getter to create JSON representation of discrete column

[surchs]

Given a column mapped to a discrete category (e.g. "Diagnosis"), create a complete, schema compliant JSON object of all annotations we have made for this column.

Example from our documentation

  "group": {
    "Annotations": {
      "IsAbout": {
        "TermURL": "bg:diagnosis",
        "Label": "Diagnosis"
      },
      "Levels": {
        "PD": {
          "TermURL": "snomed:49049000",
          "Label": "Parkinson's disease"
        },
        "CTRL": {
          "TermURL": "purl:NCIT_C94342",
          "Label": "Healthy Control"
        }
      }
    }
  }

assume that

• the column was mapped to a discrete category (has entry in state.columnToCategoryMapping)
• valueMapping is incomplete
• all other data are BIDS or schema-compliant

TODO

• [ ] combine our annotations and existing annotations
• [ ] provide human readable labels (from hard-coded for now)
• [ ] provide unit tests

Data to grab

• isAbout
  • state.columnToCategoryMap for the "Label"
  • state.categories[<categoryName>].identifier for the IRI / TermURL
• Levels (in the annotations section)
  • state.dataDictionary.annotated[<columnName>].valueMap for the TermURL
  • state.categoricalOptions[<categoryName>] and then somehow find the right term (getter?)

[surchs]

blocked by Seb lack of time

[jarmoza]

After conferring with @surchs today, the task here is only to make changes for the existing identifiers and labels found in store.state.categoricalOptions and not others used outside of the annotation tool in NeuroBagel just yet.