"""Tests for GE LLM prompt formatting (GE-L1 through GE-L4).""" import pytest from negbiodb_depmap.llm_prompts import ( GE_SYSTEM_PROMPT, GE_TASK_FORMATTERS, format_ge_l1_prompt, format_ge_l2_prompt, format_ge_l3_prompt, format_ge_l4_prompt, format_ge_prompt, ) @pytest.fixture def sample_record(): return { "context_text": "Gene: TP53\nCell line: A549_LUNG (Lung)\nScreen: CRISPR-Cas9\nGene effect: 0.05", "gene_symbol": "TP53", "cell_line": "A549_LUNG", "lineage": "Lung", } @pytest.fixture def fewshot_examples(): return [ {"context_text": "Gene: BRAF\nCell line: SKMEL5_SKIN", "gold_answer": "B"}, {"context_text": "Gene: RPS3\nCell line: HeLa_CERVIX", "gold_answer": "A"}, {"context_text": "Gene: OR1A1\nCell line: MCF7_BREAST", "gold_answer": "C"}, ] class TestL1Prompts: def test_zero_shot_returns_tuple(self, sample_record): sys, user = format_ge_l1_prompt(sample_record) assert sys == GE_SYSTEM_PROMPT assert "TP53" in user assert "A)" in user assert "D)" in user def test_zero_shot_has_answer_format(self, sample_record): _, user = format_ge_l1_prompt(sample_record) assert "single letter" in user.lower() def test_fewshot_includes_examples(self, sample_record, fewshot_examples): _, user = format_ge_l1_prompt(sample_record, config="3-shot", fewshot_examples=fewshot_examples) assert "BRAF" in user assert "Answer: B" in user def test_fewshot_no_examples_falls_back(self, sample_record): _, user = format_ge_l1_prompt(sample_record, config="3-shot", fewshot_examples=None) assert "Categories:" in user class TestL2Prompts: def test_zero_shot_json_fields(self, sample_record): _, user = format_ge_l2_prompt(sample_record) assert "gene_name" in user assert "essentiality_status" in user assert "JSON" in user def test_fewshot_includes_extraction(self, sample_record): examples = [ { "context_text": "Gene: EGFR", "gold_extraction": {"genes": [{"gene_name": "EGFR"}]}, }, ] _, user = format_ge_l2_prompt(sample_record, config="3-shot", fewshot_examples=examples) assert "EGFR" in user class TestL3Prompts: def test_zero_shot_structure(self, sample_record): _, user = format_ge_l3_prompt(sample_record) assert "TP53" in user assert "NON-ESSENTIAL" in user assert "biological plausibility" in user.lower() def test_fewshot_truncation(self, sample_record): long_example = { "context_text": "x " * 1000, "gold_reasoning": "Because " * 500, } _, user = format_ge_l3_prompt( sample_record, config="3-shot", fewshot_examples=[long_example] ) assert "[...]" in user class TestL4Prompts: def test_zero_shot_tested_format(self, sample_record): _, user = format_ge_l4_prompt(sample_record) assert "tested" in user.lower() assert "untested" in user.lower() def test_fewshot_includes_examples(self, sample_record): examples = [ {"context_text": "Gene: TP53\nCell line: A549", "gold_answer": "tested"}, ] _, user = format_ge_l4_prompt(sample_record, config="3-shot", fewshot_examples=examples) assert "Answer: tested" in user class TestDispatch: def test_all_tasks_registered(self): assert set(GE_TASK_FORMATTERS.keys()) == {"ge-l1", "ge-l2", "ge-l3", "ge-l4"} def test_dispatch(self, sample_record): sys, user = format_ge_prompt("ge-l1", sample_record) assert sys == GE_SYSTEM_PROMPT assert "TP53" in user def test_invalid_task(self, sample_record): with pytest.raises(ValueError): format_ge_prompt("ge-l99", sample_record)