To view/run the 'nightly' commands, you need the testing dependencies.
Run `pip install [--editable] .[tests]`.
"""
# Override the class used by the ixmp CLI to load Scenario objects
ixmp.cli.ScenarioClass = message_ix.Scenario
@main.command("copy-model")
@click.option(
"--set-default",
is_flag=True,
help="Set the copy to be the default used when running MESSAGE.",
)
@click.option("--overwrite", is_flag=True, help="Overwrite existing files.")
@click.argument("path", type=click.Path(file_okay=False))
def copy_model(path, overwrite, set_default):
"""Copy the MESSAGE GAMS files to a new PATH.
To use an existing set of GAMS files, you can also call:
$ message-ix config set "message model dir" PATH
"""
path = Path(path).resolve()
src_dir = Path(__file__).parent / "model"
for src in src_dir.rglob("*"):
# Skip certain files
if src.suffix in (".gdx", ".log", ".lst"):
continue
import os, sys
import click
import dentate
from dentate import plot, utils
from dentate.env import Env
script_name = os.path.basename(__file__)
@click.command()
@click.option("--config", required=True, type=str)
@click.option("--config-prefix",
required=True,
type=click.Path(exists=True, file_okay=False, dir_okay=True),
default='config')
@click.option("--features-path", '-p', required=True, type=click.Path())
@click.option("--features-namespace", '-n', type=str)
@click.option("--arena-id", '-a', type=str, required=True)
@click.option("--trajectory-id", '-t', type=str, required=True)
@click.option("--coords-path", '-c', required=True, type=click.Path())
@click.option("--distances-namespace", '-d', type=str, default='Arc Distances')
@click.option("--include", '-i', type=str, multiple=True)
@click.option("--bin-size", type=float, default=100.)
@click.option("--from-spikes", type=bool, default=True)
@click.option("--normed", type=bool, default=False, is_flag=True)
@click.option("--font-size", type=float, default=14)
@click.option("--verbose", "-v", is_flag=True)
@click.option("--save-fig", is_flag=True)
def main(config, config_prefix, features_path, coords_path, features_namespace,
arena_id, trajectory_id, distances_namespace, include, bin_size,
from_spikes, normed, font_size, verbose, save_fig):
@ops.command()
@click.option(*OPTIONS_PROJECT["args"], **OPTIONS_PROJECT["kwargs"])
@click.option(*OPTIONS_RUN_UID["args"], **OPTIONS_RUN_UID["kwargs"])
@click.option(
"--copy",
"-c",
is_flag=True,
default=False,
help="To copy the run before restarting.",
)
@click.option(
"-f",
"--file",
"polyaxonfile",
multiple=True,
type=click.Path(exists=True),
help=
"The polyaxonfiles to update with, they should be an operation preset.",
)
@click.pass_context
@clean_outputs
def restart(ctx, project, uid, copy, polyaxonfile):
"""Restart run.
Uses /docs/core/cli/#caching
Examples:
\b
$ polyaxon run --uid=8aac02e3a62a4f0aaa257c59da5eab80 restart
"""
from histogram import Histogram
from optimal_alignment_finder import OptimalAlignmentFinder
@click.command()
@click.option('--target-sequence',
'-t',
help='The target DNA sequence as a string.',
type=str,
required=True)
@click.option(
'--input-fasta-file',
'-i',
help=
'Input FASTA file. This sequence will be searched for the target sequence.',
type=click.Path(exists=True),
required=True)
def parse_input(target_sequence: str, input_fasta_file: str) -> None:
"""
parse_input
:param target_sequence: The target sequence as a string.
:param input_fasta_file: The path to a FASTA file.
"""
if not Helpers.valid_dna_sequence(target_sequence):
raise click.UsageError(
'The target sequence is not a valid DNA sequence.')
input_sequence = Helpers.fasta_file_to_sequence(input_fasta_file)
if not input_sequence:
patients do not fit in the scout field of view.
Returns image orientation and estimated distance in centimeters. These measurements
can be converted into equivalent water volumes using AAPM-published tables.
