Use Gen3 schemas in transforms

[adamstruck]

Builds off #329

[adamstruck]

From review on 6/27:

SCHEMA TODO:

• change chromosome definition
  • no “chr” prefix
• remove “GENE_TPM”
• bring over “descriptions” from gdc schemas
• check “to_one” “to_many” relationships
• rename Callset to SomaticCallset

ETL TODO:

• no multiplexed edge files (i.e. they should be named callset_alleles_allele.Edge.json.gz)
• remove “_id”
• submitter_id != gid; case by case depending on vertex type
• add id property to hold gid; remove from props during emit and validation
• fix cell lines case <-> project relationship
  • create case for each cell line
  • create edge between equivalent cases

[adamstruck]

Missing vertex summary from running bloom filter:

{
  "Transcript": 129,
  "Gene": 8,
   "Aliquot": 304,
  "GeneOntologyTerm": 11,
  "Protein": 15195,
  "PfamFamily": 3
}

Seems to be in line with our previous releases.

Need to fix missing Aliquots. fixed.

[kellrott]

👍