diff options
Diffstat (limited to 'python/tests/import_pubmed.py')
| -rw-r--r-- | python/tests/import_pubmed.py | 49 |
1 files changed, 45 insertions, 4 deletions
diff --git a/python/tests/import_pubmed.py b/python/tests/import_pubmed.py index 05a77599..0185c8c4 100644 --- a/python/tests/import_pubmed.py +++ b/python/tests/import_pubmed.py @@ -9,12 +9,12 @@ from bs4 import BeautifulSoup @pytest.fixture(scope="function") def pubmed_importer(api): with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file: - yield PubmedImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', bezerk_mode=True) + yield PubmedImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', bezerk_mode=True, lookup_refs=True) @pytest.fixture(scope="function") def pubmed_importer_existing(api): with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file: - yield PubmedImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', bezerk_mode=False) + yield PubmedImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', bezerk_mode=False, lookup_refs=True) def test_pubmed_importer(pubmed_importer): last_index = pubmed_importer.api.get_changelog(limit=1)[0].index @@ -73,8 +73,49 @@ def test_pubmed_xml_parse(pubmed_importer): assert r1.contribs[0].surname == "Blume" print(r1.extra) - # TODO: assert r1.extra['pubmed']['mesh_topics'] == ['Accounting', 'Economics, Hospital', 'Hospital Administration'] assert r1.extra['pubmed']['pub_types'] == ['Journal Article'] assert not r1.refs - # XXX: r2 tests + assert r2.title == "Synthesis and Antibacterial Activity of Metal(loid) Nanostructures by Environmental Multi-Metal(loid) Resistant Bacteria and Metal(loid)-Reducing Flavoproteins" + assert r2.subtitle == None + assert r2.original_title == None + assert r2.publisher == None + assert r2.release_type == "article-journal" + assert r2.release_stage == "published" + assert r2.license_slug == None + assert r2.ext_ids.doi == "10.3389/fmicb.2018.00959" + assert r2.ext_ids.pmid == "29869640" + assert r2.ext_ids.pmcid == "PMC5962736" + assert r2.language == "en" + assert r2.volume == "9" + assert r2.issue == None + assert r2.pages == "959" + assert str(r2.release_date) == "2018-05-15" + assert r2.release_year == 2018 + # matched by ISSN, so shouldn't be in there? + #assert extra['container_name'] == "Frontiers in microbiology" + + assert len(r2.contribs) > 3 + assert r2.contribs[0].raw_name == "Maximiliano Figueroa" + assert r2.contribs[0].given_name == "Maximiliano" + assert r2.contribs[0].surname == "Figueroa" + assert r2.contribs[0].raw_affiliation == "Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile." + assert r2.contribs[4].surname == "Muñoz-Villagrán" + assert r2.contribs[7].surname == "Latorre" + assert r2.contribs[7].raw_affiliation == "Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Beauchef, Santiago, Chile." + assert r2.contribs[7].extra['more_affiliations'] == [ + "Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.", + "Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.", + "Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.", + ] + assert r2.contribs[-1].raw_name == "Felipe Arenas" + + assert r2.abstracts[0].content.startswith("Microbes are suitable candidates to recover and decontaminate different environments from soluble metal ions, either via reduction") + assert r2.abstracts[0].lang == "en" + + print(r2.extra) + assert r2.extra['pubmed']['pub_types'] == ['Journal Article'] + + assert r2.refs[0].extra['unstructured'] == "Microbiology. 2009 Jun;155(Pt 6):1840-6" + assert r2.refs[0].extra['pmid'] == "19383690" + |