def main(
port: str,
host: str,
sql: bool,
sql_uri: str,
sql_refs_table: str,
sql_alts_table: str,
data: Optional[str],
test: bool,
with_gunicorn: bool,
lazy: bool,
workers: int,
):
"""Run the resolver app."""
if test and lazy:
click.secho('Can not run in --test and --lazy mode at the same time', fg='red')
sys.exit(0)
if test:
data = [
(prefix, identifier, name)
for prefix in ['hgnc', 'chebi', 'doid', 'go']
for identifier, name in pyobo.get_id_name_mapping(prefix).items()
]
data = pd.DataFrame(data, columns=['prefix', 'identifier', 'name'])
app = get_app(
data,
lazy=lazy,
sql=sql,
uri=sql_uri,
refs_table=sql_refs_table,
alts_table=sql_alts_table,
)
run_app(app=app, host=host, port=port, with_gunicorn=with_gunicorn, workers=workers)
def main(prefix: str, host: str, port: str, with_gunicorn: bool, workers: int):
"""Run the Gilda service for this database."""
from .app import get_app
app = get_app(prefix)
run_app(app,
host=host,
port=port,
with_gunicorn=with_gunicorn,
workers=workers)
def main(mappings_file, host: str, port: str, with_gunicorn: bool):
"""Run the mappings app."""
from .mapper import get_app
app = get_app(mappings_file)
run_app(app=app, host=host, port=port, with_gunicorn=with_gunicorn)
def main(
port: str,
host: str,
sql: bool,
sql_uri: str,
sql_refs_table: str,
sql_alts_table: str,
sql_defs_table: str,
name_data: Optional[str],
alts_data: Optional[str],
defs_data: Optional[str],
test: bool,
with_gunicorn: bool,
lazy: bool,
workers: int,
):
"""Run the resolver app."""
if test and lazy:
click.secho('Can not run in --test and --lazy mode at the same time', fg='red')
sys.exit(0)
from .resolver import get_app
if test:
from pyobo import get_id_name_mapping, get_alts_to_id, get_id_definition_mapping
import pandas as pd
prefixes = ['hgnc', 'chebi', 'doid', 'go']
name_data = pd.DataFrame(
[
(prefix, identifier, name)
for prefix in prefixes
for identifier, name in get_id_name_mapping(prefix).items()
],
columns=['prefix', 'identifier', 'name'],
)
alts_data = pd.DataFrame(
[
(prefix, alt, identifier)
for prefix in prefixes
for alt, identifier in get_alts_to_id(prefix).items()
],
columns=['prefix', 'alt', 'identifier'],
)
defs_data = pd.DataFrame(
[
(prefix, identifier, definition)
for prefix in prefixes
for identifier, definition in get_id_definition_mapping(prefix).items()
],
columns=['prefix', 'identifier', 'definition'],
)
app = get_app(
name_data=name_data,
alts_data=alts_data,
defs_data=defs_data,
lazy=lazy,
sql=sql,
uri=sql_uri,
refs_table=sql_refs_table,
alts_table=sql_alts_table,
defs_table=sql_defs_table,
)
run_app(app=app, host=host, port=port, with_gunicorn=with_gunicorn, workers=workers)