Add core support for storing analysed data in files instead of in the database

[Nicklas Nordborg]

This is related to #1029, but is only about changes needed in the core to support this. It is also related to #1051 which is about changes that is needed in the web GUI and #1052 which is about changes needed by core plug-ins.

Basically, we want to use the existing system for attaching files to raw bioassays and array designs, but without the platform concept. Under the hood this is already a separate thing so it should not be a problem. Theoretically, the data file should contain the same data that is otherwise imported into the database. This means that we need to be able to attach files on the bioassay level, and on the extra value level. We are not going to add any more meta-data columns than what is already there. But we need to duplicate the existing columns to be able to tell the difference between data in files and data in the database.

Here are the details:

• Changes for BioAssaySetData:
  • implement the FileStoreEnabledData interface
  • add numFileSpots and numFileReporters as properties

• Changes for ExtraValueData:
  • implement the FileStoreEnabledData interface
  • add numFileValues as a property

• Changes for BioAssaySet and ExtraValue:
  • implement the FileStoreEnabled interface. The getPlatform() and getVariant() methods should always return null. The getParentFileSets() method should check if the parent item has files and get those. The parent item for a BioAssaySet is the BioAssaySet it is created from and for an ExtraValue the BioAssaySet it is attached to.
  • add setter/getter methods for the meta-data properties

• The installation should create two generic DataFileType:s.
  • generic.spotdata which can be used on BioAssaySet:s
  • generic.extravaluedata which can be used on ExtraValue:s

• We need to extend the current test case with a test that uses a dummy file instead of the database.

[Nicklas Nordborg]

(In [4334]) References #1050: Add core support for storing analysed data in files instead of in the database

Everything should now be in place. Will test with #1051 before closing this ticket.

[Nicklas Nordborg]

(In [4335]) References #1050: Add core support for storing analysed data in files instead of in the database

Added BioAssayData.getNumFileSpots() and other things related to it.

[Nicklas Nordborg]

Seems to be working ok.

[Nicklas Nordborg]

(In [4378]) References #1064, #1082, #1050, #1024, #967

Updated UML diagrams as a result of new db columns added by the referenced tickets.