BatchDataImporter

Short description

Imports batches of data files into BASE, creating a single RawbioAssay for each file.

Long description

The BatchDataImporter plug-in imports a batch of individual data files into an experiment chosen by the user. It is set up to be invoked from the detail view of a single Experiment where an import tab lets the user select a zip file that contains all the data files. On invocation it proceeds to create a new subdirectory in the user's raw data directory -- this subdirectory is named after the zip file minus the extension plus a time stamp in the format ddMMyy_hhmmss. The zip file is unzipped into this directory. For each file in the directory, a single RawBioAssay object is then created, and once all the data files have been processed in this way, the RawBioAssay objects just created are attached to the Experiment where the import is run from. In the case of Affymetrix data, the raw data is kept in the cel files and these are linked to the RawBioAssay. For all other data formats, the raw data is physically inserted into the database.

Documentation

The ​README.txt contains information on how to install and use the plug-in.

Maintenance plan

Bugs will be fixed. Volunteers welcome to help extend the plug-in.

License

​GNU General Public License version 2.

Author

Micha Bayer - Plant Bioinformatics Group, Scottish Crop Research Institute
​http://www.scri.ac.uk
​http://www.scri.sari.ac.uk/MichaBayer.htm
micha dot bayer at scri dot ac dot uk

Download

plugin jar file: ​batchimporter.jar
source code: ​SVN