The validation issues have been resolved with optional fields but now they are being exported as blank values now. This may pass the BCOnexus validator but will fail in others.

[HadleyKing]

I took https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2/examples/HCV1a.json and uploaded it to the BCOnexus tool to use for testing.

The BCOnexus tool added blank values for fields that did not exist in the BCO.

For example:

{
    "date": "2017-12-12T12:30:48-0400",
    "reviewer_comment": "The revised BCO looks fine",
    "status": "approved",
    "reviewer": {
        "name": "Eric Donaldson",
        "affiliation": "FDA",
        "email": "Eric.Donaldson@fda.hhs.gov",
        "contribution": [
            "curatedBy"
        ]
    }
}

became

{
    "date": "2017-12-12T12:30:48-0400",
    "reviewer_comment": "The revised BCO looks fine",
    "status": "approved",
    "reviewer": {
        "name": "Eric Donaldson",
        "affiliation": "FDA",
        "email": "Eric.Donaldson@fda.hhs.gov",
        "contribution": [
            "curatedBy"
        ],
        "orcid": ""
    }
}

When run through the BioCompute Portal validation API the following response is returned:

{
  "https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2/examples/HCV1a.json": {
    "number_of_errors": 22,
    "error_detail": [
      {
        "[description_domain][pipeline_steps][0][prerequisite][0][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][0][prerequisite][1][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][0][prerequisite][2][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][0][prerequisite][3][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][0][prerequisite][4][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][0][input_list][0][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][0][input_list][1][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][0][output_list][0][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][1][input_list][0][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][1][output_list][0][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[description_domain][pipeline_steps][1][output_list][1][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[execution_domain][script][0][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[execution_domain][software_prerequisites][1][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][input_subdomain][0][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][input_subdomain][1][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][input_subdomain][2][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][input_subdomain][3][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][input_subdomain][4][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][input_subdomain][5][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][input_subdomain][6][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][output_subdomain][0][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      },
      {
        "[io_domain][output_subdomain][1][uri][sha1_checksum]": "'' does not match '[A-Za-z0-9]+'"
      }
    ],
    "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/fhir/fhir_extension.json": {
      "number_of_errors": 0,
      "error_detail": [
        "Extension Valid"
      ]
    },
    "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm/scm_extension.json": {
      "number_of_errors": 0,
      "error_detail": [
        "Extension Valid"
      ]
    }
  }
}