Python client
The client is one dependency-light file you drop into your project — no SDK to install, no build step. Read it here, or download the whole kit:
Download the integration kit (.tar.gz) — every file below plus the docs, bundled.
client/gi_client.py
Single-file client. Depends only on requests. Wraps sync predict, async submit + poll, the composite annotation→expression workflow, job lifecycle, and model listing; returns the unified {data, meta} envelope and raises a typed GIError on any non-2xx.
client/gi_client.py
"""Tiny client for the Genomic Intelligence API.
Wraps `requests` with bearer auth, the unified `{data, meta}` /
`{error}` envelope, and a polling helper for async jobs. Drop this file
into your project and `from gi_client import Client`.
Endpoints covered:
- the six per-task predictors, each its own published operation:
``POST /v1/tasks/{promoter,splice,enhancer,chromatin,annotation,
expression}/predict``
- the composite ``POST /v1/workflows/find-genes-and-predict-expression``
- the async job endpoints ``GET /v1/tasks/jobs[/{job_id}]``
- model discovery ``GET /v1/tasks/{task}/models``
Contract reference: https://api.genomicintelligence.ai/redoc
"""
from __future__ import annotations
import time
from typing import Any, Dict, Mapping, Optional
import requests
#: Minimum ``sequence`` length per task, in bp, measured AFTER whitespace is
#: stripped. This is a MIRROR for local pre-flight only — the authority is the
#: ``minLength`` published on each task's request schema in the live OpenAPI
#: document (``GET /v1/openapi.json``, public and unauthenticated), generated
#: from the service's ``api/core/limits.py``.
#:
#: The two can no longer disagree quietly. ``scripts/check_contract.py`` reads
#: this table straight out of this file and asserts it against
#: ``scripts/contract.json``, a pin of the live document; it runs on every PR
#: and **blocks the deploy**. ``scripts/sync_contract.py --check`` re-verifies
#: the pin against the live API daily. If you need to change a number here,
#: re-pin first and reconcile this table to the contract — never the reverse.
TASK_MIN_BP: Dict[str, int] = {
"promoter": 300,
"splice": 100,
"enhancer": 50,
"chromatin": 200,
"annotation": 1_000,
"expression": 9_198,
"find-genes-and-predict-expression": 1_000,
}
#: Maximum ``sequence`` length, in bp, for every task (same mirror caveat).
#: Also published per model as ``bio_spec.request_max_bp``.
MAX_BP = 500_000
#: Above this, the composite workflow refuses synchronous delivery with
#: ``413 sync_too_large`` — resend the same body with ``Prefer: respond-async``.
FIND_GENES_SYNC_LIMIT_BP = 50_000
class GIError(RuntimeError):
"""Raised on any non-2xx response from the API.
Attributes mirror the unified error envelope so callers can switch
on ``code`` rather than HTTP status alone:
{"error": {"code": "...", "message": "...",
"request_id": "...", "details": ...}}
``details`` is carried through verbatim and never parsed. Its shape is
keyed on the sibling ``code`` and has varied across releases — for
``validation_failed`` you may see either a bare ``[{loc, msg, type}, ...]``
array or ``{"errors": [...]}`` — and splice's response-size cap emits a
``validation_failed`` with neither (``{task, record_count,
maximum_records, sequence_length, threshold}``). Branch on ``code`` and
treat ``details`` as display-only, and you are correct against all of them.
"""
def __init__(
self,
status: int,
body: Dict[str, Any],
headers: Optional[Mapping[str, str]] = None,
):
err = (body or {}).get("error", {}) if isinstance(body, dict) else {}
self.status = status
self.code = err.get("code", "http_error")
self.message = err.get("message", "")
# The X-Request-Id header is set on every response, including any
# error whose body omits error.request_id. Fall back to it — support
# tickets always need a correlation id.
self.request_id = err.get("request_id") or (headers or {}).get("X-Request-Id")
self.details = err.get("details")
rid = self.request_id or "unset"
super().__init__(f"[{status} {self.code}] {self.message} (request_id={rid})")
class Client:
"""Thin synchronous client.
