Developer Guide

Definitions

Computing infrastructure

It is composed of computationally dedicated hardware and the software components required to operate it, including calculation management programs (distributed resource management systems, Galaxy,…).

Adaptor

It is a Django module allowing WAVES-core to communicate with a specified computing infrastructure. For each computing infrastructure, WAVES-core needs a dedicated adaptor.

Service

A service is a bioinformatic tool available online through the http protocol. It can be accessed from a web form or through REST API calls.

Submission

Many bioinformatic tools provide several distinct usages. For instance, a program can be run using the command-line interface or by providing a configuration file. Otherwise, the same tool can be run on different computing infrastructures. A submission is the combination of a usage and a computing infrastructure. Thus, a service can rely on different submissions.

Job

A job stands for a command with parameters. It is run on a dedicated computing infrastructure. It may require inputs such as files. It generates outputs: exit code, standard output and standard error, and possibly result files. A job is run each time a submission is invoked by a service.

User

A user is a client which accesses services. It can be a real person using a web browser or a software using the REST API.

Administrator

An administrator is a privileged user with granted access to the WAVES-core back-office. He manages configurations, services, submissions, adaptors and jobs.

Documentation

• 1. WAVES Deveveloper Guide
  • 1.1. Job Workflow
  • 1.2. Create a WAVES-core adaptor
    • 1.2.1. Job states constants
    • 1.2.2. Class diagram overview
  • 1.3. Overriding Services and Submissions
  • 1.4. Overriding WAVES templates
    • 1.4.1. Related urls
    • 1.4.2. Services
    • 1.4.3. Jobs
  • 1.5. Overriding API entries
    • 1.5.1. Service endpoints
    • 1.5.2. Jobs endpoints
  • 1.6. Overriding forms create template packs
• 2. WAVES API python samples code
  • 2.1. Interact with services
  • 2.2. Authenticate with token
  • 2.3. Integrate a WAVES service form
  • 2.4. Create a job
• 3. WAVES API php samples code
  • 3.1. Create functions for GET and POST requests
  • 3.2. Display the list of services
  • 3.3. Integrate a WAVES service form
  • 3.4. Create a job