File size: 11,055 Bytes
e918a5c | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
"""Tests for pathway_analysis_env (DE, ORA, compare, expert, trace)."""
from __future__ import annotations
import json
import pytest
from pathway_analysis_env.models import PathwayAction
from pathway_analysis_env.server.analysis import (
adjust_pvalues_bh,
build_sample_metadata,
ora_fisher,
overlap_genes_across_top_pathways,
pydeseq2_available,
run_deseq2_contrast,
validate_counts_case,
)
from pathway_analysis_env.server.pathway_environment import (
DATA_DIR,
PathwayEnvironment,
load_case,
)
requires_pydeseq2 = pytest.mark.skipif(
not pydeseq2_available(),
reason="PyDESeq2 required for pathway pipeline tests",
)
def test_set_case_file():
env = PathwayEnvironment(case_file="toy_case_001.json")
env.set_case_file("toy_case_legacy.json")
assert env._case_file == "toy_case_legacy.json"
def test_load_pipeline_case():
case = load_case("toy_case_001.json")
assert "counts" in case
assert "pathway_genes" in case
assert case["true_pathway"] == "MAPK signaling"
def test_load_gse235417_case_is_pipeline_mode():
case = load_case("gse235417_case.json")
assert "counts_file" in case
assert "sample_ids" in case
assert "sample_metadata" in case
assert case["default_contrast"]["reference"] == "baseline"
assert case["default_contrast"]["alternate"] == "resistant"
@requires_pydeseq2
def test_deseq2_mapk_case():
case = json.loads((DATA_DIR / "toy_case_001.json").read_text(encoding="utf-8"))
from pathway_analysis_env.server.analysis import (
build_sample_metadata,
counts_dict_to_samples_by_genes,
)
cdf = counts_dict_to_samples_by_genes(case["counts"], case["sample_ids"])
meta = build_sample_metadata(case["sample_ids"], case["sample_metadata"])
rows, err = run_deseq2_contrast(
cdf,
meta,
case["default_contrast"]["alternate"],
case["default_contrast"]["reference"],
)
assert err is None
top = [r["gene"] for r in rows[:5]]
assert "DUSP6" in top or "FOS" in top
def test_ora_fisher_structure():
universe = ["A", "B", "C", "D", "E", "F"]
pathways = {"P1": ["A", "B", "C"], "P2": ["C", "D"]}
de = ["A", "B", "C"]
ora = ora_fisher(de, pathways, universe, min_pathway_genes=2)
assert len(ora) == 2
assert ora[0]["pathway"] in ("P1", "P2")
assert "q_value" in ora[0]
def test_adjust_pvalues_bh_matches_scipy():
ps = [0.01, 0.05, 0.1]
q = adjust_pvalues_bh(ps)
assert len(q) == 3
assert all(0.0 <= x <= 1.0 for x in q)
def test_validate_counts_case():
assert validate_counts_case({}) is None
bad = {
"counts": {"G1": [1, 2], "G2": [1]},
"sample_ids": ["a", "b"],
}
assert validate_counts_case(bad) is not None
def test_build_sample_metadata_missing_sample():
with pytest.raises(ValueError, match="missing"):
build_sample_metadata(["S1", "S2"], {"S1": "a"})
def test_understand_experiment_design_summary():
env = PathwayEnvironment(case_file="toy_case_001.json")
env.reset()
obs = env.step(PathwayAction(action_type="understand_experiment_design"))
assert obs.experiment_design
assert obs.experiment_design.get("samples_per_condition")
assert env.state.design_understood is True
assert env.state.validated_reference is None
def test_understand_experiment_design_legacy_graceful():
env = PathwayEnvironment(case_file="toy_case_legacy.json")
env.reset()
obs = env.step(PathwayAction(action_type="understand_experiment_design"))
design = obs.experiment_design or {}
assert design.get("legacy_mode") is True
assert design.get("sample_level_metadata_available") is False
assert design.get("samples_per_condition") is None
assert design.get("conditions") == ["control", "treated"]
assert "legacy" in obs.message.lower()
def test_inspect_dataset_legacy_graceful():
env = PathwayEnvironment(case_file="toy_case_legacy.json")
env.reset()
obs = env.step(PathwayAction(action_type="inspect_dataset"))
meta = obs.metadata or {}
assert meta.get("legacy_mode") is True
assert meta.get("sample_level_metadata_available") is False
assert meta.get("sample_ids") == []
assert "static_top_genes" not in meta
assert "static_top_pathways" not in meta
assert "legacy" in obs.message.lower()
def test_inspect_legacy_debug_mode_shows_static_lists():
env = PathwayEnvironment(case_file="toy_case_legacy.json")
env.reset(eval_mode=False)
obs = env.step(PathwayAction(action_type="inspect_dataset"))
meta = obs.metadata or {}
assert meta.get("static_top_genes")
assert meta.get("static_top_pathways")
def test_state_never_exposes_true_pathway():
env = PathwayEnvironment(case_file="toy_case_001.json")
env.reset()
assert "true_pathway" not in env.state.model_dump()
def test_submit_blocked_without_de_in_eval_mode():
env = PathwayEnvironment(case_file="toy_case_001.json")
env.reset()
obs = env.step(
PathwayAction(action_type="submit_answer", hypothesis="MAPK signaling")
)
assert obs.metadata.get("failure_code") == "submit_prerequisite_de"
assert obs.done is False
