def _get_resolver(
name_data: Union[None, str, pd.DataFrame] = None,
alts_data: Union[None, str, pd.DataFrame] = None,
defs_data: Union[None, str, pd.DataFrame] = None,
lazy: bool = False,
sql: bool = False,
uri: Optional[str] = None,
refs_table: Optional[str] = None,
alts_table: Optional[str] = None,
defs_table: Optional[str] = None,
) -> Backend:
if sql:
logger.info("using raw SQL backend")
return RawSQLBackend(
engine=uri,
refs_table=refs_table,
alts_table=alts_table,
defs_table=defs_table,
)
if lazy:
name_lookup = None
elif name_data is None:
name_lookup = _get_lookup_from_path(ensure_ooh_na_na())
elif isinstance(name_data, str):
name_lookup = _get_lookup_from_path(name_data)
elif isinstance(name_data, pd.DataFrame):
name_lookup = _get_lookup_from_df(name_data)
else:
raise TypeError(f"invalid type for `name_data`: {name_data}")
if lazy:
alts_lookup = None
elif alts_data is None and not lazy:
alts_lookup = _get_lookup_from_path(ensure_alts())
elif isinstance(alts_data, str):
alts_lookup = _get_lookup_from_path(alts_data)
elif isinstance(alts_data, pd.DataFrame):
alts_lookup = _get_lookup_from_df(alts_data)
else:
raise TypeError(f"invalid type for `alt_data`: {alts_data}")
if lazy:
defs_lookup = None
elif defs_data is None and not lazy:
defs_lookup = _get_lookup_from_path(ensure_definitions())
elif isinstance(defs_data, str):
defs_lookup = _get_lookup_from_path(defs_data)
elif isinstance(defs_data, pd.DataFrame):
defs_lookup = _get_lookup_from_df(defs_data)
else:
raise TypeError(f"invalid type for `defs_data`: {defs_data}")
return _prepare_backend_with_lookup(
name_lookup=name_lookup,
alts_lookup=alts_lookup,
defs_lookup=defs_lookup,
)
def get_app(
name_data: Union[None, str, pd.DataFrame] = None,
alts_data: Union[None, str, pd.DataFrame] = None,
lazy: bool = False,
sql: bool = False,
uri: Optional[str] = None,
refs_table: Optional[str] = None,
alts_table: Optional[str] = None,
) -> Flask:
"""Build a flask app.
:param name_data: If none, uses the internal PyOBO loader. If a string, assumes is a gzip and reads a
dataframe from there. If a dataframe, uses it directly. Assumes data frame has 3 columns - prefix,
identifier, and name and is a TSV.
:param alts_data: If none, uses the internal PyOBO loader. If a string, assumes is a gzip and reads a
dataframe from there. If a dataframe, uses it directly. Assumes data frame has 3 columns - prefix,
alt identifier, and identifier and is a TSV.
:param lazy: don't load the full cache into memory to run
:param sql_table: Use SQL-based backend
"""
app = Flask(__name__)
Swagger(app)
Bootstrap(app)
if sql:
app.config['resolver_backend'] = RawSQLBackend(
engine=uri,
refs_table=refs_table,
alts_table=alts_table,
)
else:
if lazy:
name_lookup = None
elif name_data is None:
name_lookup = _get_lookup_from_path(ensure_ooh_na_na())
elif isinstance(name_data, str):
name_lookup = _get_lookup_from_path(name_data)
elif isinstance(name_data, pd.DataFrame):
name_lookup = _get_lookup_from_df(name_data)
else:
raise TypeError(f'invalid type for `name_data`: {name_data}')
if lazy:
alts_lookup = None
elif alts_data is None and not lazy:
alts_lookup = _get_lookup_from_path(ensure_alts())
elif isinstance(alts_data, str):
alts_lookup = _get_lookup_from_path(alts_data)
elif isinstance(alts_data, pd.DataFrame):
alts_lookup = _get_lookup_from_df(alts_data)
else:
raise TypeError(f'invalid type for `alt_data`: {alts_data}')
app.config['resolver_backend'] = _prepare_backend_with_lookup(name_lookup=name_lookup, alts_lookup=alts_lookup)
app.register_blueprint(resolve_blueprint)
return app
def _load_name(
*,
engine: Union[None, str, Engine] = None,
table: Optional[str] = None,
path: Optional[str] = None,
test: bool = False,
):
engine = _ensure_engine(engine)
_load_table(
engine=engine,
table=table or REFS_TABLE_NAME,
path=path if path else ensure_ooh_na_na(),
test=test,
target_col='name',
target_col_size=4096,
)