initial pubmed importer

1 files changed, 80 insertions, 0 deletions

diff --git a/python/tests/import_pubmed.py b/python/tests/import_pubmed.py
new file mode 100644
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+++ b/python/tests/import_pubmed.py
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+
+import json, gzip
+import pytest
+from fatcat_tools.importers import PubmedImporter, Bs4XmlFilePusher
+from fixtures import api
+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)
+
+@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)
+
+def test_pubmed_importer(pubmed_importer):
+    last_index = pubmed_importer.api.get_changelog(limit=1)[0].index
+    with open('tests/files/pubmedsample_2019.xml', 'r') as f:
+        pubmed_importer.bezerk_mode = True
+        counts = Bs4XmlFilePusher(pubmed_importer, f, "PubmedArticle").run()
+    assert counts['insert'] == 1
+    assert counts['exists'] == 0
+    assert counts['skip'] == 0
+
+    # fetch most recent editgroup
+    change = pubmed_importer.api.get_changelog_entry(index=last_index+1)
+    eg = change.editgroup
+    assert eg.description
+    assert "pubmed" in eg.description.lower()
+    assert eg.extra['git_rev']
+    assert "fatcat_tools.PubmedImporter" in eg.extra['agent']
+
+    last_index = pubmed_importer.api.get_changelog(limit=1)[0].index
+    with open('tests/files/pubmedsample_2019.xml', 'r') as f:
+        pubmed_importer.bezerk_mode = False
+        pubmed_importer.reset()
+        counts = Bs4XmlFilePusher(pubmed_importer, f, "PubmedArticle").run()
+    assert counts['insert'] == 0
+    assert counts['exists'] == 1
+    assert counts['skip'] == 0
+    assert last_index == pubmed_importer.api.get_changelog(limit=1)[0].index
+
+def test_pubmed_xml_parse(pubmed_importer):
+    with open('tests/files/pubmedsample_2019.xml', 'r') as f:
+        soup = BeautifulSoup(f, "xml")
+        r1 = pubmed_importer.parse_record(soup.find_all("PubmedArticle")[0])
+        r2 = pubmed_importer.parse_record(soup.find_all("PubmedArticle")[-1])
+
+    assert r1.title == "Hospital debt management and cost reimbursement"
+    assert r1.subtitle == None
+    assert r1.original_title == None
+    assert r1.publisher == None
+    assert r1.release_type == "article-journal"
+    assert r1.release_stage == "published"
+    assert r1.license_slug == None
+    assert r1.ext_ids.doi == None
+    assert r1.ext_ids.pmid == "973217"
+    assert r1.language == "en"
+    assert r1.volume == "3"
+    assert r1.issue == "1"
+    assert r1.pages == "69-81"
+    assert r1.release_date == None # not "1976-12-03", which is medline ingest date
+    assert r1.release_year == 1976
+    # matched by ISSN, so shouldn't be in there?
+    #assert extra['container_name'] == "Abstracts of the Papers Communicated to the Royal Society of London"
+    assert len(r1.contribs) == 1
+
+    assert r1.contribs[0].raw_name == "F R Blume"
+    assert r1.contribs[0].given_name == "F R"
+    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