def base_parser(usage=None,description=None):
"""
Create base parser with common options
"""
p = optparse.OptionParser(usage=usage,
version="%s" % get_version(),
description=description)
p.add_option('-k','--api_key',action='store',dest='api_key',
default=None,
help="specify API key to use for connecting to "
"Galaxy instance. Must be supplied if there is "
"no API key stored for the specified instance, "
"(unless --username option is specified). If "
"there is a stored API key this overrides it.")
p.add_option('-u','--username',action='store',dest='username',
default=None,
help="specify username (i.e. email) for connecting "
"to Galaxy instance, as an alternative to using "
"the API key. Prompts for a password unless one "
"is supplied via the --galaxy_password option.")
p.add_option('-P','--galaxy_password',action='store',
dest='galaxy_password',default=None,
help="supply password for connecting to Galaxy "
"instance, when using the --username option.")
p.add_option('-n','--no-verify',action='store_true',dest='no_verify',
default=False,help="don't verify HTTPS "
"connections. Use this when connecting to a Galaxy "
"instance which uses self-signed certificates.")
p.add_option('-q','--suppress-warnings',action='store_true',
dest='suppress_warnings',
default=False,help="suppress warning messages "
"from nebulizer")
p.add_option('--debug',action='store_true',dest='debug',
default=False,help="turn on debugging output")
return p
Attempts to create a Bioblend based on the supplied
arguments to the nebulizer command.
"""
email,password = handle_credentials(
self.username,
self.galaxy_password,
prompt="Password for %s: " % alias)
gi = get_galaxy_instance(alias,api_key=self.api_key,
email=email,password=password,
verify_ssl=(not self.no_verify))
return gi
pass_context = click.make_pass_decorator(Context,ensure=True)
@click.group()
@click.version_option(version=get_version())
@click.option('--api_key','-k',
help="specify API key to use for connecting to "
"Galaxy instance. Must be supplied if there is "
"no API key stored for the specified instance, "
"(unless --username option is specified). If "
"there is a stored API key this overrides it.")
@click.option('--username','-u',
help="specify username (i.e. email) for connecting "
"to Galaxy instance, as an alternative to using "
"the API key. Prompts for a password unless one "
"is supplied via the --galaxy_password option.")
@click.option('--galaxy_password','-P',
help="supply password for connecting to Galaxy "
"instance, when using the --username option.")
@click.option('--no-verify','-n',is_flag=True,
# The master toctree document. master_doc = 'index' # General information about the project. project = 'nebulizer' copyright = '2016, Peter Briggs' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(), '..'))) from nebulizer import get_version # # The short X.Y version. version = get_version() # The full version, including alpha/beta/rc tags. release = get_version() # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files.
Setup script to install nebulizer: command line utilities for managing
users, tools and data libraries in Galaxy instances via the API
Copyright (C) University of Manchester 2015-2016 Peter Briggs
"""
readme = open('README.rst').read()
# Setup for installation etc
from setuptools import setup
import nebulizer
setup(
name = "nebulizer",
version = nebulizer.get_version(),
description = "Manage users, tools and libraries in Galaxy",
long_description = readme,
url = 'https://github.com/pjbriggs/nebulizer',
maintainer = 'Peter Briggs',
maintainer_email = '*****@*****.**',
packages = ['nebulizer',],
entry_points = { 'console_scripts': [
'nebulizer = nebulizer.cli:nebulizer',
'manage_users = nebulizer.deprecated_cli:manage_users',
'manage_libraries = nebulizer.deprecated_cli:manage_libraries',
'manage_tools = nebulizer.deprecated_cli:manage_tools',]
},
license = 'AFL',
install_requires = ['bioblend',
'mako',
# The master toctree document. master_doc = 'index' # General information about the project. project = u'nebulizer' copyright = u'2016, Peter Briggs' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(), '..'))) from nebulizer import get_version # # The short X.Y version. version = get_version() # The full version, including alpha/beta/rc tags. release = get_version() # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files.