>>> c = Client(api_key="gi_…")
>>> r = c.predict("promoter", sequence="ACGT" * 500, sequence_name="demo")
>>> r["meta"]["inference_time_ms"]
"""
def __init__(
self,
api_key: str,
base_url: str = "https://api.genomicintelligence.ai",
timeout: float = 120.0,
) -> None:
self.base_url = base_url.rstrip("/")
self.timeout = timeout
self._session = requests.Session()
self._session.headers.update(
{
"Authorization": f"Bearer {api_key}",
"Content-Type": "application/json",
"Accept": "application/json",
}
)
# ------------------------------------------------------------------ helpers
def _check(self, resp: requests.Response) -> Dict[str, Any]:
try:
body = resp.json()
except ValueError:
# A response arrived but is not JSON — usually an edge proxy. Use
# http_error: error.code is a closed enum published in the schema,
# so a synthesized value outside it is one no caller can match on.
# Client-origin errors carry no request_id (the server never saw
# this one), which is how you tell them apart from server errors.
body = {"error": {"code": "http_error", "message": resp.text[:200]}}
if not resp.ok:
raise GIError(resp.status_code, body, resp.headers)
return body
# ----------------------------------------------------------------- requests
def health(self) -> Dict[str, Any]:
r = self._session.get(f"{self.base_url}/health", timeout=self.timeout)
return self._check(r)
def list_models(self, task: str) -> Dict[str, Any]:
"""``GET /v1/tasks/{task}/models`` — public; the key is sent but not needed.
Returns a FLAT ``{task, default_model, models: [...]}`` object, not
the ``{data, meta}`` envelope. Each model carries ``bio_spec`` with
``request_max_bp`` (the enforced ceiling), ``context_window_bp``
(the model's own window — compare your sequence length against it to
know whether the model saw real sequence or padding; null for
annotation and expression) and ``trained_window_bp`` (fixed
receptive field where the model has one; null for sliding-window
models). Expression models also carry ``recommended_flank_bp``.
Never hard-code a window, flank or model id: use the model your
user named, else ``default_model``, and pass it as ``model`` on
every call of a run; take F = the largest ``recommended_flank_bp``
among the listed models (one fetch serves any of them), never below
4,599 and with 2F within ``request_max_bp``. Put the TSS at offset F
of the gene-sense sequence and send ``tss_index = F``. With ``tss``
the 0-based genomic TSS position, fetch ``[tss - F, tss + F)`` on
the plus strand, or ``(tss - F, tss + F]`` reverse-complemented on
the minus strand.
``request_max_bp`` is the only cap; the window fields describe what
the model reads, not what the route accepts.
An unknown ``task`` is ``404 not_found``.
"""
r = self._session.get(
f"{self.base_url}/v1/tasks/{task}/models", timeout=self.timeout
)
return self._check(r)
@staticmethod
def _body(
sequence: str,
sequence_name: str,
model: Optional[str],
options: Optional[Dict[str, Any]],
tss_index: Optional[int] = None,
) -> Dict[str, Any]:
body: Dict[str, Any] = {"sequence": sequence, "sequence_name": sequence_name}
if model is not None:
body["model"] = model
if options is not None:
body["options"] = options
if tss_index is not None:
body["tss_index"] = tss_index
return body
def predict(
self,
task: str,
sequence: str,
sequence_name: str = "sequence",
model: Optional[str] = None,
options: Optional[Dict[str, Any]] = None,
tss_index: Optional[int] = None,
) -> Dict[str, Any]:
"""Synchronous prediction. Returns the full ``{data, meta}`` body.
``task`` is one of ``promoter``, ``splice``, ``enhancer``,
``chromatin``, ``annotation``, ``expression`` — each a separately
published operation at the same URL this method builds. An
unrecognised task is ``404 not_found``, not a validation error.
``model`` is a TOP-LEVEL field, not ``options["model"]``: every
task's ``options`` object is closed (``additionalProperties:
false``), so an unknown key — ``model`` included — is rejected with
``422 validation_failed`` at ``loc ["body","options","<key>"]``.
The accepted option keys differ per task; see the request schema in
ReDoc (``PromoterOptions``, ``SpliceOptions``, …). ``expression``
additionally *requires* ``options["description"]``.
``sequence`` must be within this task's bounds (see
:data:`TASK_MIN_BP` / :data:`MAX_BP`, measured after whitespace is
stripped); outside them is ``422 validation_failed``, never ``413``.
A sequence above the floor but shorter than the selected model's
``bio_spec.context_window_bp`` (from :meth:`list_models`) is still
accepted and scored — against a window padded out to that size.
