pdf-export

Reactome's pathway PDFs from the graph: the release's book (TheReactomeBook), the website's PDF of one pathway or reaction, and the report of an analysis, from one implementation, under loose open-source licences, with diagrams in the website's pathway browser's look. It is to replace reactome/event-pdf and, for the analysis report, reactome/analysis-report.

The analysis report (spec 002)

• pdf-export serve answers today's address, GET /AnalysisService/report/{token}/{species}/{filename}.pdf?number&resource&importableOnly, as the analysis service answers it: the species checked against the graph first, then the token against the analysis service, then the report. A report is made in the background: a request waits up to 30 s, then gets 202 with Retry-After (a browser, a page that asks again), and the same address gives the PDF once it is ready. A finished report is kept for an hour. Its settings, besides spec 001's: --work (or PDF_EXPORT_WORK), the printer's private working folder, emptied at start; the limits (two reports made at once, eight waiting, two of those per client as X-Reactome-Client names it, a 5-minute budget, 512 MB kept) are ServeLimits.
• pdf-export report --token <t> --species <s> -o <file> (--number, --resource, --importable-only, and serve's --graph, --files, --render, --analysis, --site) makes one report, for checks by hand and the comparison.
• pdf-export compare-report <today's.pdf> <new.pdf> [--expected <file>] compares a report with today's by meaning (FR-208), printing counts and salted hashes, never a name or a submitted identifier. One listed difference it marks itself: a pathway's Modified rows where it has two or more modified edits (the spec's Assumptions).

See specs/002-analysis-report/ for the address's answers (contracts/service.md) and what the report holds.

The work is specified before it is built: see specs/ and CLAUDE.md. The principles are in .specify/memory/constitution.md.

Licensed under the Apache License 2.0 (LICENSE).