\b
$ diana-plus ssde tests/resources/scouts ct_scout_01.dcm ct_scout_02.dcm
Measuring scout images
------------------------
ct_scout_01.dcm (AP): 28.0cm
ct_scout_02.dcm (LATERAL): 43.0cm
"""
@click.command(short_help="Estimate patient size from localizer",
epilog=epilog)
@click.argument('path', type=click.Path(exists=True))
@click.argument('images', nargs=-1)
def ssde(path, images):
"""Estimate patient dimensions from CT-localizer IMAGES for size-specific dose estimation."""
click.echo(click.style('Measuring scout images', underline=True,
bold=True))
D = DcmDir(path=path)
for image in images:
d = D.get(image, view=DixelView.PIXELS)
result = d.measure_scout()
click.echo("{} ({}): {}cm".format(image, result[0], round(result[1])))
pass_conf = click.make_pass_decorator(Config)
@click.group()
@click.option('--host', '-h', type=str, help='Hostname of MatterMost server')
@click.option('--token', '-t', type=str, help='Your personal access token')
@click.option('--port',
'-p',
type=int,
default=443,
help='Which port to use. Default 443')
@click.option('--config',
'-c',
type=click.Path(),
help='Path to config file for host, port and token')
@click.version_option()
@click.pass_context
def cli(ctx, host, token, port, config):
if config:
settings = configparser.ConfigParser()
settings.read(config)
if not host and 'host' in settings['Default']:
host = settings['Default']['host']
if not token and 'token' in settings['Default']:
token = settings['Default']['token']
if not port and 'port' in settings['Default']:
port = int(settings['Default']['port'])
output = format_output(title, cur, headers, None, table_format)
for line in output:
click.echo(line, nl=new_line)
@click.command()
@click.option('-h', '--host', envvar='MYSQL_HOST', help='Host address of the database.')
@click.option('-P', '--port', envvar='MYSQL_TCP_PORT', type=int, help='Port number to use for connection. Honors '
'$MYSQL_TCP_PORT')
@click.option('-u', '--user', help='User name to connect to the database.')
@click.option('-S', '--socket', envvar='MYSQL_UNIX_PORT', help='The socket file to use for connection.')
@click.option('-p', '--password', 'password', envvar='MYSQL_PWD', type=str,
help='Password to connect to the database')
@click.option('--pass', 'password', envvar='MYSQL_PWD', type=str,
help='Password to connect to the database')
@click.option('--ssl-ca', help='CA file in PEM format',
type=click.Path(exists=True))
@click.option('--ssl-capath', help='CA directory')
@click.option('--ssl-cert', help='X509 cert in PEM format',
type=click.Path(exists=True))
@click.option('--ssl-key', help='X509 key in PEM format',
type=click.Path(exists=True))
@click.option('--ssl-cipher', help='SSL cipher to use')
@click.option('--ssl-verify-server-cert', is_flag=True,
help=('Verify server\'s "Common Name" in its cert against '
'hostname used when connecting. This option is disabled '
'by default'))
# as of 2016-02-15 revocation list is not supported by underling PyMySQL
# library (--ssl-crl and --ssl-crlpath options in vanilla mysql client)
@click.option('-v', '--version', is_flag=True, help='Version of mycli.')
@click.option('-D', '--database', 'dbname', help='Database to use.')
@click.option('-R', '--prompt', 'prompt',
if simulation is True:
# TODO: Public API for mirroring existing registry
self.blockchain.interface._registry._swap_registry(filepath=self.sim_registry_filepath)
self.token_agent = NucypherTokenAgent(blockchain=self.blockchain)
self.miner_agent = MinerAgent(token_agent=self.token_agent)
self.policy_agent = PolicyAgent(miner_agent=self.miner_agent)
uses_config = click.make_pass_decorator(NucypherClickConfig, ensure=True)
@click.group()
@click.option('--version', help="Prints the installed version.", is_flag=True)
@click.option('--verbose', help="Enable verbose mode.", is_flag=True)
@click.option('--config-file', help="Specify a custom config filepath.", type=click.Path(), default="cool winnebago")
@uses_config
def cli(config, verbose, version, config_file):
"""Configure and manage a nucypher nodes"""
# validate_nucypher_ini_config(filepath=config_file)
click.echo(BANNER)
# Store config data
config.verbose = verbose
config.config_filepath = config_file
if config.verbose:
click.echo("Running in verbose mode...")