``tss_index`` applies to the ``expression`` task only: the 0-based
offset of the TSS into the whitespace-stripped ``sequence``. Every
expression model takes at least 9,198 bp with the TSS at least
4,599 bp from each end, i.e. ``4599 <= tss_index <= len(sequence) -
4599``; ``tss_index`` is required unless ``sequence`` is exactly
9,198 bp. 9,198 bp is a floor, not a target: longer TSS-centred
sequence is better, and the model list says how much (the rule and
strand handling are in :meth:`list_models`). There is no
``tes_index``. The client does not
validate any of this — the API returns ``422 validation_failed``
(the ``tss_index`` checks at ``loc ["body"]``, so switch on
``error.code``). A window dominated by ``N`` or low-complexity
repeats can also be refused with ``422``: each model needs roughly
2-3.3 kb of real sequence upstream of the TSS and 2.6 kb
downstream.
"""
body = self._body(sequence, sequence_name, model, options, tss_index)
r = self._session.post(
f"{self.base_url}/v1/tasks/{task}/predict",
json=body,
timeout=self.timeout,
)
return self._check(r)
def submit_async(
self,
task: str,
sequence: str,
sequence_name: str = "sequence",
model: Optional[str] = None,
options: Optional[Dict[str, Any]] = None,
tss_index: Optional[int] = None,
) -> str:
"""Submit a task in async mode. Returns the ``job_id``.
``Prefer: respond-async`` is a declared header parameter on all six
predict operations and on the composite workflow. Async delivery is
JSON-only: combining it with a text ``?format=`` is a ``400``.
``tss_index`` is the ``expression``-only TSS offset; see :meth:`predict`.
"""
body = self._body(sequence, sequence_name, model, options, tss_index)
r = self._session.post(
f"{self.base_url}/v1/tasks/{task}/predict",
headers={"Prefer": "respond-async"},
json=body,
timeout=self.timeout,
)
body = self._check(r)
# 202 envelope is {data: {job_id, status, links}, meta: {...}} —
# uniform with the {data, meta} shape every other successful
# response on the inference URL produces.
return body["data"]["job_id"]
# --------------------------------------------------- composite workflow
def find_genes_and_predict_expression(
self,
sequence: str,
description: str,
sequence_name: str = "sequence",
options: Optional[Dict[str, Any]] = None,
async_: bool = False,
) -> Dict[str, Any]:
"""``POST /v1/workflows/find-genes-and-predict-expression``.
Runs annotation over the region, cuts a window around each found
gene's TSS, and scores expression for each — one round trip. Each
gene is scored with the API's default expression model, using as
much flank around each TSS as the submitted region holds, so longer
regions give better predictions.
``sequence`` is 1,000–500,000 bp (the annotation stage's floor).
``description`` is the experimental context applied to every gene;
it is required (missing or empty is ``422 validation_failed``) and
is passed as ``options["description"]``. Extra ``options`` may add
``annotation_model``, ``expression_model`` and
``shift_coordinates``; the object is closed, so any
other key is a ``422``.
Above :data:`FIND_GENES_SYNC_LIMIT_BP` (50,000 bp) synchronous
delivery is refused with ``413 sync_too_large`` carrying
``details = {sequence_length, threshold}`` — resend the identical
body with ``async_=True``.
Returns the ``{data, meta}`` body; with ``async_=True`` that body is
the ``202`` acceptance ``{data: {job_id, status, links}, meta}``,
so poll :meth:`wait_for_job` on ``body["data"]["job_id"]``.
``meta.task_specific_counts`` is
``{genes_found, genes_predicted, genes_skipped}`` with
``genes_predicted + genes_skipped == genes_found``; per-gene causes
are in ``data.expression_predictions[].skip_reason``.
"""
opts: Dict[str, Any] = dict(options or {})
opts["description"] = description
body = self._body(sequence, sequence_name, None, opts)
headers = {"Prefer": "respond-async"} if async_ else None
r = self._session.post(
f"{self.base_url}/v1/workflows/find-genes-and-predict-expression",
headers=headers,
json=body,
timeout=self.timeout,
)
return self._check(r)
def get_job(self, job_id: str) -> requests.Response:
"""Single poll. The caller inspects ``status_code`` to discriminate."""
