As a LL data manager, I want to load data from publish layer into EAV (pheno model)

Scrum: ticket:1067

Acceptance criteria:

Status:

To-do's:

• Add logging (so we can see what going on when it crashes in production environment, if it ever occurs)
  • Add Thread Monitor
• How to handle/load/implement descriptive tables like LAB_BEPALING, this table is actually big list of Measurements with a lot of extra fields.
  • options:
    • Create a new type that extends Measurement and hold the additional fields
    • Merge data into the label of Category
• How to handle/load/implement the table that describes which foreign keys are used between the tables.
  • The matrix viewer should know this info as well to build correct queries
• Re-factor lifelines packages (it a little bit messy), remove old not used code anymore and place in descriptive packages
• Remove JPA dependencies
  • Many-to-many in JPA are not working properly with Labels, for example ov.setTarget_Name("x"). In JDBCMapper this is solved, but know not where and how we could best do this for JPA. This set by label should also be put into generated test
  • Remove change org.molgenis.JpaDatabase? interface to prevent this
  • trick to prevent compilation problem in Hudson, should be changed!
  • this.em = ((JpaDatabase?)db).getEntityManager().getEntityManagerFactory().createEntityManager();
  • Jpa reverse relation cause hudson to give compile error. Should be added to molgenis for non-jpa entities. And implement as @deprecated of throw unsupportedOperationException.
• Update CSV readers to be multi threaded?
• In (production) environment it's not a bad idea to put the java executable in the Oracle VM that part of the database.
• Last but not least, Test if data is loaded correctly (Test from Anco).
• We should make sure that the data is always loaded into the right format (this means that it always end up the right way in database).