Datains

Datains is an web tool for Reproducible Omics Pipeline.

Prerequisites

You will need Leiningen 2.0 or above installed.

Install Dependencies

lein deps

Initial Database

• Create Database on PostgreSQL
• Init dev-config.edn file
• migrate database by running lein run migrate

Running

To start a web server for the application, run:

lein run 

Launch a Jupyter Server for Datains

lein jupyter notebook

How to reload application without the need to restart the REPL itself

(require '[user :as u])
(u/restart)

Environment Variables for Datains

# Required
## General
PORT=
### Only support postgresql
DATABASE_URL='postgresql://localhost:5432/datains_dev?user=postgres&password=password'
### For reports/apps/projects
WORKDIR=

## App Store
APP_STORE_ACCESS_TOKEN=
APP_STORE_HOST=
APP_STORE_PORT=
APP_STORE_USER_NAME=
APP_STORE_PASSWORD=
### app_utility is a script for rendering choppy-app. where is the virtualenv for the app_utility?
APP_UTILITY_BIN=/app/external

## Cromwell
### Where is the cromwell service? More details: https://cromwell.readthedocs.io/en/stable/
CROMWELL__URL=http://localhost:8000
### Maybe you can use basic auth by nginx or httpd, e.g. 'Basic cGd4LWNyb213ZWxsOmxyb2Nr'
CROMWELL__TOKEN=

## Tasks
### More details: http://www.quartz-scheduler.org/documentation/quartz-2.3.0/tutorials/crontrigger.html
### Cron expression for submit-jobs task
TASKS__SUBMIT_JOBS__CRON=0 */1 * * * ?
### Cron expression for sync-apps task
TASKS__SYNC_APPS__CRON=0 */3 * * * ?

# Optional
DINGTALK_ACCESS_TOKEN=
DINGTALK_SECRET=

Change Log

1. Database (Model)
2. Database Handler (Controller)
3. Route (View)

TODO

Drivers

Gitea Driver

Cromwell Driver

SmartCDP Driver

Data Portal Driver

Report Driver

Scheduler

Scheduler will help us to do a series of things, such as:

1. Sync choppy apps from gitea.
2. Sync the status of all jobs from Cromwell.
3. Submit the jobs to Cromwell periodically.

So we need a plugable implement.

Async Task

License

Copyright © 2019 FIXME