flowapy 0.1.2__tar.gz → 0.2.0__tar.gz

{flowapy-0.1.2 → flowapy-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flowapy
-Version: 0.1.2
+Version: 0.2.0
 Summary: Variant literature assessment pipeline with AI extraction
 Project-URL: Homepage, https://github.com/populationgenomics/flowa
 Project-URL: Source, https://github.com/populationgenomics/flowa
@@ -47,6 +47,7 @@ Requires-Dist: pypdf
 Requires-Dist: s3fs
 Requires-Dist: tenacity
 Requires-Dist: typer
+Requires-Dist: zstandard
 Provides-Extra: anthropic
 Requires-Dist: pydantic-ai-slim[anthropic]==1.101.0; extra == 'anthropic'
 Provides-Extra: bedrock

{flowapy-0.1.2 → flowapy-0.2.0}/examples/demo/README.md

@@ -166,10 +166,10 @@ VARIANT=NM_001035_3-c_14174A_G
 rm -f assessments/$VARIANT/aggregation.json \
       assessments/$VARIANT/aggregation_raw.json
 rm -rf assessments/$VARIANT/extractions/ assessments/$VARIANT/runs/
-# Re-runs flowa.convert (which uses anchorite for PDF chunking).
-# Drop this line to reuse the cached markdown and only redo extract +
-# aggregate.
-rm -f papers/*/markdown.md papers/*/convert_raw.json
+# Re-runs flowa.convert (which uses anchorite for PDF chunking and
+# builds pdf_index.pkl.zst). Drop this line to reuse the cached markdown
+# + index and only redo extract + aggregate.
+rm -f papers/*/markdown.md papers/*/convert_raw.json papers/*/pdf_index.pkl.zst
 ```
 
 Then drive the pipeline. The demo's `scripts/start.ts` translates the
@@ -208,11 +208,13 @@ and not needed by anything downstream.
 For papers whose source license blocks redistribution (CC-BY-NC-ND,
 paywalled; see `fixtures/LICENSES.md` for the rule), do **not** delete
 the whole `papers/{encodedDoi}/` directory — only delete `source.pdf`,
-`markdown.md`, and `convert_raw.json`. Keep `metadata.json` (the
-bibliographic fields are factual data, not copyrightable) but replace
-its `abstract` field with a sentinel string, so the omission reads as
-deliberate (not a missing-data bug) when the literature view renders
-the row:
+`markdown.md`, `convert_raw.json`, and `pdf_index.pkl.zst`. The
+`pdf_index.pkl.zst` embeds the PDF's extracted text (anchorite's char
+index), so it carries the same copyright as `source.pdf` and must not
+ship in the open-source repo. Keep `metadata.json` (the bibliographic
+fields are factual data, not copyrightable) but replace its `abstract`
+field with a sentinel string, so the omission reads as deliberate (not
+a missing-data bug) when the literature view renders the row:
 
 ```bash
 python3 -c "

{flowapy-0.1.2 → flowapy-0.2.0}/examples/demo-gateway/src/demo_gateway/main.py

@@ -18,9 +18,13 @@ from typing import Annotated
 import uvicorn
 from fastapi import APIRouter, Depends, FastAPI, HTTPException, Query, Request, status
 from fastapi.middleware.cors import CORSMiddleware
-from flowa.resolve import ResolvedCitations, ResolveRequest, resolve_citations
+from flowa.resolve import (
+    ResolvedCitations,
+    ResolveRequest,
+    load_pdf_index_from_storage,
+    resolve_citations,
+)
 from flowa.schema import VariantSpec
-from flowa.storage import paper_url, read_bytes, read_text
 from pydantic import BaseModel, Field
 
 from .config import Settings
@@ -111,24 +115,15 @@ def resolve_citations_route(
 ) -> ResolvedCitations:
     """Align verbatim quotes to PDF bboxes.
 
