labioquim / visualdynamics

Web Platform made with Python and NextJS for automating GROMACS simulations

Visual Dynamics

Visual Dynamics is a web application made platform for molecular simulations. It aims to automatize the generation and execution of a molecular simulation with capabilities to generate and run dynamics of Protein and Protein + Ligand (prepared in ACPYPE or PRODRG).

Self-hosting

If you want to self-host Visual Dynamics just stick to the steps below (this only works on Linux):

1. Make sure to have nodejs, yarn, docker , docker compose and the docker plugin nfsvol.
2. Copy the file .env.example to .env and fill it. The ones you need to change are: VISUALDYNAMICS_URL (for this tutorial we'll assume this is set to visualdynamics.localhost), DB_USER, DB_PASS and DB_DATABASE, NEXTAUTH_SECRET, SMTP_USER, SMTP_HOST, SMTP_PASS and SMTP_PORT
3. Run docker compose -f docker-compose.prod.yml up -d --build
4. Enter the folder client and run yarn install.
5. Run DATABASE_URL=postgres://DB_USER:DB_PASS@localhost:5432/DB_DATABASE yarn prisma migrate deploy. Note the DB_ fields that must be the ones you set on .env
6. Run DATABASE_URL=postgres://DB_USER:DB_PASS@localhost:5432/DB_DATABASE yarn prisma db seed. Note the DB_ fields that must be the ones you set on .env
7. Now you can open a browser and access visualdynamics.localhost.

Note: This tutorial will make Visual Dynamics available on only ONE machine.

Note: If you plan to run Visual Dynamics to your whole institution, please coordinate with your IT Sector to address the intricacies of your institution infrastructure.

License

The Visual Dynamics source code is available under the MIT License. Some of the dependencies are licensed differently, so watch out for them.

visualdynamics's Issues

labioquim

LABIOQUIM

Problem with regex handling email verification

Hello, sorry to bother you
It seems that your mail verification doesn't take into account mails with several dots after the arobase, for example
[email protected] doesn't work even though it's a valid address
Thank you
Louis

FIOCRUZ RONDÔNIA

The automated release is failing 🚨

🚨 The automated release from the next branch failed. 🚨

I recommend you give this issue a high priority, so other packages depending on you can benefit from your bug fixes and new features again.

You can find below the list of errors reported by semantic-release. Each one of them has to be resolved in order to automatically publish your package. I’m sure you can fix this 💪.

Errors are usually caused by a misconfiguration or an authentication problem. With each error reported below you will find explanation and guidance to help you to resolve it.

Once all the errors are resolved, semantic-release will release your package the next time you push a commit to the next branch. You can also manually restart the failed CI job that runs semantic-release.

If you are not sure how to resolve this, here are some links that can help you:

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If those don’t help, or if this issue is reporting something you think isn’t right, you can always ask the humans behind semantic-release.

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The release 1.0.0 on branch next cannot be published as it is out of range.

Based on the releases published on other branches, only versions within the range >=1.5.0 can be published from branch next.

The following commits are responsible for the invalid release:

