File size: 8,499 Bytes
3ed6b66 01b3ee5 3ed6b66 01b3ee5 3ed6b66 01b3ee5 3ed6b66 01b3ee5 3ed6b66 01b3ee5 3ed6b66 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 | """What every endpoint shares: the client, the call budget, dates, stages and HGNC resolution.
Endpoints are plain functions — strings in, payload dicts out — and no exception escapes one
(the family tool_server contract). A failure inside one source call is a ``source_errors`` entry,
an input that a source does not know is an ``unresolved`` entry, and only an endpoint where
nothing could be looked up at all is an ``error`` payload.
"""
from __future__ import annotations
import threading
import time
from collections.abc import Iterable
from dataclasses import dataclass, field
from typing import Any
from src import config
from src.provenance import stamp
from src.tu_client import SourceError, SourceResult, ToolClient
# One endpoint call may spend at most this long across all its source calls; the orchestrator's
# own call limit is above it (300 s for annotate_genes, its default for the others).
ENDPOINT_BUDGET_SECONDS = 240
_client: ToolClient | None = None
_client_lock = threading.Lock()
def get_client() -> ToolClient:
"""The process-wide client (one cache, one set of rate limits for every endpoint)."""
global _client
with _client_lock:
if _client is None:
_client = ToolClient()
return _client
def set_client(client: ToolClient | None) -> None:
"""Tests replay recorded responses through a client of their own."""
global _client
with _client_lock:
_client = client
class Budget:
"""The endpoint's wall-clock budget. Past it, remaining inputs are reported, not looked up."""
def __init__(self, seconds: float = ENDPOINT_BUDGET_SECONDS, clock=time.monotonic):
self._clock = clock
self.seconds = seconds
self._deadline = clock() + seconds
@property
def remaining(self) -> float:
return max(0.0, self._deadline - self._clock())
@property
def spent(self) -> bool:
return self.remaining <= 0
@dataclass
class Collector:
"""Accumulates what an endpoint found, failed on and could not resolve."""
rows: list[dict[str, Any]] = field(default_factory=list)
unresolved: list[dict[str, str]] = field(default_factory=list)
source_errors: list[dict[str, str]] = field(default_factory=list)
sources_used: set[str] = field(default_factory=set)
retrieved: list[float] = field(default_factory=list)
calls: int = 0
def call(
self,
client: ToolClient,
budget: Budget,
tool: str,
args: dict[str, Any],
*,
unknown: tuple[str, str] | None = None,
) -> SourceResult | None:
"""One source call. None (with the reason recorded) if it failed or the budget ran out.
``unknown=(marker, input)``: a source error whose detail contains ``marker`` means the
source does not know ``input`` (Reactome's 404, Open Targets' "no disease for ID"). That
is an unresolved input, not a source failure.
"""
if budget.spent:
return None
result, err = self.attempt(client, budget, tool, args)
if err is None:
return result
if unknown is not None and err.reason == "source_unavailable" and unknown[0] in err.detail:
self.unresolved_input(unknown[1], f"unknown to {err.source}: {err.detail}")
else:
self.source_errors.append(err.as_payload())
return None
def attempt(
self,
client: ToolClient,
budget: Budget,
tool: str,
args: dict[str, Any],
) -> tuple[SourceResult | None, SourceError | None]:
"""One source call whose failure is handed back, not recorded: the caller may retry it.
The call's deadline never runs past ``budget``: a call started with 12 s left gets 12 s.
