Spaces:
Running
Running
File size: 9,779 Bytes
3f4c075 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 | """Unit tests for BLAST pipeline resilience.
Covers:
- check_status_until_ready: jobs are not declared STUCK before they get a
meaningful share of their poll budget (NCBI routinely exceeds RTOE).
- _run_blast (pipeline_v2): NCBI failure falls back to EBI BLAST instead of
failing the whole pipeline; result shape is normalized across providers.
- BlastTool._submit stype mapping for blastx/tblastn.
Network calls are mocked; these tests never touch the real providers.
"""
import pytest
from app.integrations.ncbi import blast as ncbi_blast
SAMPLE_XML = """<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_query-len>7</BlastOutput_query-len>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>sp|P12345|FOO_HUMAN</Hit_id>
<Hit_def>sp|P12345|FOO_HUMAN Foo protein [Homo sapiens]</Hit_def>
<Hit_accession>P12345</Hit_accession>
<Hit_len>100</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>50.0</Hsp_bit-score>
<Hsp_score>100</Hsp_score>
<Hsp_evalue>1e-5</Hsp_evalue>
<Hsp_query-from>1</Hsp_query-from>
<Hsp_query-to>7</Hsp_query-to>
<Hsp_hit-from>10</Hsp_hit-from>
<Hsp_hit-to>16</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>5</Hsp_identity>
<Hsp_positive>6</Hsp_positive>
<Hsp_gaps>1</Hsp_gaps>
<Hsp_align-len>8</Hsp_align-len>
<Hsp_qseq>AAAAA--</Hsp_qseq>
<Hsp_hseq>AAAAA--</Hsp_hseq>
<Hsp_midline>AAAAA </Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
"""
PROTEIN_SEQ = "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEA"
class _FakeClock:
"""Deterministic clock: asyncio.sleep() advances it instead of waiting."""
def __init__(self):
self.now = 0.0
def time(self):
return self.now
@pytest.fixture
def fake_clock(monkeypatch):
clock = _FakeClock()
async def _fake_sleep(seconds):
clock.now += seconds
monkeypatch.setattr(ncbi_blast.asyncio, "sleep", _fake_sleep)
monkeypatch.setattr(ncbi_blast.asyncio, "get_event_loop", lambda: clock)
return clock
async def _always_waiting(rid, fmt="XML"):
return {"status": "WAITING", "raw": "Status=WAITING", "rid": rid}
async def _ready_after(rid, threshold, fmt="XML"):
clock = ncbi_blast.asyncio.get_event_loop()
if clock.time() > threshold:
return {"status": "READY", "raw": "Status=READY", "rid": rid}
return {"status": "WAITING", "raw": "Status=WAITING", "rid": rid}
class TestStuckThreshold:
def test_slow_job_is_not_abandoned_before_half_budget(self, monkeypatch, fake_clock):
# Regression: a job WAITING for ~188s used to be declared STUCK with a
# 900s budget (old threshold max(RTOE*5, 180)). It must keep polling.
async def waiting_then_ready(rid, fmt="XML"):
return await _ready_after(rid, threshold=300)
monkeypatch.setattr(ncbi_blast, "check_status", waiting_then_ready)
result = asyncio_run(ncbi_blast.check_status_until_ready(
"RID1", max_wait_seconds=900, estimated_seconds=10,
))
assert result["status"] == "READY", result
assert fake_clock.now >= 300
def test_truly_stuck_job_declared_stuck_after_half_budget(self, monkeypatch, fake_clock):
monkeypatch.setattr(ncbi_blast, "check_status", _always_waiting)
result = asyncio_run(ncbi_blast.check_status_until_ready(
"RID2", max_wait_seconds=900, estimated_seconds=10,
))
assert result["status"] == "STUCK", result
assert fake_clock.now >= 450, f"STUCK fired too early at {fake_clock.now:.0f}s"
def test_budget_exhaustion_returns_timeout_before_stuck(self, monkeypatch, fake_clock):
