Fix bugs in automated GDC to CRDCH transformation script

[gaurav]

We still need to:

• Figure out how to determine the associated_project.
• Figure out the sample_id.
• Figure out the project_id.
• Figure out why time_between_excision_and_freezing doesn't work at present.
• Figure out the bug in generating the tissue_or_organ_of_origin value.
• Figure out the bug preventing us from generating validatable observations (probably the same as Uncomment non-validating data from the CCDH Pilot examples and fix CRDCH model so that they work correctly #39)

TODO: Once PR #22 has been merged, we should add references to the lines of code to this file.