81e4e9f2ff
All checks were successful
Test execution / Test-all (push) Successful in 2m11s
Adapt the code of `dump-things-pid-check` to the dynamic configuration changes.
116 lines
3.4 KiB
Python
116 lines
3.4 KiB
Python
from __future__ import annotations
|
|
|
|
import sys
|
|
from argparse import ArgumentParser
|
|
from collections.abc import Iterable
|
|
from pathlib import Path
|
|
|
|
from fastapi import FastAPI
|
|
|
|
from dump_things_service.abstract_config import (
|
|
get_config_labels,
|
|
read_config,
|
|
)
|
|
from dump_things_service.backends.schema_type_layer import _SchemaTypeLayer
|
|
from dump_things_service.backends.sqlite import _SQLiteBackend
|
|
from dump_things_service.exceptions import CurieResolutionError
|
|
from dump_things_service.instance_state import create_instance_state
|
|
from dump_things_service.manifest import manifest_configuration
|
|
from dump_things_service.store.model_store import _ModelStore
|
|
from dump_things_service.utils import (
|
|
create_token_store,
|
|
get_on_disk_labels,
|
|
)
|
|
|
|
parser = ArgumentParser(
|
|
prog='Check pids for resolvability',
|
|
description='This command checks for pids that are in CURIE format and '
|
|
'cannot be resolved.',
|
|
)
|
|
parser.add_argument(
|
|
'store',
|
|
help='The root directory of the store.',
|
|
)
|
|
|
|
|
|
def show_backend(model_store: _ModelStore):
|
|
backend = model_store.backend
|
|
if isinstance(backend, _SchemaTypeLayer):
|
|
backend = backend.backend
|
|
if isinstance(backend, _SQLiteBackend):
|
|
print(f'Checking: {backend.db_path}', file=sys.stderr)
|
|
else:
|
|
print(f'Checking: {backend.root}', file=sys.stderr)
|
|
|
|
|
|
def check_pids_in_stores(
|
|
stores: Iterable[_ModelStore]
|
|
) -> int:
|
|
result = 0
|
|
for store in stores:
|
|
print('checking', store.get_uri(), file=sys.stderr)
|
|
for record_info in store.get_all_objects():
|
|
pid = record_info.json_object['pid']
|
|
try:
|
|
store.pid_to_iri(pid)
|
|
except CurieResolutionError:
|
|
result += 1
|
|
print(pid, store.get_uri())
|
|
|
|
return result
|
|
|
|
|
|
def check_pids(
|
|
store_path: Path,
|
|
):
|
|
abstract_config = read_config(store_path)
|
|
instance_state = create_instance_state(
|
|
store_path=store_path,
|
|
bootstrap_token='',
|
|
fastapi_app=FastAPI(),
|
|
)
|
|
manifest_configuration(abstract_config, instance_state)
|
|
|
|
result = 0
|
|
|
|
# Check pids in curated stores
|
|
result += check_pids_in_stores(instance_state.curated_stores.values())
|
|
|
|
# Check pids in incoming stores. Incoming stores can be defined in the
|
|
# configuration, or can be generated by external authentication sources.
|
|
# In the latter case, they are manifest as directories in the incoming area
|
|
# of a collection.
|
|
for collection, collection_info in abstract_config.collections.items():
|
|
configured_labels = get_config_labels(abstract_config, collection)
|
|
on_disk_labels = get_on_disk_labels(
|
|
store_path=store_path,
|
|
abstract_config=abstract_config,
|
|
collection=collection,
|
|
)
|
|
all_labels = configured_labels.union(on_disk_labels)
|
|
|
|
token_stores = [
|
|
create_token_store(
|
|
abstract_config,
|
|
instance_state,
|
|
collection,
|
|
instance_state.store_path / collection_info.incoming / label
|
|
)
|
|
for label in all_labels
|
|
]
|
|
result += check_pids_in_stores(token_stores)
|
|
|
|
return result
|
|
|
|
|
|
def main():
|
|
arguments = parser.parse_args()
|
|
result = check_pids(Path(arguments.store).absolute())
|
|
if result > 0:
|
|
print(f'found {result} unresolvable pids', file=sys.stderr)
|
|
return 1
|
|
return 0
|
|
|
|
|
|
if __name__ == '__main__':
|
|
sys.exit(main())
|