"""
self.calls += 1
try:
result = client.call(
tool, args, max_wait=min(10.0, budget.remaining), deadline=budget.remaining
)
except SourceError as err:
return None, err
self.sources_used.add(result.source)
self.retrieved.append(result.retrieved_at)
return result, None
def unresolved_input(self, value: str, reason: str) -> None:
self.unresolved.append({"input": value, "reason": reason})
def out_of_budget(self, values: Iterable[str]) -> None:
for value in values:
self.unresolved_input(
value, f"not looked up: the {ENDPOINT_BUDGET_SECONDS} s call budget ran out"
)
def stamped(row: dict[str, Any], result: SourceResult, *, ref: str, url: str) -> dict[str, Any]:
return stamp(
row,
source=result.source,
source_tool=result.tool,
tooluniverse_version=result.tooluniverse_version,
query=result.args,
source_ref=ref,
source_url=url,
retrieved_at=result.retrieved_at,
cache=result.cache,
)
def query_dates(retrieved: Iterable[float]) -> str:
"""'2026-10-20', or '2026-10-14 to 2026-10-20' when cached answers span days."""
from src.provenance import iso_utc
days = sorted({iso_utc(t)[:10] for t in retrieved})
if not days:
return "today"
return days[0] if len(days) == 1 else f"{days[0]} to {days[-1]}"
def according_to(source_ids: Iterable[str], retrieved: Iterable[float]) -> str:
names = [config.source(s)["name"] for s in sorted(set(source_ids))]
joined = names[0] if len(names) == 1 else ", ".join(names[:-1]) + " and " + names[-1]
return f"According to {joined} (queried {query_dates(retrieved)})"
def humanise_list(items: list[str], limit: int = 5) -> str:
shown = items[:limit]
more = len(items) - len(shown)
text = ", ".join(shown)
return f"{text} and {more} more" if more > 0 else text
# Open Targets' clinical-stage vocabulary, highest first. Anything unknown sorts last and is
# shown as Open Targets wrote it.
_STAGE_ORDER = (
"APPROVAL",
"APPROVED",
"PHASE_4",
"PHASE_3",
"PHASE_2_3",
"PHASE_2",
"PHASE_1_2",
"PHASE_1",
"EARLY_PHASE_1",
"PHASE_0",
"PRECLINICAL",
)
def stage_rank(stage: str | None) -> int:
try:
return _STAGE_ORDER.index((stage or "").upper())
except ValueError:
return len(_STAGE_ORDER)
def stage_label(stage: str | None) -> str:
if not stage:
return "stage not stated"
text = stage.upper()
if text in ("APPROVAL", "APPROVED"):
return "approved"
return (
text.replace("_", " ")
.lower()
.replace("phase 1 2", "phase 1/2")
.replace("phase 2 3", "phase 2/3")
)
@dataclass(frozen=True)
class Gene:
"""An input resolved through HGNC."""
input: str
symbol: str
hgnc_id: str
name: str
locus_type: str
ensembl_gene_id: str | None
uniprot_ids: tuple[str, ...]
provenance_row: dict[str, Any]
HGNC = "HGNC_fetch_gene_by_symbol"
def resolve_symbols(
symbols: list[str], client: ToolClient, budget: Budget, out: Collector
) -> list[Gene]:
"""HGNC symbol → approved record. Unknown symbols go to ``unresolved``."""
genes: list[Gene] = []
for i, symbol in enumerate(symbols):
if budget.spent:
out.out_of_budget(symbols[i:])
break
result = out.call(client, budget, HGNC, {"symbol": symbol})
if result is None:
continue
data = result.data or {}
if not data.get("symbol"):
out.unresolved_input(symbol, "not a current, previous or alias symbol in HGNC")
continue
row = stamped(
{"input": symbol, "symbol": data["symbol"], "hgnc_id": data["hgnc_id"]},
result,
ref=data["hgnc_id"],
url=f"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/{data['hgnc_id']}",
)
genes.append(
Gene(
input=symbol,
symbol=data["symbol"],
hgnc_id=data["hgnc_id"],
name=data.get("name") or "",
locus_type=data.get("locus_type") or "",
ensembl_gene_id=data.get("ensembl_gene_id"),
uniprot_ids=tuple(data.get("uniprot_ids") or ()),
provenance_row=row,
)
)
return genes
def resolution_rows(genes: list[Gene]) -> list[dict[str, Any]]:
"""The identifier mapping each answer rests on, with HGNC's provenance."""
return [g.provenance_row for g in genes]
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