• ci: trying to fix rel version (ad79b07)
• chore(release): 1.0.0-next.2 [skip ci] (9e2b0dd)
• ci: fix pnpm-lock location (689bcf0)
• chore(release): 1.0.0-next.1 [skip ci] (37a4092)
• ci: downgrade semantic-release (1c089fc)
• ci: i'm losing my mind on this one (3fa448e)
• ci: trigger release (0b3c5c0)
• ci: trigger release (72f37d6)
• ci: trigger release (1ffc1da)
• ci: trigger release (6c1e61b)
• ci: add missing deps (2b3287f)
• ci: go back to pat (5f3f97f)
• ci: use github token from actions (f591094)
• ci: fix pre-release version (4bf8e85)
• ci: add missing dev dependency (19745b0)
• ci: trying with PAT (f1dc773)
• ci: trying again (d5d41bd)
• ci: trying again (7772c26)
• ci: trying to fix pnpm (7bcbd68)
• ci: fix package manager (234a8cc)
• feat: dynamics -> simulations (#13) (a74996e)
• fix: running dynamic page should now work (21734ce)
• fix: disable preload data on running page (089f96b)
• fix: disable preload of my-dynamics (575dd88)
• chore: update ecosystem (5311fda)
• fix: use full baseurl if not development (d5be1d6)
• fix: server start command (ac38ebc)
• fix: add SSL to server (c5c098c)
• fix: add _npt.gro to results download (8be8f77)
• chore: add first post (66f6ec8)
• chore: update translations (f0d24e4)
• chore: remove unneeded file (f5ccd7d)
• fix: instruct users to contact admin for old simulations (b83f6ee)
• fix: missing translations (4b8e2b3)
• feat: add download archive button (6603ed7)
• fix: update translations and images (22f02a1)
• fix: update db schema (d2c21cc)
• fix: navbar scroll, email sending (b19a616)
• chore: remove unneeded console.log (a9e3264)
• fix: mobile navbar positioning, initial theme load (e0daf89)
• chore: update prisma version (f55bd9c)
• chore: reworking directories (eb8066e)
• fix: get initial theme synchronously (0085537)
• revert: going back to pm2 for client deploy (1016d6f)
• fix: moving thread number to config file (5af7e96)
• chore: update readme (c7562cd)
• fix(acpype | prodrg): usage of box_distance and ignore (97cb69f)
• fix: change redis default port (1478e2c)
• chore: deploy scheme ready (e6a42cd)
• fix: dockerization almost done (2a4c2ba)
• feat: containerization in progress (cb720da)
• chore: moving deploy to docker (4058b33)
• fix: minimum python version (a3ae014)
• fix(client): smooth transition on dynamic form submit button (4899a38)
• feat(client): improvements to sidebar, animations and loading states (ef01b75)
• fix(client): behaviour and style merging (9d8c732)
• fix(server): not returning command list when requestes (1c794a2)
• feat(client): use framer-motion for animations (60657be)
• chore(repo): move to yarn (b5280e2)
• chore: add institutions logo (fc5bb32)
• chore: rename acpype test pdb (b26c593)
• feat: only process molecules with 5000 or less atoms (234e596)
• fix: i18n namespace loading on dynamic forms (8933cc2)
• feat: move to next-translate instead of next-i18next (e1dcbf3)
• feat: updated posts view (73c3033)
• fix: show loading state on route changing (0f6631d)
• fix: migrate from nextjs-progressbar to next-progress (62baae0)
• feat: redirect user from vd1 to reset password screen on first login (4e3d463)
• fix(client): fix page viewport on mobile (2788fbb)
• fix(client): blog page not rendering tab title (395e3ad)
• fix(client): sign up form loading state not showing up (f9b3e4b)
• fix(client): sign in form loading state not showing up (fd377ef)
• feat(client): added ability to reset password (c780d68)
• fix: revert tailwind dark mode enabler (1561325)
• fix: correct and re-enabled gray color (ef07c5c)
• docs(client): added storybook and Button stories (787bfa3)
• chore: fixes for production (da24e51)
• chore(client): add log to mailer (16f2538)
• fix(server): download logic (95d02d0)
• fix(client): disable prisma log query (1cfa7c5)
• chore: fix pm2 ecosystem file (d73014a)
• chore: pm2 ecosystem file (bed728e)
• chore: pm2 ecosystem file (b33ceb4)
• chore: pm2 ecosystem file (0e6da7e)
• chore: for tests (2ea6a66)
• chore: pm2 ecosystem file (0699e48)
• chore: pm2 ecosystem file (7dfbac3)
• chore: pm2 ecosystem file (00c0645)
• chore: pm2 ecosystem file (a05ecb9)
• chore: pm2 ecosystem file (66130bb)
• chore: pm2 ecosystem file (e075dde)
• chore: pm2 ecosystem file (e714ff9)
• chore: pm2 ecosystem file (f5aba4a)
• chore: pm2 ecosystem file (a86f1a5)
• chore: pm2 ecosystem file (aecca37)
• chore: pm2 ecosystem file (e28b76e)
• chore: pm2 ecosystem file (976fd15)
• fix(server): fix nthreads to 10 (dc4b249)
• fix(server): min python 3.9 (fcf83f6)
• fix(client): improve blog managing (10de12d)
• fix(client): reduced usage of useState in forms, built static blogs for all languages (9470688)
• fix(client): admin cron job fix (e876cf5)
• fix(client): send mail url (e413957)
• fix(client): admin sign up request list item behaviour on small screens (b46f09c)
• fix(server): run server on networ IP (bcbc78d)
• feat(client): re-enabled PRODRG dynamic execution (add8e05)
• feat: migrate PRODRG to linux commands (0fb1f45)
• feat(mail): send mail on admin approval/rejection (539b81e)
