auth_conf_xml).findall('authenticator'): auth_type = auth.find('type') if auth_type is not None: self.authenticators.append(auth_type.text) except OSError: 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()] # Parse error report config error_report_yml = self.config.get( "error_report_file", join(dirname(self.config_file), 'error_report.yml')) try: with open(error_report_yml) as f: error_reporters = yaml.safe_load(f) self.error_report_modules = [er.get('type', None) for er in error_reporters] except OSError: pass # Parse file sources config file_sources_conf_yml = self.config.get( "file_sources_config_file", join(dirname(self.config_file), 'file_sources_conf.yml')) if exists(file_sources_conf_yml): with open(file_sources_conf_yml) as f: file_sources_conf = yaml.safe_load(f) else: file_sources_conf = [] self.file_sources = [c.get('type', None) for c in file_sources_conf]
[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_mysqlclient(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.univa:UnivaJobRunner" in self.job_runners)
[docs] def check_galaxycloudrunner(self): return ("galaxycloudrunner.rules" in self.job_rule_modules)
[docs] def check_pbs_python(self): return "galaxy.jobs.runners.pbs:PBSJobRunner" in self.job_runners
[docs] def check_pykube(self): return "galaxy.jobs.runners.kubernetes:KubernetesJobRunner" in self.job_runners or which('kubectl')
[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_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_kamaki(self): return 'pithos' in self.object_stores
[docs] def check_python_irodsclient(self): return 'irods' in self.object_stores
[docs] def check_fs_dropboxfs(self): return 'dropbox' in self.file_sources
[docs] def check_fs_webdavfs(self): return 'webdav' in self.file_sources
[docs] def check_fs_s3fs(self): # pyfilesystem plugin access to s3 return 's3' in self.file_sources
[docs] def check_fs_anvilfs(self): # pyfilesystem plugin access to terra on anvil return 'anvil' in self.file_sources
[docs] def check_s3fs(self): # use s3fs directly (skipping pyfilesystem) for direct access to more options return 's3fs' in self.file_sources
[docs] def check_watchdog(self): install_set = {'auto', 'True', 'true', 'polling', True} 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 check_python_gitlab(self): return 'gitlab' in self.error_report_modules
[docs] def check_pygithub(self): return 'github' in self.error_report_modules
[docs] def check_influxdb(self): return 'influxdb' in self.error_report_modules
[docs] def check_keras(self): return asbool(self.config["enable_tool_recommendations"])
[docs] def check_tensorflow(self): return asbool(self.config["enable_tool_recommendations"])
[docs]def optional(config_file=None): if not config_file: config_file = find_config_file(['galaxy', 'universe_wsgi'], include_samples=True) 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