bilbomd-ui

bilbomd-ui is the frontend GUI for BilboMD. It is a Single Page Application SPA. The deploy instructions are outlined in more detail the bilbomd repo, and give instructions for deploying a production instance to https://bilbomd.bl1231.als.lbl.gov, but if you want to start a development version you can just check this code out and fire it up interactively.

Getting Started with Vite

This project uses Vite for bundling, to provide a dev server, and we are beginning to use the closly related Vitest to help us write unit tests. Have a look at the Vite documentation to see why we use it.

Available Scripts

There are a number of scripts defined in the package.json file:

  "scripts": {
    "clean": "rimraf dist/*",
    "dev": "GIT_HASH=$(git rev-parse --short HEAD) vite",
    "prebuild": "tsc",
    "build": "vite build",
    "lint": "eslint",
    "preview": "vite preview",
    "optimize": "vite optimize"
  }

npm run dev

Runs the app in the development mode, and will serve on port 3002.\

Open http://localhost:3002 to view the developemnt instance in the browser.

The page will automagically refresh if you make edits. You will also see any linting errors in the console.

npm run build

Will transpile the Typescript code using tsc then optimize for production. Output goes into dist directory.

npm run lint

Will run eslint on code.

Deploy production

The production instance is served from an ngnix Docker container. Have a look at the bilbomd-ui.dockerfile for details of the docker build. The entire production ecosystem is deployed as a single Docker compose setup. Details are in the bilbomd repo.

NERSC Notes

When deployed to NERSC/SPIN in order to develop the frontend with a simple npm run dev you must forward the backend proxy. We can expose a loadbalancing port from the Rancher K8 control plane and then use SSH tunnels.

ssh -L 3501:backend-loadbalancer.bilbomd.development.svc.spin.nersc.org:5432 perlmutter

Then you should be able to start a local development instance of bilbomd-ui with npm run dev and point your browser to localhost:3002 and you should be connected to the development backend service running on SPIN.

Authors

• Scott Classen sclassen at lbl dot gov
• Shreyas Prabhakar shreyasprabhakar at lbl dot gov
• Michal Hammel mhammel at lbl dot gov

