Exemplo n.º 1
0
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()
Exemplo n.º 2
0
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()
Exemplo n.º 3
0
 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()
         ]
     )
Exemplo n.º 4
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 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()
     ])
Exemplo n.º 5
0
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)
Exemplo n.º 6
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
        
Exemplo n.º 7
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"""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"
Exemplo n.º 8
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"""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")

Exemplo n.º 9
0
#  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
Exemplo n.º 10
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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
Exemplo n.º 11
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#!/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:
Exemplo n.º 12
0
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
Exemplo n.º 13
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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

Exemplo n.º 14
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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()
Exemplo n.º 15
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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
Exemplo n.º 16
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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:
Exemplo n.º 17
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Arquivo: main.py Projeto: derks/boss
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')))
Exemplo n.º 18
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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()
Exemplo n.º 19
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"""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'
Exemplo n.º 20
0
"""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"