diff options
Diffstat (limited to 'python/tests')
| -rw-r--r-- | python/tests/files/datacite/datacite_doc_30.json | 72 | ||||
| -rw-r--r-- | python/tests/files/datacite/datacite_result_30.json | 39 | ||||
| -rw-r--r-- | python/tests/files/example_shadow.json | 10 | ||||
| -rw-r--r-- | python/tests/import_datacite.py | 3 | ||||
| -rw-r--r-- | python/tests/import_shadow.py | 61 |
5 files changed, 183 insertions, 2 deletions
diff --git a/python/tests/files/datacite/datacite_doc_30.json b/python/tests/files/datacite/datacite_doc_30.json new file mode 100644 index 00000000..5f851bbb --- /dev/null +++ b/python/tests/files/datacite/datacite_doc_30.json @@ -0,0 +1,72 @@ +{ + "id": "10.17912/micropub.biology.000143", + "type": "dois", + "attributes": { + "doi": "10.17912/micropub.biology.000143", + "identifiers": null, + "creators": [ + { + "raw_name": "Celja J Uebel", + "givenName": "Celja J", + "familyName": "Uebel", + "affiliation": [], + "role": "author" + }, + { + "raw_name": "Carolyn M Phillips", + "givenName": "Carolyn M", + "familyName": "Phillips", + "affiliation": [], + "role": "author" + } + ], + "titles": [ + { + "title": "Phase-separated protein dynamics are affected by fluorescent tag choice" + } + ], + "publisher": "microPublication Biology", + "container": {}, + "publicationYear": 2019, + "subjects": [], + "contributors": [], + "dates": null, + "language": null, + "types": { + "resourceTypeGeneral": "DataPaper" + }, + "relatedIdentifiers": [], + "sizes": [], + "formats": [], + "version": null, + "rightsList": [], + "descriptions": [ + { + "description": "Biological liquid-liquid phase separation", + "descriptionType": "Abstract" + } + ], + "geoLocations": [], + "fundingReferences": [], + "url": "https://www.micropublication.org/journals/biology/micropub.biology.000143", + "contentUrl": null, + "metadataVersion": 0, + "schemaVersion": null, + "source": null, + "isActive": true, + "state": "findable", + "reason": null, + "created": "2019-08-19T14:43:08.000Z", + "registered": "2019-08-19T14:43:09.000Z", + "published": "2019", + "updated": "2019-11-09T12:32:02.000Z" + }, + "relationships": { + "client": { + "data": { + "id": "caltech.micropub", + "type": "clients" + } + } + } +} diff --git a/python/tests/files/datacite/datacite_result_30.json b/python/tests/files/datacite/datacite_result_30.json new file mode 100644 index 00000000..fc2c4dfc --- /dev/null +++ b/python/tests/files/datacite/datacite_result_30.json @@ -0,0 +1,39 @@ +{ + "abstracts": [ + { + "content": "Biological liquid-liquid phase separation", + "lang": "fr", + "mimetype": "text/plain" + } + ], + "contribs": [ + { + "index": 0, + "given_name": "Celja J", + "surname": "Uebel", + "raw_name": "Celja J Uebel", + "role": "author" + }, + { + "index": 1, + "given_name": "Carolyn M", + "raw_name": "Carolyn M Phillips", + "surname": "Phillips", + "role": "author" + } + ], + "ext_ids": { + "doi": "10.17912/micropub.biology.000143" + }, + "extra": { + "datacite": { + "resourceTypeGeneral": "DataPaper" + }, + "container_name": "microPublication Biology" + }, + "refs": [], + "release_stage": "published", + "release_year": 2019, + "publisher": "microPublication Biology", + "title": "Phase-separated protein dynamics are affected by fluorescent tag choice" +} diff --git a/python/tests/files/example_shadow.json b/python/tests/files/example_shadow.json new file mode 100644 index 00000000..3386f481 --- /dev/null +++ b/python/tests/files/example_shadow.json @@ -0,0 +1,10 @@ +{"shadow":{"shadow_corpus":"scimag","shadow_id":"12703034","sha1hex":"0000002922264275f11cca7b1c3fb662070d0dd7","doi":"10.1371/journal.pmed.0020124","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"0000002922264275f11cca7b1c3fb662070d0dd7","sha256hex":"b4728210cc0f70d8a8f8c39bd97fcbbab3eaca4309ac4bdfbce5df3b66c82f79","md5hex":"debd8db178fa08a7a0aaec6e42832a8e","size_bytes":206121,"mimetype":"application/pdf"},"cdx":{"url":"https://link.springer.com/content/pdf/10.1007%2Fs11626-008-9119-8.pdf","datetime":"20180729135948","sha1hex":"0000002922264275f11cca7b1c3fb662070d0dd7","cdx_sha1hex":null,"mimetype":"application/pdf","warc_path":"UNPAYWALL-PDF-CRAWL-2018-07-20180729132538992-15980-16048-wbgrp-svc281/UNPAYWALL-PDF-CRAWL-2018-07-20180729135708800-16009-11693~wbgrp-svc281.us.archive.org~8443.warc.gz","warc_csize":32497,"warc_offset":105265425,"row_created":"2019-08-09T23:25:44.571943+00:00"}} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"51052483","sha1hex":"00000119fa780ce368ebd96563afdb3eebb90ad3","doi":"10.1191/0266355403gh289oa","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"00000119fa780ce368ebd96563afdb3eebb90ad3","sha256hex":"57ce460db4410b9bfaf500ed652fd29e64d46b40c17e28f1156ba03736edf91b","md5hex":"96133eec3a6c533993213e7bdf446251","size_bytes":164344,"mimetype":"application/pdf"},"cdx":null} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"2476283","sha1hex":"0000017a31547caf347fab66282a40831b9ceb08","doi":"10.1016/0042-207x(62)90512-2","pmid":"54321","isbn13":null},"file_meta":{"sha1hex":"0000017a31547caf347fab66282a40831b9ceb08","sha256hex":"e8d0c607b024ff6ffd58a35f76c454844b70ad19fe3f78a573af1ae53f53ad9d","md5hex":"b53318522b9f35a42b7e53f150fe70b2","size_bytes":116735,"mimetype":"application/pdf"},"cdx":null} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"8760871","sha1hex":"000001abf3dbf936d5053d14f41699722531b8c6","doi":"10.1016/s0042-207x(79)80945-8","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"000001abf3dbf936d5053d14f41699722531b8c6","sha256hex":"8a69b4a6dff98682ad43e7d4139221c1557c1bd202b615490af8a2c7dcbb71d2","md5hex":"29e1cfac8ecfbc8be57a1ec8b465c4be","size_bytes":138218,"mimetype":"application/pdf"},"cdx":null} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"11473618","sha1hex":"0000022e387be46ef797f6686d36c9899cbd6856","doi":"10.1038/ng.2339","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"0000022e387be46ef797f6686d36c9899cbd6856","sha256hex":"a72517e8e72d78bc07a6ef7ff3a6d1d3e04325df986cb8f1bbb4e809f7a9dbdd","md5hex":"9cb8a6e056c9cc740d3bed0c50cd53dc","size_bytes":80992,"mimetype":"application/pdf"},"cdx":null} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"47301218","sha1hex":"0000029209536bda5f22e5110e573c5bd8ceb43a","doi":"10.2307/23406551","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"0000029209536bda5f22e5110e573c5bd8ceb43a","sha256hex":"315f1d39a00ccf256fa15d92a14869dbda48d31500989aaacb11368f906a5827","md5hex":"8141b42ec3bb41fa87099633a1b61d93","size_bytes":305236,"mimetype":"application/pdf"},"cdx":null} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"30603850","sha1hex":"000002c1abd521f18aa23d9e8f464e697e218ab1","doi":"10.1109/spire.1998.712983","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"000002c1abd521f18aa23d9e8f464e697e218ab1","sha256hex":"777e2c472e9d2fec3bbd26bad788562cf1e08e5850315c25cfb6e46d38e7e4af","md5hex":"3a3c92fabaf6cf437bb596d9e9255ff6","size_bytes":113768,"mimetype":"application/pdf"},"cdx":{"url":"http://proteomics.bioprojects.org/pavel/papers/SST_versus_EST_in_gene_recognition..pdf","datetime":"20081121222143","sha1hex":"000002c1abd521f18aa23d9e8f464e697e218ab1","cdx_sha1hex":null,"mimetype":"application/pdf","warc_path":"1227992340180_31-c/1227992509265_9.arc.gz","warc_csize":61212,"warc_offset":62956683,"row_created":"2020-01-07T02:06:33.965383+00:00"}} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"9311918","sha1hex":"000002d4f7d4174451e4214475d5ba59f1f6a593","doi":"10.1111/j.1439-0507.2008.01572.x","pmid":"18721331","isbn13":null},"file_meta":{"sha1hex":"000002d4f7d4174451e4214475d5ba59f1f6a593","sha256hex":"713758ce0417f604c0a4b0bf5b5eea571a9b08ca4cc81a98d602c43f42abfe37","md5hex":"0df123e6305c617ffd38ebef90b1e318","size_bytes":178664,"mimetype":"application