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"""Test local xsearch + xfetch against a local PubMed archive.
Requires EDIRECT_LOCAL_ARCHIVE to point to a PubMed archive directory
(e.g. /export3/PubMed/Source) and edirect tools on PATH.
Run with: EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source python3 -m unittest tests.test_local_xfetch -v
"""
import os
import subprocess
import unittest
ARCHIVE = os.environ.get("EDIRECT_LOCAL_ARCHIVE", "/export3/PubMed/Source")
@unittest.skipUnless(os.path.isdir(ARCHIVE),
f"EDIRECT_LOCAL_ARCHIVE not found: {ARCHIVE}")
class TestLocalXfetch(unittest.TestCase):
def test_xsearch_xfetch_penk_stress(self):
"""Local xsearch + xfetch for Penk + stress, expect PMIDs."""
env = os.environ.copy()
env["EDIRECT_LOCAL_ARCHIVE"] = ARCHIVE
result = subprocess.run(
["sh", "-c",
'xsearch -db pubmed -query "(stress) AND (Penk [tiab])" '
'| xfetch -db pubmed'],
capture_output=True, text=True, timeout=120, env=env)
self.assertEqual(result.returncode, 0, result.stderr)
output = result.stdout.strip()
self.assertGreater(len(output), 0, "Expected non-empty XML output")
self.assertIn("PubmedArticle", output,
"Expected PubmedArticle XML elements")
# Count articles -- local index may be incomplete compared to NCBI
# (depends on how far the indexing pipeline ran)
count = output.count("<PubmedArticle>")
print(f" Found {count} PubmedArticle records for Penk+stress (local)")
self.assertGreater(count, 5, "Expected at least 5 PubmedArticles")
if __name__ == "__main__":
unittest.main()
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