def init(context, force, demo, auto, root_dir):
"""Bootstrap a new chanjo setup."""
is_bootstrapped = False
root_path = Path(root_dir)
LOG.info("setting up chanjo under: %s", root_path)
db_uri = context.obj.get('database')
db_uri = db_uri or "sqlite:///{}".format(
root_path.joinpath(DB_NAME).abspath())
# test setup of sambamba
sambamba_bin = find_executable('sambamba')
if sambamba_bin is None: # pragma: no cover
LOG.warning("'sambamba' command not found")
else:
LOG.debug("'sambamba' found: %s", sambamba_bin)
if demo:
LOG.info("copying demo files: %s", root_dir)
setup_demo(root_dir, force=force)
LOG.info("configure new chanjo database: %s", db_uri)
chanjo_db = ChanjoDB(db_uri)
chanjo_db.set_up()
is_bootstrapped = True
elif auto or click.confirm('Bootstrap HGNC transcript BED?'):
pull(root_dir, force=force)
LOG.info("configure new chanjo database: %s", db_uri)
chanjo_db = ChanjoDB(db_uri)
chanjo_db.set_up()
is_bootstrapped = True
# setup config file
root_path.makedirs_p()
conf_path = root_path.joinpath('chanjo.yaml')
with codecs.open(conf_path, 'w', encoding='utf-8') as conf_handle:
data = {'database': db_uri}
data_str = ruamel.yaml.dump(data, Dumper=ruamel.yaml.RoundTripDumper)
LOG.info("writing config file: %s", conf_path)
conf_handle.write(data_str)
if is_bootstrapped:
click.echo('Chanjo bootstrap successful! Now run: ')
bed_path = root_path.joinpath(DEMO_BED_NAME if demo else BED_NAME)
click.echo("chanjo --config {} link {}".format(conf_path, bed_path))
def init(context, force, demo, auto, root_dir):
"""Bootstrap a new chanjo setup."""
is_bootstrapped = False
root_path = Path(root_dir)
LOG.info("setting up chanjo under: %s", root_path)
db_uri = context.obj.get('database')
db_uri = db_uri or "sqlite:///{}".format(root_path.joinpath(DB_NAME).abspath())
# test setup of sambamba
sambamba_bin = find_executable('sambamba')
if sambamba_bin is None: # pragma: no cover
LOG.warning("'sambamba' command not found")
else:
LOG.debug("'sambamba' found: %s", sambamba_bin)
if demo:
LOG.info("copying demo files: %s", root_dir)
setup_demo(root_dir, force=force)
LOG.info("configure new chanjo database: %s", db_uri)
chanjo_db = ChanjoDB(db_uri)
chanjo_db.set_up()
is_bootstrapped = True
elif auto or click.confirm('Bootstrap HGNC transcript BED?'):
pull(root_dir, force=force)
LOG.info("configure new chanjo database: %s", db_uri)
chanjo_db = ChanjoDB(db_uri)
chanjo_db.set_up()
is_bootstrapped = True
# setup config file
root_path.makedirs_p()
conf_path = root_path.joinpath('chanjo.yaml')
with codecs.open(conf_path, 'w', encoding='utf-8') as conf_handle:
data = {'database': db_uri}
data_str = ruamel.yaml.dump(data, Dumper=ruamel.yaml.RoundTripDumper)
LOG.info("writing config file: %s", conf_path)
conf_handle.write(data_str)
if is_bootstrapped:
click.echo('Chanjo bootstrap successful! Now run: ')
bed_path = root_path.joinpath(DEMO_BED_NAME if demo else BED_NAME)
click.echo("chanjo --config {} link {}".format(conf_path, bed_path))
def init(context, force, demo, auto, root_dir):
"""Bootstrap a new chanjo setup."""
root_path = path(root_dir).abspath()
log.info("setting up chanjo under: %s", root_path)
db_uri = context.obj.get('database')
abs_db_path = root_path.joinpath(DB_NAME)
db_uri = db_uri or "sqlite:///{}".format(abs_db_path)
# test setup of sambamba
sambamba_bin = find_executable('sambamba')
if sambamba_bin is None: # pragma: no cover
log.warn("'sambamba' command not found")
else:
log.debug("'sambamba' found: %s", sambamba_bin)
if demo:
log.info("copying demo files: %s", root_dir)
setup_demo(root_dir, force=force)
elif auto or click.confirm('Bootstrap CCDS transcript BED?'):
# ensure root dir exists
root_path.makedirs_p()
pull(root_dir, force=force)
log.info("configure new chanjo database: %s", db_uri)
chanjo_db = ChanjoDB(db_uri)
chanjo_db.set_up()
# setup config file
conf_path = root_path.joinpath('chanjo.yaml')
with codecs.open(conf_path, 'w', encoding='utf-8') as conf_handle:
data = {'database': db_uri}
data_str = yaml.dump(data, default_flow_style=False)
log.info("writing config file: %s", conf_path)
conf_handle.write(data_str)
click.echo('Chanjo bootstrap successful! Now run: ')
bed_path = root_path.joinpath(BED_NAME)
click.echo("chanjo --config {} link {}".format(conf_path, bed_path))
def existing_db(tmpdir):
db_path = tmpdir.join("coverage.sqlite3")
chanjo_db = ChanjoDB(str(db_path))
chanjo_db.set_up()
yield chanjo_db
chanjo_db.tear_down()
def chanjo_db():
_chanjo_db = ChanjoDB("sqlite://")
_chanjo_db.set_up()
yield _chanjo_db
_chanjo_db.tear_down()
def existing_db(tmpdir):
db_path = tmpdir.join('coverage.sqlite3')
chanjo_db = ChanjoDB(str(db_path))
chanjo_db.set_up()
yield chanjo_db
chanjo_db.tear_down()
def chanjo_db():
_chanjo_db = ChanjoDB('sqlite://')
_chanjo_db.set_up()
yield _chanjo_db
_chanjo_db.tear_down()