return self._session.get(
f"{self.base_url}/v1/tasks/jobs/{job_id}", timeout=self.timeout
)
def wait_for_job(
self,
job_id: str,
poll_interval: float = 2.0,
max_wait: float = 30 * 60,
on_progress=None,
) -> Dict[str, Any]:
"""Poll until terminal. Returns ``{data, meta}`` on success, raises ``GIError``."""
deadline = time.monotonic() + max_wait
while True:
r = self.get_job(job_id)
if r.status_code == 200:
return r.json()
if r.status_code == 202:
if on_progress is not None:
try:
# 202 poll body is also {data: {progress: {...}}, meta}.
on_progress((r.json().get("data") or {}).get("progress") or {})
except Exception:
pass
if time.monotonic() > deadline:
raise TimeoutError(f"job {job_id} did not finish within {max_wait}s")
time.sleep(poll_interval)
continue
# Terminal error
try:
body = r.json()
except ValueError:
# http_error for the same reason as _check above: the code must
# come from the published enum.
body = {"error": {"code": "http_error", "message": r.text[:200]}}
raise GIError(r.status_code, body, r.headers)
def list_jobs(self, limit: int = 50) -> Dict[str, Any]:
r = self._session.get(
f"{self.base_url}/v1/tasks/jobs",
params={"limit": limit},
timeout=self.timeout,
)
return self._check(r)
client/quickstart.py
Runs every task end to end against the bundled real sequences. The fastest way to confirm your key works before you write any code.
client/quickstart.py
"""Genomic Intelligence API — partner quickstart.
Hits every public task endpoint with a real, biologically meaningful
sequence drawn from the bundled ``sequences/`` directory (the same
fixtures the service uses for its golden numeric-regression tests).
Sync calls are sized so each task completes in a few seconds on a warm
GPU; ``annotation`` is the one outlier and is intentionally exercised
both sync and async.
pip install -r requirements.txt
export GI_API_KEY=gi_xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
export GI_BASE_URL=https://api.genomicintelligence.ai # optional
python quickstart.py
"""
from __future__ import annotations
import os
import pathlib
import sys
import requests
from gi_client import Client, GIError
SEQ_DIR = pathlib.Path(__file__).parent / "sequences"
def load_fasta(filename: str) -> tuple[str, str]:
"""Return (sequence_name, sequence) from a single-record FASTA file."""
text = (SEQ_DIR / filename).read_text()
lines = text.splitlines()
header = lines[0].lstrip(">").strip()
sequence = "".join(line.strip() for line in lines[1:] if line.strip())
return header, sequence.upper()
def _section(title: str) -> None:
print(f"\n=== {title} ===")
def _summary(label: str, body: dict) -> None:
meta = body.get("meta", {})
counts = meta.get("task_specific_counts", {})
print(
f"{label:<22} model={meta.get('model'):<32} "
f"{meta.get('inference_time_ms', '?')} ms counts={counts}"
)
def main() -> int:
api_key = os.environ.get("GI_API_KEY")
if not api_key:
print("ERROR: set GI_API_KEY (your gi_… bearer key)", file=sys.stderr)
return 2
base_url = os.environ.get("GI_BASE_URL", "https://api.genomicintelligence.ai")
client = Client(api_key=api_key, base_url=base_url)
_section("Health")
print(client.health())
# All sequences are real biological inputs from the service's golden
# fixtures — see client/sequences/. Each FASTA carries
# provenance in its header (gene symbol, coordinates, assembly).
tp53_name, tp53_seq = load_fasta("promoter_tp53.fa") # human, ~26 kb, gene-sense (TP53 is - strand)
hbb_name, hbb_seq = load_fasta("splice_hbb.fa") # human, ~4 kb
eve_name, eve_seq = load_fasta("enhancer_eve.fa") # drosophila, ~10 kb, eve developmental enhancer (+ strand)
chr19_name, chr19_seq = load_fasta("chromatin_active_promoter_chr19.fa") # human, ~40 kb
hbb_tss_name, hbb_tss_seq = load_fasta("expression_hbb_k562.fa") # human, 9,198 bp (the minimum), TSS-centered
_section("Sync inference (real biological sequences)")
try:
_summary("promoter (TP53)",
client.predict("promoter", tp53_seq, tp53_name))
_summary("splice (HBB)",
client.predict("splice", hbb_seq, hbb_name))