def test_gene_list_blocked_in_eval_mode():
env = PathwayEnvironment(case_file="toy_case_legacy.json")
env.reset()
env.step(PathwayAction(action_type="run_differential_expression"))
obs = env.step(
PathwayAction(
action_type="run_pathway_enrichment",
gene_list=["DUSP6", "FOS"],
)
)
assert obs.metadata.get("failure_code") == "ora_gene_list_blocked"
@requires_pydeseq2
def test_understand_validated_contrast_matches_explicit_de():
env = PathwayEnvironment(case_file="toy_case_001.json")
env.reset()
u = env.step(
PathwayAction(
action_type="understand_experiment_design",
condition_a="control",
condition_b="treated",
)
)
assert u.experiment_design and u.experiment_design.get("validated_contrast")
assert env.state.validated_reference == "control"
assert env.state.validated_alternate == "treated"
a = env.step(
PathwayAction(
action_type="run_differential_expression",
condition_a="control",
condition_b="treated",
)
)
env2 = PathwayEnvironment(case_file="toy_case_001.json")
env2.reset()
env2.step(
PathwayAction(
action_type="understand_experiment_design",
condition_a="control",
condition_b="treated",
)
)
b = env2.step(PathwayAction(action_type="run_differential_expression"))
assert a.de_genes and b.de_genes
assert [r.get("gene") for r in a.de_genes[:10]] == [r.get("gene") for r in b.de_genes[:10]]
def test_no_step_after_episode_done():
env = PathwayEnvironment(case_file="toy_case_legacy.json")
env.reset()
env.step(PathwayAction(action_type="run_differential_expression"))
env.step(PathwayAction(action_type="run_pathway_enrichment"))
env.step(PathwayAction(action_type="submit_answer", hypothesis="MAPK signaling"))
late = env.step(PathwayAction(action_type="inspect_dataset"))
assert late.done
assert late.metadata.get("error") == "episode_done"
assert late.metadata.get("failure_code") == "episode_already_done"
def test_overlap_summary():
ora = [
{
"pathway": "a",
"p_value": 0.01,
"overlap_genes": ["G1", "G2"],
},
{
"pathway": "b",
"p_value": 0.02,
"overlap_genes": ["G2", "G3"],
},
]
ov = overlap_genes_across_top_pathways(ora, top_k=2)
assert "G2" in ov["genes_supporting_multiple_top_pathways"]
@requires_pydeseq2
def test_episode_pipeline_success():
env = PathwayEnvironment(case_file="toy_case_001.json")
obs0 = env.reset(episode_id="ep-test-1")
assert obs0.metadata.get("pipeline_mode") is True
assert obs0.trace_path
a = PathwayAction(
action_type="run_differential_expression",
condition_a="control",
condition_b="treated",
)
obs1 = env.step(a)
assert obs1.de_genes
assert obs1.top_genes
b = PathwayAction(action_type="run_pathway_enrichment")
obs2 = env.step(b)
assert obs2.pathway_enrichment
assert "MAPK signaling" in obs2.top_pathways[:3]
assert obs2.overlap_summary is not None
c = PathwayAction(
action_type="compare_pathways",
pathway_a="MAPK signaling",
pathway_b="ERK cascade",
)
obs3 = env.step(c)
assert obs3.pathway_comparison
assert "shared_de_support" in obs3.pathway_comparison
obs4 = env.step(
PathwayAction(action_type="submit_answer", hypothesis="MAPK signaling")
)
assert obs4.done
assert obs4.metadata.get("correct") is None
assert env.episode_outcome is not None
assert env.episode_outcome.get("correct") is True
def test_legacy_fixture():
env = PathwayEnvironment(case_file="toy_case_legacy.json")
obs0 = env.reset()
assert obs0.metadata.get("pipeline_mode") is False
env.step(PathwayAction(action_type="run_differential_expression"))
env.step(PathwayAction(action_type="run_pathway_enrichment"))
fin = env.step(
PathwayAction(action_type="submit_answer", hypothesis="MAPK signaling")
)
assert fin.done
assert env.episode_outcome and env.episode_outcome.get("correct") is True
def test_orchestrator_mode_exposes_correct_metadata():
env = PathwayEnvironment(case_file="toy_case_legacy.json")
env.reset(orchestrator_mode=True)
env.step(PathwayAction(action_type="run_differential_expression"))
env.step(PathwayAction(action_type="run_pathway_enrichment"))
fin = env.step(
PathwayAction(action_type="submit_answer", hypothesis="MAPK signaling")
)
assert fin.metadata.get("correct") is True
@requires_pydeseq2
def test_strict_invalid_counts_matrix():
env = PathwayEnvironment(case_file="toy_case_001.json")
env.reset(strict=True)
env._case["counts"]["DUSP6"] = [1, 2]
obs = env.step(
PathwayAction(
action_type="run_differential_expression",
condition_a="control",
condition_b="treated",
)
)
assert obs.done and obs.metadata.get("strict_failure") is True
assert obs.metadata.get("failure_code") == "de_invalid_counts_matrix"
@requires_pydeseq2
def test_strict_mode_missing_contrast():
env = PathwayEnvironment(case_file="toy_case_no_default.json")
env.reset(strict=True)
obs = env.step(PathwayAction(action_type="run_differential_expression"))
assert obs.done is True
assert obs.metadata.get("strict_failure") is True
assert obs.metadata.get("failure_code") == "de_missing_contrast"
|