-    Sync `def` so FastAPI auto-runs it in the threadpool — anchorite's PDF
-    parsing is CPU-bound and would block the asyncio loop otherwise.
+    Sync `def` so FastAPI auto-runs it in the threadpool — deserialising the
+    PdfIndex pickle and aligning quotes is CPU-bound and would block the
+    asyncio loop otherwise.
     """
     base = str(settings.demo_data_dir)
-
-    def pdf_loader(doi: str) -> bytes | None:
-        try:
-            return read_bytes(paper_url(base, doi, 'source.pdf'))
-        except FileNotFoundError:
-            return None
-
-    def md_loader(doi: str) -> str | None:
-        try:
-            return read_text(paper_url(base, doi, 'markdown.md'))
-        except FileNotFoundError:
-            return None
-
-    return resolve_citations(body.citations, pdf_loader=pdf_loader, markdown_loader=md_loader)
+    return resolve_citations(
+        body.citations,
+        index_provider=lambda doi: load_pdf_index_from_storage(base, doi),
+    )
 
 
 @asynccontextmanager

{flowapy-0.1.2 → flowapy-0.2.0}/examples/demo-gateway/tests/test_resolve.py

@@ -1,24 +1,13 @@
 """HTTP shape tests for /resolve-citations.
 
 Library-level resolver behaviour is covered in flowa's `tests/test_resolve.py`;
-here we just check that the route plumbs Settings → loader → flowa.resolve
-correctly and returns the expected wire shape.
+here we just check that the route plumbs Settings → index_provider →
+flowa.resolve correctly and returns the expected wire shape.
 """
 
-from pathlib import Path
-
 from fastapi.testclient import TestClient
-from flowa import resolve as flowa_resolve_module
-from flowa.storage import encode_doi
-
-from demo_gateway.config import Settings
-
 
-def _write_fake_paper(data_dir: Path, doi: str, pdf: bytes = b'fake-pdf', markdown: str = '# fake md') -> None:
-    paper_dir = data_dir / 'papers' / encode_doi(doi)
-    paper_dir.mkdir(parents=True, exist_ok=True)
-    (paper_dir / 'source.pdf').write_bytes(pdf)
-    (paper_dir / 'markdown.md').write_text(markdown)
+import demo_gateway.main as demo_main
 
 
 def test_post_resolve_citations_rejects_malformed_body(client: TestClient) -> None:
@@ -26,8 +15,8 @@ def test_post_resolve_citations_rejects_malformed_body(client: TestClient) -> No
     assert response.status_code == 422
 
 
-def test_post_resolve_citations_returns_errors_for_missing_pdfs(client: TestClient) -> None:
-    """When source.pdf is absent, the DOI surfaces in `errors` rather than `resolved`."""
+def test_post_resolve_citations_returns_errors_for_missing_index(client: TestClient) -> None:
+    """When pdf_index.pkl.zst is absent, the DOI surfaces in `errors` rather than `resolved`."""
     response = client.post(
         '/resolve-citations',
         json={'citations': [{'doi': '10.1/missing', 'quotes': ['anything']}]},
@@ -35,15 +24,11 @@ def test_post_resolve_citations_returns_errors_for_missing_pdfs(client: TestClie
     assert response.status_code == 200
     body = response.json()
     assert body['resolved'] == {}
-    assert body['errors'] == {'10.1/missing': 'source.pdf not found'}
+    assert body['errors'] == {'10.1/missing': 'pdf_index not available'}
 
 
-def test_post_resolve_citations_returns_resolved_bboxes(
-    client: TestClient,
-    settings: Settings,
-    monkeypatch,
-) -> None:
-    """When source.pdf exists, the route resolves quotes to bboxes via the library."""
+def test_post_resolve_citations_returns_resolved_bboxes(client: TestClient, monkeypatch) -> None:
+    """When the index loads, the route resolves quotes to bboxes via the library."""
 
     class _FakeBbox:
         def __init__(self, top: int, left: int, bottom: int, right: int) -> None:
@@ -53,16 +38,16 @@ def test_post_resolve_citations_returns_resolved_bboxes(
             self.right = right
 
     class _FakePdfIndex:
-        def __init__(self, _pdf_bytes: bytes, *, markdown: str | None = None) -> None:
-            pass
-
         def resolve(self, quotes: list[str]) -> dict[str, list[tuple[int, _FakeBbox]]]:
             # 0-indexed page from anchorite — the +1 boundary wrap in resolve.py
             # turns this into page=1 on the wire.
             return {q: [(0, _FakeBbox(top=10, left=20, bottom=30, right=40))] for q in quotes}
 
-    monkeypatch.setattr(flowa_resolve_module, 'PdfIndex', _FakePdfIndex)
-    _write_fake_paper(settings.demo_data_dir, '10.1/present')
+    monkeypatch.setattr(
+        demo_main,
+        'load_pdf_index_from_storage',
+        lambda _base, doi: _FakePdfIndex() if doi == '10.1/present' else None,
+    )
 
     response = client.post(
         '/resolve-citations',

{flowapy-0.1.2 → flowapy-0.2.0}/examples/demo-gateway/uv.lock

@@ -3,14 +3,14 @@ revision = 3
 requires-python = "==3.13.*"
 
