Plugin architecture

Most of the ISA tools could/should get a Plugin mechanism. This will allow to modularize the code, or to combine tools into one, and include custom functionality which is specific for an institute's local installation.

• A generic plugin could provide a beanshell, with full access to the ISA objects, so that a beanshell script could call external shell scripts, R code, ...

• A possible local script could check for an instrument type in an assay, and auto-fill a number of derived values, compliant with local SOPs to reduce manual editing. On the other hand, providing the auto-fill functionality ISA-wide could be problematic and lead to wrong annotations.

• Another possible local script could take care of integrating local lab equipment.

• A special plugin for the ISAcreator could be the wrapped ISAvalidator, which allows to have a more stringent validation before creating and uploading an ISA archive.

• A special plugin for the ISAcreator could be the wrapped ISAloader, which allows to submit an ISAarchive right from within ISAcreator, without using the standalone loader.

The latter two plugins serve the use case where a BII instance is installed locally, and users / curators and submitters are actually the same person.