csv2caDSR

A very simple program for harmonizing CSV files against Common Data Elements from the caDSR, which we access using the caDSR-on-FHIR service.

How to use

Using csv2caDSR is an overly complicated process (it will be improved in later versions if needed):

1. sbt "run --csv example.csv --to-json example.json"

   • Creates a JSON file describing the columns in the CSV file.

2. Fill in the caDSR values in the CSV file.

3. sbt "run --json example-with-caDSRs.json --to-json example-with-values.json"

   • Fills in values for caDSR values.

4. Map CSV values to caDSR values.

5. sbt "run --json example-with-values.json --to-json example-with-enumValues.json"

   • Retrieve descriptions and concept identifiers for the mapped caDSR values.

6. sbt "run --csv example.csv --json example-with-enumValues.json --to-csv example-mapped.csv"

   • Map CSV file to CDEs based on the mapping information in example-with-enumValues.json.

7. sbt "run --csv example.csv --json example-with-enumValues.json --to-pfb examples/avro/example.avro"

   • Convert CSV file to a PFB file in Avro.

8. sbt "run --csv example.csv --json example-with-enumValues.json --to-cedar examples/cedar/prefix --upload-to-cedar --cedar-upload-folder-url https://repo.metadatacenter.org/folders/bba27862-cbfb-474b-a6d0-bbf03c297df9"

   • Convert CSV file to CEDAR instance data (using the prefix provided, in this example at examples/cedar/prefix.instance.${index}.json), generate a CEDAR template (in this example, at examples/cedar/prefix.template.json), and optionally upload it to a particular CEDAR template.

9. sbt "run --csv example.csv --json example-with-enumValues.json --to-jsonld examples/jsonld/prefix --generate-shacl"

   • Convert CSV file to JSON-LD (using the prefix provided, in this example at examples/jsonld/prefix.instance.${index}.jsonld) and generate a SHACL file (in this example, at examples/jsonld/prefix.shacl.ttl).