https://github.com/gersteinlab/stressserver
Server code for STRESS
https://github.com/gersteinlab/stressserver
Last synced: 3 months ago
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Server code for STRESS
- Host: GitHub
- URL: https://github.com/gersteinlab/stressserver
- Owner: gersteinlab
- Created: 2015-09-26T19:31:49.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2018-11-17T20:02:22.000Z (about 7 years ago)
- Last Synced: 2025-06-16T03:10:58.194Z (7 months ago)
- Language: C
- Size: 3.32 MB
- Stars: 0
- Watchers: 18
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
Allosteric Web
=============
Repo for website of an allosteric project in Gersten lab
All code from DC in code folder
## Note about potential security vulnerability
The current version of this server has a security vulnerability. This vulnerability, which is in the rack module, has been classified by GitHub as a moderate severity security vulnerability. More information can be found here:
https://nvd.nist.gov/vuln/detail/CVE-2018-16471
and here:
https://nvd.nist.gov/vuln/detail/CVE-2015-3225
## Tasks
- [x] Allow users to upload files
- [x] Allow users to give PDB ID and then fetch files from PDB
- [x] Let users select which module they want to run (BL or/and GN)
- [x] Run two programs and report results
- [x] Pipeline all programs using bash (Shantao)
- [x] Install & configure MMTK on an AWS instance (Richard)
- [x] Email notification for users after the job is done
- [x] Archive finished results in SQL database, automatically query
- [x] Fix GN module
- [N] Batch processing (user can submit multiple PDB ids or upload multiple PDB files and retrieve all the results in one zip file)
- [x] Random job id
- [N] Delete user submitted PDB files and results after 1 week
- [N] Prepopulate database with selected PDB IDs and results
- [ ] Front end design, descriptions, instructions, email content, etc.
- [N] Progress indicator
- [ ] Quick mode?
- [ ] Docker image
- [ ] Make code available: BL/GN, server code, sample data & output, docker image
- [ ] Database flat file showing all results: Bulk paper results and accumulated results
- [ ] Documentation
- [N] Caps to prevent overuse
- [N] DNS naming
- [N] Visualization (optional)?
- [D] Fix autoscaling
- [ ] Web server setup packaging and distribution
## Implementation Notes
- Paperclip used to manage PDB file attachments
- Validations for user-uploaded PDB files and user-specified PDB ids
- Run `pipeline_BL [INPUTPDB]` to execute BL module and `pipeline_GN [INPUTPD]`
- But in order to remove MMTK dependency, pass `fnm_10` as the 2nd param
- GN Module not working now...I need to ask DC about the weird VMD dependency and python script (Shantao)
- `pipeline_BL.sh` writes output files to the current working directory
## AWS Notes
- 1 web server tier for processing HTTP requests, 1 worker tier for processing background jobs. Auto-scaling enabled.
- 1 RDS database and 1 S3 bucket for cloud-based storage. Allows both tiers to share data.
- RDS t2.micro: max_connections is 26