def main():
defaults = backend.defaults('wight', 'log')
defaults['log']['level'] = 'WARN'
app = WightApp(config_defaults=defaults)
app.register_controllers()
bright_yellow = "%s%s" % (Fore.YELLOW, Style.BRIGHT)
bright_magenta = "%s%s" % (Fore.MAGENTA, Style.BRIGHT)
dim_red = "%s%s" % (Fore.RED, Style.DIM)
dim_white = "%s%s" % (Fore.WHITE, Style.DIM)
reset = "%s%s" % (Style.RESET_ALL, dim_white)
try:
app.setup()
app.run()
except UnauthenticatedError:
print "\n%sYou need to be logged to use this command. Use '%swight login%s %s<user e-mail>%s%s' to login.%s\n" % (
dim_red, bright_yellow, reset, bright_magenta, reset, dim_red,
reset)
except TargetNotSetError:
print "\n%sYou need to set the target to use wight. Use '%swight target-set%s %s<url of target>%s%s' to login.%s\n" % (
dim_red, bright_yellow, reset, bright_magenta, reset, dim_red,
reset)
finally:
app.close()
def main():
defaults = backend.defaults('wight', 'log')
defaults['log']['level'] = 'WARN'
app = WightApp(config_defaults=defaults)
app.register_controllers()
bright_yellow = "%s%s" % (Fore.YELLOW, Style.BRIGHT)
bright_magenta = "%s%s" % (Fore.MAGENTA, Style.BRIGHT)
dim_red = "%s%s" % (Fore.RED, Style.DIM)
dim_white = "%s%s" % (Fore.WHITE, Style.DIM)
reset = "%s%s" % (Style.RESET_ALL, dim_white)
try:
app.setup()
app.run()
except UnauthenticatedError:
print "\n%sYou need to be logged to use this command. Use '%swight login%s %s<user e-mail>%s%s' to login.%s\n" % (
dim_red, bright_yellow, reset, bright_magenta, reset, dim_red, reset
)
except TargetNotSetError:
print "\n%sYou need to set the target to use wight. Use '%swight target-set%s %s<url of target>%s%s' to login.%s\n" % (
dim_red, bright_yellow, reset, bright_magenta, reset, dim_red, reset
)
finally:
app.close()
def test_main_instantiate_app(self, app_mock):
main()
defaults = backend.defaults('wight', 'log')
defaults['log']['level'] = 'WARN'
app_mock.assert_called_with(config_defaults=defaults)
expect(app_mock.mock_calls).to_be_like(
[
call(config_defaults={'wight': {}, 'log': {'level': 'WARN'}}),
call().register_controllers(),
call().setup(),
call().run(),
call().close()
]
)
def test_main_instantiate_app(self, app_mock):
main()
defaults = backend.defaults('wight', 'log')
defaults['log']['level'] = 'WARN'
app_mock.assert_called_with(config_defaults=defaults)
expect(app_mock.mock_calls).to_be_like([
call(config_defaults={
'wight': {},
'log': {
'level': 'WARN'
}
}),
call().register_controllers(),
call().setup(),
call().run(),
call().close()
])
def main(argv=None):
myname = 'cement-demo'
defaults = backend.defaults(myname)
defaults[myname]['foo'] = "BAR!"
