leonarski_f
511be0c366
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* `rugnux --model` adopts the model's space group as a label where the data were merged in its enantiomorph, instead of reindexing the reflections - which swapped I(+) with I(-). * `rugnux --model` warns, naming the atom, when the anomalous density at the model's atoms comes out inverted, which means the data and the model are in opposite hands. * `rugnux --model` writes an anomalous difference map (`<prefix>_anom.ccp4`) when the merge kept the Bijvoet split, and names the ten model atoms it peaks highest on as `ANOMALOUS_SITE_01`..`_10`. * `MEAN_ATOM_DENSITY_SIGMA` is read from the map by cubic rather than linear interpolation and comes out around a tenth higher; it is no longer comparable with the figure earlier versions printed. * `rugnux --model` reads an mmCIF coordinate file as well as a PDB one, gzipped or not, taking the format from the file's content rather than its name. * A model `rugnux --model` cannot use is reported as a `WARNING:` line in the results report instead of only in the log. * The rugnux results report has a `10. MODEL VALIDATION` section when `--model` was given; `REPORT_VERSION` is 4, `WARNINGS` moves to section 11 and no existing key changed. * The rugnux results report records how the run was invoked, what it cost and what it ran on: `COMMAND_LINE=`, `WALL_TIME=` and `GPU_COUNT=` / `GPU=`. * rugnux says which GPUs it can see before it starts processing. * `rugnux --export-unmerged` also writes `<prefix>_unmerged.mtz` on a `--no-merge` run, and is ignored on a run with no output prefix instead of writing a file called `_unmerged.mtz`. * `/start` asks the writer whether the run can be written before the detector is armed, so a run whose master file already exists, or whose output directory cannot be created, is refused up front with the writer's own message. This needs the TCP image stream or the built-in HDF5 writer; the ZeroMQ stream is unchanged. * A calibration that fails goes to `Error` carrying the reason instead of `Inactive`, so `/wait_till_done` and `/wait_until_running` report it; a cancelled calibration still goes to `Inactive`. * `/wait_till_done` answers 500 with the message when a collection ended in an error. A cancelled collection and a collection that only triggered a warning still answer 200. * A pending start failure is discarded by `/cancel` and `/deactivate`, as it already was by `/start` and `/initialize`. * `/scan_result` no longer reports the previous run's images after a collection that failed to start, or after `/deactivate`. * The TCP image stream protocol version is 4. `jfjoch_writer` and `jfjoch_broker` have to be of the same release, as before. Reviewed-on: #75
Jungfraujoch Frontend
Building
To build web interface:
cd frontend_ui
npm install
npm run openapi
npm run build
Available Scripts
In the project directory, you can run:
npm start
Runs the app in the development mode.
The page will reload if you make edits.
You will also see any lint errors in the console.
npm test
Launches the test runner in the interactive watch mode.
See the section about running tests for more information.
npm run build
Builds the app for production to the dist folder.
It correctly bundles React in production mode and optimizes the build for the best performance.
The build is minified and the filenames include the hashes.
Your app is ready to be deployed!
npm run openapi
npm audit findings
npm audit currently reports 17 advisories (3 high, 13 moderate, 1 low). All of
them live in build-time tooling and never reach the production bundle
shipped to the browser. Summary of the chains:
| Source dep | Vulnerable transitives | When it runs |
|---|---|---|
@redocly/cli |
@opentelemetry/*, dompurify (via redoc), ws (via simple-websocket), js-yaml, protobufjs, @babel/core |
npm run redocly / redocly4broker — static OpenAPI HTML generation |
vite |
esbuild@0.27.x |
Dev server and dep pre-bundling. Production build uses Rollup. |
vite-plugin-svgr |
@babel/core, js-yaml (via cosmiconfig) |
Vite build plugin |
openapi-typescript-codegen |
js-yaml |
npm run openapi — TS client generation |
Notes on the high-severity items:
esbuildGHSA-gv7w-rqvm-qjhr is a Deno-specific RCE viaNPM_CONFIG_REGISTRY; GHSA-g7r4-m6w7-qqqr is an arbitrary-file-read in the dev server on Windows. Neither applies to a Linux build of the production bundle.wsGHSA-96hv-2xvq-fx4p only matters whensimple-websocketopens a socket, which happens during docs generation, not at runtime.
npm audit fix cannot resolve any of these without downgrading
@redocly/cli (no real fix) or jumping vite to a major that switches the
bundler to Rolldown.