Home

#The Loading Tool for the ESD Relational Database

This is a command line tool to manipulate SampleTab submissions into the EBI's Biosamples database.

Available Commands:

• Loading, for loading a SampleTab file into a relational database like our Oracle instances.
• Unloading, for unloading data related to a given SampleTab file.
• Permission Control, for manipulating data visibility and user ownership.

##Configuration The commands above uses hibernate.properties to set up the JDBC database that backs the data. This is a standard Hibernate configuration file (see Hibernate documentation about that).

Both the loader and unloader uses the generic_invoker.sh script to launch proper Java classes. This is relevant to you want to use a JDBC driver that is not build with the command line package. Currently, we officially support Oracle only, but we ship the BioSD command line package with drivers for MySQL, H2, HSQL. We test against MySQL and H2 from time to time, we regularly test code against HSQL during development. We do final tests against Oracle, before releasing and deploying.

##EBI Deployment The commands above can be accessed from:
/ebi/microarray/home/biosamples-dev/loader_relational/biosd_loader_shell_X.Y-SNAPSHOT