diff options
| -rwxr-xr-x | scripts/index-genenetwork | 18 |
1 files changed, 14 insertions, 4 deletions
diff --git a/scripts/index-genenetwork b/scripts/index-genenetwork index 2779abc..0544bc7 100755 --- a/scripts/index-genenetwork +++ b/scripts/index-genenetwork @@ -514,9 +514,14 @@ def xapian_compact(combined_index: pathlib.Path, indices: List[pathlib.Path]) -> @click.argument("xapian_directory") @click.argument("sql_uri") @click.argument("sparql_uri") +@click.option("-v", "--virtuoso-ttl-directory", + type=pathlib.Path, + default=pathlib.Path("/var/lib/data/"), + show_default=True) def is_data_modified(xapian_directory: str, sql_uri: str, - sparql_uri: str) -> None: + sparql_uri: str, + virtuoso_ttl_directory: pathlib.Path) -> None: dir_ = pathlib.Path(xapian_directory) with locked_xapian_writable_database(dir_) as db, database_connection(sql_uri) as conn: checksums = "-1" @@ -529,7 +534,7 @@ def is_data_modified(xapian_directory: str, ]) # Return a zero exit status code when the data has changed; # otherwise exit with a 1 exit status code. - generif = pathlib.Path("/var/lib/data/") + generif = virtuoso_ttl_directory if (db.get_metadata("generif-checksum").decode() == md5hash_ttl_dir(generif) and db.get_metadata("checksums").decode() == checksums): sys.exit(1) @@ -540,9 +545,14 @@ def is_data_modified(xapian_directory: str, @click.argument("xapian_directory") @click.argument("sql_uri") @click.argument("sparql_uri") +@click.option("-v", "--virtuoso-ttl-directory", + type=pathlib.Path, + default=pathlib.Path("/var/lib/data/"), + show_default=True) # pylint: disable=missing-function-docstring def create_xapian_index(xapian_directory: str, sql_uri: str, - sparql_uri: str) -> None: + sparql_uri: str, + virtuoso_ttl_directory: pathlib.Path) -> None: logging.basicConfig(level=os.environ.get("LOGLEVEL", "DEBUG"), format='%(asctime)s %(levelname)s: %(message)s', datefmt='%Y-%m-%d %H:%M:%S %Z') @@ -587,7 +597,7 @@ def create_xapian_index(xapian_directory: str, sql_uri: str, logging.info("Writing generif checksums into index") db.set_metadata( "generif-checksum", - md5hash_ttl_dir(pathlib.Path("/var/lib/data/")).encode()) + md5hash_ttl_dir(virtuoso_ttl_directory).encode()) for child in combined_index.iterdir(): shutil.move(child, xapian_directory) logging.info("Index built") |