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OMERO.mapr is an OMERO.web app that enables browsing of data through attributes linked to images in the form of Map Annotations.
It is used extensively by the Image Data Resource <https://idr.openmicroscopy.org/>_,
allowing users to find data by various categories such as Genes, Phenotypes, Organism etc.
In OMERO, Map Annotations are lists of named attributes or "Key-Value Pairs" that can be used to
annotate many types of data. Annotations can be assigned a namespace
to indicate the origin and purpose of the annotation.
Map Annotations created by users via the Insight client or webclient all have the
namespace openmicroscopy.org/omero/client/mapAnnotation, whereas other
Map Annotations created via the OMERO API by other tools should have their own distinct
namespace.
We can configure OMERO.mapr to search for Map Annotations of specified namespace,
looking for Values under specifed Keys.
For example, seach for values under key Gene Symbol or Gene Identifier
and namespace openmicroscopy.org/mapr/gene.
.. image:: https://user-images.githubusercontent.com/900055/36256919-d8a19fb6-124c-11e8-8628-d792ff29bd22.png
This section assumes that an OMERO.web is already installed. NB: Configuration of the settings (see below) is not optional and is required for the app to work.
Install the app using pip <https://pip.pypa.io/en/stable/>_:
::
$ pip install omero-maprAdd the app to the list of installed apps:
::
$ omero config append omero.web.apps '"omero_mapr"'You need to configure the namespaces and keys that you want users to be able to search for. A general config is structured like this:
::
$ omero config append omero.web.mapr.config '{"menu": "gene", "config": {"default": ["Gene Symbol"], "all": ["Gene Symbol", "Gene Identifier"], "ns": ["openmicroscopy.org/mapr/gene"], "wildcard": {"enabled": true}, "case_sensitive": "true", "label": "Gene"}}'
With the following meanings:
omero.web.ui.top_links.omero.web.ui.top_links.Phenotype search <https://idr.openmicroscopy.org/mapr/phenotype/?experimenter=-1>_ serves as an example for this behaviour.In general, the IDR config (here <https://github.com/IDR/deployment/blob/master/ansible/group_vars/omero-hosts.yml>_ as a yaml representation) serves as a great example containing an extensive omero.web.mapr.config.
Map Annotations that are added using the webclient or Insight in the Key-Value panel
use a specific "client" namespace. We can therefore configure OMERO.mapr to search
for these annotations using the namespace openmicroscopy.org/omero/client/mapAnnotation.
For example, to search for "Primary Antibody" or "Secondary Antibody" values, we can add:
::
$ omero config append omero.web.mapr.config '{"menu": "antibody", "config":{"default":["Primary Antibody"], "all":["Primary Antibody", "Secondary Antibody"], "ns":["openmicroscopy.org/omero/client/mapAnnotation"], "label":"Antibody"}}'We can add an "Antibodies" link to the top of the webclient page to take us to the Antibodies search page.
The link tooltip is "Find Antibody values".
The viewname should be in the form maprindex_{menu} where {menu} is the the menu value in the previous config.
::
$ omero config append omero.web.ui.top_links '["Antibodies", {"viewname": "maprindex_antibody"}, {"title": "Find Antibody values"}]'After restarting web, we can now search for Antibodies:
.. image:: https://user-images.githubusercontent.com/900055/40605069-063ff29a-6259-11e8-9295-3887dde0441f.png
We can also specify an empty list of keys to search for any value.
::
$ omero config append omero.web.mapr.config '{"menu": "anyvalue", "config":{"default":["Any Value"], "all":[], "ns":["openmicroscopy.org/omero/client/mapAnnotation"], "label":"Any"}}'
# Top link
$ omero config append omero.web.ui.top_links '["Any Value", {"viewname": "maprindex_anyvalue"}, {"title": "Find Any Value"}]'After restarting web, we can now search for any Value, such as "INCENP":
.. image:: https://user-images.githubusercontent.com/900055/40605101-1cd1925c-6259-11e8-93a8-e72af2e570d3.png
In this example we want to search
for Map Annotations of namespace openmicroscopy.org/mapr/gene searching for
attributes under the Gene Symbol and Gene Identifier keys.
