That class allows to convert a PSI XML file into Intact data.
That processing is done in 3 steps:
(1) Parsing of the PSI XML file using DOM and materialisation as an immutable (read-only) and defensive
object model (defensive in the sense that it doesn't allow the user to create rubbish data),
(2) Checking if all the required Intact object are present in the database (CVs, Proteins, Biosources...)
The proteins are created/updated during that phase.
(3) Making the Experiments and Interactions persistent.
Features:
- Use the DOM XML API for parsing the data (that's not the fastest but this can be changed if need's be),
- Use of commons-cli to parse the
command line options,
- Test suite for some part of the API (eg. parsing, model)
- A couple of options are available:
> Halt of the processing after Parsing (-upToParsing)
> Halt of the processing after Checking (-upToChecking)
hence no interaction or experiment created,
> Auto assign default biosource (-useTaxidWhenMissing)
> Auto assign interaction type for an Interaction (-useInteractionTypeWhenMissing)
> Reuse of existing proteins instead of doing unnecessary (and slow) update (-reuseExistingProtein)
Not requesting that option forces the update of all proteins,
> Display progress bar during long tasks like protein update and interaction creation (-gui),
> Debug mode that give more verbose (-debug)