# Enhancer model is Drosophila-trained — use a fly enhancer.
_summary("enhancer (eve)",
client.predict("enhancer", eve_seq, eve_name))
_summary("chromatin (chr19)",
client.predict("chromatin", chr19_seq, chr19_name))
except GIError as exc:
print(f"sync task failed: {exc}", file=sys.stderr)
return 1
except requests.RequestException as exc:
# Transport-level: DNS, TLS, connection refused, read timeout.
# Routine for a hosted service and not a request problem.
print(f"sync task failed: network error: {type(exc).__name__}: {exc}", file=sys.stderr)
return 1
_section("Expression (HBB in K562, TSS-centered)")
# Every expression model takes at least 9,198 bp with the TSS at least
# 4,599 bp from each end. Anything shorter is a hard 422 -- no padding, no
# truncation. The bundled fixture is that minimum for HBB, centered on its
# canonical TSS, so the quickstart runs offline of any genome fetch; with
# the K562 cell-type description this should report HIGH expression
# (HBB is highly expressed in K562 erythroleukemia cells).
#
# At exactly 9,198 bp, tss_index is optional and defaults to 4599. The
# floor is not a target: for real use, longer TSS-centred sequence is
# better, and the model list says how much. From
# client.list_models("expression") take the model your user named, else
# default_model (pass it as model= on every call of a run), and
# F = the largest bio_spec.recommended_flank_bp among the listed models,
# never below 4,599 and with 2F within request_max_bp. Never hard-code a
# window, flank or model id. With tss the 0-based genomic TSS position,
# fetch [tss - F, tss + F) on the plus strand, or (tss - F, tss + F] and
# reverse-complement it on the minus strand, so the TSS sits at offset F.
# Then pass
# tss_index=<0-based TSS offset into the whitespace-stripped sequence>; it
# is REQUIRED at any other length and must satisfy
# 4599 <= tss_index <= len(sequence) - 4599. Note "whitespace-stripped":
# an index counted over line-wrapped FASTA characters is off by the newline
# count and can silently score the wrong region, so assert on the
# scored_window echoed back below.
try:
body = client.predict(
"expression",
sequence=hbb_tss_seq,
sequence_name=hbb_tss_name,
options={
"description": (
"assay term name is polyA plus RNA-seq. "
"biosample summary is Homo sapiens K562."
),
},
)
pred = body.get("data", {}).get("prediction", {})
counts = body.get("meta", {}).get("task_specific_counts", {})
print(
f"expression: {pred.get('expression_log_tpm')} log(TPM+1) "
f"({pred.get('expression_tpm')} TPM)"
)
# Windowing provenance: confirm the server scored the window you meant.
print(
f" tss_index={counts.get('tss_index')} "
f"scored_window={counts.get('scored_window')}"
)
except GIError as exc:
print(f"expression failed: {exc}", file=sys.stderr)
except requests.RequestException as exc:
print(f"expression failed: network error: {type(exc).__name__}: {exc}", file=sys.stderr)
_section("Async job — annotation on TP53 (~26 kb)")
# Annotation is the slowest atomic task and the one where async
# actually matters. TP53 is well-annotated; expect at least one
# transcript in the response.
try:
job_id = client.submit_async(
"annotation",
sequence=tp53_seq,
sequence_name=tp53_name,
)
print(f"submitted job_id={job_id}")
def progress(p):
pct = p.get("current_percent")
msg = p.get("message", "")
print(f" {pct:>3}% {msg}")
body = client.wait_for_job(job_id, poll_interval=2.0, on_progress=progress)
meta = body.get("meta", {})
counts = meta.get("task_specific_counts", {})
transcripts = body.get("data", {}).get("transcripts", []) or []
print(
f"done — counts={counts} "
f"transcripts={len(transcripts)} "
f"total_time_ms={meta.get('inference_time_ms')}"
)
except GIError as exc:
print(f"annotation failed: {exc}", file=sys.stderr)
return 1
except requests.RequestException as exc:
print(f"annotation failed: network error: {type(exc).__name__}: {exc}", file=sys.stderr)
return 1
except TimeoutError as exc:
# wait_for_job gives up rather than polling forever.
print(f"annotation timed out: {exc}", file=sys.stderr)
return 1
_section("Recent jobs")
print(client.list_jobs(limit=5))
return 0
if __name__ == "__main__":
raise SystemExit(main())
client/requirements.txt
The client's only runtime dependency.
client/requirements.txt
requests>=2.31
Example sequences
Real sequences the quickstart and recipes run against — download or curl them directly: