Description

The BioCASe Provider Software (BPS), an xml data binding middleware, is used as an abstraction layer in front of a database. After installation and configuration the database is accessible as a BioCASe service - as defined by the BioCASe protocol - and can be used to create distributed heterogenous information systems. The BPS is agnostic to the kind of data being exchanged and any conceptual schema, such as ABCD (Access to Biological Collections Data) for the BioCASe networks, can be used to set up distributed networks.

The Provider Software is a software package to be installed on the data provider's web server. Core component is the PyWrapper software, an XML/CGI database interface written in object-oriented Python that allows a standard access to a variety of database management systems and arbitrarily structured databases. The use of Python makes the software platform-independent, so it can be used on most of the current operating systems.

The connection to the database is done by different database modules that use SQL templates. This way it is easy to build new DB modules for different DB vendors. Non SQL capable databases are not be supported (with the exception of Excel, which ships with an ODBC driver). Most of the current relational DBMSs are supported by the wrapper - for a complete list of supported databases see the documentation.

Documentation

PyWrapper Wiki The PyWrapper Wiki is the perfect spot for getting to know the BioCASe Provider Software. You will find a beginner's guide, detailed tutorials on installation, configuration, mapping, debugging of the software as well as the version history and a comprehensive list of FAQs.

Download

provider_software_3.7.1.tar.gz (11M)

The latest stable version provided as a gzipped tarball archive for download. It is suitable for Windows, Linux, MacOS X, Solaris and probably all other Unixes. If you use Subversion, you download the latest stable version directly from the repository via anonymous access: http://ww2.biocase.org/svn/bps2/branches/stable.

In addition to a regular installation, you can install BioCASe as a Docker container (Docker is an operating-system-level virtualization software). This makes it very easy to install BioCASe (from a Docker image) and also to update or remove BioCASe installations. More on installing BioCASe as a Docker container can be found in the installation tutorial. If you don't know yet what Docker is, you should read the Get Started Guide.
If you're famliar with Docker, we suggest to use the Docker path for installing BioCASe!

Find detailed tutorials for installation and configuration on the PyWrapper Wiki, also a list of new features and bugfixes in the version history. The Provider Software requires Python 2.5+ to run. On most Linux systems, Python 2.7 will be pre-installed, which works fine with BioCASe.

Note for BiNHum/GGBN providers: If you want to use the ABCD2.1(GGBN) schema with BioCASe, you need to do download an additional file that is not part of the regular release. Please download the ABCD 2.1 schema definition for the BiNHum network or the ABCD-GGBN schema definition for the GGBN network and copy this file to the folder templates/cmf of your BioCASe installation.

If you have questions or problems installing or configuring the Provider Software, please contact the BioCASe Helpdesk at the Botanical Museum Berlin, which willoffer assistance in the process.