app = foundation.CementApp(myname, config_defaults=defaults)
try:
app.setup()
app.args.add_argument('-f', '--foo', action='store',
metavar='STR', help='set foo')
app.run()
print("Hello world from cement-demo")
if app.pargs.foo:
app.log.info("Argument Foo == {}".format(app.pargs.foo))
if app.config.has_key(myname, 'foo'):
app.log.info(
"Config Foo == {}".format(app.config.get(myname, 'foo')))
finally:
app.close()
return(0)
#!/usr/bin/env python
#
# @description@
#
# Created by: @creator@ <@email@>
# License: @license@
# URL: @url@
#
from cement.core import foundation, backend
from cement.core.controller import CementBaseController, expose
from cement.core.exc import FrameworkError, CaughtSignal
defaults = backend.defaults('@module@')
defaults['@module@'] = dict(
debug=False,
foo='bar',
)
class @class_prefix@BaseController(CementBaseController):
class Meta:
label = 'base'
description = '@module@ base controller'.capitalize()
arguments = [
( ['-f', '--foo'], dict(help='the notorious foo option')),
]
@expose(hide=True)
def default(self):
raise NotImplementedError
"""Configuration settings"""
import os
from cement.core import backend
config_defaults = backend.defaults('production', 'archive', 'config', 'project','log', 'distributed', 'db')
config_defaults['production']['root'] = None
config_defaults['production']['swestore'] = None
config_defaults['archive']['root'] = None
config_defaults['project']['root'] = None
config_defaults['project']['repos'] = None
config_defaults['project']['finished'] = None
config_defaults['config']['ignore'] = ["slurm*", "tmp*"]
config_defaults['log']['level'] = "INFO"
config_defaults['log']['file'] = os.path.join(os.getenv("HOME"), "log", "pm.log")
config_defaults['distributed']['jobaccount'] = None
config_defaults['db']['url'] = None
config_defaults['db']['password'] = None
config_defaults['db']['username'] = None
config_defaults['db']['samples'] = "samples"
config_defaults['db']['projects'] = "projects"
config_defaults['db']['flowcells'] = "flowcells"
"""pm configuration settings"""
import os
from cement.core import backend
config_defaults = backend.defaults('log')
config_defaults['log']['level'] = "INFO"
config_defaults['log']['file'] = os.path.join(os.getenv("HOME"), "log", "pm.log")
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Created September 4, 2012
@author: Justin Hammond, Rackspace Hosting
"""
from cement.core import backend, foundation
import aiclib
INVALID_VALUE = "N/A"
defaults = backend.defaults('queries')
defaults['queries']['debug'] = False
app = foundation.CementApp('queries', config_defaults=defaults)
def invalid_switch_ports(json=False, username="******", password="******",
uri="https://nvp"):
nvp = aiclib.nvp.Connection(uri, username=username, password=password)
query = nvp.lswitch_port('*').query().length(1000)
results = query.relations(['LogicalQueueConfig',
'LogicalSwitchConfig']).results()
output = {} if json else ""
msg = "Port:\t%s\nType:\t%s\nQRate:\t%s\nIP:\t%s\nMAC:\t%s\n\n"
while results:
if len(results['results']) == 0:
break
sys.path.append(module_path)
from ntr.cli.controllers.base import NotarioBaseController
from ntr.core import exc as ntr_exc
# Ugly, but how to improve?
USER_PATH = os.path.expanduser('~')
USER_PATH_CONFIG = USER_PATH + '/.notario/config'
# TODO: figure out if we want to have also a ~/notario.ini
file_path = os.path.abspath(__file__)
base_path = os.path.dirname(file_path)
config_path = os.path.join(module_path, 'data/config/notario.cfg')
# Default values for the config.
defaults = backend.defaults('notario')
defaults['notario']['dir'] = "/.notes/"
defaults['notario']['ext'] = ".txt"
defaults['notario']['edt'] = "subl"
"""
Entry point for the Notario.minion application.
"""
class NotarioApp(foundation.CementApp):
class Meta:
label = 'notario'
bootstrap = 'ntr.cli.bootstrap'
base_controller = NotarioBaseController
#!/usr/bin/env python
from cement.core import controller, foundation, backend, handler
import boto
import sys
import string
defaults = backend.defaults('base')
defaults['base']['AWS_REGIONS'] = ['us-east-1', 'us-west-2', 'us-west-1', 'eu-west-1',
'ap-southeast-1', 'ap-northeast-1', 'sa-east-1']
class BaseController(controller.CementBaseController):
class Meta:
label = 'base'
description = 'AWS CLI.'
configuration_defaults = defaults
arguments = [
(['-r', '--region'], dict(
default=defaults['base']['AWS_REGIONS'][0],
choices=defaults['base']['AWS_REGIONS'],
nargs=1,
help="Set AWS regional context."))
