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galaxy_config.py
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galaxy_config.py
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from __future__ import absolute_import
from collections import namedtuple
import contextlib
import os
import shutil
import urllib
from string import Template
from tempfile import mkdtemp
from six.moves.urllib.request import urlretrieve
import click
from planemo import galaxy_run
from planemo.io import warn
from galaxy.tools.deps import commands
NO_TEST_DATA_MESSAGE = (
"planemo couldn't find a target test-data directory, you should likely "
"create a test-data directory of pass an explicit path using --test-data."
)
WEB_SERVER_CONFIG_TEMPLATE = """
[server:main]
use = egg:Paste#http
port = ${port}
host = ${host}
use_threadpool = True
threadpool_kill_thread_limit = 10800
[app:main]
paste.app_factory = galaxy.web.buildapp:app_factory
"""
TOOL_CONF_TEMPLATE = """<toolbox>
<section id="data_source" name="Data Source">
<tool file="data_source/upload.xml" />
</section>
<section id="testing" name="Test Tools">
${tool_definition}
</section>
</toolbox>
"""
EMPTY_JOB_METRICS_TEMPLATE = """<?xml version="1.0"?>
<job_metrics>
</job_metrics>
"""
BREW_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
<homebrew />
<!--
<homebrew versionless="true" />
-->
</dependency_resolvers>
"""
SHED_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
<tool_shed_tap />
</dependency_resolvers>
"""
# Provide some shortcuts for simple/common dependency resolutions strategies.
STOCK_DEPENDENCY_RESOLUTION_STRATEGIES = {
"brew_dependency_resolution": BREW_DEPENDENCY_RESOLUTION_CONF,
"shed_dependency_resolution": SHED_DEPENDENCY_RESOLUTION_CONF,
}
EMPTY_TOOL_CONF_TEMPLATE = """<toolbox></toolbox>"""
DOWNLOADS_URL = ("https://raw.githubusercontent.com/"
"jmchilton/galaxy-downloads/master/")
LATEST_URL = DOWNLOADS_URL + "latest.sqlite"
FAILED_TO_FIND_GALAXY_EXCEPTION = (
"Failed to find Galaxy root directory - please explicitly specify one "
"with --galaxy_root."
)
GalaxyConfig = namedtuple(
'GalaxyConfig',
['galaxy_root', 'config_directory', 'env', 'test_data_dir']
)
@contextlib.contextmanager
def galaxy_config(ctx, tool_path, for_tests=False, **kwds):
test_data_dir = __find_test_data(tool_path, **kwds)
tool_data_table = __find_tool_data_table(
tool_path,
test_data_dir=test_data_dir,
**kwds
)
if kwds.get("install_galaxy", None):
galaxy_root = None
else:
galaxy_root = __find_galaxy_root(ctx, **kwds)
config_directory = kwds.get("config_directory", None)
def config_join(*args):
return os.path.join(config_directory, *args)
created_config_directory = False
if not config_directory:
created_config_directory = True
config_directory = mkdtemp()
try:
if __install_galaxy_if_needed(config_directory, kwds):
galaxy_root = config_join("galaxy-central-master")
__handle_dependency_resolution(config_directory, kwds)
__handle_job_metrics(config_directory, kwds)
tool_definition = __tool_conf_entry_for(tool_path)
empty_tool_conf = config_join("empty_tool_conf.xml")
tool_conf = config_join("tool_conf.xml")
database_location = config_join("galaxy.sqlite")
preseeded_database = True
try:
template_url = DOWNLOADS_URL + urllib.urlopen(LATEST_URL).read()
urlretrieve(template_url, database_location)
except Exception:
