Export data from ICAT into BagIt packages
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
demo
scripts
.gitignore
LICENSE.txt
MANIFEST.in
Makefile
README.rst
icat-bagit-tool.spec
setup.py

README.rst

icat-bagit-tool - Export data from ICAT into BagIt packages

This tool implements the export scientific data from an ICAT into a BagIt package as defined by the RDA Research Data Repository Interoperability WG.

System requirements

Python:

  • Python 2.7, or 3.2 and newer.

Required library packages:

  • python-icat
  • bagit
  • lxml (optional, will fall back on xml.etree.ElementTree from the standard library if not available.)

Installation

python-icat uses the distutils Python standard library package and follows its conventions of packaging source distributions. See the documentation on Installing Python Modules for details or to customize the install process.

  1. Download the sources, unpack, and change into the source directory.

  2. Build:

    $ python setup.py build
    
  3. Install:

    $ python setup.py install
    

The last step might require admin privileges in order to write into the site-packages directory of your Python installation.

Bugs and limitations

  • For the time being, only the export part is implemented. The tool does not support the import of BagIt packages into ICAT.
  • The data in the ICAT is arranged in terms of investigations, datasets, and datafiles. The investigation is a central entity in the ICAT schema. An investigation may be composed of any number of datasets, which in turn may contain any number of datafiles. The export script only supports exporting one single investigation as a whole. It is assumed that the investigation is unambiguously determind by name and visitId and furthermore that these attributes do not contain a colon. These are mostly a limitations of the command line interface of the script and can easily be changed at the expense of rendering this interface somewhat more complicated.
  • The export script puts a zip file per dataset in the payload directory of the package. It probably should rather create subdirectories per dataset with the corresponding datafiles instead. Even better, it should have a command line switch to control this behavior.
  • The package is exported as one single dataset, even though the investigation may comprise many datasets in the ICAT schema. Export as a collection of individual datasets is currently not supported.
  • Due to shortcomings in the ICAT schema, the metadata contained in the datacite.xml file in the package is not entirely compliant to the DataCite schema (e.g. format of names). Furthermore object attributes from the ICAT schema are mapped onto DataCite properties, although the semantics of those attributes and properties does not always match. For instance, users related to the investigation in ICAT are denominated creator of the dataset in the DataCite metadata, which may or may not be correct.
  • Serialization of the exported package should be supported.
  • Documentation is entirely missing.

Copyright and License

Copyright 2018 Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.