107 lines
3.8 KiB
Python
107 lines
3.8 KiB
Python
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from pathlib import Path
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import pytest
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from gfa_core.extension_stage.api_converter import (
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ApiConversionError,
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_build_repair_prompt,
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_validate_spec,
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)
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def test_validate_spec_preserves_input_roles_and_param_placeholders():
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spec = _validate_spec({
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"original_command": "seqtk subseq At.pep.fa At.id > out.fa",
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"command_template": "seqtk subseq {input_fasta} {input_file} > {output_dir}/hits.fa --min {param_min_length}",
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"input_roles": {
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"input_fasta": {"role": "target_pep_fasta", "resolve_by": "config_species"},
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"input_file": {"role": "target_id_list", "resolve_by": "species_final_gfmembers_id"},
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},
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"parameters": {
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"min-length": {"default": 80, "editable": True},
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"internal flag": {"default": "legacy", "editable": False},
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},
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})
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assert spec["input_roles"]["input_fasta"]["role"] == "target_pep_fasta"
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assert spec["input_roles"]["input_file"]["required"] is True
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assert "min_length" in spec["parameters"]
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assert spec["parameters"]["internal_flag"]["editable"] is False
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assert spec["requires_user_confirmation"] is False
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def test_validate_spec_rejects_editable_parameter_not_used_by_template():
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with pytest.raises(ApiConversionError, match="editable parameter"):
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_validate_spec({
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"original_command": "blastp -evalue 1e-5",
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"command_template": "blastp -query {input_fasta} -out {output_dir}/blast.tsv -evalue 1e-5",
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"parameters": {"evalue": {"default": "1e-5", "editable": True}},
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})
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def test_repair_prompt_does_not_forbid_parameter_placeholders(tmp_path: Path):
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raw_code = tmp_path / "code"
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raw_data = tmp_path / "data"
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raw_code.mkdir()
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raw_data.mkdir()
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(raw_code / "run.sh").write_text("echo test\n", encoding="utf-8")
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(raw_data / "At.id").write_text("AT1G01010\n", encoding="utf-8")
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prompt = _build_repair_prompt(
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extension={
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"template_type": "shell_pipeline",
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"entrypoint": {"command_template": "echo {input_file} > {output_dir}/out.txt"},
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"parameters": {},
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"inputs": {},
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"outputs": {},
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"requirements": {},
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"runtime": {},
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},
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raw_code=raw_code,
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raw_data=raw_data,
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validation_context={"status": "failed", "error": "missing value"},
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attempt=1,
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max_attempts=3,
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lessons=[],
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)
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assert "For v1, do not put parameter placeholders" not in prompt
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assert "Every parameter with editable=true must be used" in prompt
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assert "input_roles" in prompt
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def test_repair_prompt_includes_phase_specific_rules(tmp_path: Path):
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raw_code = tmp_path / "code"
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raw_data = tmp_path / "data"
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raw_code.mkdir()
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raw_data.mkdir()
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(raw_code / "run.sh").write_text("echo test\n", encoding="utf-8")
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(raw_data / "input.fa").write_text(">g1\nMA\n", encoding="utf-8")
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prompt = _build_repair_prompt(
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extension={
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"template_type": "shell_pipeline",
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"entrypoint": {"command_template": "bash {code_dir}/run.sh > {output_dir}/out.txt"},
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"parameters": {},
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"inputs": {},
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"outputs": {},
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"requirements": {},
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"runtime": {},
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},
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raw_code=raw_code,
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raw_data=raw_data,
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validation_context={
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"repair_phase": "publish_gate",
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"status": "failed",
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"error": "Publish gate failed",
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"publish_checks": {"errors": ["golden original-vs-converted comparison did not pass"]},
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},
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attempt=1,
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max_attempts=20,
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lessons=[],
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)
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assert '"repair_phase": "publish_gate"' in prompt
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assert "If repair_phase is publish_gate" in prompt
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assert "writes outputs under work/current directory instead of {output_dir}" in prompt
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