data (rd3): add emx2 mapping script

[davidruvolo51]

The purpose of this PR is to add the mapping script for EMX2 migration. This includes the steps to reshape the data, recoding the values to the new ontologies, and the new EMX1 to EMX2 column name mappings.

What are the main changes you did

• solverd_subjects to

  • Individuals
  • Pedigree: relationships need to be mapped and linked here
    • Pedigree members: we can accurately detect parent-patient relationships.
  • Individual Observations
    • Clinical observations
    • Disease History
    • Phenotypic Features

• solverd_samples

  • Biosamples

• solverd_labinfo

  • Protocol parameters (this needs more planning)

• solverd_samples

  • Files: for file paths, multiple paths should be collapsed into a comma separated string

To do

Questions and issues

• Mismatch between ontology table names and dataset names: For some ontologies, the table names do not match the name of the corresponding csv file. For example, "gender at birth" is the ontology table name, but the file is "assigned gender at birth". We need to make sure all table names are in sync