https://github.com/wtsi-hgi/genestack-uploader
A HTTP server providing an API and a frontend for easy uploading to Genestack
https://github.com/wtsi-hgi/genestack-uploader
Last synced: about 2 months ago
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A HTTP server providing an API and a frontend for easy uploading to Genestack
- Host: GitHub
- URL: https://github.com/wtsi-hgi/genestack-uploader
- Owner: wtsi-hgi
- License: gpl-3.0
- Created: 2021-10-05T16:20:37.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2023-02-16T04:42:23.000Z (about 2 years ago)
- Last Synced: 2025-01-26T18:48:43.475Z (3 months ago)
- Language: Python
- Size: 455 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Genestack Uplaoder
A HTTP server providing an API and a frontend for easy uploading to Genestack
## Build & Run Docker Image -- by Fei
1. If any change is applied, version number (`config.py`) should be updated.
```
VERSION = "2.4"
```
2. `hgi-docker.sh` can build dev and production images automatically with right `frontend/.env` files.
It creates `mercury/genestack-uploader:2.4.dev` and `mercury/genestack-uploader:2.4.prod` with the appropriate configuration in the image.
```
sudo ./hgi-docker.sh 2.4
```
Check built imgages
```
sudo docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
mercury/genestack-uploader 2.4.prod ff7989cfc80c 14 minutes ago 1.3GB
mercury/genestack-uploader 2.4.dev 2cdf3ab5dbe3 14 minutes ago 1.3GB
```
3. push the image to DockerHub
Log in docker with mercury first. (check secrets). Then push.
```
sudo docker login
sudo docker push mercury/genestack-uploader:2.4.dev
sudo docker push mercury/genestack-uploader:2.4.prod
```
4. log in dev and production (details on Confluence Swarm Page)
5. Update running image
```
docker pull mercury/genestack-uploader:2.4.dev
docker service scale mystack_genestack-uploader=1
docker service scale mystack_genestack-uploader=0
docker service update --image=mercury/genestack-uploader:2.4.dev mystack_genestack-uploader
docker service scale mystack_genestack-uploader=1
```
## Running with Docker 🐳 -- by Michael
1. Update `frontend/.env` and `config.py` if needed. (See `docs/spec/main-spec-updates/1.md` for discussion about base URL paths.)
2. Build the image, i.e.
```
docker build -t mercury/genestack-uploader:0.1.dev .
```
The tagging scheme used on this project is `mercury/genestack-uploader:X.Y.{prod|dev}`, where X.Y is the version number, and the final tag is `prod` or `dev`, describing which URL is specified in `.env` and `config.py`. (This is also described in more detail in `docs/spec/main-spec-updates/1.md`.)
If deploying in the HGI environments, the script `hgi-docker.sh`, passing the argument of the verison number will build the images as we need, for example `./hgi-docker.sh 2.0` will create `mercury/genestack-uploader:2.0.dev` and `mercury/genestack-uploader:2.0.prod` with the appropriate configuration in the image.
3. Run the image. You must:
- provide the env variable `GSSERVER` with a value of either `qc` or `default`
- link to config files `/root/.genestack.cfg` and `/root/.s3cfg`
- link SSH key files to `/root/.ssh/id_rsa_genestack` and `/root/.ssh/id_rsa_genestack.pub`
Optional Environment Variables:
- `JOB_EXPIRY_HOURS`: defaults to `168` (hours in a week) - this is how long a job should be kept after it has completed for it to be accessed using the `/jobs/{uuid}` API endpoint
- `LOG_LEVEL`: one of `DEBUG`, `INFO`, `WARNING`, `ERROR`, `CRITICAL` (defaults to `INFO`) - the minimum level of logs to be reported
The app runs on port 5000 on a Docker network, so that can be used to forward it, such as in a nginx container.
To test, you can also expose port 5000, i.e.
```
docker run -p 80:5000 -e GSSERVER=default -v /home/ubuntu/genestack-uploader/configs:/root -d --name genestack-uploader mercury/genestack-uploader:0.1.dev
```
## Version Numbering -- by Michael
There are two important version numbers to keep track of.
- The version number of the `uploadtogenestack` package
- This is updated in the package's `setup.py` file, and is given a tag on GitLab
- This tag number is then used in this repositories Dockerfile to install the right version
- The version number of this web app
- This is updated in `config.py` and is also reflected in the Docker image tag
Ensure that these are kept up to date, as it really helps find bugs when you know which versions of each a particular image is running. The version numbers are displayed at the bottom of the homepage.