if version:
next(reader) # skip headers
for company_id, company_name, count in reader:
company_id, count = int(company_id), int(count)
company_name_norm = cg.preprocessor(company_name)
if not company_name_norm:
logger.info(
f"Skipping {company_name} - it appears in stoplist")
continue
else:
rows.append(
NameEdge(source=company_name, target=company_id, n=count))
return rows
@click.command()
@click.argument("input-file", type=click.Path(exists=True))
@click.argument("output-file", type=click.Path())
@click.option("--min-count", default=10)
def append_data(input_file, output_file, min_count):
cg = CompanyGraph()
new_rows = read_rows(input_file, cg)
g = cg.graph
for row in new_rows:
if g.has_edge(row.source, row.target):
g[row.source][row.target]["n"] += row.n
else:
if row.n >= min_count:
g.add_edge(row.source, row.target, n=row.n)
# Names should have 1 possible id candidate
# IMX Image: Base options
@click.group(context_settings=dict(help_option_names=['-?', '--help']), help=DESCRIP)
@click.version_option(VERSION, '-v', '--version')
def cli():
click.echo()
# IMX Image: List IMX boot img content
@cli.command(short_help="List i.MX boot image content")
@click.option('-t', '--type', type=click.Choice(['auto', '67RT', '8M', '8QXP_A0', '8QM_A0', '8X']),
default='auto', show_default=True, help="Image type")
@click.option('-o', '--offset', type=UINT, default=0, show_default=True, help="File Offset")
@click.option('-s', '--step', type=UINT, default=0x100, show_default=True, help="Parsing step")
@click.argument('file', nargs=1, type=click.Path(exists=True))
def info(offset, type, step, file):
""" List i.MX boot image content """
try:
with open(file, 'rb') as stream:
stream.seek(offset)
if type == "auto":
boot_image = parse(stream, step)
else:
img_type = {'67RT': BootImg2,
'8M': BootImg2,
'8QXP_A0': BootImg3a,
'8QM_A0': BootImg3b,
'8X': BootImg4}
boot_image = img_type[type].parse(stream, step)
def visit_class(self, cls: ClassDefinition) -> bool:
if cls.mixin or cls.abstract or not cls.slots:
return False
if cls.description:
for dline in cls.description.split('\n'):
print(f'// {dline}')
print(f'message {camelcase(cls.name)}')
print(" {")
self.relative_slot_num = 0
return True
def end_class(self, cls: ClassDefinition) -> None:
print(" }")
def visit_class_slot(self, cls: ClassDefinition, aliased_slot_name: str, slot: SlotDefinition) -> None:
qual = 'repeated ' if slot.multivalued else 'optional ' if not slot.required or slot.primary_key else ''
slotname = lcamelcase(aliased_slot_name)
slot_range = self.obj_name(slot.range)
self.relative_slot_num += 1
print(f" {qual}{slotname} {slot_range} = {self.relative_slot_num}")
@click.command()
@click.argument("yamlfile", type=click.Path(exists=True, dir_okay=False))
@click.option("--format", "-f", default='proto', type=click.Choice(['proto']),
help="Output format")
def cli(yamlfile, format):
""" Generate proto representation of biolink model """
print(ProtoGenerator(yamlfile, format).serialize())
import sys
import click
import pylint.lint
import getaddons
import travis_helpers
from getaddons import get_modules_changed
from git_run import GitRun
try:
import ConfigParser
except ImportError:
import configparser as ConfigParser
CLICK_DIR = click.Path(exists=True, dir_okay=True, resolve_path=True)
def get_extra_params(odoo_version):
"""Get extra pylint params by odoo version
Transform a seudo-pylint-conf to params,
it to overwrite base-pylint-conf values.
Use a seudo-inherit of configuration file.
To avoid have a 2 config files (stable and pr-conf) by each odoo-version
Example:
pylint_master.conf
pylint_master_pr.conf
pylint_90.conf
pylint_90_pr.conf
pylint_80.conf
for infileName in tqdm(self.currentfiles, total=len(self.currentfiles)))
yecho("Done converting csv to hdf5.")
def mergetelescopefiles(self):
yecho("Merging telescope files.")
self.get_currentfiles(DIRECTORIES[0]+M12+CSV)
files1, files2 = self.split_currentfiles()
self.currentfiles = Parallel(n_jobs=20)\
(delayed(mt.mc_append_and_merge)
([m1], [m2], self.rootdir+DIRECTORIES[-3], easy_merge=True)
for m1, m2 in tqdm(zip(files1, files2), total=len(files1)))
yecho("Done merging telescope files.")
