diff options
Diffstat (limited to 'python/tests')
| -rw-r--r-- | python/tests/files/datacite_1k_records.jsonl.gz | bin | 0 -> 684605 bytes | |||
| -rw-r--r-- | python/tests/files/datacite_sample.jsonl | 1 | ||||
| -rw-r--r-- | python/tests/import_datacite.py | 108 |
3 files changed, 92 insertions, 17 deletions
diff --git a/python/tests/files/datacite_1k_records.jsonl.gz b/python/tests/files/datacite_1k_records.jsonl.gz Binary files differnew file mode 100644 index 00000000..28ea6e37 --- /dev/null +++ b/python/tests/files/datacite_1k_records.jsonl.gz diff --git a/python/tests/files/datacite_sample.jsonl b/python/tests/files/datacite_sample.jsonl new file mode 100644 index 00000000..dba3e267 --- /dev/null +++ b/python/tests/files/datacite_sample.jsonl @@ -0,0 +1 @@ +{"id":"10.18730/8dym9","type":"dois","attributes":{"doi":"10.18730/8dym9","identifiers":[{"identifier":"https://doi.org/10.18730/8dym9","identifierType":"DOI"},{"identifier":"ICDW 20791","identifierType":"Other"}],"creators":[{"name":"GLIS Of The ITPGRFA","affiliation":[]}],"titles":[{"title":"Triticum turgidum L. subsp. durum (Desf.) Husn. 97090"}],"publisher":"International Centre for Agricultural Research in Dry Areas","container":{},"publicationYear":2017,"subjects":[{"subject":"Plant Genetic Resource for Food and Agriculture"}],"contributors":[{"name":"International Centre For Agricultural Research In Dry Areas","affiliation":[]}],"dates":[{"date":"1986","dateType":"Accepted"},{"date":"1978-06-03","dateType":"Collected"},{"date":"2017","dateType":"Issued"}],"language":"en","types":{"ris":"GEN","bibtex":"misc","citeproc":"article","schemaOrg":"CreativeWork","resourceType":"PGRFA Material","resourceTypeGeneral":"PhysicalObject"},"relatedIdentifiers":[{"schemeUri":"http://www.fao.org/plant-treaty/areas-of-work/global-information-system/descriptors","schemeType":"XML","relationType":"HasMetadata","relatedIdentifier":"https://ssl.fao.org/glisapi/v1/pgrfas?doi=10.18730/8DYM9","relatedIdentifierType":"URL","relatedMetadataScheme":"GLIS Descriptors"},{"schemeUri":"http://rs.tdwg.org/dwc/terms/guides/text/index.htm","schemeType":"DwC-A","relationType":"HasMetadata","relatedIdentifier":"https://ssl.fao.org/glisapi/v1/pgrfas?_format=dwc&doi=10.18730/8DYM9","relatedIdentifierType":"URL","relatedMetadataScheme":"Darwin Core Archive"}],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[{"description":"Plant Genetic Resource.<br>Taxonomy: Triticum turgidum L. subsp. durum (Desf.) Husn.<br>Common name(s): Wheat<br>Conserved by: International Centre for Agricultural Research in Dry Areas (ICARDA), Lebanon<br>Local sample unique identifier: 97090<br>Method of creation: Acquisition<br>Date: 1986<br>Biological status: Traditional cultivar/landrace<br>Other identifiers: ICDW 20791<br>MLS status: Included<br>Historical: No","descriptionType":"Abstract"}],"geoLocations":[{"geoLocationPlace":"Collecting site","geoLocationPoint":{"pointLatitude":"35.5","pointLongitude":"23.7333"}}],"fundingReferences":[],"url":"https://ssl.fao.org/glis/doi/10.18730/8DYM9","contentUrl":null,"metadataVersion":3,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"created":"2017-11-11T12:26:01.000Z","registered":"2017-11-11T12:26:02.000Z","published":"2017","updated":"2019-08-02T16:34:56.000Z"},"relationships":{"client":{"data":{"id":"fao.itpgrfa","type":"clients"}}}} diff --git a/python/tests/import_datacite.py b/python/tests/import_datacite.py index 0bbaba2e..9c542fc6 100644 --- a/python/tests/import_datacite.py +++ b/python/tests/import_datacite.py @@ -1,25 +1,99 @@ """ Test datacite importer. +""" -Datacite is a aggregator, hence inputs are quite varied. +import datetime +import pytest +import gzip +from fatcat_tools.importers import DataciteImporter, JsonLinePusher +from fixtures import api +import json -Here is small sample of ID types taken from a sample: - 497344 "DOI" - 65013 "URL" - 22210 "CCDC" - 17853 "GBIF" - 17635 "Other" - 11474 "uri" - 9170 "Publisher ID" - 7775 "URN" - 6196 "DUCHAS" - 5624 "Handle" - 5056 "publisherId" +@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) -A nice tool, not yet existing tool (maybe named indigo) would do the following: +@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) - $ shuf -n 100000 datacite.ndjson | indigo -t md > data.md -TODO(martin): Write tests. -""" +@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 |