# No network access - just roll forward from null.
preseeded_database = False
template_args = dict(
port=kwds.get("port", 9090),
host="127.0.0.1",
temp_directory=config_directory,
database_location=database_location,
tool_definition=tool_definition % tool_path,
tool_conf=tool_conf,
debug=kwds.get("debug", "true"),
master_api_key=kwds.get("master_api_key", "test_key"),
id_secret=kwds.get("id_secret", "test_secret"),
log_level=kwds.get("log_level", "DEBUG"),
)
properties = dict(
file_path="${temp_directory}files",
new_file_path="${temp_directory}/tmp",
tool_config_file=tool_conf,
check_migrate_tools="False",
manage_dependency_relationships="False",
job_working_directory="${temp_directory}/job_working_directory",
template_cache_path="${temp_directory}/compiled_templates",
citation_cache_type="file",
citation_cache_data_dir="${temp_directory}/citations/data",
citation_cache_lock_dir="${temp_directory}/citations/lock",
collect_outputs_from="job_working_directory",
database_auto_migrate="True",
cleanup_job="never",
master_api_key="${master_api_key}",
id_secret="${id_secret}",
log_level="${log_level}",
debug="${debug}",
tool_data_table_config_path=tool_data_table,
integrated_tool_panel_config=("${temp_directory}/"
"integrated_tool_panel_conf.xml"),
# Use in-memory database for kombu to avoid database contention
# during tests.
amqp_internal_connection="sqlalchemy+sqlite://",
migrated_tools_config=empty_tool_conf,
test_data_dir=test_data_dir, # TODO: make gx respect this
)
if not for_tests:
properties["database_connection"] = \
"sqlite:///${database_location}?isolation_level=IMMEDIATE"
__handle_kwd_overrides(properties, kwds)
# TODO: consider following property
# watch_tool = False
# datatypes_config_file = config/datatypes_conf.xml
# welcome_url = /static/welcome.html
# logo_url = /
# sanitize_all_html = True
# serve_xss_vulnerable_mimetypes = False
# track_jobs_in_database = None
# outputs_to_working_directory = False
# retry_job_output_collection = 0
env = __build_env_for_galaxy(properties, template_args)
__build_test_env(properties, env)
# No need to download twice - would GALAXY_TEST_DATABASE_CONNECTION
# work?
if preseeded_database:
env["GALAXY_TEST_DB_TEMPLATE"] = os.path.abspath(database_location)
env["GALAXY_TEST_UPLOAD_ASYNC"] = "false"
web_config = __sub(WEB_SERVER_CONFIG_TEMPLATE, template_args)
open(config_join("galaxy.ini"), "w").write(web_config)
tool_conf_contents = __sub(TOOL_CONF_TEMPLATE, template_args)
open(tool_conf, "w").write(tool_conf_contents)
open(empty_tool_conf, "w").write(EMPTY_TOOL_CONF_TEMPLATE)
yield GalaxyConfig(galaxy_root, config_directory, env, test_data_dir)
finally:
if created_config_directory:
shutil.rmtree(config_directory)
def __find_galaxy_root(ctx, **kwds):
galaxy_root = kwds.get("galaxy_root", None)
if galaxy_root:
return galaxy_root
elif ctx.global_config.get("galaxy_root", None):
return ctx.global_config["galaxy_root"]
else:
par_dir = os.getcwd()
while True:
run = os.path.join(par_dir, "run.sh")
config = os.path.join(par_dir, "config")
if os.path.isfile(run) and os.path.isdir(config):
return par_dir
new_par_dir = os.path.dirname(par_dir)
if new_par_dir == par_dir:
break
par_dir = new_par_dir
raise Exception(FAILED_TO_FIND_GALAXY_EXCEPTION)
def __find_test_data(path, **kwds):
