Develop a complete Example Data Workflow for CRDCH

[gaurav]

An Example Data Workflow would automatically pull data from nodes, transform it into CRDCH instance data using the Python Data Classes from cancerDHC/ccdhmodel, and then validate that CRDCH instance data using the validation schemas from cancerDHC/ccdhmodel. This allows us to:

• Tests that the LinkML model and its artifacts are being generated correctly, by ensuring that the Python Data Classes and the validation schemas generated by LinkML work as expected.
• Ensure that transformation code can be written to transform node data into CRDCH data.
• Generates example data for use elsewhere in the project.
  • e.g. Provide example instance data in the CRDCH model documentation ccdhmodel#67

Covers the following issues:

• https://github.com/cancerDHC/example-data/milestone/1
  • Add support for extracting the full sample/portion/analyte hierarchy from GDC example-data#6
  • Add PDC import and show how the CCDH model can be used to synthesize data between GDC and PDC example-data#9
• Get the ccdhmodel python code into PyPI as a package ccdhmodel#69

[gaurav]

While many of the pieces are in place for this, our focus on the CRDC-H model this quarter prevented us from making much progress on this goal. However, this ticket is still valid, but should be completed next quarter.