@click.command()
@click.option('--rootdir', "-rd", default="./", type=click.Path(file_okay=False, writable=True),
help='RootDir from which to read the files')
@click.option('--subdir', "-sd", default="", type=click.Path(file_okay=False),
help='subdir from which to read the files in each processing subdir.')
@click.option('--root2csv', "-rtc", default="False", type=bool,
help='Convert root to csv or not. Also filters the events. Needs processed star and superstar files.')
@click.option('--csv2hdf5', "-cth", default="True", type=bool,
help='Convert csv to hdf5 or not.')
@click.option('--mergehdf5', "-mh", default="False", type=bool,
help='Merge the hdf5files or not.')
@click.option('--mergetelescopes', "-mt", default="True", type=bool,
help='Merge the telescope files or not.')
@click.option('--normalize', "-no", default="True", type=click.Choice(['True', 'False', 'pixelwise', 'camerawise']),
help='Whether to merge the telescope files. Defaults to pixelwise. `True` also defaults to pixelwise.')
@click.option('--normfile', "-nf", default=None, type=click.Path(dir_okay=False, resolve_path=True, exists=True),
help='Location of the normfile.')
for symbol in unique_symbols:
if symbol in result:
dataset[-1].append(1)
else:
dataset[-1].append(0)
if result[-1] == "SPAM":
dataset[-1].append(SPAM_LABEL)
else:
dataset[-1].append(HAM_LABEL)
return dataset
@click.command()
@click.option('--ham', type=click.Path(exists=True))
@click.option('--spam', type=click.Path(exists=True))
@click.option('--out', type=click.Path())
def main(ham, spam, out):
""" Runs data processing scripts to turn raw data from (../raw) into
cleaned data ready to be analyzed (saved in ../processed).
python make_dataset.py --ham ../../data/processed/ham.scan_results.txt --spam ../../data/processed/spam.scan_results.txt --out ../../data/processed/dataset.txt
"""
logger = logging.getLogger(__name__)
logger.info('making final data set from raw data')
ham_scan_results = []
spam_scan_results = []
if ham:
from warnings import warn
import os
import shutil
import click
"""
Script assumes figures are exactly one directory deep.
E.g. under 'figures', not 'figures/eps'
"""
@click.command()
@click.argument('flatdir',
type=click.Path(exists=True, file_okay=False, dir_okay=True))
@click.argument('figdir',
type=click.Path(exists=True, file_okay=False, dir_okay=True))
def main(flatdir, figdir):
figprefix = os.path.basename(figdir)
for filename in os.listdir(flatdir):
if filename.startswith(figprefix + '_'):
targetfilename = os.path.splitext(filename)[0] + '.eps'
sourcefilename = targetfilename[len(figprefix) + 1:]
sourcepathname = os.path.join(figdir, sourcefilename)
targetpathname = os.path.join(flatdir, targetfilename)
if os.path.exists(sourcepathname):
shutil.copy(sourcepathname,
targetpathname,
follow_symlinks=True)
else:
warn("Missing eps file '{}'".format(sourcepathname))
# -*- coding: utf-8 -*-
import logging
from pathlib import Path
import click
from dotenv import find_dotenv, load_dotenv
@click.command()
@click.argument("source_path", type=click.Path(exists=True))
@click.argument("external_path", type=click.Path(exists=True))
@click.argument("processed_path", type=click.Path())
def main(source_path, external_path, processed_path):
"""Runs data processing scripts to turn source data into
processed data ready to be analyzed.
"""
logger = logging.getLogger(__name__)
logger.info("making final data set from raw data")
if __name__ == "__main__":
log_fmt = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
logging.basicConfig(level=logging.INFO, format=log_fmt)
project_dir = Path(__file__).resolve().parents[2]
load_dotenv(find_dotenv())
main()
import parglare.termui as t
@click.group()
@click.option('--debug/--no-debug', default=False, help="Debug/trace output")
@click.option('--colors/--no-colors', default=True, help="Output coloring")
@click.pass_context
def pglr(ctx, debug, colors):
"""
Command line interface for working with parglare grammars.