Version History

• 1.14.1 (11/22/2024)
  • Add feature toggle to hide BilboMD if necessary
  • Add Alert warning if no jobs available for a BilboMD Multi run
• 1.14.0 (11/21/2024)
  • Add BilboMD Multi pipeline
• 1.13.9 (11/19/2024)
  • Fix an issue where the AutoRg calculation would fail silently if the Access Token expired before selecting the SAXS dat file for a BilboMD Classic job.
• 1.13.8 (11/15/2024)
  • Fix display of job steps
  • Update the details link and text of c1/c2 fix option for Scoper job form
• 1.13.7 (11/14/2024)
  • Add clarification about new option to fix c1/c2 values in Scoper runs
• 1.13.6 (11/12/2024)
  • Fix display of progress and steps for Scoper jobs
• 1.13.5 (11/12/2024)
  • Add checkbox for users to fix c1/c2 values during multifoxs step
• 1.13.4 (11/08/2024)
  • Fixes for NERSC status step display
  • Add NERSC state and overall progress to Jobs list table
• 1.13.3 (11/04/2024)
  • Add experimental Rg to all new job form submissions.
• 1.13.2 (11/04/2024)
  • Inform users of NERSC vs. SIBYLS versions of BilboMD
  • Fix the condition display of job steps on NERSC
• 1.13.1 (10/21/2024)
  • Improve colors for the Home component
  • Add dark mode schematic image files
• 1.13.0 (10/18/2024)
  • Add User Account component that allows user to change email address and delete account
  • Implement Vitest and add a few initial tests
  • Improve the Home page component seen by unauthenticated users
• 1.12.4 (10/10/2024)
  • Add schematic diagrams for BilboMD AF and BilboMD SANS pipelines
• 1.12.3
  • Improve error handling for the Jobs page when user has no jobs
• 1.12.2
  • Add schematic diagrams showing various steps of BilboMD pipelines
• 1.12.1
  • Add feedback components and conditionally display based on presence in MongoDB
• 1.12.0
  • Add initial BilboMD SANS forms
  • Add @bl1231/bilbomd-mongodb-schema as a dependency
• 1.11.3
  • Remove line length validation (70 character limit) for user-uploaded const.inp files.
  • Instead we will sanitize const.inp files on the backend.
• 1.11.2
  • Add line length validation (70 character limit) for user-uploaded const.inp files
• 1.11.1
  • Add "experimental" tag to the MolStar Viewer
  • Single Job Page loads with NERSC Steps Accordian unexpanded if job is Completed
• 1.11.0
  • Add BilboMD AF (AlphaFold) job type
  • Add NERSC status checker so that new jobs cannot be submitted if Perlmutter is down.
  • Various UI improvements
• 1.10.3
  • Add Perlmutter outage notices to the NERSC status component
• 1.10.2
  • Improve caching during GitHub Actions
  • Migrate MUI Grid to Grid2
• 1.10.1
  • Fix git hash value display in footer
  • Add checks for null/undefined data in FoXSAnalysis component
• 1.10.0
  • Add config information table to the Admin panel
  • Improvements to CI/CD workflow
• 1.9.7
  • Use new config API for config info (e.g. dev/prod, useNersc, repo, etc.)
  • remove all VITE_* references from frontend code
• 1.9.6
  • Implement separate "latest" and "versioned" GitHub Actions for building Docker images
• 1.9.5
  • Improvements to the NERSC Status component
  • Add conditional visibility to some columns in Jobs table
  • Add NERSC logo to header when deployed to SPIN
  • Increase maximum allowed file size for uploaded PAE json files
• 1.9.4
  • Add CI/CD GitHub action workflow to build docker images on push to main
  • Add validation function for SAXS data files
  • Add validation function for RNA
  • Improvements to Instructions
  • Many dependency updates including to eslint 9.x
• 1.9.3
  • Add new NERSC step status component
  • Fix the unresponsive footer
• 1.9.2
  • Use .env to toggle NERSC-specific UI elements.
  • Add clarification to some instructions
  • Remove pm2 dependency
• 1.9.1
  • Changes for NERSC deployment
• 1.9.0
  • Using Content-Disposition headers for more precise results downloading
  • Fix to inp Jiffy to handle PDB files with more than A-Z ChainIDs.
  • All File Select input elements now enforce specific file suffixes.
• 1.8.4
  • Adjust INP Jiffy to procude inp files with CHARMM-specific segid naming.
  • Update summary information on the unauthenticated home page.
• 1.8.3
  • Add a slider to control the weight value used by igraph cluster_leiden() function.
• 1.8.2
  • Changes to allow PDB or CRD/PSF files for BilboMD Classic
  • Now using createBrowserRouter from react-router-dom
  • Add global ErrorBoundary
  • Convert some *.js file to *.ts
• 1.8.1
  • Improve NERSC status component
  • Fix bug in INP Jiffy multistep form
• 1.8.0
  • Mainly changes to allow building and deploying on local laptop and NERSC SPIN.
  • Added new Admin panel with view of BullMQ queues
• 1.7.3
  • INP Jiffy now accepts only PDB files instead of CRD.
• 1.7.2
  • PAE Jiffy now accepts only PDB files instead of CRD.
• 1.7.1
  • Hide delete button for jobs that are "Submitted" or "Running"
  • Comment out some verbose unneeded console logs
• 1.7.0
  • Add components for displaying FoXS analysis for BilboMD classic/auto jobs.
• 1.6.2
  • Fix bug when rg_min and rg_max are too close.
• 1.6.1
  • Better feedback about status of bilbomd and scoper BullMQ queues.
• 1.6.0
  • Add ability to toggle between Dark and Light mode.
• 1.5.1
  • Refactor and improve the Scoper job details page
• 1.5.0
  • Add rechart dependency for displaying FoXS plots.
  • Display FoXS plots and Chi^2 values for Scoper results
• 1.4.2
  • Improvements to the Molstar viewer.
• 1.4.1
  • Forgot to merge the feature branch... oops.
  • Now we should have a Molstar viewer.
• 1.4.0
  • Add Molstar viewer for Scoper Job detail page.
• 1.3.1
  • Add better Scoper status information in the SingleJobPage It still needs work, but I want to release what's been done so far.
• 1.3.0
  • Add new Scoper options for RNA
• 1.2.4
  • Upgrade redux and redux toolkit
• 1.2.3
  • Some improvements to the Job details component
  • Changes to allow Docker deployment for UI
  • update Vite from 4.5.0 to 5.0.0
• 1.2.2
  • Add better information about number of MD runs and conformation to Job details
• 1.2.1
  • Fix bug in Job/Jobs components when there is no BullMQ entry
  • Changed default conformational_sampling to 3 for BilboMD Auto jobs
• 1.2.0
  • Changes to accomodate new Typescript backend code
• 1.1.2
  • Increase max upload for PAE json files in af2paeJiffySchema
• 1.1.1
  • Fix bug when directly loading Job component with error
• 1.1.0
  • Add better error reporting for CHARMM steps
• 1.0.0
  • Add BilboMD Auto job submission form
  • Fix bug in MultiFoXS with Eigne library
  • Simplify the result PDBs bundled into results.tar.gz
• 0.0.20
  • Increase the max allowed file size of uploaded `PAE.json`` files from 20MB to 40MB
• 0.0.19
  • Add necessary changes to make compatible with the new v1 API
• 0.0.18
  • Bug fixes for AutoRg
• 0.0.17
  • Add AutoRG functionality to the New Job Form
• 0.0.16
  • Update NPM dependencies
  • Bump NodeJS to 18.18.0
• 0.0.15
  • Add Number of Workers to BullMQ Summary component
• 0.0.14
  • Add BullMQ Summary component
• 0.0.13
  • Improve Job Detail page
  • Add step indicators for BilboMD
  • Display information about queue position in the Job List page
• 0.0.12
  • Update the Welcome component
  • Add better references to Welcome page
  • Update nodejs dependencies
• 0.0.11
  • Add PAE jiffy (creates const.inp from AlphaFold PAE JSON input file).