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()