]
@controller.expose(hide=True, aliases=['run', 'help'])
def default(self):
print self._usage_text
print self._help_text
class StackController(controller.CementBaseController):
class Meta:
from pm.experiment import setup_project
from pm.utils import test
import logbook
LOG = logbook.Logger(__name__)
has_ngstestdata = False
try:
import ngstestdata as ntd
has_ngstestdata = True
datadir = os.path.join(os.path.dirname(ntd.__file__), os.pardir, "data")
except ImportError:
LOG.warn("Module ngstestdata not found. Not running full tests")
filedir = os.path.dirname(__file__)
config_defaults = backend.defaults('config', 'projects','log', 'bcbio')
config_defaults['log']['level'] = "INFO"
config_defaults['log']['file'] = os.path.join(os.curdir, "log", "pm.log")
config_defaults['projects']['J.Doe_00_01'] = {'alias':"null", 'path':os.path.join(filedir, "data", "projects", "J.Doe_00_01")}
config_defaults['projects']['J.Doe_00_02'] = {'alias':"null", 'path':os.path.join(filedir, "data", "projects", "J.Doe_00_02")}
config_defaults['projects']['J.Doe_00_03'] = {'alias':"null", 'path':os.path.join(filedir, "data", "projects", "J.Doe_00_03")}
config_defaults['config']['project'] = "projects.yaml"
config_defaults['config']['sample'] = "samples.yaml"
samples = {'P001_101_index3': {'120924_AC003CCCXX': {'1_120924_AC003CCCXX_TGACCA': {'id': '1_120924_AC003CCCXX_3', 'analysis': []}}, '121015_BB002BBBXX': {'1_121015_BB002BBBXX_TGACCA': {'id': '1_121015_BB002BBBXX_3', 'analysis': []}}}, 'P001_102_index6': {'120924_AC003CCCXX': {'2_120924_AC003CCCXX_ACAGTG': {'id': '2_120924_AC003CCCXX_5', 'analysis': []}}}}
# Add plugin directory
class PmBcbioTestApp(test.PmTestApp):
class Meta(PmMainApp.Meta):
plugin_dir = os.path.join(filedir, os.pardir, "plugin")
config_defaults = config_defaults
import os
from cement.core import backend, handler, output
from cement.utils import test, shell
LOG = backend.minimal_logger(__name__)
BASEDIR = os.path.join(os.path.dirname(__file__), os.pardir)
from pm.cli import PmMainApp
## Set default configuration
filedir = os.path.abspath(os.curdir)
config_defaults = backend.defaults('config', 'project','log')
config_defaults['project']['root'] = os.path.join(filedir, "data", "projects")
config_defaults['config']['ignore'] = ["slurm*", "tmp*"]
config_defaults['log']['level'] = "INFO"
config_defaults['log']['file'] = os.path.join(filedir, "log", "pm.log")
def safe_makedir(dname):
"""Make directory"""
if not os.path.exists(dname):
try:
os.makedirs(dname)
except OSError:
if not os.path.isdir(dname):
raise
else:
print "Directory %s already exists" % dname
return dname
import os
import glob
from cement.core import backend, foundation, handler
from cli import JSONConfigParserHandler
from cli import controllers
CONFIG_DIR = os.path.join(__path__[0], './config')
CONFIG_FILES = glob.glob(os.path.join(CONFIG_DIR, '*.json'))
# defined app first and handlers afterwards
app = foundation.CementApp('credovi',
config_defaults=backend.defaults('credovi'),
config_handler='JSONConfigParser',
config_files=CONFIG_FILES)
# hooks must be registered afterwards
from cli.hooks import *
handler.register(JSONConfigParserHandler)
handler.register(controllers.BaseController)
handler.register(controllers.DatabaseController)
handler.register(controllers.CredoController)
handler.register(controllers.CredoStandAloneController)
handler.register(controllers.MMCIFController)
handler.register(controllers.LigandController)
handler.register(controllers.ModuleController)
# setup the application
app.setup()
import sys
