OMERO.autotag
================
OMERO.autotag is a plugin for `OMERO.web <https://github.com/ome/omero-web>`_ that automates the application of tags to images based on the
original filename, path, and extensions of the images.
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 autotag, the following are now required. To use autotag on older OMERO systems (running Python 2),
please use versions older than 3.1.0.
* Python 3.5 or later
* omero-web 5.6 or later
* django 1.11 or later
User Documentation
==================
http://help.openmicroscopy.org/web-tagging.html
Installation
============
The recommended way to install autotag 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-autotag
# Add autotag to webclient
omero config append omero.web.apps '"omero_autotag"'
# Add autotag to centre panel
omero config append omero.web.ui.center_plugins '["Auto Tag", "omero_autotag/auto_tag_init.js.html", "auto_tag_panel"]'
Upgrade from omero-webtagging-autotag to omero-autotag
======================================================
Since 3.2.2, the package was renamed to `omero-autotag`. 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-autotag
pip install omero-autotag
# Then open the OMERO.web configuration editor
omero config edit
# Update the two configurations called 'omero.web.apps' and 'omero.web.ui.center_plugins'
# In 'omero.web.apps': 'omero_webtagging_autotag' -> 'omero_autotag'
# In 'omero.web.ui.center_plugins': '["Auto Tag", "omero_webtagging_autotag/auto_tag_init.js.html", "auto_tag_panel"]' -> '["Auto Tag", "omero_autotag/auto_tag_init.js.html", "auto_tag_panel"]'
# 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-autotag`, 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-autotag==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
===========
Uses node and webpack.
This will detect changes and rebuild `static/autotag/js/bundle.js` when there
are any. This works in conjunction with django development server as that
will be monitoring `bundle.js` for any changes.
To build the node components on changes
::
cd omero_webtagging_autotag
npm install
node_modules/webpack/bin/webpack.js --watch
To install using pip in development mode (in appropriate virtualenv)
::
# In the top-level autotag 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 autotag 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.
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"description": "OMERO.autotag\n================\nOMERO.autotag is a plugin for `OMERO.web <https://github.com/ome/omero-web>`_ that automates the application of tags to images based on the\noriginal filename, path, and extensions of the images.\n\nThis 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.\n\nRequirements\n============\n\nAs Python 2 has now reached end-of-life, OMERO 5.6 now\nrequires Python 3. With release 3.1.0 of autotag, the following are now required. To use autotag on older OMERO systems (running Python 2),\nplease use versions older than 3.1.0.\n\n* Python 3.5 or later\n* omero-web 5.6 or later\n* django 1.11 or later\n\nUser Documentation\n==================\n\nhttp://help.openmicroscopy.org/web-tagging.html\n\nInstallation\n============\n\nThe recommended way to install autotag is using `pip`, but it is also possible\nto install it manually as described `here <https://www.openmicroscopy.org/site/support/omero5/developers/Web/CreateApp.html#add-your-app-location-to-your-pythonpath>`_.\n\n::\n\n # In the python environment of OMERO.web (virtualenv or global)\n pip install omero-autotag\n\n # Add autotag to webclient\n omero config append omero.web.apps '\"omero_autotag\"'\n\n # Add autotag to centre panel\n omero config append omero.web.ui.center_plugins '[\"Auto Tag\", \"omero_autotag/auto_tag_init.js.html\", \"auto_tag_panel\"]'\n\nUpgrade from omero-webtagging-autotag to omero-autotag\n======================================================\n\nSince 3.2.2, the package was renamed to `omero-autotag`. 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.\n\nYou can perform the upgrade as follow:\n\n::\n\n # stop omero web\n # Install the new package and uninstall the old one\n pip uninstall omero-webtagging-autotag\n pip install omero-autotag\n \n # Then open the OMERO.web configuration editor\n omero config edit\n # Update the two configurations called 'omero.web.apps' and 'omero.web.ui.center_plugins'\n # In 'omero.web.apps': 'omero_webtagging_autotag' -> 'omero_autotag'\n # In 'omero.web.ui.center_plugins': '[\"Auto Tag\", \"omero_webtagging_autotag/auto_tag_init.js.html\", \"auto_tag_panel\"]' -> '[\"Auto Tag\", \"omero_autotag/auto_tag_init.js.html\", \"auto_tag_panel\"]'\n # start omero web\n\nNote that installing the latest `omero-webtagging-autotag` is not functional but has a dependency on `omero-autotag`. \nThus, if you wish to use the old version `omero-webtagging-autotag`, make sure to specify the latest working version:\n\n::\n\n # ONLY IF YOU WANT TO USE AN OLDER VERSION OF THE PLUGIN\n # stop omero web\n pip install omero-webtagging-autotag==3.2.0\n # And set the configuration accordingly\n # start omero web\n\n\nDocumentation\n=============\n\nAvailable on the `OMERO website <http://help.openmicroscopy.org/web-tagging.html>`_.\n\n\nDevelopment\n===========\n\nUses node and webpack.\n\nThis will detect changes and rebuild `static/autotag/js/bundle.js` when there\nare any. This works in conjunction with django development server as that\nwill be monitoring `bundle.js` for any changes.\n\nTo build the node components on changes\n\n::\n\n cd omero_webtagging_autotag\n npm install\n node_modules/webpack/bin/webpack.js --watch\n\nTo install using pip in development mode (in appropriate virtualenv)\n\n::\n\n # In the top-level autotag directory containing setup.py\n pip install -e .\n cd $OMERO_PREFIX\n\nOMERO development server can then be started in the usual way. Remember to\nconfigure the autotag settings the same as above.\n\nProject Maintenance\n===================\n\nI (Douglas) am no longer actively developing\nOMERO.webtagging. I am thrilled to hand over\nmaintainence and development to\n`German Bioimaging <https://gerbi-gmb.de/i3dbio/i3dbio-about/>`_.\n\nAcknowledgements\n================\n\nOMERO.webtagging was created by Douglas P. W. Russell\n(dpwrussell@gmail.com) while at Oxford University and\nHarvard Medical School, then later extended by DPWR\nConsulting Ltd.\n\nThese plugins were developed originally with the\nsupport of [Micron Advanced Bioimaging Unit](https://micronoxford.com/)\nfunded by the Wellcome Trust Strategic Award 091911,\nand [Open Microscopy](https://www.openmicroscopy.org/).\n\nContinued development was supported by [The Laboratory\nof Systems Pharmacology, Harvard Medical School](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/research-program/) and\n[Research Computing, Harvard Medical School](https://it.hms.harvard.edu/our-services/research-computing).\n\nContinued development was sponsored by\n[Micron Advanced Bioimaging Unit](https://micronoxford.com/)\nfunded by the Wellcome Trust Strategic Award 107457.\n\n\n",
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