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🧹 Refactor artifact creation logic in bionemo_scientist.py #19

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🧹 Refactor artifact creation logic in bionemo_scientist.py #19

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125 changes: 42 additions & 83 deletions bionemo_scientist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,16 @@ class RunArtifact:
label: str


def write_artifact(name: str, filename: str, content: Any, label: str, is_json: bool = False) -> RunArtifact:
OUTPUTS.mkdir(parents=True, exist_ok=True)
file_path = OUTPUTS / filename
if is_json:
write_json(file_path, content)
else:
write_text(file_path, content)
return RunArtifact(name, str(file_path), label)


def load_repo_env() -> None:
env_path = ROOT / ".env"
if not env_path.exists():
Expand Down Expand Up @@ -477,43 +487,26 @@ def save_hosted_artifacts(sequence: str, msa_result: dict[str, Any], fold_result
"msa_result": msa_result,
"fold_result": fold_result,
}
OUTPUTS.mkdir(parents=True, exist_ok=True)
msa_json = OUTPUTS / "bionemo_msa_search.json"
msa_a3m = OUTPUTS / "bionemo_msa_alignment.a3m"
fold_json = OUTPUTS / "bionemo_openfold3_response.json"
fold_cif = OUTPUTS / "bionemo_openfold3_structure.cif"
write_json(msa_json, msa_result)
write_text(msa_a3m, msa_primary)
write_json(fold_json, fold_result)
structure = fold_result["outputs"][0]["structures_with_scores"][0]["structure"]
write_text(fold_cif, structure)
OUTPUTS.mkdir(parents=True, exist_ok=True)
write_json(OUTPUTS / "bionemo_scientist_artifacts.json", {**msa_all, "run": run_meta})
return [
RunArtifact("msa_json", str(msa_json), "REAL"),
RunArtifact("msa_a3m", str(msa_a3m), "REAL"),
RunArtifact("fold_json", str(fold_json), "REAL"),
RunArtifact("fold_cif", str(fold_cif), "REAL"),
write_artifact("msa_json", "bionemo_msa_search.json", msa_result, "REAL", is_json=True),
write_artifact("msa_a3m", "bionemo_msa_alignment.a3m", msa_primary, "REAL"),
write_artifact("fold_json", "bionemo_openfold3_response.json", fold_result, "REAL", is_json=True),
write_artifact("fold_cif", "bionemo_openfold3_structure.cif", structure, "REAL"),
]


def save_hosted_failure_artifacts(msa_result: dict[str, Any], error: Exception, request_id: str, run_meta: dict[str, Any]) -> list[RunArtifact]:
OUTPUTS.mkdir(parents=True, exist_ok=True)
msa_json = OUTPUTS / "bionemo_msa_search.json"
msa_a3m = OUTPUTS / "bionemo_msa_alignment.a3m"
error_path = OUTPUTS / "bionemo_openfold3_error.txt"
write_json(msa_json, msa_result)
write_text(msa_a3m, msa_result["alignments"]["Uniref30_2302"]["a3m"]["alignment"])
write_text(
error_path,
"\n".join(
[
f"request_id: {request_id}",
f"error_type: {type(error).__name__}",
f"error: {error}",
]
)
+ "\n",
)
error_content = "\n".join(
[
f"request_id: {request_id}",
f"error_type: {type(error).__name__}",
f"error: {error}",
]
) + "\n"
write_json(
OUTPUTS / "bionemo_scientist_artifacts.json",
{
Expand All @@ -525,9 +518,9 @@ def save_hosted_failure_artifacts(msa_result: dict[str, Any], error: Exception,
},
)
return [
RunArtifact("msa_json", str(msa_json), "REAL"),
RunArtifact("msa_a3m", str(msa_a3m), "REAL"),
RunArtifact("fold_error", str(error_path), "FAILED"),
write_artifact("msa_json", "bionemo_msa_search.json", msa_result, "REAL", is_json=True),
write_artifact("msa_a3m", "bionemo_msa_alignment.a3m", msa_result["alignments"]["Uniref30_2302"]["a3m"]["alignment"], "REAL"),
write_artifact("fold_error", "bionemo_openfold3_error.txt", error_content, "FAILED"),
]