/pdf"},"cdx":null} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"7757772","sha1hex":"000002f8966a4c5547f8a47f43661fcc3edc34ea","doi":"10.1007/s10464-011-9424-3","pmid":"21287262","isbn13":null},"file_meta":{"sha1hex":"000002f8966a4c5547f8a47f43661fcc3edc34ea","sha256hex":"ee1bce27134ae55b3d67f9b31f66571e41ac496fc3fb526dec2d53513b8f6deb","md5hex":"e72c5cf3d61635821e78ca0306c98887","size_bytes":337857,"mimetype":"application/pdf"},"cdx":null} +{"shadow":{"shadow_corpus":"scimag","shadow_id":"74272862","sha1hex":"000003a94022be58305ccc2a018a6359eeb226db","doi":"10.1002/slct.201802783","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"000003a94022be58305ccc2a018a6359eeb226db","sha256hex":"f277eefc7b1466df814a7a892ab8e2e7f08db1faae0bf73b893211e5f5b37193","md5hex":"27534b8494f54ba5de47c16fb2590b04","size_bytes":1372272,"mimetype":"application/pdf"},"cdx":null} diff --git a/python/tests/import_datacite.py b/python/tests/import_datacite.py index 669a6984..15650375 100644 --- a/python/tests/import_datacite.py +++ b/python/tests/import_datacite.py @@ -287,10 +287,9 @@ def test_datacite_conversions(datacite_importer): for now. """ datacite_importer.debug = True - for i in range(30): + for i in range(31): src = 'tests/files/datacite/datacite_doc_{0:02d}.json'.format(i) dst = 'tests/files/datacite/datacite_result_{0:02d}.json'.format(i) - print('testing mapping from {} => {}'.format(src, dst)) with open(src, 'r') as f: re = datacite_importer.parse_record(json.load(f)) result = entity_to_dict(re) diff --git a/python/tests/import_shadow.py b/python/tests/import_shadow.py new file mode 100644 index 00000000..70a918d2 --- /dev/null +++ b/python/tests/import_shadow.py @@ -0,0 +1,61 @@ + +import json +import pytest +from fatcat_tools.importers import ShadowLibraryImporter, JsonLinePusher +from fixtures import api + + +@pytest.fixture(scope="function") +def shadow_importer(api): + yield ShadowLibraryImporter(api) + +# TODO: use API to check that entities actually created... +def test_shadow_importer_basic(shadow_importer): + with open('tests/files/example_shadow.json', 'r') as f: + JsonLinePusher(shadow_importer, f).run() + +def test_shadow_importer(shadow_importer): + last_index = shadow_importer.api.get_changelog(limit=1)[0].index + with open('tests/files/example_shadow.json', 'r') as f: + shadow_importer.bezerk_mode = True + counts = JsonLinePusher(shadow_importer, f).run() + assert counts['insert'] == 2 + assert counts['exists'] == 0 + assert counts['skip'] == 8 + + # fetch most recent editgroup + change = shadow_importer.api.get_changelog_entry(index=last_index+1) + eg = change.editgroup + assert eg.description + assert "shadow library" in eg.description.lower() + assert eg.extra['git_rev'] + assert "fatcat_tools.ShadowLibraryImporter" in eg.extra['agent'] + + # re-insert; should skip + with open('tests/files/example_shadow.json', 'r') as f: + shadow_importer.reset() + shadow_importer.bezerk_mode = False + counts = JsonLinePusher(shadow_importer, f).run() + assert counts['insert'] == 0 + assert counts['exists'] == 2 + assert counts['skip'] == 8 + +def test_shadow_dict_parse(shadow_importer): + with open('tests/files/example_shadow.json', 'r') as f: + raw = json.loads(f.readline()) + f = shadow_importer.parse_record(raw) + + assert f.sha1 == "0000002922264275f11cca7b1c3fb662070d0dd7" + assert f.md5 == "debd8db178fa08a7a0aaec6e42832a8e" + assert f.sha256 == "b4728210cc0f70d8a8f8c39bd97fcbbab3eaca4309ac4bdfbce5df3b66c82f79" + assert f.mimetype == "application/pdf" + assert f.size == 206121 + assert len(f.urls) == 2 + for u in f.urls: + if u.rel == "publisher": + assert u.url.startswith("https://link.springer.com/content/pdf/10.1007%2Fs11626-008-9119-8.pdf") + if u.rel == "webarchive": + assert u.url.startswith("https://web.archive.org/") + assert "20180729135948" in u.url + assert len(f.release_ids) == 1 + |