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.
The Django web site has a very good tutorial to get you familiar with the Django framework. The more you know about Django, the easier you will find it working with the OmeroWeb framework. One major feature of Django that we do not use in OmeroWeb is the Django database mapping, since all data comes from the OMERO server and is saved back there. You will notice that the models.py files in each app are empty.
In order to deploy OMERO.web in a development or testing environment please follow the instructions under OMERO.web deployment for developers.
You should make sure that you can access the webclient on your local machine before starting to develop your own code. Be sure to use the correct port number, e.g.:
When you edit and save your app, Django will automatically detect this and you only need to refresh your browser to see the changes.
If you want to make changes to the OMERO.web code itself, you should see Editing OMERO.web.
You can place your app anywhere on your PYTHONPATH, as long as it can be imported by OMERO.web.
We suggest you use GitHub (as we do) since it is much easier for us to help you with any problems you have if we can see your code. The steps below describe how to create a stand-alone git repository for your app, similar to webtagging. If you do not want to use GitHub, simply ignore the steps related to GitHub.
The steps below describe how to set up a new app. You should choose an appropriate name for your app and use it in place of <your-app>:
Your app needs to be within a directory that is on your PYTHONPATH. We usually create a new container for a new app, and add it to the PYTHONPATH.
$ mkdir PARENT-APP-DIR
$ cd PARENT-APP-DIR
$ export PYTHONPATH=$PYTHONPATH:/path/to/PARENT-APP-DIR
OR you could simply choose an existing location:
$ cd /somewhere/on/your/pythonpath/
Login to your GitHub account homepage (e.g. https://github.com/<your-name>/) and click “New repository”
Enter the name of <your-app>, add a description and choose to add a README.
Check out your new repository (into a new directory)
$ git clone git@github.com:<your-name>/<your-app>.git
OR: If you have not used git to create your app directory above, then
$ mkdir <your-app>
In either case, you should now have a directory called your-app within a directory that is on your PYTHONPATH.
Create an empty file <your-app>/__init__.py (NB: both double underscores)
Create urls.py
from django.conf.urls import *
from <your-app> import views
urlpatterns = patterns('django.views.generic.simple',
# index 'home page' of the <your-app> app
url( r'^$', views.index, name='<your-app>_index' ),
)
Create views.py
from django.http import HttpResponse
def index(request):
"""
Just a place-holder while we get started
"""
return HttpResponse("Welcome to your app home-page!")
For more details on how to write views, forms, using templates, etc. check the Django documentation.
omero.web.apps adds your custom application to the INSTALLED_APPS, so that URLs are registered etc.
Note
Here we use single quotes around double quotes, since we are passing a double-quoted string as a json object.
$ bin/omero config append omero.web.apps '"<your-app>"'
Now you can view the home-page we created above (NB: you will need to restart the OMERO.web server for the config settings to take effect).
$ bin/omero web stop
$ bin/omero web start
Go to http://localhost:4080/<your-app>/ OR http://localhost:8000/<your-app>/ and you should see ‘Welcome’.
$ git status (see new files, plus .pyc files)
$ echo "*.pyc" > .gitignore # ignore .pyc files
$ echo ".gitignore" >> .gitignore # ALSO ignore .gitignore
$ git add ./
$ git commit -m "Initial commit of bare-bones OMERO.web app"
$ git push origin master
We have got our new app working, but it is not connecting to OMERO yet. Let us create a simple “stack preview” for an Image with multiple Z-sections. We are going to display the image name and 5 planes evenly spaced across the Z-stack. You should be able to add the appropriate code to urls.py, views.py that you created above, and add a template under /omeroweb/<your-app>/templates/<your-app>/
Note
note that /<your-app>/ appears twice in that path (need an extra folder under templates).
The following example can be found in the OMERO.webtest repository.
urls.py
url( r'^stack_preview/(?P<imageId>[0-9]+)/$', views.stack_preview,
name="<your-app>_stack_preview" ),
views.py Here we are using the @login_required decorator to retrieve a connection to OMERO from the session key in the HTTP request (or provide a login page and redirect here). conn is passed to the method arguments. NB: Note a couple of new imports to add at the top of your page.
from omeroweb.webclient.decorators import login_required
from django.shortcuts import render
@login_required()
def stack_preview (request, imageId, conn=None, **kwargs):
""" Shows a subset of Z-planes for an image """
image = conn.getObject("Image", imageId) # Get Image from OMERO
image_name = image.getName()
sizeZ = image.getSizeZ() # get the Z size
# 5 Z-planes
z_indexes = [0, int(sizeZ*0.25),
int(sizeZ*0.5), int(sizeZ*0.75), sizeZ-1]
return render(request, 'webtest/stack_preview.html',
{'imageId':imageId,
'image_name':image_name,
'z_indexes':z_indexes})
<your-app>/templates/<your-app>/stack_preview.html
<html>
<head>
<title>Stack Preview</title>
</head>
<body>
<h1>{{ image_name }}</h1>
{% for z in z_indexes %}
<img src="{% url 'webgateway.views.render_image' imageId z 0 %}"
style="max-width: 200px; max-height:200px"/>
{% endfor %}
</body>
</html>
Viewing the page at http://localhost:4080/<your-app>/stack_preview/<image-id>/ should give you the image name and 5 planes from the Z stack. You will notice that we are using the webgateway to handle the image rendering using a URL auto-generated by Django - see WebGateway.