"""
ctx.obj = {'debug': debug, 'colors': colors}
@pglr.command()
@click.argument('grammar_file', type=click.Path())
@click.pass_context
def check(ctx, grammar_file):
debug = ctx.obj['debug']
colors = ctx.obj['colors']
check_get_grammar_table(grammar_file, debug, colors)
@pglr.command()
@click.argument('grammar_file', type=click.Path())
@click.pass_context
def viz(ctx, grammar_file):
debug = ctx.obj['debug']
colors = ctx.obj['colors']
t.colors = colors
grammar, table = check_get_grammar_table(grammar_file, debug, colors)
is_flag=True,
callback=set_ctx_obj_option,
is_eager=True,
expose_value=False,
help="Enable safe mode; disables all third party plugins.")
]
return bulk_options(options)
#~~ helper for settings legacy options we still have to support on "octoprint"
legacy_options = bulk_options([
hidden_option("--host", type=click.STRING, callback=set_ctx_obj_option),
hidden_option("--port", type=click.INT, callback=set_ctx_obj_option),
hidden_option("--logging", type=click.Path(), callback=set_ctx_obj_option),
hidden_option("--debug", "-d", is_flag=True, callback=set_ctx_obj_option),
hidden_option("--daemon",
type=click.Choice(["start", "stop", "restart"]),
callback=set_ctx_obj_option),
hidden_option("--pid",
type=click.Path(),
default="/tmp/octoprint.pid",
callback=set_ctx_obj_option),
hidden_option("--iknowwhatimdoing",
"allow_root",
is_flag=True,
callback=set_ctx_obj_option),
hidden_option("--ignore-blacklist",
"ignore_blacklist",
is_flag=True,
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import click
import os
from pkg_resources import resource_filename
import yaml
from ..workflow import integrate, summarize
@click.command()
@click.option('-i',
'--in-seq',
type=click.Path(exists=True, dir_okay=False),
required=True,
help='Input sequence file (can be gzip file.')
@click.option('-o',
'--out-file',
type=click.Path(exists=False, dir_okay=False),
required=True,
help='Output annotation file.')
@click.option('-d',
'--annot-dir',
type=click.Path(file_okay=False),
required=True,
help='directory that has the outputs of annotation tools.')
@click.option('--out-fmt',
type=click.Choice(['gff3', 'genbank']),
default='gff3',
import click
import pandas as pd
@click.command()
@click.argument('exp_table',
type=click.Path(dir_okay=False, exists=True),
required=True)
@click.argument('cutoff', type=click.FLOAT, default=1)
def main(exp_table, cutoff):
exp_df = pd.read_table(exp_table, index_col=0)
ubi_genes = exp_df.T.min() > cutoff
ubi_genes = ubi_genes[ubi_genes].index
for each in ubi_genes:
print each
if __name__ == '__main__':
main()
@click.option("-q", "--psm-fdr-threshold", default=0.05, type=float,
help='Minimum FDR Threshold to use for filtering GPSMs when selecting identified glycopeptides')
@click.option("-s", "--tandem-scoring-model", default='coverage_weighted_binomial', type=click.Choice(
glycopeptide_tandem_scoring_functions.keys()),
help="Select a scoring function to use for evaluating glycopeptide-spectrum matches")
@click.option("-x", "--oxonium-threshold", default=0.05, type=float,
help=('Minimum HexNAc-derived oxonium ion abundance '
'ratio to filter MS/MS scans. Defaults to 0.05.'))
@click.option("-a", "--adduct", 'adducts', multiple=True, nargs=2,
help=("Adducts to consider. Specify name or formula, and a"
" multiplicity."))
@processes_option
@click.option("--export", type=click.Choice(
['csv', 'html']), multiple=True,
help="export command to after search is complete")
@click.option("-o", "--output-path", default=None, type=click.Path(writable=True), help=(
"Path to write resulting analysis to."))