::
$ omero config append omero.web.mapr.config '{"menu": "gene","config": {"default": ["Gene Symbol"],"all": ["Gene Symbol", "Gene Identifier"],"ns": ["openmicroscopy.org/mapr/gene"],"label": "Gene"}}'Now add a top link of Genes with tooltip Find Gene annotations that will take us to the gene search page. The query_string parameters are added to the URL, with "experimenter": -1
specifying that we want to search across all users.
::
$ omero config append omero.web.ui.top_links '["Genes", {"viewname": "maprindex_gene", "query_string": {"experimenter": -1}}, {"title": "Find Gene annotations"}]'Finally, we can add a map annotation to an Image that is in a Screen -> Plate -> Well
or Project -> Dataset -> Image hierarchy.
This code uses the OMERO Python API <https://docs.openmicroscopy.org/latest/omero/developers/Python.html>_ to
add a map annotation corresponding to the configuration above:
::
key_value_data = [["Gene Identifier","ENSG00000117399"],
["Gene Identifier URL", "http://www.ensembl.org/id/ENSG00000117399"],
["Gene Symbol","CDC20"]]
map_ann = omero.gateway.MapAnnotationWrapper(conn)
map_ann.setValue(key_value_data)
map_ann.setNs("openmicroscopy.org/mapr/gene")
map_ann.save()
image = conn.getObject('Image', 2917)
image.linkAnnotation(map_ann)Now restart OMERO.web as normal for the configuration above to take effect.
You should now be able to browse to a Genes page and search for
CDC20 or ENSG00000117399.
Note that if you create multiple Map Annotations with the same Namespace, this will result in a more verbose layout in the webclient UI. It is preferable to combine all Key-Value pairs for a particular Namespace into a single Map Annotation.
External URL Favicons ^^^^^^^^^^^^^^^^^^^^^
Mapr can automatically convert URLs into favicon links.
To use this feature the key such as Gene Identifier must be in the "all" list of a config
as shown above and the Gene Identifier key-value pair must be followed by a key-value pair
called Gene Identifier URL.
A favicon linked to the external URL will be appended to the Gene Identifier row, and the
Gene Identifier URL key-value pair will be hidden.
OMERO.web must be configured with the Django redis cache
https://docs.openmicroscopy.org/omero/5/sysadmins/unix/install-web/walkthrough/omeroweb-install-centos7-ice3.6.html?highlight=redis#configuring-omero-web
which is used to cache the favicons that are obtained using a Google service.
If your IT structure utilizes a proxy and you are unwilling to set the proxy on a system level for the OMERO(.web) server you can set one directly in the requests.get() method <https://github.com/ome/omero-mapr/blob/99dfb1a17418dbc996b9cb402e35db9d8e4b79f8/omero_mapr/views.py#L669>_ like this
::
proxies = {'http':'http://wwwproxy.<youproxy>.de:80','https':'http://wwwproxy.<yourproxy>.de:80'}
r = requests.get(
"%s%s" % (mapr_settings.FAVICON_WEBSERVICE, favdomain),
stream=True, proxies = proxies)Map Annotations on Wells/Images ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ For Plates the same Map Annotation that is on an Image has to also be on its corresponding Well for the Values to be correctly findable in the search function. The reasons for this rather unintuitive behaviour are partly historical, as in the past no Annotations were shown for Images when browsing Screen-Plate-Well data, and partly performance related, as the query runs quicker by saving a JOIN when you're trying to find matching Plates if you only need to query Wells instead of Images.
Testing MAPR requires OMERO.server running. Run tests (includes self-contained OMERO.server, requires docker)::
docker-compose -f docker/docker-compose.yml up --build --abort-on-container-exit
docker-compose -f docker/docker-compose.yml rm -fvMAPR is released under the AGPL.
2016-2021, The Open Microscopy Environment