# Find test data directory associated with path.
test_data = kwds.get("test_data", None)
if test_data:
return os.path.abspath(test_data)
else:
test_data = __search_tool_path_for(path, "test-data")
if test_data:
return test_data
warn(NO_TEST_DATA_MESSAGE)
return None
def __find_tool_data_table(path, test_data_dir, **kwds):
tool_data_table = kwds.get("tool_data_table", None)
if tool_data_table:
return os.path.abspath(tool_data_table)
else:
extra_paths = [test_data_dir] if test_data_dir else []
return __search_tool_path_for(
path,
"tool_data_table_conf.xml.test",
extra_paths,
) or __search_tool_path_for( # if all else fails just use sample
path,
"tool_data_table_conf.xml.sample"
)
def __search_tool_path_for(path, target, extra_paths=[]):
if not os.path.isdir(path):
tool_dir = os.path.dirname(path)
else:
tool_dir = path
possible_dirs = [tool_dir, "."] + extra_paths
for possible_dir in possible_dirs:
possible_path = os.path.join(possible_dir, target)
if os.path.exists(possible_path):
return os.path.abspath(possible_path)
return None
def __tool_conf_entry_for(tool_path):
if os.path.isdir(tool_path):
tool_definition = '''<tool_dir dir="%s" />'''
else:
tool_definition = '''<tool file="%s" />'''
return tool_definition
def __install_galaxy_if_needed(config_directory, kwds):
installed = False
if kwds.get("install_galaxy", None):
install_cmds = [
"cd %s" % config_directory,
galaxy_run.DOWNLOAD_GALAXY,
"tar -zxvf master | tail",
"cd galaxy-central-master",
"type virtualenv >/dev/null 2>&1 && virtualenv .venv",
galaxy_run.ACTIVATE_COMMAND,
]
commands.shell(";".join(install_cmds))
installed = True
return installed
def __build_env_for_galaxy(properties, template_args):
env = {}
for key, value in properties.iteritems():
var = "GALAXY_CONFIG_OVERRIDE_%s" % key.upper()
value = __sub(value, template_args)
env[var] = value
return env
def __build_test_env(properties, env):
# Keeping these environment variables around for a little while but they
# many are probably not needed as of the following commit.
# https://bitbucket.org/galaxy/galaxy-central/commits/d7dd1f9
test_property_variants = {
'GALAXY_TEST_MIGRATED_TOOL_CONF': 'migrated_tools_config',
'GALAXY_TEST_SHED_TOOL_CONF': 'migrated_tools_config', # Hack
'GALAXY_TEST_TOOL_CONF': 'tool_config_file',
'GALAXY_TEST_FILE_DIR': 'test_data_dir',
'GALAXY_TOOL_DEPENDENCY_DIR': 'tool_dependency_dir',
# Next line would be required for tool shed tests.
# 'GALAXY_TEST_TOOL_DEPENDENCY_DIR': 'tool_dependency_dir',
}
for test_key, gx_key in test_property_variants.items():
value = properties.get(gx_key, None)
if value is not None:
env[test_key] = value
def __handle_dependency_resolution(config_directory, kwds):
resolutions_strategies = [
"brew_dependency_resolution",
"dependency_resolvers_config_file",
"shed_dependency_resolution",
]
selected_strategies = 0
for key in resolutions_strategies:
if kwds.get(key):
selected_strategies += 1
if selected_strategies > 1:
message = "At most one option from [%s] may be specified"
raise click.UsageError(message % resolutions_strategies)
for key in STOCK_DEPENDENCY_RESOLUTION_STRATEGIES:
if kwds.get(key):
resolvers_conf = os.path.join(
config_directory,
"resolvers_conf.xml"
)
conf_contents = STOCK_DEPENDENCY_RESOLUTION_STRATEGIES[key]
open(resolvers_conf, "w").write(conf_contents)
dependency_dir = os.path.join("config_directory", "deps")
kwds["tool_dependency_dir"] = dependency_dir
kwds["dependency_resolvers_config_file"] = resolvers_conf
def __handle_job_metrics(config_directory, kwds):
metrics_conf = os.path.join(config_directory, "job_metrics_conf.xml")
open(metrics_conf, "w").write(EMPTY_JOB_METRICS_TEMPLATE)
kwds["job_metrics_config_file"] = metrics_conf
def __handle_kwd_overrides(properties, kwds):
kwds_gx_properties = [
'job_config_file',
'job_metrics_config_file',
'dependency_resolvers_config_file',
'tool_dependency_dir',
]
for prop in kwds_gx_properties:
val = kwds.get(prop, None)
if val:
properties[prop] = val
def __sub(template, args):
if template is None:
return ''
return Template(template).safe_substitute(args)
__all__ = ["galaxy_config"]