Uchuva - A Scientific web Portal

Currently, under heavy development, keep in touch :).

Features

• A visual editor for workflows
• A virtual file system
• A visual command line opts and args library generator
• Submit workflows to HTCondor (Dagman), Slurm, OpenLava (LSF), Torque (PBS) and OAR.
• Rest Api with Swagger
• Vagrant
• Docker
• Tested using mocha/chai: unit testing, regression, integration and aceptance test (selenium)
• i8ln
• Easy to monitor with ELK stack (logger)

For more information please visit the wiki

Installing

If you want to try it out as quickly as possible, please install MongoDB, ensure that you have the right compilers installed (for OSX, XCode4 will work, for Ubuntu, the build-essential and libssl-dev packages) and then use Docker:

Native

Dependencies

• Node.js
• MongoDB
• Git

Optional Deps

• Git
• make, g++, curl
• HTCondor/OpenLava/Torque/Slurm
• Web browser

Ubuntu Linux (32 and 64 bits)

Update and install the essential packages

apt-get update
apt-get install -y git curl sudo python make build-essential g++

Install NodeJS 6.9

curl -sL https://deb.nodesource.com/setup_6.x | sudo -E bash -
sudo apt-get install -y nodejs mongodb

Clone this repo and install the Node dependencies

git clone https://github.com/carlochess/uchuva
cd uchuva/prototipo
npm install

Install MongoDB

Start uchuva

npm start

Centos 7

DEB Linux (doesn't work for now)

Install using dpkg

$ apt-get update
$ apt-get install -y git curl sudo python build-essential g++
$ curl -sL https://deb.nodesource.com/setup_6.x | sudo -E bash -
$ sudo apt-get install -y nodejs mongodb
$ sudo dpkg -i uchuva_0.0.1_all.deb
$ sudo apt-get -f install

All the files for Uchuva install are listed here.

/var/lib/uchuva      #contains the binaries
/usr/share/uchuva    #contains the start script
/var/log/uchuva      #contains the agent logs
/etc/default/uchuva  #contains all the environment variables with default values. These variable values can be changed as per requirement

Docker

Using Docker to test this project is the better choise you can make. Please, install Docker engine

$ curl -fsSL https://get.docker.com/ | sudo sh
$ sudo gpasswd -a ${USER} docker
$ newgrp docker

Then Docker-compose

$ curl -L "https://github.com/docker/compose/releases/download/1.8.1/docker-compose-$(uname -s)-$(uname -m)" > docker-compose
$ sudo mv docker-compose /usr/local/bin/docker-compose
$ chmod +x /usr/local/bin/docker-compose
$ docker-compose --version

And finally, download and create Uchuva container

$ git clone --depth=1 https://github.com/carlochess/uchuva/ && cd uchuva
$ docker-compose up -d

It may take from 10 to 60 minutes to complete (The first time).

You can now visit the host page

$ firefox localhost:3000

Vagrant

Go to vagrant/{HTCondor/sola,OpenLava,Torque,Slurm} folder and run

$ vagrant up

Visit the wiki vagrant entry

Windows

Download The HTCondor.msi currently stable release. Then you have two choises: manually download and install MongoDB, Nodejs and Git installers

Or using Chocolatey package manager, automatically download and install nodejs, mongodb and git.

choco install nodejs.install 
choco install mongodb 
choco install git 

Remember to start MongoDB Service:

md \data\db
"C:\Program Files\MongoDB\Server\3.2\bin\mongod.exe" --dbpath c:\data\db

Open another terminal, clone Uchuva

git clone https://github.com/carlochess/uchuva
cd uchuva/prototipo
npm install
npm start

Mac OS

brew update
brew install node mongodb git

Open another terminal, clone Uchuva

git clone https://github.com/carlochess/uchuva
cd uchuva/prototipo
npm install
npm start

And go to the website

NPM package

Isn't working right now You can install uchuva using a node package manager (npm or yarn)

$ npm install -g uchuva

Test

cd prototipo
npm test

API

You can generate your api client or server from swagger, the spec is saved in prototipo/static/swagger/api.json

• Using the code editor http://editor.swagger.io/
• Using a code gen from an image: see prototipo/utils/generadores/generate.sh

This is an exampĺe

require 'swagger_client'

SwaggerClient.configure do |config|
     config.host= "127.0.0.1"
end

apikey = "hzeQHLaKmgg4bdB25Jio"
dagapi   = SwaggerClient::DagApi.new

result = dagapi.user_get(apikey)
puts "Number of dags", result.length

Documentation

You can read my bacherlor thesis (Spanish) in the doc/ folder

Related projects

Pegasus, Swift parallel scripting language, Dagman, Taverna, Apache airavata, Galaxy, OnlineHPC, Kepler, makeflow, Askaban, Luigi, Agave API,

Why does my project is call by a super heroe name?

Because i believe that your project would save too many lives and therefore the planet :)

Issues

Please report any issues using Github issue tracker.

• Do include a detailed description of the problem.
• Do include a link to a gist with any interesting stack traces/logs (you may also attach these directly to the bug report).
• Do include a reduced test case.
• Use the issue tracker to submit basic help requests.
• Do not post empty "I see this too" or "Any updates?" comments. These provide no additional information and clutter the log.

Disclaimer

• Thanks to Colorado Reed's for creating the d3.graph.editor.
• Also thanks to the creators of Angular file manager
• Agave project for Torque and Slurm Docker images
• Puppet for their HTCondor, Mongo, Docker, etc modules
• Swagger for the api generator
• TTY.js for such amazing web terminal
• Graph ordering and rendering: Dagre

Roadmap

See TODO.md