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Richard Liang
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WIP: A little more test coverage.
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‎tests/update_frequency_file_lib_test.py‎

Lines changed: 144 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,16 @@
1+
from collections import Counter
2+
from io import StringIO
3+
14
import pytest
25

36
from easyhla.models import HLAProteinPair
47
from easyhla.update_frequency_file_lib import (
8+
FrequencyRowDict,
59
NewName,
610
OldName,
711
OtherLocusException,
812
parse_nomenclature,
13+
update_old_frequencies,
914
)
1015
from easyhla.utils import HLA_LOCUS
1116

@@ -161,9 +166,6 @@ def test_new_name_to_frequency_format(
161166
assert new_name.to_frequency_format() == expected_result
162167

163168

164-
# dict[OldName, NewName], list[str], list[tuple[str, str]], list[tuple[str, str]]
165-
166-
167169
@pytest.mark.parametrize(
168170
(
169171
"rows, expected_remapping, expected_deprecated, "
@@ -237,6 +239,7 @@ def test_new_name_to_frequency_format(
237239
("B*505002", "B*49:32:11"),
238240
("B*570101", "B*57:01:01"),
239241
("Cw*223344", "C*22:122"),
242+
("Cw*223445", "None"),
240243
("DPB1*020102", "DPB1*02:01:02"),
241244
],
242245
{
@@ -246,10 +249,12 @@ def test_new_name_to_frequency_format(
246249
OldName("B", "50", "50"): NewName("B", "49", "32"),
247250
OldName("B", "57", "01"): NewName("B", "57", "01"),
248251
OldName("C", "22", "33"): NewName("C", "22", "122"),
252+
OldName("C", "22", "34"): NewName(None, "", ""),
249253
},
250254
[
251255
"A*020120",
252256
"B*505001",
257+
"Cw*223445",
253258
],
254259
[("A*020120", NewName("A", "02", "01"))],
255260
[("B*505002", NewName("B", "49", "32"))],
@@ -279,3 +284,139 @@ def test_parse_nomenclature(
279284
assert result[1] == expected_deprecated
280285
assert result[2] == expected_deprecated_maps_to_other
281286
assert result[3] == expected_mapping_overrides_deprecated
287+
288+
289+
@pytest.mark.parametrize(
290+
(
291+
"old_frequency_lines, remapping, expected_updated_frequencies, "
292+
"expected_unmapped_alleles, expected_deprecated_alleles_seen"
293+
),
294+
[
295+
pytest.param(
296+
["1234,5678,5701,5603,2233,4455"],
297+
{
298+
OldName("A", "12", "34"): NewName("A", "12", "34"),
299+
OldName("A", "56", "78"): NewName("A", "56", "78"),
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OldName("B", "57", "01"): NewName("B", "57", "01"),
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OldName("B", "56", "03"): NewName("B", "56", "03"),
302+
OldName("C", "22", "33"): NewName("C", "22", "33"),
303+
OldName("C", "44", "55"): NewName("C", "44", "55"),
304+
},
305+
[
306+
{
307+
"a_first": "12:34",
308+
"a_second": "56:78",
309+
"b_first": "57:01",
310+
"b_second": "56:03",
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"c_first": "22:33",
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"c_second": "44:55",
313+
},
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],
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Counter(),
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Counter(),
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id="one_row_all_trivial",
318+
),
319+
pytest.param(
320+
["1234,5678,5701,5603,2233,4455"],
321+
{
322+
OldName("A", "12", "34"): NewName("A", "12", "340"),
323+
OldName("A", "56", "78"): NewName("A", "56", "110"),
324+
OldName("B", "57", "01"): NewName("B", "55", "02"),
325+
OldName("B", "56", "03"): NewName("B", "53", "04"),
326+
OldName("C", "22", "33"): NewName("C", "22", "115"),
327+
OldName("C", "44", "55"): NewName("C", "43", "02"),
328+
},
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[
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{
331+
"a_first": "12:340",
332+
"a_second": "56:110",
333+
"b_first": "55:02",
334+
"b_second": "53:04",
335+
"c_first": "22:115",
336+
"c_second": "43:02",
337+
},
338+
],
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Counter(),
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Counter(),
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id="one_row_all_nontrivial",
342+
),
343+
pytest.param(
344+
["1234,5678,5701,5603,2233,4455"],
345+
{},
346+
[
347+
{
348+
"a_first": "unmapped",
349+
"a_second": "unmapped",
350+
"b_first": "unmapped",
351+
"b_second": "unmapped",
352+
"c_first": "unmapped",
353+
"c_second": "unmapped",
354+
},
355+
],
356+
Counter(
357+
{
358+
("A", "1234"): 1,
359+
("A", "5678"): 1,
360+
("B", "5701"): 1,
361+
("B", "5603"): 1,
362+
("C", "2233"): 1,
363+
("C", "4455"): 1,
364+
}
365+
),
366+
Counter(),
367+
id="one_row_all_unmapped",
368+
),
369+
pytest.param(
370+
["1234,5678,5701,5603,2233,4455"],
371+
{
372+
OldName("A", "12", "34"): NewName(None, "", ""),
373+
OldName("A", "56", "78"): NewName(None, "", ""),
374+
OldName("B", "57", "01"): NewName(None, "", ""),
375+
OldName("B", "56", "03"): NewName(None, "", ""),
376+
OldName("C", "22", "33"): NewName(None, "", ""),
377+
OldName("C", "44", "55"): NewName(None, "", ""),
378+
},
379+
[
380+
{
381+
"a_first": "deprecated",
382+
"a_second": "deprecated",
383+
"b_first": "deprecated",
384+
"b_second": "deprecated",
385+
"c_first": "deprecated",
386+
"c_second": "deprecated",
387+
},
388+
],
389+
Counter(),
390+
Counter(
391+
{
392+
("A", "1234"): 1,
393+
("A", "5678"): 1,
394+
("B", "5701"): 1,
395+
("B", "5603"): 1,
396+
("C", "2233"): 1,
397+
("C", "4455"): 1,
398+
}
399+
),
400+
id="one_row_all_deprecated",
401+
),
402+
],
403+
)
404+
def test_update_old_frequencies(
405+
old_frequency_lines: list[str],
406+
remapping: dict[OldName, NewName],
407+
expected_updated_frequencies: list[FrequencyRowDict],
408+
expected_unmapped_alleles: Counter[tuple[HLA_LOCUS, str]],
409+
expected_deprecated_alleles_seen: Counter[tuple[HLA_LOCUS, str]],
410+
):
411+
fake_old_frequency_file: StringIO = StringIO("\n".join(old_frequency_lines))
412+
updated_frequencies: list[FrequencyRowDict]
413+
unmapped_alleles: Counter[tuple[HLA_LOCUS, str]]
414+
deprecated_alleles_seen: Counter[tuple[HLA_LOCUS, str]]
415+
416+
updated_frequencies, unmapped_alleles, deprecated_alleles_seen = (
417+
update_old_frequencies(fake_old_frequency_file, remapping)
418+
)
419+
420+
assert updated_frequencies == expected_updated_frequencies
421+
assert unmapped_alleles == expected_unmapped_alleles
422+
assert deprecated_alleles_seen == expected_deprecated_alleles_seen

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