Expand All @@ -542,16 +535,6 @@ def save_hosted_openfold2_artifacts(sequence: str, msa_result: dict[str, Any], f
"pTM": output.get("ptm_score"),
}
OUTPUTS.mkdir(parents=True, exist_ok=True)
msa_json = OUTPUTS / "bionemo_msa_search.json"
msa_a3m = OUTPUTS / "bionemo_msa_alignment.a3m"
fold_json = OUTPUTS / "bionemo_openfold2_response.json"
fold_pdb = OUTPUTS / "bionemo_openfold2_structure.pdb"
score_json = OUTPUTS / "bionemo_openfold2_scores.json"
write_json(msa_json, msa_result)
write_text(msa_a3m, msa_primary)
write_json(fold_json, fold_result)
write_text(fold_pdb, structure)
write_json(score_json, {"request_id": request_id, "sequence": sequence, "scores": score})
write_json(
OUTPUTS / "bionemo_scientist_artifacts.json",
{
Expand All @@ -563,25 +546,17 @@ def save_hosted_openfold2_artifacts(sequence: str, msa_result: dict[str, Any], f
},
)
return [
RunArtifact("msa_json", str(msa_json), "REAL"),
RunArtifact("msa_a3m", str(msa_a3m), "REAL"),
RunArtifact("fold_json", str(fold_json), "REAL"),
RunArtifact("fold_pdb", str(fold_pdb), "REAL"),
RunArtifact("fold_scores", str(score_json), "REAL"),
write_artifact("msa_json", "bionemo_msa_search.json", msa_result, "REAL", is_json=True),
write_artifact("msa_a3m", "bionemo_msa_alignment.a3m", msa_primary, "REAL"),
write_artifact("fold_json", "bionemo_openfold2_response.json", fold_result, "REAL", is_json=True),
write_artifact("fold_pdb", "bionemo_openfold2_structure.pdb", structure, "REAL"),
write_artifact("fold_scores", "bionemo_openfold2_scores.json", {"request_id": request_id, "sequence": sequence, "scores": score}, "REAL", is_json=True),
]


def save_demo_artifacts(sequence: str, request_id: str, run_meta: dict[str, Any]) -> list[RunArtifact]:
demo = simulate_local_structure(sequence, request_id)
OUTPUTS.mkdir(parents=True, exist_ok=True)
msa_json = OUTPUTS / "bionemo_msa_search.json"
msa_a3m = OUTPUTS / "bionemo_msa_alignment.a3m"
fold_json = OUTPUTS / "bionemo_openfold3_response.json"
fold_cif = OUTPUTS / "bionemo_openfold3_structure.cif"
write_json(msa_json, demo["msa"])
write_text(msa_a3m, demo["msa_a3m"])
write_json(fold_json, demo["fold"])
write_text(fold_cif, demo["structure_cif"])
write_json(
OUTPUTS / "bionemo_scientist_artifacts.json",
{
Expand All @@ -593,23 +568,15 @@ def save_demo_artifacts(sequence: str, request_id: str, run_meta: dict[str, Any]
},
)
return [
RunArtifact("msa_json", str(msa_json), "DEMO"),
RunArtifact("msa_a3m", str(msa_a3m), "DEMO"),
RunArtifact("fold_json", str(fold_json), "DEMO"),
RunArtifact("fold_cif", str(fold_cif), "DEMO"),
write_artifact("msa_json", "bionemo_msa_search.json", demo["msa"], "DEMO", is_json=True),
write_artifact("msa_a3m", "bionemo_msa_alignment.a3m", demo["msa_a3m"], "DEMO"),
write_artifact("fold_json", "bionemo_openfold3_response.json", demo["fold"], "DEMO", is_json=True),
write_artifact("fold_cif", "bionemo_openfold3_structure.cif", demo["structure_cif"], "DEMO"),
]


