Web application to host the pre calculated analyses by SelectZyme.
Prerequisite for all installs is to clone the repository.
git clone https://github.com/ipb-halle/SelectZyme-app.git
cd SelectZyme-app
docker-compose up
docker-compose down # shut down services
Access the server from your browser at: localhost/selectzyme/
Install dependencies defined in the pyproject.toml and SelectZyme without dependencies.
pip install .
pip install --no-dependencies git+https://github.com/ipb-halle/SelectZyme.git
Usage:
python app.py # runs example analysis 'demo' by default
python app.py -i=petase
-i= specify the case study to load. Available case studies are listed here with their names (here as an example petase).
Access the server for your analysis from your browser at: localhost:8050
graph TD;
B[Demo analysis] --> D[data/demo/:/app/data_container/];
C[Petase analysis] --> E[data/petase/:/app/data_container/];
A[Proxy - Nginx] -->|/selectzyme/demo/| B[Demo analysis];
A[Proxy - Nginx] -->|/selectzyme/petase/| C[Petase analysis];
subgraph Docker Network;
A[Proxy - Nginx];
B[Demo analysis];
C[Petase analysis];
end
Target server: biocloud Service: SelectZyme
In order to automatically (re-)start the service (e.g. with a cronjob) please perform these steps:
./sz.sh install # register service 1st time
./sz.sh start
systemctl status sz.service # test status
./sz.sh stop # stop service
Use sz.sh update to update the service.
Additional notes on the current workflow to build docker images with a workflow: Because of a restricted company network, images (github: packages) are build using a CI workflow. The packages appear in the repo on the right, clicking on them you can change the visibility. They should inherit visibility from the repo but the company can have restrictions so ask the organization owner to enable public visibility of your package (image).
sequenceDiagram
actor User
participant BP as Biocloud Proxy
participant SDP as Selectzyme Demo Proxy (nginx)
participant SDA as Selectzyme Demo App
User->>+BP: Request resource
BP->>+SDP: Forward request (e.g., to selectzyme-proxy.selectzyme-network)
SDP->>+SDA: Proxy request to Selectzyme Demo App
SDA-->>-SDP: App response
SDP-->>-BP: Forward response
BP-->>-User: Response
- Changes: Biocloud proxy sits on top of SelectZyme proxy
This project uses the following tools to improve code quality:
Ocean server development (ocean_ip) http://ocean_ip/selectzyme/demo/
MIT License