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🧹 Refactor duplicated requests.post logic into helper function #5

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🧹 Refactor duplicated requests.post logic into helper function #5

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99 changes: 24 additions & 75 deletions bionemo_scientist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -226,6 +226,25 @@ def annotate_artifacts(artifacts: list[RunArtifact], run_meta: dict[str, Any]) -
return annotated


def _post_hosted(url: str, key: str, payload: dict[str, Any], timeout: int = 900) -> dict[str, Any]:
response = requests.post(
url,
headers={
"Content-Type": "application/json",
"Authorization": f"Bearer {key}",
},
json=payload,
timeout=timeout,
)
if response.status_code >= 400:
raise requests.HTTPError(
f"{response.status_code} Server Error: {response.text[:500]}",
response=response,
)
response.raise_for_status()
return response.json()


def call_hosted_msa_search(sequence: str, request_id: str) -> dict[str, Any]:
key = resolve_key()
if not key:
Expand All @@ -239,17 +258,7 @@ def call_hosted_msa_search(sequence: str, request_id: str) -> dict[str, Any]:
"max_msa_sequences": 128,
"output_alignment_formats": ["a3m"],
}
response = requests.post(
MSA_SEARCH_HOSTED_URL,
headers={
"Content-Type": "application/json",
"Authorization": f"Bearer {key}",
},
json=payload,
timeout=600,
)
response.raise_for_status()
return response.json()
return _post_hosted(MSA_SEARCH_HOSTED_URL, key, payload, timeout=600)


def call_hosted_rfdiffusion(goal: str, request_id: str) -> dict[str, Any]:
Expand All @@ -261,22 +270,7 @@ def call_hosted_rfdiffusion(goal: str, request_id: str) -> dict[str, Any]:
"contigs": "80-120",
"diffusion_steps": 50,
}
response = requests.post(
RFDIFFUSION_HOSTED_URL,
headers={
"Content-Type": "application/json",
"Authorization": f"Bearer {key}",
},
json=payload,
timeout=900,
)
if response.status_code >= 400:
raise requests.HTTPError(
f"{response.status_code} Server Error: {response.text[:500]}",
response=response,
)
response.raise_for_status()
return response.json()
return _post_hosted(RFDIFFUSION_HOSTED_URL, key, payload, timeout=900)


def call_hosted_proteinmpnn(backbone_pdb: str, request_id: str) -> dict[str, Any]:
Expand All @@ -290,22 +284,7 @@ def call_hosted_proteinmpnn(backbone_pdb: str, request_id: str) -> dict[str, Any
"use_soluble_model": False,
"ca_only": False,
}
response = requests.post(
PROTEINMPNN_HOSTED_URL,
headers={
"Content-Type": "application/json",
"Authorization": f"Bearer {key}",
},
json=payload,
timeout=900,
)
if response.status_code >= 400:
raise requests.HTTPError(
f"{response.status_code} Server Error: {response.text[:500]}",
response=response,
)
response.raise_for_status()
return response.json()
return _post_hosted(PROTEINMPNN_HOSTED_URL, key, payload, timeout=900)


def call_hosted_openfold3(sequence: str, msa_alignment: str, request_id: str) -> dict[str, Any]:
Expand Down Expand Up @@ -338,22 +317,7 @@ def call_hosted_openfold3(sequence: str, msa_alignment: str, request_id: str) ->
}
],
}
response = requests.post(
OPENFOLD3_HOSTED_URL,
headers={
"Content-Type": "application/json",
"Authorization": f"Bearer {key}",
},
json=payload,
timeout=900,
)
if response.status_code >= 400:
raise requests.HTTPError(
f"{response.status_code} Server Error: {response.text[:500]}",
response=response,
)
response.raise_for_status()
return response.json()
return _post_hosted(OPENFOLD3_HOSTED_URL, key, payload, timeout=900)


def call_hosted_openfold2(sequence: str, msa_alignment: str, request_id: str) -> dict[str, Any]:
Expand All @@ -375,22 +339,7 @@ def call_hosted_openfold2(sequence: str, msa_alignment: str, request_id: str) ->
"relax_prediction": False,
"use_templates": False,
}
response = requests.post(
OPENFOLD2_HOSTED_URL,
headers={
"Content-Type": "application/json",
"Authorization": f"Bearer {key}",
},
json=payload,
timeout=900,
)
if response.status_code >= 400:
raise requests.HTTPError(
f"{response.status_code} Server Error: {response.text[:500]}",
response=response,
)
response.raise_for_status()
return response.json()
return _post_hosted(OPENFOLD2_HOSTED_URL, key, payload, timeout=900)


def simulate_local_structure(sequence: str, request_id: str) -> dict[str, Any]:
Expand Down