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OMERO.tagsearch

OMERO.tagsearch is a plugin for OMERO.web <https://github.com/ome/omero-web>_ that enables searching of data using tags, with the search continuously refined as available search terms are entered and further term suggestions based on the entered terms are offered. This can be used in a way that is similar to navigating a file system hierarchy.

This was formerly part of OMERO.webtagging <https://github.com/German-BioImaging/webtagging>_, the umbrella name for tools developed to enhance use of text annotations (tags) in OMERO.

Requirements

As Python 2 has now reached end-of-life, OMERO 5.6 now requires Python 3. With release 3.1.0 of tagsearch, the following are now required. To use tagsearch on older OMERO systems (running Python 2), please use versions older than 3.1.0.

• Python 3.8 or later
• omero-web 5.6 or later
• django 4.2 or later

User Documentation

http://help.openmicroscopy.org/web-tagging.html

Installation

The recommended way to install tagsearch is using pip, but it is also possible to install it manually as described here <https://www.openmicroscopy.org/site/support/omero5/developers/Web/CreateApp.html#add-your-app-location-to-your-pythonpath>_.

::

In the python environment of OMERO.web (virtualenv or global)

pip install omero-tagsearch

Add tagsearch to webclient

omero config append omero.web.apps '"omero_tagsearch"'

Add a top-link to tagsearch designer

omero config append omero.web.ui.top_links '["Tag Search", "tagsearch"]'

Upgrade from omero-webtagging-tagsearch to omero-tagsearch

Since 3.2.2, the package was renamed to omero-tagsearch. This is a breaking change for OMERO.web, as the old package must be removed from the OMERO.web config and replaced by the new package.

You can perform the upgrade as follow:

::

stop omero web

Install the new package and uninstall the old one

pip uninstall omero-webtagging-tagsearch
pip install omero-tagsearch

Then open the OMERO.web configuration editor

omero config edit

Update the configuration called 'omero.web.apps'

In 'omero.web.apps': 'omero_webtagging_tagsearch' -> 'omero_tagsearch'

start omero web

Note that installing the latest omero-webtagging-autotag is not functional but has a dependency on omero-autotag. Thus, if you wish to use the old version omero-webtagging-tagsearch, make sure to specify the latest working version:

::

ONLY IF YOU WANT TO USE AN OLDER VERSION OF THE PLUGIN

stop omero web

pip install omero-webtagging-tagsearch==3.2.0

And set the configuration accordingly

start omero web

Documentation

Available on the OMERO website <http://help.openmicroscopy.org/web-tagging.html>_.

Development

Pure javascript so does not require a node build step.

To install using pip in development mode (in appropriate virtualenv)

::

In the top-level tagsearch directory containing setup.py

pip install -e . cd $OMERO_PREFIX

OMERO development server can then be started in the usual way. Remember to configure the tagsearch settings the same as above.

Project Maintenance

I (Douglas) am no longer actively developing OMERO.webtagging. I am thrilled to hand over maintainence and development to German Bioimaging <https://gerbi-gmb.de/i3dbio/i3dbio-about/>_.

Acknowledgements

OMERO.webtagging was created by Douglas P. W. Russell (dpwrussell@gmail.com) while at Oxford University and Harvard Medical School, then later extended by DPWR Consulting Ltd.

These plugins were developed originally with the support of Micron Advanced Bioimaging Unit <https://micronoxford.com/> funded by the Wellcome Trust Strategic Award 091911, and Open Microscopy <https://www.openmicroscopy.org/>.

Continued development was supported by The Laboratory of Systems Pharmacology, Harvard Medical School <https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/research-program/> and Research Computing, Harvard Medical School <https://it.hms.harvard.edu/our-services/research-computing>.

Continued development was sponsored by Micron Advanced Bioimaging Unit <https://micronoxford.com/>_ funded by the Wellcome Trust Strategic Award 107457.