 [options]
-exclude-newer = "2026-05-19T00:00:39.870651Z"
+exclude-newer = "0001-01-01T00:00:00Z" # This has no effect and is included for backwards compatibility when using relative exclude-newer values.
 exclude-newer-span = "P7D"
 
 [options.exclude-newer-package]
-pydantic-ai-slim = { timestamp = "2026-05-26T00:00:39.87066Z", span = "PT0S" }
-anchorite = { timestamp = "2026-05-26T00:00:39.870656Z", span = "PT0S" }
-seq-smith = { timestamp = "2026-05-26T00:00:39.87066Z", span = "PT0S" }
-pydantic-graph = { timestamp = "2026-05-26T00:00:39.870661Z", span = "PT0S" }
+pydantic-ai-slim = { timestamp = "0001-01-01T00:00:00Z", span = "PT0S" }
+anchorite = { timestamp = "0001-01-01T00:00:00Z", span = "PT0S" }
+seq-smith = { timestamp = "0001-01-01T00:00:00Z", span = "PT0S" }
+pydantic-graph = { timestamp = "0001-01-01T00:00:00Z", span = "PT0S" }
 
 [[package]]
 name = "aiohappyeyeballs"
@@ -415,7 +415,7 @@ wheels = [
 
 [[package]]
 name = "flowapy"
-version = "0.1.2"
+version = "0.2.0"
 source = { editable = "../../" }
 dependencies = [
     { name = "anchorite" },
@@ -431,6 +431,7 @@ dependencies = [
     { name = "s3fs" },
     { name = "tenacity" },
     { name = "typer" },
+    { name = "zstandard" },
 ]
 
 [package.optional-dependencies]
@@ -466,6 +467,7 @@ requires-dist = [
     { name = "s3fs" },
     { name = "tenacity" },
     { name = "typer" },
+    { name = "zstandard" },
 ]
 provides-extras = ["anthropic", "bedrock", "google", "openai"]
 
@@ -2109,3 +2111,28 @@ sdist = { url = "https://files.pythonhosted.org/packages/30/21/093488dfc7cc8964d
 wheels = [
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 ]
+
+[[package]]
+name = "zstandard"
+version = "0.25.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/fd/aa/3e0508d5a5dd96529cdc5a97011299056e14c6505b678fd58938792794b1/zstandard-0.25.0.tar.gz", hash = "sha256:7713e1179d162cf5c7906da876ec2ccb9c3a9dcbdffef0cc7f70c3667a205f0b", size = 711513, upload-time = "2025-09-14T22:15:54.002Z" }
+wheels = [
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+]

{flowapy-0.1.2 → flowapy-0.2.0}/packages/chat-service/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@flowajs/chat-service",
-  "version": "0.0.3",
+  "version": "0.0.4",
   "description": "Stateless service that orchestrates LLM conversations over flowa artifacts.",
   "license": "MIT",
   "type": "module",
@@ -71,7 +71,7 @@
     "zod": "4.4.3"
   },
   "peerDependencies": {
-    "@ai-sdk/amazon-bedrock": "^4.0.0",
+    "@ai-sdk/amazon-bedrock": "^4.0.101",
     "@ai-sdk/anthropic": "^3.0.0",
     "@ai-sdk/google": "^3.0.0",
     "@ai-sdk/google-vertex": "^4.0.0",

flowapy-0.2.0/prompts/generic/aggregation_schema.py

@@ -0,0 +1,36 @@
+"""Aggregation schema for generic ACMG-style variant assessment.
+
+This module defines the output structure for aggregation across papers.
+The AggregationResult class is loaded dynamically by Flowa.
+
+Interface requirements (accessed by Flowa's validation logic):
+    - results[].category must exist
+    - results[].claims[].paper_id and .citations[].quote must exist
+    - results[].papers[].paper_id must exist
+
+Strict structured outputs (Bedrock/Anthropic/OpenAI NativeOutput) clobber
+additionalProperties to false, collapsing dict[str, X] fields to empty objects.
+Use a list shape with the category carried as a field inside each entry.
+"""
+
+from pydantic import BaseModel, Field
+
+from flowa.artifact import CategoryResult as BaseCategoryResult
+
+
+class CategoryResult(BaseCategoryResult):
+    """ACMG-classification result for a single assessment category."""
+
+    classification: str = Field(
+        description='ACMG classification: Pathogenic, Likely Pathogenic, VUS, Likely Benign, or Benign.'
+    )
+    classification_rationale: str = Field(description='Brief explanation of why this classification was selected.')
+
+
+class AggregationResult(BaseModel):
+    """Multi-category aggregation result for ACMG-style variant assessment."""
+
+    results: list[CategoryResult] = Field(
+        description='List of assessment results, one per selected category. '
+        'Each entry carries its own `category` identifier.'
+    )