@click.option("-w", "--workload-size", default=500, type=int, help="Number of spectra to process at once")
@click.option("--save-intermediate-results", default=None, type=click.Path(), required=False,
help='Save intermediate spectrum matches to a file', cls=HiddenOption)
def search_glycopeptide(context, database_connection, sample_path, hypothesis_identifier,
analysis_name, output_path=None, grouping_error_tolerance=1.5e-5, mass_error_tolerance=1e-5,
msn_mass_error_tolerance=2e-5, psm_fdr_threshold=0.05, peak_shape_scoring_model=None,
tandem_scoring_model=None, oxonium_threshold=0.15,
save_intermediate_results=None, processes=4,
workload_size=500, adducts=None, export=None):
"""Identify glycopeptide sequences from processed LC-MS/MS data
"""
if output_path is None:
output_path = make_analysis_output_path("glycopeptide")
if peak_shape_scoring_model is None:
@click.command()
@click.option(
"--clusters",
type=CommaSeparatedValues(),
help="Comma separated list of Kubernetes API server URLs (default: {})".
format(DEFAULT_CLUSTERS),
envvar="CLUSTERS",
)
@click.option(
"--cluster-registry",
metavar="URL",
help="URL of Cluster Registry to discover clusters to report on",
)
@click.option("--kubeconfig-path",
type=click.Path(exists=True),
help="Path to kubeconfig file")
@click.option(
"--kubeconfig-contexts",
type=CommaSeparatedValues(),
help=
"List of kubeconfig contexts to use (default: use all defined contexts)",
envvar="KUBECONFIG_CONTEXTS",
)
@click.option(
"--application-registry",
metavar="URL",
help="URL of Application Registry to look up team by application ID",
)
@click.option("--use-cache",
is_flag=True,
)
@rnax.command()
@pass_pipe
@arggist
def show(pipe: Pipe):
"""Prints current selection to stdout, in tsv format."""
# TODO allow storing plain matrix, i.e. without multiindex
data = getattr(pipe, pipe.selection, pipe.matrix)
data.to_csv(sys.stdout, sep='\t')
@rnax.command()
@click.argument('out',
type=click.Path(writable=True, dir_okay=False, file_okay=True),
default='-')
@click.option("--mode",
"-m",
type=click.Choice(['csv', 'pickle', 'auto']),
default='auto')
@pass_pipe
@arggist
def store(pipe: Pipe, out: str, mode: str):
"""Save current selection in given file; in tsv format."""
# TODO allow storing plain matrix, i.e. without multiindex
data = getattr(pipe, pipe.selection, pipe.matrix)
compression = 'infer'
if mode == 'auto':
if out.endswith('.gz'):
f = out.rstrip('.gz')
import netifaces
import os
from mixer.config import ConfigCheck
from rtmidi import midiutil
def print_midiports(ctx, param, value):
if not value or ctx.resilient_parsing:
return
click.echo(midiutil.list_output_ports())
ctx.exit()
@click.command()
@click.argument('config', type=click.Path(exists=True))
@click.option('--gui', is_flag=True)
@click.option('--restapi', is_flag=True)
@click.option('--port', default=5000, type=int)
@click.option('--debug', is_flag=True)
@click.option('--listmidi',
is_flag=True,
is_eager=True,
expose_value=False,
callback=print_midiports)
def start(config, gui, restapi, port, debug):
"""
Read config and start the app
"""
c = ConfigCheck(config)
Log the name of the file being processed and check the input file
size against identify.FILE_TOO_LARGE_THRESHOLD for too large input.
"""
for filename in utils.walk(file_or_dirs):
log(f'* {filename:}', nl=False)
if os.path.getsize(filename) > identify.FILE_TOO_LARGE_THRESHOLD:
log(' ... SKIP')
continue
yield filename
@click.command('extract')
@click.argument('src',
nargs=-1,
type=click.Path(exists=True, resolve_path=True))
@click.option('--output',
'-o',
type=click.File('w'),
default='-',
help='Output file.')
@click.option('--existing',
'-e',
type=click.Path(exists=True),
help='Existing Beancount ledger for de-duplication.')
@click.option('--reverse',
'-r',
is_flag=True,
help='Sort entries in reverse order.')
@click.option('--failfast',
'-x',
import click
from strephit.commons.classification import reverse_gazetteer
from sklearn.externals import joblib
from sklearn.svm import LinearSVC
from strephit.classification.feature_extractors import FactExtractorFeatureExtractor
logger = logging.getLogger(__name__)
@click.command()
@click.argument('training-set', type=click.File('r'))
@click.argument('language')
@click.option('-o',
'--outfile',
type=click.Path(dir_okay=False, writable=True),
default='output/classifier_model.pkl',
help='Where to save the model')
@click.option('-c', default=1.0, help='Penalty parameter C of the error term.')
