Kemal Yaylali
1e46fff2ff
docs/blog/rarelens.tex builds a 10-page write-up covering the Nextflow DSL2 pipeline, the three execution backends behind one API call, the Argo and ArgoCD track, Terraform, the external systems integrated, the ranking, the benchmark and the model. It is deliberately as much an account of what was wrong as of what works: the components that scored evidence nobody had looked up, the missense AUROC that fell from 0.872 to 0.500 once allele frequency was removed, the ontology walk that silently dropped 399 terms, and the propagation change that measured slightly worse than what it replaced and was kept anyway with the numbers published. Figures come from one headless-browser script. Screenshots are of the running application; the six diagrams are hand-written HTML styled from the same palette, rendered by the same script. Keeping both in one place is what stops the article drifting from the system, and every number in a diagram has to be changed deliberately.
The technical introduction
rarelens.tex is a standalone technical write-up of the platform — pipeline, event-driven
execution, infrastructure, the ranking, the model, and the parts that turned out to be wrong.
rarelens.pdf is the built article (10 pages).
make # build the PDF (uses a Docker TeX Live; nothing to install locally)
make figures # re-capture every figure, then rebuild
make clean
Where the figures come from
Both kinds of figure are produced by one headless-browser script, diagram-sources/shoot.mjs, so
the article cannot drift away from the thing it describes:
- Screenshots (
01–06) are taken from the running application.make figuresneeds it up —make up && make migrate && make hpo, the API on:8000, the UI on:5173— and a case that has been analysed. The published Loeys–Dietz case is the default; override withCASE_ID. - Diagrams (
arch,events,pipeline,evidence,benchmark,model) are HTML pages indiagram-sources/, styled from the same palette as the application, rendered to PNG by the same script. They are hand-written rather than generated, so any number in them has to be updated deliberately when the measurement changes — which is the point.
Figures are committed because rebuilding them needs a running stack and a browser. If a
measurement in the article changes, change it in the diagram source, re-run make figures, and
say so in the commit.