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.
You will need to have an OMERO server running that you can connect to. This will typically be on your own machine, although it does not necessarily have to be. If you want to connect to another server (not localhost) you can edit the server list as described on the OMERO.web deployment page (see Unix or Windows version) and choose that server when you log in. That page also describes how to set debug to ‘True’ which is important when developing with OMERO.web and you should also be using the Django ‘development’ server.
You can either add your app to the omeroweb under an OMERO.server release build, or run directly from the OMERO.web source code:
If all your edits will be under your own app, and you are not editing or building the OMERO.web source code, then the simplest option is to directly add your app to the server build under lib/python/omeroweb. This code is run when you start the Django server with
$ bin/omero web start
Starting django development webserver...
Validating models...
0 errors found
Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://0.0.0.0:4080/
Quit the server with CONTROL-C.
Note
Port number is 4080
When you edit and save the code, under lib/python/omeroweb/, Django automatically detects this and you only need to refresh your browser to see the changes. You can see this in the OMERO.web intro movie.
Alternatively,if you have checked out the OMERO.server source code and are building from source, you will have 2 copies of the OMERO.web code - source code is under components/tools/OmeroWeb/omeroweb and the server build is under dist/lib/python/omeroweb. You should be editing the source code since any edits to the build code will get wiped out each time you build! In order to run Django directly from the source code you need to follow a few steps (commands are shown below):
Set $OMERO_HOME, so that OMERO.web knows where to find config, write logs etc.
Note
You should not set $OMERO_HOME on production servers
Make sure that the Django libraries that are under the build: dist/lib/python/django are on your PYTHONPATH.
Remove the built omeroweb folder, otherwise this will get used instead of the source omeroweb
Note
You have to do this again if you build the server
From the source omeroweb/ folder, manually run the Django development server
$ export OMERO_HOME = ~/Desktop/OMERO/dist # Example server build path
# Make sure the Django code etc can be imported
$ export PYTHONPATH=$OMERO_HOME/lib/python/:$PYTHONPATH
$ cd $OMERO_HOME
# need to remove the built omeroweb code so it doesn't get imported
$ rm -rf lib/python/omeroweb/
$ cd ../components/tools/OmeroWeb/omeroweb
$ python manage.py runserver
Validating models...
0 errors found
Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://127.0.0.1:8000/
Quit the server with CONTROL-C.
Note
Default port number is 8000. To specify port, use E.g: $ python manage.py runserver 0.0.0.0:4080
You should make sure that you can access the webclient and webadmin on your local machine before starting to develop your own code. Be sure to use the correct port number as mentioned above, either:
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 github steps below.
The steps below describe setting up a new app. You should choose an appropriate name for your app and use it in place of <your-app> in the examples below:
Login to your github account homepage (E.g. https://github.com/<your-name>/) and click “New repository”
Enter the name of <your-app>, add description and choose to add README.
Change into the /omeroweb/ directory:
# running from build
$ cd lib/python/omeroweb/
# OR: running from source:
$ cd components/tools/OmeroWeb/omeroweb
Checkout your new repository (into a new directory)
$ git clone git@github.com:<your-name>/<your-app>.git
OR: If you haven’t used git to create your app directory above, then
$ mkdir <your-app>
Create an empty file <your-app>/__init__.py (NB: both double underscores)
Create urls.py
from django.conf.urls.defaults import *
from omeroweb.<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!")
This will add your app to the INSTALLED_APPS, so that urls are registered etc.
$ bin/omero config set omero.web.apps '["<your-app>"]'
Note
For releases before 4.4, you need to ‘register’ your app with Django manually by adding it to the INSTALLED_APPS list in omeroweb/settings.py following the pattern of existing apps there. You also need to edit omeroweb/urls.py to add your app’s urls.py file to the list of “urlpatterns”. Again, you should be able to follow the existing examples there. You can also specify at this point the url under which your app will be found.
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>/ 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). This example can be found in webtest.
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_to_response
@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_to_response('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 webgateway to handle the image rendering using a url auto-generated by Django - see WebGateway.
The webtest app has a number of examples. If you go to the webtest homepage E.g. http://localhost:8000/webtest you will see an introduction to some of them. This page tries to find random image and dataset from your OMERO server to use in the webtest examples.
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.
This functionality is under development:
An alternative is to bring your content into the existing webclient. See omeroweb/settings.py “omero.web.ui.right_plugins” and “omero.web.ui.center_plugins”.