import logging
from cement.core import backend, foundation, controller, handler
logo_ascii = """
_ _ _ _
_ __ _ _| |_| |_ ___ _ _ ___ __ _ _ _| |_ _ _ ___| |_
| '_ \ || | _| ' \/ _ \ ' \___/ _` | '_| _| ' \/ -_) _|
| .__/\_, |\__|_||_\___/_||_| \__,_|_| \__|_||_\___|\__|
|_| |__/
"""
defaults = backend.defaults('base')
defaults['base']['address'] = '<broadcast>'
log = logging.getLogger(__name__)
def run(name, config, controller=None):
mod = __import__('artnet.scripts', globals(), locals(), [name], -1)
try:
getattr(mod, name).main(config, controller)
except:
log.error("Couldn't find lighting script named %r" % name)
class ArtnetBaseController(controller.CementBaseController):
class Meta:
label = 'base'
description = "%s\nBasic artnet protocol support." % logo_ascii
import os
from cement.core import backend, handler, output
from cement.utils import test, shell
from scilifelab.pm import PmApp
from data import setup_data_files
from empty_files import setup_empty_files
## Set default configuration
filedir = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
config_defaults = backend.defaults("production", "archive", "config", "project", "log", "db")
config_defaults["production"]["root"] = os.path.join(filedir, "data", "production")
config_defaults["archive"]["root"] = os.path.join(filedir, "data", "archive")
config_defaults["project"]["root"] = os.path.join(filedir, "data", "projects")
config_defaults["project"]["repos"] = os.path.join(filedir, "data", "repos")
config_defaults["config"]["ignore"] = ["slurm*", "tmp*"]
config_defaults["log"]["level"] = "INFO"
config_defaults["log"]["file"] = os.path.join(filedir, "data", "log", "pm.log")
config_defaults["db"]["url"] = "localhost"
config_defaults["db"]["user"] = "******"
config_defaults["db"]["password"] = "******"
config_defaults["db"]["samples"] = "samples-test"
config_defaults["db"]["flowcells"] = "flowcells-test"
config_defaults["db"]["projects"] = "projects-test"
def safe_makedir(dname):
"""Make directory"""
if not os.path.exists(dname):
try:
os.makedirs(dname)
except OSError:
import os
import sys
from cement.core import foundation, backend
from cement.core import exc as cement_exc
from cement.utils import fs
from boss.cli.controllers.base import BossBaseController
from boss.core import exc as boss_exc
if sys.version_info[0] >= 3:
from imp import reload
defaults = backend.defaults('boss', 'answers')
defaults['boss']['data_dir'] = '~/.boss/'
class BossApp(foundation.CementApp):
class Meta:
label = 'boss'
bootstrap = 'boss.cli.bootstrap'
base_controller = BossBaseController
config_defaults = defaults
config_files = [
'/etc/boss/boss.conf',
'~/.boss.conf',
'~/.boss/config',
]
def validate_config(self):
# fix up paths
self.config.set('boss', 'data_dir',
fs.abspath(self.config.get('boss', 'data_dir')))
from cement.core import backend
from skyler import Skyler
defaults = backend.defaults('base', 'keystone')
defaults['base']['rabbitmq_host'] = 'localhost'
defaults['base']['rabbitmq_user'] = '******'
defaults['base']['rabbitmq_password'] = '******'
defaults['base']['heat_endpoint'] = 'http://172.16.0.201:8004/v1'
defaults['base']['templates'] = '/vagrant/skyler-cli/skyler/templates'
defaults['base']['docker-registry'] = 'localhost:5042'
defaults['base']['neutron_endpoint'] = 'http://localhost:9696/'
# defaults['base']['network'] = 'sky-net'
defaults['base']['subnet'] = 'private-subnet'
defaults['base']['network'] = 'private'