@click.option('--loss',
default='squared_hinge',
help='Specifies the loss function.',
type=click.Choice(['hinge', 'squared_hinge']))
@click.option('--penalty',
default='l2',
help='Specifies the norm used in the penalization.',
type=click.Choice(['l1', 'l2']))
@click.option(
'--dual',
is_flag=True,
help=
Command-line interface for the retrieval of a protein<->kcat mapping of a model.
"""
# IMPORTS
# External modules
import click
# Internal modules
from submodules.get_reactions_kcat_mapping import get_reactions_kcat_mapping
# Set-up console arguments using click decorators
@click.command()
@click.option("--sbml_path",
required=True,
type=click.Path(exists=True, file_okay=True, dir_okay=True),
prompt="Analyzed SBML",
help="Full path to the SBML of the metabolic model that shall be sMOMENT-enhanced")
@click.option("--project_folder",
required=True,
type=click.Path(exists=True, dir_okay=True),
prompt="Project folder",
help="Path to the project folder in which the reactions<->kcat mapping JSON will be created.")
@click.option("--project_name",
required=True,
type=str,
prompt="Project name",
help="Name of the current project. The generated reactions<->kcat mapping JSON will have this name as prefix.")
@click.option("--organism",
required=True,
type=str,
covariate=conditions,
condition_type=condition_type,
output_dir=output_dir,
model_name=model_name)
# Group analysis - PyBASC
@group.command()
@click.argument('group_config')
def basc(group_config):
import CPAC.pipeline.cpac_group_runner as cpac_group_runner
cpac_group_runner.run_basc(group_config)
@group.command(name="mdmr")
@click.argument("group_config", type=click.Path(exists=True))
def group_mdmr(group_config):
from CPAC.pipeline.cpac_group_runner import run_cwas
run_cwas(group_config)
@group.command(name="isc")
@click.argument("group_config", type=click.Path(exists=True))
def group_isc(group_config):
from CPAC.pipeline.cpac_group_runner import run_isc
run_isc(group_config)
# Utilities
@main.group()
def utils():
def app_group(parent):
"""App CLI group"""
formatter = cli.make_formatter(cli.AppPrettyFormatter)
@parent.group(name='app')
def app():
"""Manage app configuration"""
pass
@app.command()
@cli.admin.ON_EXCEPTIONS
def list(): # pylint: disable=W0622
"""List apps"""
for appname in master.list_scheduled_apps(context.GLOBAL.zk.conn):
print(appname)
@app.command()
@click.option('-m',
'--manifest',
type=click.Path(exists=True, readable=True),
required=True)
@click.option('--env',
help='Proid environment.',
required=True,
type=click.Choice(['dev', 'qa', 'uat', 'prod']))
@click.option('--proid', help='Proid.', required=True)
@click.option('-n', '--count', type=int, default=1)
@click.argument('app')
@cli.admin.ON_EXCEPTIONS
def schedule(app, manifest, count, env, proid):
"""Schedule app(s) on the cell master"""
with open(manifest, 'rb') as fd:
data = yaml.load(fd.read())
# TODO: should we delete all potential attributes starting
# with _ ?
if '_id' in data:
del data['_id']
data['environment'] = env
if 'affinity' not in data:
# TODO: allow custom affinity formats.
data['affinity'] = '{0}.{1}'.format(*app.split('.'))
data['proid'] = proid
scheduled = master.create_apps(context.GLOBAL.zk.conn, app, data,
count)
for app_id in scheduled:
print(app_id)
@app.command()
@click.argument('instance')
@cli.admin.ON_EXCEPTIONS
def configure(instance):
"""View app instance configuration"""
scheduled = master.get_app(context.GLOBAL.zk.conn, instance)
cli.out(formatter(scheduled))
@app.command()
@click.argument('apps', nargs=-1)
@cli.admin.ON_EXCEPTIONS
def delete(apps):
"""Deletes (unschedules) the app by pattern"""
master.delete_apps(context.GLOBAL.zk.conn, apps)
del list
del schedule
del delete
del configure
def test_data_option():
return planemo_option(
"--test_data",
type=click.Path(exists=True, file_okay=False, resolve_path=True),
help="test-data directory to for specified tool(s).",
)
