CHAPaaS

CHAP as a Service (a.k.a CHAPBook) provides a web based service (interface) for rapid development of CHESS analysis workflows within CHESS Analysis Pipeline (CHAP) framework.

Requirements

CHAPaaS is written in GoLang and can be build using standard GoLang build procedure. Please use provided Makefile and build it using

make

But in order to run CHAPaaS we need the following:

• jupyter notebook where CHAP code will be executed
• miniconda or conda
• corresponding python environments for supported workflows
  • tomo/conda.yml
  • saxswaxs/conda.yml To install given environment please do the following:

conda env create -f <workflow>/conda.yml

Running CHAPaaS

To run the service please follow these steps:

1. Setup jupyter notebook server elsewhere, it can be local installation or remote one
   • configure your notebook to allow access from CHAPaaS. Here is an example of local jupyter setup:

c.NotebookApp.tornado_settings = {
    "headers": {
        "Content-Security-Policy": "frame-ancestors 'self' http://localhost:8182"
    }
}
c.NotebookApp.token = "jupyter-token"
c.NotebookApp.open_browser = False
c.NotebookApp.port = 18889
c.NotebookApp.ip = '*'

Feel free to provide your own token value, and adjust ports as necessary. In this example port 8182 refers to CHAPaaS port, while 18889 is notebook server port. 2. Install either miniconda or coda tool

• install all supported workflow environments, e.g.

git clone [email protected]:CHESSComputing/CHAPBookWorkflows.git
conda env create -f CHAPBookWorkflows/tomo/conda.yml
conda env create -f CHAPBookWorkflows/saxswaxs/conda.yml
...

3. Install ChessAnalysisPipeline and make it accessible in your PATH.
4. Create proper configuration file, e.g. config.json

{
    "base": "",
    "verbose": 1,
    "chap": "/path/CHAPaaS/scripts/chap.sh",
    "chap_dir": "/path/ChessAnalysisPipeline",
    "user_dir": "/path/CHAPaaS/chap/users",
    "user_repo": "/tmp/CHAPBook",
    "scripts_dir": "/path/CHAPaaS/scripts",
    "redirect_url": "http://localhost:8182",
    "oauth": [
        {
            "provider": "github",
            "client_id" : "123",
            "client_secret": "xyz"
        }
    ],
    "jupyter_root": "/tmp/jupyter",
    "jupyter_token": "jupyter-token",
    "jupyter_host": "http://localhost:18889",
    "workflows_root": "/path/CHAPaaS/examples",
    "github_token": "/path/CHAPaaS/token",
    "doi": "666131920",
    "development_mode": true,
    "port": 8182
}

5. Start the service

./chapaas -config config.json