schema update

[lindaxiang]

• [x] add 4 new fields

  1. gene name
  2. diagnostic pcr Ct value
  3. sample collection date null reason
  4. host age null reason

• [x] make sure the following fields are NOT required fields in schema as we are not going to expect them in the submitted TSV

  1. sample collection date precision
  2. NML submitted specimen type
  3. Ns per 100 kbp
  4. consensus genome length
  5. geo_loc_name (city)
  6. library ID
  7. lineage/clade analysis software name
  8. lineage/clade analysis software version
  9. lineage/clade name
  10. sequencing date
  11. variant designation
  12. variant evidence
  13. variant evidence details

• [x] rename field sequencing_protocol_name to sequencing_protocol

• [x] update some CV terms in the schema to sync with latest DH

[lindaxiang]

Addressed by: https://github.com/cancogen-virus-seq/metadata-schemas/pull/5

[lindaxiang]

• [x] One new column fasta header name need to be added.

• This field in the TSV will specify how the sample is labeled in FASTA.

• [x] Column isolate

• This field is reserved for GISAID virus names. So samples don't meet GISAID quality threshold won't have a GISAID virus name

• It's possible the isolate column to be null

[rosibaj]

@lindaxiang as discussed, we need one more update to remove teh 1 from the field names. the added names should be like so:

gene_name
diagnostic_pcr_ct_value

[lindaxiang]

Addressed by https://github.com/cancogen-virus-seq/metadata-schemas/pull/6

[rosibaj]

has been updated in prod