• fix: send mail on dynamic status changed (922b12a)
• fix(cron): don't send email when no inactive users (c0ca8b7)
• fix: rename admin requests cron job (7394fe9)
• feat: mailer (accd472)
• chore: add logo for email (dd0ee45)
• feat: md_pr update (02afc10)
• chore(client): restructure components (323e6be)
• fix: changed generate routes, added update mdpr route (4d7b180)
• fix(client): type errors and title positioning (53c342f)
• fix(client): dynamic card sṕinner color (7091d5a)
• fix(server): command running pid saving on wrong place (6e19b0a)
• fix(client): disable abort button when the request is running (fb9271e)
• fix: abort task route, improvements on UI and more (1165112)
• fix(server): update default celety services (a9cda03)
• fix(client): improvements to layout (fd4a9b9)
• chore(tests): add testfiles (982e2d5)
• fix(server): fixes for admin page to view all running dynamics (1f106a0)
• feat(client): admin page to view all running dynamics (eeddab9)
• fix(client): cleanup on unused imports on admin approval/reject page (62c9124)
• feat(client): admin request approval/reject page (8db28aa)
• fix(client): add info about signup (588ad4f)
• fix(client): screen scroll, signin error messages (fbe6b3f)
• feat(client): signup page (5e0fe33)
• fix(client): move some pages away from getServerSideProps (9b03c48)
• fix(client): min height on mobile, link to admin page (78f63cf)
• fix(client): tailwindcss auto classname sorter (bdda700)
• fix(client): behaviour on mobile and desktop (9523855)
• fix(client): improvements to mobile UI (2d2b316)
• chore(vscode): always prefer non-relative imports (7814ca4)
• fix(server): send last log lines reversed (1fb1965)
• fix(client): improvements to dynamic related pages (1618f8f)
• fix(client): update main (8f07e77)
• fix(client): improve colors (d121046)
• fix(client): font family (3912c6d)
• fix(client): lazy load some default components (4de545a)
• fix(client): search bar wrong color on dark mode (5bfcca8)
• fix(client): drop multi color theme in favor of light and dark theme (f5bdc6a)
• fix: remove unneeded component (12398cc)
• feat(client): redone layout (4f55ca7)
• fix(client): icon size on buttons (c09080d)
• fix(client): mobile nav lock body scroll (3b4ed6f)
• fix(client): add spacing in about sections (7a97449)
• fix: add title to work icon on maintainer card (8fa963d)
• fix: improved about page (6fb771b)
• fix: lockfile, add .env.example (4c9807d)
• feat(client): add progressbar on top, and fix loading state on page transition (55b77d3)
• fix(client): color scheme persistence (465ac29)
• feat(client): loading state on auth form, added some content to home page (f2a7122)
• fix: translations (5021b51)
• chore: trigger deploy (f749850)
• feat(client): fixes and about page with some initial content (aa4f646)
• fix(client): backend url from env (a84a1e8)
• fix(client): 404 page title (2dfe246)
• fix(client): custom 404 page, prodrg force fields (c7ed6b1)
• feat(client): added prodrg page, some fixes to failing api calls (5246a43)
• fix(client): don't use node as edge backend (7bbb1a6)
• fix(client): duplicated header links (2afffcb)
• fix: vercel build (ea6112c)
• fix: vercel build (641e80b)
• fix: vercel build (687af35)
• fix: vercel build (542e9c6)
• fix: improvements (f885bc4)
• feat(client): authentication done (d3a9d1b)
• fix(client): improvements to breadcrumb (0fccc0a)
• feat(client): improved page transitions, translations and components (cf91a86)
• fix(server): download command list for running and queued dynamics (3a84a83)
• feat: added file downloads for dynamics ran on server (40668fa)
• feat: added acpype dynamic, improved visuals (56152f2)
• feat: added acpype dynamic, dynamic cancellation (6cb44ac)
• feat(server): improved the way running data is returne (15b5307)
• feat(client): added dynamic breadcrumb, finished running page, started translations (6528324)
• chore(repo): update pnpm-lock (db547f6)
• feat(client): you can now generate and start a APO dynamic (be9cb52)
• feat(server): big changes on APO dynamic generation and dynamic execution (6e4f8f9)
• feat(server): run route now just calls celery process (2306af0)
• chore: flower.service -> celery-flower.service, docs on setting up celery (5eafc63)
• feat: added celery to run dynamics (2695f41)
• feat(server): added route to get user dynamic run status (ee3bbac)
• feat: ability to start APO dynamic (ba2a914)
• fix(client): improved select/input border color, fixed future form translation keys (fee3c74)
• feat(client): a bunch more things (d9c4efc)
• feat(client): started redoing layout (c96855a)
• feat(apps): added base code for client and server (c79c56f)

Those commits should be moved to a valid branch with git merge or git cherry-pick and removed from branch next with git revert or git reset.

A valid branch could be main or next.

See the workflow configuration documentation for more details.

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Good luck with your project ✨

Your semantic-release bot 📦🚀