# With a small budget, TIMEOUT (end of budget) must win over STUCK.
monkeypatch.setattr(ncbi_blast, "check_status", _always_waiting)
result = asyncio_run(ncbi_blast.check_status_until_ready(
"RID3", max_wait_seconds=120, estimated_seconds=1000,
))
assert result["status"] == "TIMEOUT", result
assert fake_clock.now >= 120
class TestPipelineBlastFallback:
def test_ncbi_success_shape(self, monkeypatch):
from app.routers import pipeline_v2
async def fake_run_blast_with_retry(*args, **kwargs):
return {"raw": SAMPLE_XML, "rid": "RID-X"}
monkeypatch.setattr(pipeline_v2.ncbi_blast, "run_blast_with_retry", fake_run_blast_with_retry)
result = asyncio_run(pipeline_v2._run_blast(PROTEIN_SEQ))
assert result["source"] == "ncbi"
assert result["count"] == 1
assert result["query_sequence_type"] == "protein"
assert result["database"] == "nr"
assert result["top_hit"]["accession"] == "P12345"
assert result["top_hit"]["evalue"] == 1e-5
assert result["hits"][0]["hit_alignment"] == "AAAAA--"
assert result["hits"][0]["query_alignment"] == "AAAAA--"
assert result["hits"][0]["midline"] == "AAAAA "
def test_ncbi_failure_falls_back_to_ebi(self, monkeypatch):
from app.routers import pipeline_v2
async def fake_run_blast_with_retry(*args, **kwargs):
return {"error": "BLAST STUCK after polling (attempt 3/3): Job stuck in WAITING for 188.75s"}
class FakeEbiTool:
async def run_uncached(self, input):
assert input["database"] == "uniprotkb" # nr mapped to EBI db
assert input["program"] == "blastp"
return {
"hits": [{
"accession": "Q9H2H9",
"id": "tr|Q9H2H9|Q9H2H9_HUMAN",
"description": "CCHC-type zinc finger protein 3",
"organism": "Homo sapiens",
"evalue": 1e-30,
"bit_score": 210.0,
"identity_pct": 98.7,
"alignment_length": 152,
"query_coverage_pct": 0,
"query_from": 1,
"query_to": 152,
"hit_from": 1,
"hit_to": 152,
}],
"count": 1,
"source": "EBI BLAST",
"database": "uniprotkb",
}
monkeypatch.setattr(pipeline_v2.ncbi_blast, "run_blast_with_retry", fake_run_blast_with_retry)
monkeypatch.setattr(pipeline_v2, "BlastTool", FakeEbiTool)
result = asyncio_run(pipeline_v2._run_blast(PROTEIN_SEQ))
assert result["source"] == "ebi"
assert result["count"] == 1
assert result["top_hit"]["accession"] == "Q9H2H9"
assert result["database"] == "nr" # reports the requested db, not EBI's
assert result["hits"][0]["organism"] == "Homo sapiens"
assert result["hits"][0]["hit_alignment"] == "" # EBI lacks alignment text
assert result["hits"][0]["query_coverage_pct"] == pytest.approx(round(152 / len(PROTEIN_SEQ) * 100, 1))
def test_both_providers_fail_returns_error(self, monkeypatch):
from app.routers import pipeline_v2
async def fake_run_blast_with_retry(*args, **kwargs):
return {"error": "BLAST STUCK after polling (attempt 3/3): Job stuck in WAITING for 188.75s"}
class EmptyEbiTool:
async def run_uncached(self, input):
return {"error": "EBI down", "hits": []}
monkeypatch.setattr(pipeline_v2.ncbi_blast, "run_blast_with_retry", fake_run_blast_with_retry)
monkeypatch.setattr(pipeline_v2, "BlastTool", EmptyEbiTool)
result = asyncio_run(pipeline_v2._run_blast(PROTEIN_SEQ))
assert result["error"]
assert "STUCK" in result["error"]
assert result["count"] == 0
assert result["hits"] == []
def test_ebi_fallback_skips_unmapped_database(self):
from app.routers.pipeline_v2 import _run_ebi_blast_fallback
result = asyncio_run(_run_ebi_blast_fallback(PROTEIN_SEQ, "blastp", "no_such_db", "protein", 10))
assert result is None
class TestEbiToolSubmit:
async def test_stype_mapping(self, monkeypatch):
from app.tools.blast import BlastTool
captured = {}
class FakeResp:
text = "RID=abc\nRTOE=5"
def raise_for_status(self):
pass
class FakeClient:
def __init__(self, **kwargs):
pass
async def __aenter__(self):
return self
async def __aexit__(self, *args):
pass
async def post(self, url, **kwargs):
captured["data"] = kwargs["data"]
return FakeResp()
monkeypatch.setattr("app.tools.blast.httpx.AsyncClient", lambda **kw: FakeClient())
tool = BlastTool()
await tool._submit("MKTAYIAKQRQISFVKSHFSRQDIL", "blastx", "nr")
assert captured["data"]["stype"] == "protein" # blastx queries a protein
await tool._submit("ATGCATGC", "tblastn", "nt")
assert captured["data"]["stype"] == "dna"
def asyncio_run(coro):
import asyncio
return asyncio.run(coro)
|