import gzip import json import pytest from fixtures import api from fatcat_tools.importers import CrossrefImporter, JsonLinePusher @pytest.fixture(scope="function") def crossref_importer(api): with open("tests/files/ISSN-to-ISSN-L.snip.txt", "r") as issn_file: yield CrossrefImporter( api, issn_file, extid_map_file="tests/files/example_map.sqlite3", bezerk_mode=True ) @pytest.fixture(scope="function") def crossref_importer_existing(api): with open("tests/files/ISSN-to-ISSN-L.snip.txt", "r") as issn_file: yield CrossrefImporter( api, issn_file, extid_map_file="tests/files/example_map.sqlite3", bezerk_mode=False ) @pytest.mark.skip( reason="slow/huge crossref import is a corner-case and slows tests significantly" ) def test_crossref_importer_huge(crossref_importer): last_index = crossref_importer.api.get_changelog(limit=1)[0].index with gzip.open("tests/files/huge_crossref_doi.json.gz", "rt") as f: crossref_importer.bezerk_mode = True line = f.readline() mega_blob = [line for i in range(95)] counts = JsonLinePusher(crossref_importer, mega_blob).run() assert counts["insert"] == 95 change = crossref_importer.api.get_changelog_entry(index=last_index + 1) release = crossref_importer.api.get_release(change.editgroup.edits.releases[0].ident) assert len(release.contribs) == 1014 def test_crossref_importer(crossref_importer): last_index = crossref_importer.api.get_changelog(limit=1)[0].index with open("tests/files/crossref-works.2018-01-21.badsample.json", "r") as f: crossref_importer.bezerk_mode = True counts = JsonLinePusher(crossref_importer, f).run() assert counts["insert"] == 14 assert counts["exists"] == 0 assert counts["skip"] == 0 # fetch most recent editgroup change = crossref_importer.api.get_changelog_entry(index=last_index + 1) eg = change.editgroup assert eg.description assert "crossref" in eg.description.lower() assert eg.extra["git_rev"] assert "fatcat_tools.CrossrefImporter" in eg.extra["agent"] last_index = crossref_importer.api.get_changelog(limit=1)[0].index with open("tests/files/crossref-works.2018-01-21.badsample.json", "r") as f: crossref_importer.bezerk_mode = False crossref_importer.reset() counts = JsonLinePusher(crossref_importer, f).run() assert counts["insert"] == 0 assert counts["exists"] == 14 assert counts["skip"] == 0 assert last_index == crossref_importer.api.get_changelog(limit=1)[0].index def test_crossref_mappings(crossref_importer): assert crossref_importer.map_release_type("journal-article") == "article-journal" assert crossref_importer.map_release_type("asdf") is None assert crossref_importer.map_release_type("book-series") is None assert crossref_importer.map_release_type("standard") == "standard" def test_crossref_importer_create(crossref_importer): crossref_importer.create_containers = True with open("tests/files/crossref-works.2018-01-21.badsample.json", "r") as f: JsonLinePusher(crossref_importer, f).run() def test_crossref_dict_parse(crossref_importer): with open("tests/files/crossref-works.single.json", "r") as f: # not a single line raw = json.loads(f.read()) r = crossref_importer.parse_record(raw) # ensure the API server is ok with format JsonLinePusher(crossref_importer, [json.dumps(raw)]).run() print(r.extra) assert ( r.title == "Renormalized perturbation theory by the moment method for degenerate states: Anharmonic oscillators" ) assert r.publisher == "Wiley-Blackwell" assert r.release_type == "article-journal" assert r.release_stage == "published" assert r.license_slug == "CC-BY-NC-ND" assert r.original_title == "Renormalized perturbation theory auf deutsch" assert r.ext_ids.doi == "10.1002/(sici)1097-461x(1998)66:4<261::aid-qua1>3.0.co;2-t" assert r.ext_ids.isbn13 == "978-3-16-148410-0" assert r.language == "fr" assert r.subtitle is None assert "subtitle" not in r.extra assert "subtitle" not in r.extra["crossref"] assert "funder" not in r.extra assert "funder" not in r.extra["crossref"] # matched by ISSN, so shouldn't be in there # assert extra['container_name'] == "International Journal of Quantum Chemistry" assert r.extra["aliases"] == ["some other title"] assert r.extra["crossref"]["archive"] == ["Portico", "LOCKSS"] assert len(r.contribs) == 6 assert r.contribs[0].raw_name == "Marcelo D. Radicioni" assert r.contribs[0].given_name == "Marcelo D." assert r.contribs[0].surname == "Radicioni" assert r.contribs[0].index == 0 assert r.contribs[0].extra["seq"] == "first" assert r.contribs[1].raw_affiliation == "Some University" assert r.contribs[1].extra["more_affiliations"] == ["Some Department"] assert r.contribs[1].role == "author" assert r.contribs[4].role == "editor" assert r.contribs[4].index is None assert r.contribs[4].extra is None assert r.contribs[5].role == "translator" assert r.contribs[5].index is None assert len(r.refs) == 25 assert r.refs[0].key == "BIB1" assert r.refs[0].year == 1972 assert r.refs[0].locator == "1734" assert r.refs[0].container_name == "J. Chem. Phys." assert r.refs[0].extra == { "volume": "57", "authors": ["Swenson"], "doi": "10.1063/1.1678462", "medium": "DVD", } assert r.refs[2].key == "BIB3" assert r.refs[2].extra.get("author") is None assert ( r.refs[2].container_name == "Hypervirial Theorem's, Lecture Notes in Chemistry <3" ) assert ( r.refs[3].container_name == "Large Order Perturbation Theory and Summation Methods in Quantum Mechanics, Lecture Notes in Chemistry" ) def test_crossref_subtitle(crossref_importer): """ Tests new subtitle field, explicitly """ with open("tests/files/crossref-works.single.json", "r") as f: # not a single line raw = json.loads(f.read()) raw["subtitle"] = ["some bogus subtitle", "blah"] r = crossref_importer.parse_record(raw) # ensure the API server is ok with format JsonLinePusher(crossref_importer, [json.dumps(raw)]).run() print(r.extra) assert ( r.title == "Renormalized perturbation theory by the moment method for degenerate states: Anharmonic oscillators" ) assert r.subtitle == "some bogus subtitle" assert "subtitle" not in r.extra assert "subtitle" not in r.extra["crossref"] def test_stateful_checking(crossref_importer_existing): with open("tests/files/crossref-works.single.json", "r") as f: # not a single line, a whole document raw = f.read() # might not exist yet... crossref_importer_existing.push_record(json.loads(raw)) crossref_importer_existing.finish() # make sure we wouldn't insert again entity = crossref_importer_existing.parse_record(json.loads(raw)) assert crossref_importer_existing.try_update(entity) is False