OMERO figure creation app
Project description
OMERO.figure
An OMERO.web app for creating figures from images in OMERO.
For full details see SUPPORT.md.
Requirements
OMERO 5.4.0 or newer.
Installing from PyPI
This section assumes that an OMERO.web is already installed.
Install the app using pip:
$ pip install -U omero-figure
Add figure custom app to your installed web apps:
$ bin/omero config append omero.web.apps '"omero_figure"'
Display a link to ‘Figure’ at the top of the webclient:
$ bin/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:
$ bin/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 on the OMERO.server machine.
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/python2.7/site-packages. Go to that directory.
Option 1: Connect to the OMERO server and upload 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 $ path/to/OMERO.server/bin/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 from distribution packages. For example, install on CentOS 7:
$ yum install python-reportlab
Optional: Figure legends can be formatted using Markdown syntax. To see this correctly in the exported PDF info page, we need Python Markdown. For example, install on CentOS 7:
$ yum install python-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: $ path/to/OMERO.server/bin/omero script list # Replace the script $ cd omero_figure/scripts $ path/to/OMERO.server/bin/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
To update the demo figure app at http://figure.openmicroscopy.org/demo/ we have a grunt task that concats and moves js files into demo/. It also replaces Django template tags in index.html and various js code fragments with static app code. This is all handled by the grunt task:
$ grunt demo
This puts everything into the omero-figure/demo/ directory. This can be tested locally via:
$ cd demo/ $ python -m SimpleHTTPServer
Go to http://localhost:8000/ to test it. This will not install the script and dependencies required to export the figure as PDF.
To update the figure.openmicroscopy.org site:
Copy the demo directory and replace the demo directory in gh-pages-staging branch
Commit changes and open PR against ome/gh-pages-staging as described https://github.com/ome/omero-figure/tree/gh-pages-staging
It is also possible to run the demo in docker without installing anything locally:
$ docker build -t figure-demo . $ docker run -ti --rm -p 8000:8000 figure-demo
License
OMERO.figure is released under the AGPL.
Copyright
2016, The Open Microscopy Environment
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