The OMERO.webtest app has a number of examples. Once installed, you can go to the webtest homepage e.g. http://localhost:4080/webtest and you will see an introduction to some of them. This page tries to find random images and datasets from your OMERO server to use in the webtest examples.
OMERO.web uses the jQuery and jQuery UI javascript libraries extensively. If you need these libraries, you can include the OMERO.web versions of these libraries in your own pages. The alternative is to provide a specific version of jQuery or jQuery UI in your own app if, for example, you think that a version change may cause problems in your code. If you need to make use of these resources in your own pages, you can add the following statements to the <head> of your page templates:
<!-- jQuery -->
{% include "webgateway/base/includes/script_src_jquery.html" %}
<!-- jQuery UI - includes js and css -->
{% include "webgateway/base/includes/jquery-ui.html" %}
The OMERO 5.1.0 release included an upgrade to jQuery 1.11.1 and jQuery UI 1.10.4. We have added jQuery-migrate library (1.2.1) to reduce the effects of this upgrade. You should inspect the javascript console during development to observe any warning messages.
We provide several HTML templates in webgateway/templates/webgateway/base. This is a nice way of giving users the feeling that they have not left the webclient, if you are providing additional functionality for webclient users. You may choose not to use this if you are building a ‘stand-alone’ web application. In either case, it is good practice to create your own templates with common components (links, logout etc.), so you can make changes to all your pages at once. See Writing page templates in OMERO.web for more info.
You can add settings to your app that allow configuration via the command line in the same way as for the base OMERO.web. The list of CUSTOM_SETTINGS_MAPPINGS in components/tools/OmeroWeb/omeroweb/settings.py is a good source for examples of the different data types and parsers you can use.
For example, if you want to create a user-defined setting yourapp.foo, that contains a dictionary of key-value pairs, you can add to CUSTOM_SETTINGS_MAPPINGS in yourapp/settings.py:
import json
CUSTOM_SETTINGS_MAPPINGS = {
"omero.web.yourapp.foo": ["FOO", '{"key": "val"}', json.loads]
}
From somewhere else in your app, you can then access the settings:
from yourapp import settings
print settings.FOO
Users can then configure this on the command line as follows:
$ bin/omero config set omero.web.yourapp.foo '{"userkey": "userval"}'
You can configure omero.web.ui.top_links to add links to the list of links at the top of the webclient main pages.
Name your URL in urls.py (optional). Preferably we use URL names to refer to URLs. For example, the homepage of your app might be named like this in yourapp/urls.py.
url( r'^$', views.index, name='figure_index' ),
You can then refer to the link defined above using this name, or you can simply use a full URL for external links.
Update configuration Use the OMERO command line interface to append the link to the top_links list.
Links use the format ["Label", "URL_name"] or you can follow this example:
$ bin/omero config append omero.web.ui.top_links '["Figure", "figure_index"]'
From OMERO 5.1, you can add additional attributes to links using the format ['Link Text', 'link', attrs]. This can be used to add tool-tips and to open the link in a new “target” tab. For example:
$ bin/omero config append omero.web.ui.top_links '["Homepage", "http://myhome.com", {"title": "Homepage", "target": "new"}]'
If you have created your own image viewer and would like to have it replace the existing image viewer in the webclient, this can be configured using omero.web.viewer.view.
You will need your views.py method to take an Image ID with a parameter named iid. For example, see channel_overlay_viewer from the omero-webtest app:
@login_required()
def channel_overlay_viewer(request, iid, conn=None, **kwargs):
You can then configure the webclient to use this viewer by providing the full path name to this view method. For example, if you have omero-webtest installed you can use the channel_overlay_viewer:
$ bin/omero config set omero.web.viewer.view webtest.views.channel_overlay_viewer
This will now direct the image viewer url at webclient/img_detail/<iid>/ to this viewer. However, the existing viewer will still be available under webgateway at webgateway/img_detail/<iid>/.
If you want to use a different viewer for different images, you can conditionally redirect to the webgateway viewer or elsewhere. For example:
if image.getSizeC() == 1:
return HttpResponseRedirect(reverse("webgateway.views.full_viewer", args=(iid,)))
If you want to display content from your app within the webclient UI, please see Webclient Plugins.