{flowapy-0.1.2 → flowapy-0.2.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "flowapy"
-version = "0.1.2"
+version = "0.2.0"
 description = "Variant literature assessment pipeline with AI extraction"
 readme = "README.md"
 requires-python = "==3.13.*"
@@ -27,6 +27,7 @@ dependencies = [
     "s3fs",   # S3/MinIO support for fsspec
     "tenacity",
     "typer",
+    "zstandard",
 ]
 
 [project.optional-dependencies]

{flowapy-0.1.2 → flowapy-0.2.0}/src/flowa/aggregate.py

@@ -15,7 +15,7 @@ from pydantic_ai import Agent, ModelRetry, NativeOutput, RunContext
 from flowa.clinvar import format_clinvar_for_prompt, query_clinvar
 from flowa.models import create_model, get_model_settings
 from flowa.prompts import load_prompt_and_schema
-from flowa.resolve import CitationQuery, resolve_citations
+from flowa.resolve import CitationQuery, load_pdf_index_from_storage, resolve_citations
 from flowa.schema import AGGREGATION_SCHEMA_VERSION, with_schema_version
 from flowa.settings import ModelConfig, Settings
 from flowa.storage import (
@@ -23,9 +23,7 @@ from flowa.storage import (
     encode_doi,
     exists,
     paper_url,
-    read_bytes,
     read_json,
-    read_text,
     write_bytes,
     write_json,
 )
@@ -158,16 +156,14 @@ def create_aggregate_agent(
 def resolve_aggregate_citations(
     aggregate_dict: dict[str, Any],
     paper_id_to_doi: dict[str, str],
-    pdf_bytes_cache: dict[str, bytes],
-    markdown_cache: dict[str, str],
+    base: str,
     metadata_cache: dict[str, dict[str, Any]],
 ) -> None:
     """Post-process aggregate output: resolve quotes to bboxes on claim citations.
 
-    Delegates the actual alignment to `flowa.resolve.resolve_citations` with
-    cache-backed loaders, then attaches the resulting bboxes onto each claim's
-    citations in place. Claims are grouped by paper_id so every (paper_id,
-    quote) pair resolves to exactly one paper.
+    Loads each paper's pre-built `pdf_index.pkl.zst` via the same path the
+    gateway uses; the convert step that ran earlier in this pipeline wrote
+    the artifact, so it's guaranteed to be present.
     """
     # Collect all (doi, quote) pairs, grouped by DOI.
     doi_quotes: dict[str, list[str]] = {}
@@ -180,8 +176,7 @@ def resolve_aggregate_citations(
     citations_input = [CitationQuery(doi=doi, quotes=quotes) for doi, quotes in doi_quotes.items()]
     result = resolve_citations(
         citations_input,
-        pdf_loader=pdf_bytes_cache.get,
-        markdown_loader=markdown_cache.get,
+        index_provider=lambda doi: load_pdf_index_from_storage(base, doi),
     )
 
     # Attach resolved bboxes onto each claim's citations.
@@ -229,14 +224,11 @@ async def aggregate_evidence_async(
     clinvar_data = query_clinvar(hgvs_c_full, ncbi_api_key)
     clinvar_text = format_clinvar_for_prompt(clinvar_data)
 
-    # Load extractions and metadata for each paper. PDF bytes and Markdown are
-    # cached for post-LLM citation resolution: PdfIndex takes both (markdown
-    # denoises the indexed PDF chars). Both files are produced together by the
-    # pipeline; a missing markdown.md at this point is a storage corruption and
-    # surfaces as FileNotFoundError below.
+    # Load extractions and metadata for each paper. PDF bytes and markdown
+    # are NOT loaded here — the post-LLM citation resolver loads the paper's
+    # pre-built `pdf_index.pkl.zst` directly from storage, so this step only
+    # needs the LLM inputs.
     evidence_extractions: list[dict[str, Any]] = []
-    pdf_bytes_cache: dict[str, bytes] = {}
-    markdown_cache: dict[str, str] = {}
     metadata_cache: dict[str, dict[str, Any]] = {}
 
     for doi in dois:
@@ -252,8 +244,6 @@ async def aggregate_evidence_async(
             log.info('Skipping %s: variant not discussed', doi)
             continue
 
