OMERO.figure

An OMERO.web app for creating figures from images in OMERO.

For full details see SUPPORT.md.

Requirements

• OMERO.web 5.6.0 or newer.

Installing from PyPI

This section assumes that an OMERO.web is already installed.

Install the app using pip:

NB: You need to ensure that you are running pip from the python environment where omero-web is installed. Depending on your install, you may need to call pip with, for example: /path/to_web_venv/venv/bin/pip install ...

$ pip install -U omero-figure

Add figure custom app to your installed web apps:

$ omero config append omero.web.apps '"omero_figure"'

Display a link to 'Figure' at the top of the webclient:

$ omero config append omero.web.ui.top_links '["Figure", "figure_index",
  {"title": "Open Figure in new tab", "target": "_blank"}]'

Add 'Figure' to the 'Open with' options, available from context menu on the webclient tree:

$ omero config append omero.web.open_with '["omero_figure", "new_figure",
  {"supported_objects":["images"], "target": "_blank", "label": "OMERO.figure"}]'

Now restart OMERO.web as normal.

Enabling figure export

This section assumes that an OMERO.server is already installed.

Figures can be exported as PDF or TIFF files using a script that runs on the OMERO.server. This script needs to be uploaded to the OMERO.server and its dependencies installed in the OMERO.server virtual environment.

The script can be uploaded using two alternative workflows, both of which require you to have the correct admin privileges. To find where OMERO.figure has been installed using pip, run:

$ pip show omero-figure

The command will display the absolute path to the directory where the application is installed e.g. ~/<virtualenv_name>/lib/python3.6/site-packages. Go to that directory.

Option 1: Connect to the OMERO server and upload the script via the CLI. It is important to be in the correct directory when uploading so that the script is uploaded with the full path: omero/figure_scripts/Figure_To_Pdf.py:

$ cd omero_figure/scripts
$ omero script upload omero/figure_scripts/Figure_To_Pdf.py --official

Option 2: Alternatively, before starting the OMERO.server, copy the script from the figure install /omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py to the OMERO.server path/to/OMERO.server/lib/scripts/omero/figure_scripts. Then restart the OMERO.server.

Now install the script's dependencies:

• Install reportlab PDF python package. This needs to be installed in the virtual environment where the OMERO.server is installed. Depending on your install, you may need to call pip with, for example: /path/to_server_venv/venv/bin/pip install ...

$ pip install "reportlab<3.6"

• Optional: Figure legends can be formatted using Markdown syntax. To see this correctly in the exported PDF info page, we need Python Markdown:

$ pip install markdown

Upgrading OMERO.figure

After upgrading OMERO.figure with:

$ pip install -U omero-figure

You need to update the Figure export script using one of the 2 options described above. If using Option 1, you need to replace the existing script:

# Get the ID of the existing Figure_To_Pdf script:
$ omero script list

# Replace the script
$ cd omero_figure/scripts
$ omero script replace <SCRIPT_ID> omero/figure_scripts/Figure_To_Pdf.py

Development

We use Grunt for various tools. See http://figure.openmicroscopy.org/2014/05/01/testing-with-jshint-jasmine-grunt.html for an introduction.

Install Node from https://nodejs.org, then:

$ cd omero-figure
$ npm install

Install Grunt CLI as described on http://gruntjs.com/using-the-cli.

To build various resources into omero_figure/static run:

$ grunt build

This will concatenate js files into a single figure.js file, compile the underscore templates into templates.js and also copy the shape-editor.js from node_modules.

During development, you will want to peform the concatenation (concat) and template compilation (jst) tasks whenever the JavaScript or template files change. This can be achieved with:

$ grunt watch

It is also possible to develop figure in docker without installing anything locally. The Docker image is built on top of openmicroscopy/omero-web-standalone:latest, so you will have a fully functional omero-web environment while developing omero-figure. First build the Docker image:

$ docker build -t figure-devel .

To develop omero-figure you can either make all the changes within the Docker container itself by running:

$ docker run -ti -e OMEROHOST=YOUR_HOST -p 4080:4080 figure-devel

The preferred option is to mount the repository containing the omero-figure code. Make the changes locally and see the changes in the docker container. To do so, run:

::

$ docker run -ti -e OMEROHOST=YOUR_HOST -p 4080:4080 -v /PATH_TO_GIT_REPO/omero-figure:/home/figure/src figure-devel

After starting the container, run docker ps in another terminal to find the ID of the container. Then run:

$ docker exec -u 0 -it CONTAINER_ID bash   # replace CONTAINER_ID by the correct value
$ cd /home/figure/src
$ grunt watch

Release process

This repository uses bump2version to manage version numbers. To tag a release run:

$ bumpversion release

This will remove the .dev0 suffix from the current version, commit, and tag the release.

To switch back to a development version run:

$ bumpversion --no-tag [major|minor|patch]

specifying major, minor or patch depending on whether the development branch will be a major, minor or patch release. This will also add the .dev0 suffix.

Remember to git push all commits and tags.

License

OMERO.figure is released under the AGPL.

Copyright

2016-2022, The Open Microscopy Environment