OMERO.web for developers

OME Meeting, Dundee 2017

Will Moore | Jean-Marie Burel

Outline

• The OMERO.web framework
• JSON api
• Example apps
• Extension points: top-links, webclient-plugin, open-with
• App installation via PyPI
• Decoupling of OMERO.web deployment
• Getting Started

OMERO.web framework

OMERO.web apps

JSON API app

• ✔ Access JSON API from language of choice: Java, Python, JavaScript, Matlab etc
• ✔ Don't need ICE
• ✔ Not tied to specific version of OMERO
• ✔ Installed by individual users (instead of sysadmin)
• ✔ Developers don't need to install OMERO.web
• ✘ Currently limited API coverage
• ✘ May be less performant than ICE for large queries?
• ✘ Stateless only. No stateful services

JSON API

• OMERO.web app /api/
• JSON generated by omero-marshal from OMERO.model objects
• Login via POST to /api/v0/login/
• 5.3.0 supports GET Project, Dataset, Image, Screen, Plate, Well
• 5.3.2 adds GET ROIs and Shapes
• Can Create, Update and Delete Projects, Datasets & Screens only
• Doesn't use jsonp (webgateway does). Use CORS instead
• Urls included in JSON to facilitate exploring in browser
• See JSON API docs

JSON API in the browser

JSON API with Python

import requests
session = requests.Session()
# Set CSRF token
token = session.get("http://server.org/api/v0/token/").json()['data']
session.headers.update({'X-CSRFToken': token,
                        'Referer': "http://server.org/api/v0/token/"})
# Login
session.post("http://server.org/api/v0/login/", data={'username': USERNAME,
                                                      'password': PASSWORD,
                                                      'server': 1})
# List Projects
rsp = session.get("http://server.org/api/v0/m/projects/").json()
for p in rsp['data']:
    print p['@id'], p['Name']

JSON Login via CORS

webgateway API

• Json data: e.g. Image json webgateway/imgData/<imageId>/
• Image rendering: webgateway/render_image/<imageId>/<z>/<t>/

See WebGateway documentation

App examples

• Ship with OMERO.web:
  • webgateway | webclient | webadmin | api
• External apps:
  • Stowers ODR | JCB DataViewer | OMERO.webtagging |
    OMERO.forms | CATMAID | FPBioimage
• OME projects:
  • OMERO.figure | OMERO.iviewer |
    OMERO.mapr (used by IDR)
• Examples & Prototypes:
  • webtest | OMERO.gallery | OMERO.player

Custom Repos

• Stowers ODR
• JCB DataViewer
• Harvard Medical School (HMS) LINCS

OMERO.gallery

• HTML pages generated via Django templates
• Suitable for mobile devices
• Prototype / example app (not actively developed)

OMERO.figure

OMERO.iviewer

• First release 0.1.0 on 25th May 2017
• Uses aurelia js framework with Open Layers
• Loads data via /api/ and /webgateway/ urls
• Developed by Harald Waxenegger. See: omero-iviewer

OMERO.mapr (IDR)

• Extends webclient Django-based pages
• Many custom API queries of map annotations
• IDR uses the Public user to allow auto-login via OMERO.web
• See: omero-mapr

OMERO.webtagging

• Auto-tag: Add Tags to Images based on file path
• Tag-searcher: Filter data by series of Tags
• Douglas Russell (Micron, Oxford) See: OMERO.webtagging

OMERO.forms

• Create forms to validate metadata input
• Douglas Russell (Sorger Lab, HMS). See: OMERO.forms

3rd party viewers

• CATMAID loading image data via OMERO-CATMAID by L'École polytechnique
  
• FPBioimage 3D viewer from Laser Analytics Group, Cambridge packaged as OMERO-FPBioimage by OME

Webclient plugins

• Links and hooks to access apps from webclient
• See Linking from webclient and webclient plugin docs

Open With...

$ bin/omero config append omero.web.open_with '["omero_iviewer", "omero_iviewer_index",
  {"supported_objects":["image"], "script_url": "omero_iviewer/openwith.js"}]'
                    

// openwith.js
OME.setOpenWithUrlProvider("omero_iviewer", function(selected, url) {
    // Add image Id to url
    url += selected[0].id + "/";

    // We try to traverse the jstree, to find parent of selected image
    var inst = $.jstree.reference('#dataTree');
    var parent = OME.getTreeImageContainerBestGuess(selected[0].id);
    url += '?' + parent.type + '=' + parent.data.id

    return url;
});
                    

Open with from OMERO.figure

App JavaScript frameworks

*prototype app

App installation via PyPI

• Make OMERO.web apps "pip installable"
• Easier to deploy in CI environment for testing
• Easier for users to install

$ pip install omero-iviewer
$ bin/omero config append omero.web.apps '"omero_iviewer"'

Decoupling of OMERO.web deployment

• OMERO.web installed on different machine / environment from OMERO.server
• Use virtualenv to control Python version & dependencies
• Independent deployment & testing
• See OMERO.web deployment docs

Getting Started

Summary

• Try installing some apps
• Create your own apps and share!

Thank you