-        pdf_bytes_cache[doi] = read_bytes(paper_url(base, doi, 'source.pdf'))
-        markdown_cache[doi] = read_text(paper_url(base, doi, 'markdown.md'))
         metadata = read_json(paper_url(base, doi, 'metadata.json'))
         metadata_cache[doi] = metadata
 
@@ -332,7 +322,7 @@ async def aggregate_evidence_async(
     # Post-LLM: resolve quotes to bboxes, replace paper_id with DOI
     aggregate_dict = output.model_dump()
     with logfire.span('flowa.resolve_citations', paper_count=len(paper_id_to_doi)):
-        resolve_aggregate_citations(aggregate_dict, paper_id_to_doi, pdf_bytes_cache, markdown_cache, metadata_cache)
+        resolve_aggregate_citations(aggregate_dict, paper_id_to_doi, base, metadata_cache)
 
     # Store structured aggregation result
     write_json(aggregation_url, with_schema_version(aggregate_dict, AGGREGATION_SCHEMA_VERSION))

flowapy-0.2.0/src/flowa/artifact.py

@@ -0,0 +1,73 @@
+"""Shared schema primitives for aggregation prompt sets.
+
+`CategoryResult` is the citation-grounded base each deployment derives from
+to add its own classification field(s) — e.g. generic ACMG sets add
+`classification` + `classification_rationale`; private deployments may add
+their own classification dimensions. Each deployment also defines its own
+`AggregationResult` with `results: list[CategoryResult]` pointing at its
+own `CategoryResult` subclass (Pydantic doesn't covariantly substitute the
+parent's parameterised generic).
+
+This module is the Python analog of `@flowajs/chat-service`'s
+`artifactFields` / `ArtifactSchema` export: it exists so prompt-set schemas
+share their citation-grounded structure rather than duplicating it.
+
+The schema-side descriptions here are deliberately structural — they
+describe what each field IS. Behavioural guidance (how to populate
+`description`, ranking conventions, claim-emission criteria) belongs in the
+aggregation prompt template, not the schema.
+"""
+
+from pydantic import BaseModel, Field
+
+
+class AggregateCitation(BaseModel):
+    """A citation quoting a specific passage from a source paper."""
+
+    quote: str = Field(
+        description='A short, distinctive verbatim quote from the paper text that identifies this evidence.'
+    )
+
+
+class Claim(BaseModel):
+    """A factual statement supporting a synthesis, sourced from one paper."""
+
+    paper_id: str = Field(description='AuthorYear identifier of the source paper; must appear in papers[].')
+    text: str = Field(
+        description='The factual statement as the curator reads it in triage. '
+        'May synthesise across citations from the same paper.'
+    )
+    citations: list[AggregateCitation] = Field(
+        description='One or more supporting quotes from paper_id.',
+        min_length=1,
+    )
+
+
+class RankedPaper(BaseModel):
+    """A paper in the ranked papers list. List position encodes importance."""
+
+    paper_id: str = Field(description='AuthorYear identifier; must match the key used in paper_id_mapping.')
+    rank_rationale: str = Field(description='One sentence explaining why this paper sits at this rank.')
+
+
+class CategoryResult(BaseModel):
+    """Citation-grounded base for an aggregation result.
+
+    Deployments subclass to add classification-specific fields. The five
+    fields here are the contract that `flowa.aggregate` reads at validation
+    time.
+    """
+
+    category: str = Field(description='Assessment-category identifier.')
+    description: str = Field(description='Short human-readable summary of the synthesis.')
+    notes: str = Field(
+        description='Long-form synthesis in Markdown. Uses inline citation links: '
+        '[text](#cite:paper_id "verbatim quote") to reference specific paper evidence locations.'
+    )
+    papers: list[RankedPaper] = Field(
+        description='Source documents contributing to the synthesis, ordered by importance. '
+        'List position is the rank; paper_id values must be unique.'
+    )
+    claims: list[Claim] = Field(
+        description='Factual claims supporting the synthesis, grouped by paper_id in the same order as papers[].'
+    )