# defaults['base']['cidr_start'] = '10.0.1.0/28'
# defaults['base']['gateway'] = '10.0.1.1'
# TODO: remove this from conf, read from env vars
defaults['keystone']['auth_url'] = 'http://localhost:35357/v2.0'
defaults['keystone']['username'] = '******'
defaults['keystone']['password'] = '******'
defaults['keystone']['tenant'] = 'demo'
app = Skyler('skyler', config_defaults=defaults)
app.setup()
CONFIG = app.config
app.close()
"""classes for full test"""
import os
from cement.core import backend, handler, output
from cement.utils import test
from scilifelab.pm import PmApp
filedir = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
config_defaults = backend.defaults('production', 'archive', 'config', 'project','log', 'runqc', 'db')
config_defaults['production']['root'] = os.path.join(filedir, "data", "production")
config_defaults['archive']['root'] = os.path.join(filedir, "data", "archive")
config_defaults['project']['root'] = os.path.join(filedir, "data", "projects")
config_defaults['project']['repos'] = os.path.join(filedir, "data", "repos")
config_defaults['runqc']['root'] = os.path.join(filedir, "data", "archive")
config_defaults['runqc']['production'] = os.path.join(filedir, "data", "production")
config_defaults['runqc']['rsync_sample_opts'] = "-amnv --include=*/ --include='[0-9][0-9]_\*.txt' --include='bcbb_software_versions.txt' --include='*.yaml*' --include='*screen.txt' --include='*summary.txt' --include='*fastqc_data.txt' --include='*metrics' --exclude='tmp' --exclude='*'"
config_defaults['config']['ignore'] = ["slurm*", "tmp*"]
config_defaults['log']['level'] = "INFO"
config_defaults['log']['file'] = os.path.join(filedir, "data", "log", "pm.log")
config_defaults['db']['url'] = "localhost"
config_defaults['db']['user'] = "******"
config_defaults['db']['password'] = "******"
config_defaults['db']['samples'] = "samples-test"
config_defaults['db']['flowcells'] = "flowcells-test"
config_defaults['db']['projects'] = "projects-test"
## Output handler for tests
class PmTestOutputHandler(output.CementOutputHandler):
class Meta:
label = 'pmfulltest'
"""classes for full test"""
import os
from cement.core import backend, handler, output
from cement.utils import test
from scilifelab.pm import PmApp
filedir = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
config_defaults = backend.defaults('production', 'archive', 'config',
'project', 'log', 'runqc', 'db')
config_defaults['production']['root'] = os.path.join(filedir, "data",
"production")
config_defaults['archive']['root'] = os.path.join(filedir, "data", "archive")
config_defaults['project']['root'] = os.path.join(filedir, "data", "projects")
config_defaults['project']['repos'] = os.path.join(filedir, "data", "repos")
config_defaults['runqc']['root'] = os.path.join(filedir, "data", "archive")
config_defaults['runqc']['production'] = os.path.join(filedir, "data",
"production")
config_defaults['runqc'][
'rsync_sample_opts'] = "-amnv --include=*/ --include='[0-9][0-9]_\*.txt' --include='bcbb_software_versions.txt' --include='*.yaml*' --include='*screen.txt' --include='*summary.txt' --include='*fastqc_data.txt' --include='*metrics' --exclude='tmp' --exclude='*'"
config_defaults['config']['ignore'] = ["slurm*", "tmp*"]
config_defaults['log']['level'] = "INFO"
config_defaults['log']['file'] = os.path.join(filedir, "data", "log", "pm.log")
config_defaults['db']['url'] = "localhost"
config_defaults['db']['user'] = "******"
config_defaults['db']['password'] = "******"
config_defaults['db']['samples'] = "samples-test"
config_defaults['db']['flowcells'] = "flowcells-test"
config_defaults['db']['projects'] = "projects-test"