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"""
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
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