ckanext-papaya 0.0.1

Papaya viewer extension for CKAN

ckanext-papaya

This is an extension for CKAN that uses Papaya (https://github.com/rii-mango/Papaya) to provide views for NIFTI (.nii) and DICOM (.dcm) file formats. It provides views for both single DICOM files as well as DICOM directories uploaded to CKAN as a ZIP file.

Requirements

Tested with CKAN 2.9.0a.

Installation

To install ckanext-papaya:

1. Activate your CKAN virtual environment, for example:

   . /usr/lib/ckan/default/bin/activate

2. Install the ckanext-papaya Python package into your virtual environment:

   pip install ckanext-papaya

3. Add papaya to the ckan.plugins setting in your CKAN config file (by default the config file is located at /etc/ckan/default/production.ini). To avoid having the Papaya viewer enabled for all ZIP files, regardless of whether they contain DICOM files, do not add papaya to ckan.views.default_views.

4. Restart CKAN. For example if you’ve deployed CKAN with Apache on Ubuntu:

   sudo service apache2 reload

Config settings

None at present. NIFTI files and DICOM directories tend to be rather large, so you may have to increase the maximum resource size to allow users to upload these file formats.

Developer installation

To install ckanext-papaya for development, activate your CKAN virtualenv and do:

git clone https://github.com//ckanext-papaya.git
cd ckanext-papaya
python setup.py develop
pip install -r dev-requirements.txt

Tests

To run the tests, do:

nosetests --nologcapture --with-pylons=test.ini

To run the tests and produce a coverage report, first make sure you have coverage installed in your virtualenv (pip install coverage) then run:

nosetests --nologcapture --with-pylons=test.ini --with-coverage --cover-package=ckanext.papaya --cover-inclusive --cover-erase --cover-tests

Using the Extension

The extension automatically creates a view using the Papaya Viewer for single DICOM files (with file extension .dcm), NIFTI files (with file extension .nii), and ZIP archives that contain one or more DICOM files. If a ZIP archive contains other file types besides DICOM files, or DICOM files without the .dcm extension, they will simply be ignored when displaying correctly-formatted files in Papaya.

To view zipped DICOM files, the extension temporarily unzips the archive and passes the contents of the files with .dcm extensions to Papaya. The unzipped files are deleted immediately to prevent them from taking up space on the server. Papaya can’t actually read local files, since it’s a JavaScript framework, so it is necessary to pass the raw contents of the files rather than the paths to the files themselves on to Papaya. Users may experience some lag when trying to view large DICOM directories, but most of this lag comes from Papaya reading the individual DICOM files rather than from the CKAN extension passing the data to Papaya.

Unlike our ParaView extension (https://github.com/SFB-ELAINE/ckanext-paraview), this extension runs directly in CKAN and does not require a separate server. Once it is installed in a CKAN instance and added to the config file, it will work without further setup.

This extension will automatically create Papaya views for newly-uploaded files, but existing resources with NIFTI files, single DICOM files, or DICOM directories may need to have the Papaya view added manually.