Creating an app =============== The Django web site has a very good :djangodoc:`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 files in each app are empty. Getting set up -------------- In order to deploy OMERO.web in a development or testing environment please follow the instructions under :doc:`Deployment`. 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.: - `http://localhost:4080/webclient/ `_ 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 :doc:`/developers/Web/EditingOmeroWeb`. You can place your app anywhere on your :envvar:`PYTHONPATH`, as long as it can be imported by OMERO.web. Creating an app --------------- 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 : Add your app to your PYTHONPATH ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Your app needs to be within a directory that is on your :envvar:`PYTHONPATH`. We usually create a new container for a new app, and add it to the :envvar:`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/ Create and check out a new GitHub repository OR manually create a new directory ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Login to your GitHub account homepage (e.g. ``_\ /) and click "New repository" - Enter the name of , add a description and choose to add a README. - Check out your new repository (into a new directory) :: $ git clone - OR: If you have not used git to create your app directory above, then :: $ mkdir - In either case, you should now have a directory called ``your-app`` within a directory that is on your :envvar:`PYTHONPATH`. Add the essential files to your app ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Create an empty file ``/`` (NB: both double underscores) - Create :file:`` :: from django.conf.urls import * from import views urlpatterns = patterns('django.views.generic.simple', # index 'home page' of the app url( r'^$', views.index, name='_index' ), ) - Create :file:`` :: 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 :djangodoc:`Django documentation `. Add your app to OMERO.web ^^^^^^^^^^^^^^^^^^^^^^^^^ :property:`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 '""' 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/ `_\ / OR `http://localhost:8000/ `_\ / and you should see 'Welcome'. Commit your code and push to GitHub ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ :: $ 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 Connect to OMERO: example ^^^^^^^^^^^^^^^^^^^^^^^^^ 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 :file:``, :file:`` that you created above, and add a template under /omeroweb//templates// .. note:: note that // appears twice in that path (need an extra folder under templates). The following example can be found in the `OMERO.webtest `_ repository. - **** :: url( r'^stack_preview/(?P[0-9]+)/$', views.stack_preview, name="_stack_preview" ), - **** 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}) - **/templates//stack\_preview.html** :: Stack Preview

{{ image_name }}

{% for z in z_indexes %} {% endfor %} Viewing the page at http://localhost:4080//stack_preview// 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 :doc:`/developers/Web/WebGateway`. Resources for writing your own code ----------------------------------- The `OMERO.webtest `_ app has a number of examples. Once installed, you can go to the webtest homepage e.g. ``_ 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. .. _jquery_and_jquery_ui: Using jQuery and jQuery UI from OMERO.web ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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 ```` of your page templates: :: {% include "webgateway/base/includes/script_src_jquery.html" %} {% 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. Extending templates ^^^^^^^^^^^^^^^^^^^ 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 :doc:`/developers/Web/WritingTemplates` for more info. App settings ------------ 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 :sourcedir:`components/tools/OmeroWeb/omeroweb/` 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, that contains a dictionary of key-value pairs, you can add to ``CUSTOM_SETTINGS_MAPPINGS`` in ``yourapp/``: :: import json CUSTOM_SETTINGS_MAPPINGS = { "": ["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 '{"userkey": "userval"}' OMERO.web top links ^^^^^^^^^^^^^^^^^^^ You can configure :property:`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** (optional). Preferably we use URL names to refer to URLs. For example, the homepage of your app might be named like this in yourapp/ :: 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", "", {"title": "Homepage", "target": "new"}]' Custom image viewer ^^^^^^^^^^^^^^^^^^^ 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 :property:`omero.web.viewer.view`. You will need your :file:`` 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//`` to this viewer. However, the existing viewer will still be available under webgateway at ``webgateway/img_detail//``. 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,))) OMERO.web plugins ----------------- If you want to display content from your app within the webclient UI, please see :doc:`/developers/Web/WebclientPlugin`.