""" Test datacite importer. """ import datetime import pytest import gzip from fatcat_tools.importers import DataciteImporter, JsonLinePusher from fixtures import api import json @pytest.fixture(scope="function") def datacite_importer(api): with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file: yield DataciteImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', bezerk_mode=True) @pytest.fixture(scope="function") def datacite_importer_existing(api): with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file: yield DataciteImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', bezerk_mode=False) @pytest.mark.skip(reason="larger datacite import slows tests down") def test_datacite_importer_huge(datacite_importer): last_index = datacite_importer.api.get_changelog(limit=1)[0].index with gzip.open('tests/files/datacite_1k_records.jsonl.gz', 'rt') as f: datacite_importer.bezerk_mode = True counts = JsonLinePusher(datacite_importer, f).run() assert counts['insert'] == 998 change = datacite_importer.api.get_changelog_entry(index=last_index+1) release = datacite_importer.api.get_release(change.editgroup.edits.releases[0].ident) assert len(release.contribs) == 3 def test_datacite_importer(datacite_importer): last_index = datacite_importer.api.get_changelog(limit=1)[0].index with open('tests/files/datacite_sample.jsonl', 'r') as f: datacite_importer.bezerk_mode = True counts = JsonLinePusher(datacite_importer, f).run() assert counts['insert'] == 1 assert counts['exists'] == 0 assert counts['skip'] == 0 # fetch most recent editgroup change = datacite_importer.api.get_changelog_entry(index=last_index+1) eg = change.editgroup assert eg.description assert "datacite" in eg.description.lower() assert eg.extra['git_rev'] assert "fatcat_tools.DataciteImporter" in eg.extra['agent'] last_index = datacite_importer.api.get_changelog(limit=1)[0].index with open('tests/files/datacite_sample.jsonl', 'r') as f: datacite_importer.bezerk_mode = False datacite_importer.reset() counts = JsonLinePusher(datacite_importer, f).run() assert counts['insert'] == 0 assert counts['exists'] == 1 assert counts['skip'] == 0 assert last_index == datacite_importer.api.get_changelog(limit=1)[0].index def test_datacite_dict_parse(datacite_importer): with open('tests/files/datacite_sample.jsonl', 'r') as f: raw = json.load(f) r = datacite_importer.parse_record(raw) # ensure the API server is ok with format JsonLinePusher(datacite_importer, [json.dumps(raw)]).run() print(r.extra) assert r.title == "Triticum turgidum L. subsp. durum (Desf.) Husn. 97090" assert r.publisher == "International Centre for Agricultural Research in Dry Areas" assert r.release_type == "article" assert r.release_stage == "published" assert r.license_slug == None assert r.original_title == "Triticum turgidum L. subsp. durum (Desf.) Husn. 97090" assert r.ext_ids.doi == "10.18730/8dym9" assert r.ext_ids.isbn13 == None assert r.language == "enc" assert r.subtitle == None assert r.release_date == None assert r.release_year == 1986 assert 'subtitle' not in r.extra assert 'subtitle' not in r.extra['datacite'] assert 'funder' not in r.extra assert 'funder' not in r.extra['datacite'] # matched by ISSN, so shouldn't be in there #assert extra['container_name'] == "International Journal of Quantum Chemistry" assert r.extra['datacite']['url'] == 'https://ssl.fao.org/glis/doi/10.18730/8DYM9' assert r.extra['datacite']['subjects'] == [{'subject': 'Plant Genetic Resource for Food and Agriculture'}] assert len(r.abstracts) == 1 assert len(r.abstracts[0].content) == 421 assert len(r.contribs) == 1 assert r.contribs[0].raw_name == "GLIS Of The ITPGRFA" assert r.contribs[0].given_name == None assert r.contribs[0].surname == None assert len(r.refs) == 0