torchcell.literature

The literature capture subsystem. It reads papers and supplementary files from Zotero (zotero), OCRs or extracts them into markdown (ocr, extract, scanned), fetches supplementary data (si_data), and records a sha256 provenance manifest for every stored artifact (manifest, provenance) in the on-disk mirror. server is the read-only HTTP endpoint (tc-lit-server) that serves the mirrored artifacts, and sync reconciles the mirror against a Zotero collection.

Classes

BackfillReport	Summary of a mirror-wide backfill run.
Manifest	Provenance + integrity record for one paper's captured artifact.
LiteratureServerConfig	Runtime configuration for the literature endpoint.
LiteratureKeys	The shared ApiKeys model bound to the TC_LIT_* variables.
ZoteroConfig	Credentials for a single Zotero library.
ZoteroLibrary	Synchronous handle to one Zotero library.

Functions

backfill_key	Regularize one citation-key directory to a manifest.json.
backfill_mirror	Backfill manifests for every citation-key directory under root.
capture_by_doi	Capture a paper's full artifact from Zotero + external SI data.
generate_citation_key	Generate a Better BibTeX-style citation key from paper metadata.
build_manifest	Scan an artifact directory and build its manifest.
write_manifest	Write manifest.json into the artifact directory; return its path.
ocr_artifact	OCR every PDF in an artifact directory: paper.pdf and each si/si*.pdf.
ocr_pdf	OCR one PDF to markdown next to it (<stem>.pdf -> <stem>.md).
create_app	Build the FastAPI app bound to config (config stored on app.state).
create_app_from_env	Factory for uvicorn --factory torchcell.literature.server:create_app_from_env.
dryad_files	Resolve a DRYAD dataset DOI to [(filename, download_url), ...].
fetch_si_data	Download SI data files into <artifact_dir>/si/si_data/.
make_zotero_client	Construct a pyzotero client from a ZoteroConfig.
with_zotero_retry	Run a zero-arg Zotero call with bounded exponential-backoff retry.