def link(context, bed_stream):
"""Link related genomic elements."""
chanjo_db = ChanjoDB(uri=context.obj['database'])
result = link_elements(bed_stream)
with click.progressbar(result.models, length=result.count,
label='adding transcripts') as bar:
for tx_model in bar:
chanjo_db.add(tx_model)
try:
chanjo_db.save()
except IntegrityError:
LOG.exception('elements already linked?')
chanjo_db.session.rollback()
click.echo("use 'chanjo db setup --reset' to re-build")
context.abort()
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 link(context, bed_stream):
"""Link related genomic elements."""
chanjo_db = ChanjoDB(uri=context.obj['database'])
result = link_elements(bed_stream)
with click.progressbar(result.models, length=result.count,
label='adding transcripts') as bar:
for tx_model in bar:
chanjo_db.add(tx_model)
try:
chanjo_db.save()
except IntegrityError:
log.exception('elements already linked?')
chanjo_db.session.rollback()
click.echo("use 'chanjo db setup --reset' to re-build")
context.abort()
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 load(context, sample, group, name, group_name, threshold, bed_stream):
"""Load Sambamba output into the database for a sample."""
chanjo_db = ChanjoDB(uri=context.obj['database'])
source = os.path.abspath(bed_stream.name)
result = load_transcripts(bed_stream, sample_id=sample, group_id=group,
source=source, threshold=threshold)
result.sample.name = name
result.sample.group_name = group_name
try:
chanjo_db.add(result.sample)
with click.progressbar(result.models, length=result.count,
label='loading transcripts') as bar:
for tx_model in bar:
chanjo_db.add(tx_model)
chanjo_db.save()
except IntegrityError as error:
LOG.error('sample already loaded, rolling back')
LOG.debug(error.args[0])
chanjo_db.session.rollback()
context.abort()
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 test_no_dialect():
# GIVEN not explicity specifying SQLite dialect
# WHEN setting up the API
chanjo_db = ChanjoDB(':memory:')
# THEN chanjo should guess it
assert chanjo_db.dialect == 'sqlite'