Note

This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.

OMERO.web framework

OMERO.web is a framework for building web applications for OMERO. It uses Django to generate HTML pages from data retrieved from the OMERO server. OMERO.web acts as a Python client of the OMERO server using the OMERO API, as well as being a web server itself (see ‘infrastructure’ info below). It uses Django ‘apps’ to provide modular web tools, such as the webclient (working with image data, administrator management). This modular framework makes it possible to extend OMERO.web with your own apps.

One of the apps, WebGateway, provides utility methods for accessing data and rendering images, as well as handling the connection to OMERO server.

OMERO.web infrastructure

OMERO Python API

The OMERO.web framework is all based on the OMERO Python API, using the Blitz Gateway (see OMERO Python language bindings). The OMERO.web framework provides functionality for creating and retrieving connections to OMERO (see example below and Writing OMERO.web views for more details)

Web gateway

The webgateway is a Django app that provides utility functionality for the other web components. This includes a full image viewer, as well as methods for rendering images etc. You can browse the webgateway URLs, or see the WebGateway page for more info.

Web apps

The OMERO.web framework consists of several Django apps denoted by folders named ‘web....’. These include webgateway, as discussed above, as well as released tools (webclient) and other apps in development:

webclient

Main web client for viewing images, annotating, administration of user and group settings etc. More information available under OMERO.web.

webgateway

A web services interface, providing rendered images and data. See WebGateway.

Note

Although it is possible to access functionality from any installed app, ONLY webgateway should be considered as a stable public API. URLs and methods within other web apps are purely designed to provide internal functionality for the app itself and may change in minor releases without warning.

Additional apps can be easily added to your OMERO.web deployment. One example is the OMERO.webtest app that contains several code samples mentioned in the following pages. You will find install instructions on the OMERO.webtest repository itself.

Getting started

The preferred workflow for extending OMERO.web is to create a new Django app. Django apps provide a nice way for you to keep all your code in one place and make it much easier to port your app to new OMERO releases or share it with other users. To get started, see Creating an app. Further documentation on editing the core OMERO.web code is at Editing OMERO.web. If you want to have a quick look at some example code, see below.

Quick example - OMERO.webtest

This tiny example gives you a feel for how the OMERO.web framework gets data from OMERO and displays it on a web page. You can find this and other examples in the OMERO.webtest repository.

There are 3 parts to each page: url, view and template. For example, this code below is for generating an HTML page of a Dataset (see screen-shot). If you have OMERO.web running, you can view the page under http://servername.example.org/webtest/dataset/<datasetId>.

• url goes in omeroweb/omero_webtest/urls.py This maps the URL ‘webtest/dataset/<datasetId>/’ to the View function ‘dataset’, passing it the datasetId.

  url( r'^dataset/(?P<datasetId>[0-9]+)/$', views.dataset ),
  

• View function, in omeroweb/omero_webtest/views.py. NB: @login_required decorator retrieves connection to OMERO as ‘conn’ passed in args to method. See Writing OMERO.web views for more details.

  from omeroweb.webclient.decorators import login_required
  # handles login (or redirects). Was @isUserConnected before OMERO 4.4
  @login_required()
  def dataset(request, datasetId, conn=None, **kwargs):
      ds = conn.getObject("Dataset", datasetId)
      # generate html from template
      return render(request, 'webtest/dataset.html', {'dataset': ds})
  

• Template: The template web page, in omero-webtest/omero_webtest/templates/webtest/dataset.html

  <html><body>
  
  <h1>{{ dataset.getName }}</h1>
  
  {% for i in dataset.listChildren %}
      <div style="float:left; padding:10px">
          <img src="{% url 'webgateway.views.render_thumbnail' i.id %}" />
          <br />
          {{ i.getName }}
      </div>
  {% endfor %}
  
  </body></html>
  

• Next: Get started by OMERO.web deployment for developers....