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"info": {
"author": "The Open Microscopy Team",
"author_email": "ome-devel@lists.openmicroscopy.org.uk",
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"Development Status :: 5 - Production/Stable",
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"Framework :: Django",
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"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: JavaScript",
"Programming Language :: Python :: 2",
"Topic :: Internet :: WWW/HTTP",
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"description": ".. image:: https://travis-ci.org/ome/omero-mapr.svg?branch=master\n :target: https://travis-ci.org/ome/omero-mapr\n\n.. image:: https://badge.fury.io/py/omero-mapr.svg\n :target: https://badge.fury.io/py/omero-mapr\n\n\nMAPR\n====\n\nOMERO.mapr is an OMERO.web app that enables browsing of data through attributes linked to images\nin the form of Map Annotations.\n\nIt is used extensively by the `Image Data Resource `_,\nallowing users to find data by various categories such as Genes, Phenotypes, Organism etc.\n\nIn OMERO, Map Annotations are lists of named attributes or \"Key-Value Pairs\" that can be used to\nannotate many types of data. Annotations can be assigned a ``namespace``\nto indicate the origin and purpose of the annotation.\n\nMap Annotations created by users via the Insight client or webclient all have the\nnamespace ``openmicroscopy.org/omero/client/mapAnnotation``, whereas other\nMap Annotations created via the OMERO API by other tools should have their own distinct\nnamespace.\n\nWe can configure OMERO.mapr to search for Map Annotations of specified ``namespace``,\nlooking for ``Values`` under specifed ``Keys``.\nFor example, seach for values under key ``Gene Symbol`` or ``Gene Identifier``\nand namespace ``openmicroscopy.org/mapr/gene``.\n\n.. image:: https://user-images.githubusercontent.com/900055/36256919-d8a19fb6-124c-11e8-8628-d792ff29bd22.png\n\n\nRequirements\n============\n\n* OMERO 5.3 or newer.\n\nInstalling from Pypi\n====================\n\nThis section assumes that an OMERO.web is already installed.\nNB: Configuration of the settings (see below) is not optional\nand is required for the app to work.\n\nInstall the app using `pip `_:\n\n::\n\n $ pip install omero-mapr\n\nAdd the app to the list of installed apps:\n\n::\n\n $ bin/omero config append omero.web.apps '\"omero_mapr\"'\n\n\nConfig Settings\n===============\n\nYou need to configure the namespaces and keys that you want users to be able to search for.\n\nUser-edited Map Annotations\n---------------------------\n\nMap Annotations that are added using the webclient or Insight in the Key-Value panel\nuse a specific \"client\" namespace. We can therefore configure OMERO.mapr to search\nfor these annotations using the namespace ``openmicroscopy.org/omero/client/mapAnnotation``.\nFor example, to search for \"Primary Antibody\" or \"Secondary Antibody\" values, we can add:\n\n::\n\n $ bin/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\"}}'\n\nWe can add an \"Antibodies\" link to the top of the webclient page to take us to the Antibodies search page.\nThe link tooltip is \"Find Antibody values\".\nThe ``viewname`` should be in the form ``maprindex_{menu}`` where ``{menu}`` is the the ``menu`` value in the previous config.\n\n::\n\n $ bin/omero config append omero.web.ui.top_links '[\"Antibodies\", {\"viewname\": \"maprindex_antibody\"}, {\"title\": \"Find Antibody values\"}]'\n\nAfter restarting web, we can now search for Antibodies:\n\n.. image:: https://user-images.githubusercontent.com/900055/40605069-063ff29a-6259-11e8-9295-3887dde0441f.png\n\n\nWe can also specify an empty list of keys to search for *any* value.\n\n::\n\n $ bin/omero config append omero.web.mapr.config '{\"menu\": \"anyvalue\", \"config\":{\"default\":[\"Any Value\"], \"all\":[], \"ns\":[\"openmicroscopy.org/omero/client/mapAnnotation\"], \"label\":\"Any\"}}'\n\n # Top link\n $ bin/omero config append omero.web.ui.top_links '[\"Any Value\", {\"viewname\": \"maprindex_anyvalue\"}, {\"title\": \"Find Any Value\"}]'\n\nAfter restarting web, we can now search for any Value, such as \"INCENP\":\n\n.. image:: https://user-images.githubusercontent.com/900055/40605101-1cd1925c-6259-11e8-93a8-e72af2e570d3.png\n\n\nOther Map Annotations\n---------------------\n\nIn this example we want to search\nfor Map Annotations of namespace ``openmicroscopy.org/mapr/gene`` searching for\nattributes under the ``Gene Symbol`` and ``Gene Identifier`` keys.\n\n::\n\n $ bin/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\"}}'\n\nNow 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``\nspecifying that we want to search across all users.\n\n::\n\n $ bin/omero config append omero.web.ui.top_links '[\"Genes\", {\"viewname\": \"maprindex_gene\", \"query_string\": {\"experimenter\": -1}}, {\"title\": \"Find Gene annotations\"}]'\n\n\nFinally, we can add a map annotation to an Image that is in a Screen -> Plate -> Well\nor Project -> Dataset -> Image hierarchy.\nThis code uses the OMERO `Python API `_ to\nadd a map annotation corresponding to the configuration above:\n\n::\n\n key_value_data = [[\"Gene Identifier\",\"ENSG00000117399\"],\n [\"Gene Identifier URL\", \"http://www.ensembl.org/id/ENSG00000117399\"],\n [\"Gene Symbol\",\"CDC20\"]]\n map_ann = omero.gateway.MapAnnotationWrapper(conn)\n map_ann.setValue(key_value_data)\n map_ann.setNs(\"openmicroscopy.org/mapr/gene\")\n map_ann.save()\n image = conn.getObject('Image', 2917)\n image.linkAnnotation(map_ann)\n\n\nNow restart OMERO.web as normal for the configuration above to take effect.\nYou should now be able to browse to a ``Genes`` page and search for\n``CDC20`` or ``ENSG00000117399``.\n\n\nTesting\n=======\n\nTesting MAPR requires OMERO.server running.\nRun tests (includes self-contained OMERO.server, requires docker)::\n\n docker-compose -f docker/docker-compose.yml up --build --abort-on-container-exit\n docker-compose -f docker/docker-compose.yml rm -fv\n\nLicense\n-------\n\nMAPR is released under the AGPL.\n\n\nCopyright\n---------\n\n2016, The Open Microscopy Environment",
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