From dfc70003775a006d6f9ccd34aa12359f5e9645e2 Mon Sep 17 00:00:00 2001 From: jo-pol Date: Tue, 17 Dec 2024 15:59:32 +0100 Subject: [PATCH] fixed at least file restriction changes --- pyproject.toml | 1 + .../{scripts => }/open_access_archeodepot.py | 69 +++++++++++-------- 2 files changed, 41 insertions(+), 29 deletions(-) rename src/datastation/{scripts => }/open_access_archeodepot.py (80%) diff --git a/pyproject.toml b/pyproject.toml index 0e9d4fc..ffa9502 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,4 +54,5 @@ ingest-flow = "datastation.ingest_flow:main" dv-dataverse-root-collect-storage-usage = "datastation.dv_dataverse_root_collect_storage_usage:main" dv-dataverse-root-collect-permission-overview = "datastation.dv_dataverse_root_collect_permission_overview:main" datastation-get-component-versions = "datastation.datastation_get_component_versions:main" +open-access-archeodepot = "datastation.open_access_archeodepot:main" dv-dataverse-role-assignment = "datastation.dv_dataverse_role_assignment:main" diff --git a/src/datastation/scripts/open_access_archeodepot.py b/src/datastation/open_access_archeodepot.py similarity index 80% rename from src/datastation/scripts/open_access_archeodepot.py rename to src/datastation/open_access_archeodepot.py index acabc8a..b961467 100644 --- a/src/datastation/scripts/open_access_archeodepot.py +++ b/src/datastation/open_access_archeodepot.py @@ -4,9 +4,10 @@ import json import logging import re +import os -from datastation.batch_processing import batch_process -from datastation.config import init +from datastation.common.batch_processing import BatchProcessor +from datastation.common.config import init from datastation.dv_api import publish_dataset, get_dataset_metadata, change_access_request, replace_dataset_metadata, \ change_file_restrict @@ -16,27 +17,35 @@ def open_access_archeodepot(datasets_file, licenses_file, must_be_restricted_fil doi_to_keep_restricted = read_doi_to_keep_restricted(must_be_restricted_files) server_url = dataverse_config['server_url'] api_token = dataverse_config['api_token'] - logging.debug("is dry run: {}".format(dry_run)) - time_stamp = datetime.datetime.now().strftime("%Y-%m-%d_%H.%M.%S") - batch_process(doi_to_license_uri.items(), - lambda doi_to_license: update_license( - "doi:" + doi_to_license[0], - doi_to_license[1], - doi_to_keep_restricted.get(to_key(doi_to_license[0]), []), - server_url, - api_token, - dry_run, - create_csv("datasets", - ["DOI", "Modified", "OldLicense", "NewLicense", "OldRequestEnabled", - "NewRequestEnabled"], time_stamp), - create_csv("datafiles", - ["DOI", "FileID", "Modified", "OldRestricted", "NewRestricted"], time_stamp)), - delay) - - -def create_csv(datasets, fieldnames, now): - file_name = "archeodepot-{}-{}.csv".format(datasets, now) - csv_writer = csv.DictWriter(open(file_name, 'w'), fieldnames=fieldnames) + logging.info("is dry run: {}".format(dry_run)) + now = datetime.datetime.now().strftime("%Y-%m-%d_%H.%M.%S") + processor = BatchProcessor(wait=delay) + dataset_writer = create_csv( + "datasets", now, + ["DOI", "Modified", "OldLicense", "NewLicense", "OldRequestEnabled", "NewRequestEnabled"]) + datafiles_writer = create_csv( + "datafiles", now, + ["DOI", "FileID", "Modified", "OldRestricted", "NewRestricted"]) + processor.process_entries( + doi_to_license_uri.items(), + lambda doi_to_license: update_license( + "doi:" + doi_to_license[0], + doi_to_license[1], + doi_to_keep_restricted.get(to_key(doi_to_license[0]), []), + server_url, + api_token, + dry_run, + dataset_writer, + datafiles_writer + ) + ) + + +def create_csv(object_type, time_stamp, fieldnames): + file_name = "archeodepot-{}-{}.csv".format(object_type, time_stamp) + fd = os.open(file_name, os.O_WRONLY | os.O_CREAT) + file = os.fdopen(fd, 'w', newline='') + csv_writer = csv.DictWriter(file, fieldnames=fieldnames) csv_writer.writeheader() return csv_writer @@ -45,6 +54,7 @@ def read_doi_to_license(datasets_file, rights_holder_to_license_uri): doi_to_license_uri = {} with open(datasets_file, "r") as input_file_handler: csv_reader = csv.DictReader(input_file_handler, delimiter=',', fieldnames=["DOI"], restkey="rest") + logging.info(next(csv_reader)) for row in csv_reader: key = to_key(row["rest"][-1].strip()) uri = rights_holder_to_license_uri.get(key, "") @@ -79,7 +89,8 @@ def to_key(name): return re.sub("[^a-zA-Z0-1]", "_", name) -def update_license(doi, new_license_uri, must_be_restricted, server_url, api_token, dry_run, datasets_writer, datafiles_writer): +def update_license(doi, new_license_uri, must_be_restricted, server_url, api_token, dry_run, datasets_writer, + datafiles_writer): resp_data = get_dataset_metadata(server_url, api_token, doi) change_to_restricted = list(filter( lambda file: not file['restricted'] and file_path(file) in must_be_restricted, @@ -133,11 +144,11 @@ def change_file(doi, restricted_value: bool, files, server_url, api_token, dataf return False else: for file_id in list(map(lambda file: file['dataFile']['id'], files)): - logging.debug("updating {}".format(file_id)) - datafiles_writer.writerow( - {"DOI": doi, "FileID": file_id, "Modified": modified(), - "OldRestricted": not restricted_value, - "NewRestricted": restricted_value}) + value_ = {"DOI": doi, "FileID": file_id, "Modified": modified(), + "OldRestricted": not restricted_value, + "NewRestricted": restricted_value} + datafiles_writer.writerow(value_) + logging.debug("updating dry_run={} {}".format(dry_run, value_)) if not dry_run: change_file_restrict(server_url, api_token, file_id, restricted_value) return True