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Elarwei001claude
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test(ref): cover remaining lines for codecov (#179)
Add a network-free TestAssemblyReportOffline class that mocks requests to cover assembly_report (accession validation, parent-dir and report HTTP errors, no-folder/missing-header errors, parsing, verbose, and json/save/CSV branches) and the ref(assembly_report=True) delegation. All PR-added lines are now covered except the json_package.dump rename deep in the Ensembl network save path (un-coverable network-free). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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‎tests/test_ref.py‎

Lines changed: 93 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,11 @@
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import json
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import os
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import tempfile
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import unittest
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from unittest.mock import patch
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4-
from gget.gget_ref import ref
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import gget.gget_ref as gget_ref
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from gget.gget_ref import assembly_report, ref
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from .from_json import from_json
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@@ -12,3 +16,91 @@
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class TestRef(unittest.TestCase, metaclass=from_json(ref_dict, ref)):
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pass # all tests are loaded from json
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class _FakeResp:
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"""Minimal stand-in for a requests.Response used to test assembly_report offline."""
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def __init__(self, text="", status_code=200):
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self.text = text
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self.status_code = status_code
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# A parent-directory listing containing the assembly's folder, and a minimal
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# tab-delimited assembly report (with a comment header and a blank line).
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_PARENT_HTML = '<html><body><a href="GCF_000001405.40_GRCh38.p14/">GCF_000001405.40_GRCh38.p14/</a></body></html>'
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_REPORT_TEXT = (
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"# Assembly name: GRCh38.p14\n"
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"# Sequence-Name\tSequence-Role\tGenBank-Accn\tRefSeq-Accn\tUCSC-style-name\n"
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"1\tassembled-molecule\tCM000663.2\tNC_000001.11\tchr1\n"
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"\n"
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)
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class TestAssemblyReportOffline(unittest.TestCase):
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"""Network-free tests of assembly_report and the ref() delegation (issue #179)."""
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def test_invalid_accession_raises(self):
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with self.assertRaises(ValueError):
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assembly_report("not-an-accession", verbose=False)
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@patch.object(gget_ref.requests, "get")
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def test_parse_verbose_json_and_save(self, mock_get):
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# Happy path: verbose log, blank-line skip, parsing, then json/save/csv branches.
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mock_get.side_effect = [_FakeResp(_PARENT_HTML), _FakeResp(_REPORT_TEXT)]
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df = assembly_report("GCF_000001405.40", verbose=True)
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self.assertEqual(list(df["Sequence-Name"]), ["1"])
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self.assertEqual(df.iloc[0]["UCSC-style-name"], "chr1")
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mock_get.side_effect = [_FakeResp(_PARENT_HTML), _FakeResp(_REPORT_TEXT)]
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result = assembly_report("GCF_000001405.40", json=True, verbose=False)
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self.assertIsInstance(result, list)
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self.assertEqual(result[0]["RefSeq-Accn"], "NC_000001.11")
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with tempfile.TemporaryDirectory() as tmp:
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cwd = os.getcwd()
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os.chdir(tmp)
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try:
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mock_get.side_effect = [_FakeResp(_PARENT_HTML), _FakeResp(_REPORT_TEXT)]
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assembly_report("GCF_000001405.40", save=True, verbose=False)
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self.assertTrue(os.path.exists("GCF_000001405.40_assembly_report.csv"))
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mock_get.side_effect = [_FakeResp(_PARENT_HTML), _FakeResp(_REPORT_TEXT)]
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assembly_report("GCF_000001405.40", json=True, save=True, verbose=False)
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self.assertTrue(os.path.exists("GCF_000001405.40_assembly_report.json"))
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finally:
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os.chdir(cwd)
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@patch.object(gget_ref.requests, "get")
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def test_parent_dir_non_200_raises(self, mock_get):
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mock_get.return_value = _FakeResp("", status_code=404)
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with self.assertRaises(RuntimeError):
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assembly_report("GCF_000001405.40", verbose=False)
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@patch.object(gget_ref.requests, "get")
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def test_no_folder_found_raises(self, mock_get):
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mock_get.return_value = _FakeResp("<html>no matching links</html>", status_code=200)
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with self.assertRaises(RuntimeError):
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assembly_report("GCF_000001405.40", verbose=False)
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@patch.object(gget_ref.requests, "get")
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def test_report_non_200_raises(self, mock_get):
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mock_get.side_effect = [_FakeResp(_PARENT_HTML), _FakeResp("", status_code=500)]
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with self.assertRaises(RuntimeError):
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assembly_report("GCF_000001405.40", verbose=False)
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@patch.object(gget_ref.requests, "get")
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def test_report_missing_header_raises(self, mock_get):
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# No "# Sequence-Name" header line -> columns stay None -> RuntimeError.
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mock_get.side_effect = [_FakeResp(_PARENT_HTML), _FakeResp("# only comments\nfoo\tbar\n")]
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with self.assertRaises(RuntimeError):
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assembly_report("GCF_000001405.40", verbose=False)
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def test_ref_assembly_report_requires_species(self):
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with self.assertRaises(ValueError):
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ref(None, assembly_report=True, verbose=False)
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@patch.object(gget_ref, "_assembly_report_fn")
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def test_ref_delegates_to_assembly_report(self, mock_fn):
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mock_fn.return_value = "DELEGATED"
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self.assertEqual(ref("GCF_000001405.40", assembly_report=True, verbose=False), "DELEGATED")
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mock_fn.assert_called_once()

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