def save_hosted_design_artifacts(goal: str, design_result: dict[str, Any], mpnn_result: dict[str, Any], request_id: str, run_meta: dict[str, Any]) -> list[RunArtifact]:
OUTPUTS.mkdir(parents=True, exist_ok=True)
design_json = OUTPUTS / "bionemo_rfdiffusion_response.json"
design_pdb = OUTPUTS / "bionemo_rfdiffusion_backbone.pdb"
mpnn_json = OUTPUTS / "bionemo_proteinmpnn_response.json"
mpnn_fasta = OUTPUTS / "bionemo_proteinmpnn_sequences.fa"
write_json(design_json, design_result)
write_text(design_pdb, design_result["output_pdb"])
write_json(mpnn_json, mpnn_result)
write_text(mpnn_fasta, mpnn_result["mfasta"])
write_json(
OUTPUTS / "bionemo_scientist_artifacts.json",
{
Expand All @@ -622,23 +589,15 @@ def save_hosted_design_artifacts(goal: str, design_result: dict[str, Any], mpnn_
},
)
return [
RunArtifact("design_json", str(design_json), "REAL"),
RunArtifact("design_pdb", str(design_pdb), "REAL"),
RunArtifact("mpnn_json", str(mpnn_json), "REAL"),
RunArtifact("mpnn_fasta", str(mpnn_fasta), "REAL"),
write_artifact("design_json", "bionemo_rfdiffusion_response.json", design_result, "REAL", is_json=True),
write_artifact("design_pdb", "bionemo_rfdiffusion_backbone.pdb", design_result["output_pdb"], "REAL"),
write_artifact("mpnn_json", "bionemo_proteinmpnn_response.json", mpnn_result, "REAL", is_json=True),
write_artifact("mpnn_fasta", "bionemo_proteinmpnn_sequences.fa", mpnn_result["mfasta"], "REAL"),
]


def save_demo_design_artifacts(goal: str, design_result: dict[str, Any], request_id: str, run_meta: dict[str, Any]) -> list[RunArtifact]:
OUTPUTS.mkdir(parents=True, exist_ok=True)
design_json = OUTPUTS / "bionemo_rfdiffusion_response.json"
design_pdb = OUTPUTS / "bionemo_rfdiffusion_backbone.pdb"
mpnn_json = OUTPUTS / "bionemo_proteinmpnn_response.json"
mpnn_fasta = OUTPUTS / "bionemo_proteinmpnn_sequences.fa"
write_json(design_json, design_result["design"])
write_text(design_pdb, design_result["designed_backbone_pdb"])
write_json(mpnn_json, design_result["sequence_design"])
write_text(mpnn_fasta, design_result["sequence_design"]["mfasta"])
write_json(
OUTPUTS / "bionemo_scientist_artifacts.json",
{
Expand All @@ -651,10 +610,10 @@ def save_demo_design_artifacts(goal: str, design_result: dict[str, Any], request
},
)
return [
RunArtifact("design_json", str(design_json), "DEMO"),
RunArtifact("design_pdb", str(design_pdb), "DEMO"),
RunArtifact("mpnn_json", str(mpnn_json), "DEMO"),
RunArtifact("mpnn_fasta", str(mpnn_fasta), "DEMO"),
write_artifact("design_json", "bionemo_rfdiffusion_response.json", design_result["design"], "DEMO", is_json=True),
write_artifact("design_pdb", "bionemo_rfdiffusion_backbone.pdb", design_result["designed_backbone_pdb"], "DEMO"),
write_artifact("mpnn_json", "bionemo_proteinmpnn_response.json", design_result["sequence_design"], "DEMO", is_json=True),
write_artifact("mpnn_fasta", "bionemo_proteinmpnn_sequences.fa", design_result["sequence_design"]["mfasta"], "DEMO"),
]


Expand Down