{flowapy-0.1.2 → flowapy-0.2.0}/src/flowa/convert.py

@@ -17,9 +17,11 @@ from pydantic_ai import Agent
 from pydantic_ai.messages import BinaryContent
 
 from flowa.models import create_model, get_model_settings
+from flowa.pdf_index_cache import build as build_pdf_index_payload
+from flowa.pdf_index_cache import serialize as serialize_pdf_index_payload
 from flowa.prompts import load_text_prompt
 from flowa.settings import ModelConfig, Settings
-from flowa.storage import exists, paper_url, read_bytes, write_bytes, write_text
+from flowa.storage import exists, paper_url, read_bytes, read_text, write_bytes, write_text
 
 log = logging.getLogger(__name__)
 
@@ -120,14 +122,22 @@ async def transcribe(
 
 
 async def convert_paper_async(base: str, doi: str, model: ModelConfig, prompt_set: str = 'generic') -> None:
-    """Convert a single paper's PDF to Markdown.
+    """Convert a single paper's PDF to Markdown and persist its `PdfIndex`.
 
-    Reads PDF from papers/{encoded_doi}/source.pdf in object storage.
-    Stores result to papers/{encoded_doi}/markdown.md.
+    Reads PDF from papers/{encoded_doi}/source.pdf and writes
+    papers/{encoded_doi}/markdown.md plus papers/{encoded_doi}/pdf_index.pkl.zst
+    (consumed by the gateway's resolve endpoint).
+
+    Either artifact can be missing independently — if a previous run failed
+    or pre-dates the pdf_index step, the next call fills in only what's
+    missing without re-transcribing or re-building work that's already done.
     """
     md_url = paper_url(base, doi, 'markdown.md')
+    index_url = paper_url(base, doi, 'pdf_index.pkl.zst')
+    md_needed = not exists(md_url)
+    index_needed = not exists(index_url)
 
-    if exists(md_url):
+    if not md_needed and not index_needed:
         log.info('Already converted: %s', md_url)
         return
 
@@ -138,21 +148,36 @@ async def convert_paper_async(base: str, doi: str, model: ModelConfig, prompt_se
         log.info('Skipping DOI %s: PDF not available', doi)
         return
 
-    log.info(
-        'Converting DOI %s (%d bytes, model: %s, chunk: %d pages)', doi, len(pdf_bytes), model.name, PAGES_PER_CHUNK
-    )
-
-    prompt = load_text_prompt('transcription', prompt_set)
-    t0 = time.monotonic()
-    result = await transcribe(pdf_bytes, model=model, prompt=prompt, page_count=PAGES_PER_CHUNK)
-    elapsed = time.monotonic() - t0
-
-    write_text(md_url, result.markdown)
-
-    raw_url = paper_url(base, doi, 'convert_raw.json')
-    write_bytes(raw_url, json.dumps(result.all_messages).encode())
-
-    log.info('Converted DOI %s: %d chars in %.1fs', doi, len(result.markdown), elapsed)
+    markdown: str | None = None
+    if md_needed:
+        log.info(
+            'Converting DOI %s (%d bytes, model: %s, chunk: %d pages)', doi, len(pdf_bytes), model.name, PAGES_PER_CHUNK
+        )
+        prompt = load_text_prompt('transcription', prompt_set)
+        t0 = time.monotonic()
+        result = await transcribe(pdf_bytes, model=model, prompt=prompt, page_count=PAGES_PER_CHUNK)
+        elapsed = time.monotonic() - t0
+
+        markdown = result.markdown
+        write_text(md_url, markdown)
+        write_bytes(paper_url(base, doi, 'convert_raw.json'), json.dumps(result.all_messages).encode())
+        log.info('Converted DOI %s: %d chars in %.1fs', doi, len(markdown), elapsed)
+
+    if index_needed:
+        # PdfIndex construction is CPU-bound (~8s on the deployed gateway
+        # hardware) and dominates per-call latency at `/api/v1/resolve` if
+        # rebuilt on every call. Pay the cost here once per paper and ship
+        # the result; see `flowa.pdf_index_cache` for the storage format.
+        # `asyncio.to_thread` keeps the rest of the convert pipeline (other
+        # papers being transcribed concurrently) unblocked.
+        if markdown is None:  # index missing but markdown already on disk
+            markdown = read_text(md_url)
+        t0 = time.monotonic()
+        blob = await asyncio.to_thread(
+            lambda: serialize_pdf_index_payload(build_pdf_index_payload(pdf_bytes, markdown))
+        )
+        write_bytes(index_url, blob)
+        log.info('Wrote pdf_index for DOI %s: %.1f MB in %.1fs', doi, len(blob) / 1e6, time.monotonic() - t0)
 
 
 def convert_paper(