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dnanexus's Issues

Execution Domain

  • URI is the only required field in script or software_prerequisites

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.

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": "[email protected]",
        "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": "[email protected]",
        "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"
      ]
    }
  }
}

Test Issue

Is your feature request related to a problem? Please describe.
Creating a test issue

Describe the solution you'd like
None

Describe alternatives you've considered
NA

Additional context
NA

Django items

When starting the app I get this notification:
You have 18 unapplied migration(s). Your project may not work properly until you apply the migrations for app(s): admin, auth, contenttypes, sessions. Run 'python manage.py migrate' to apply them.

When trying to use the admin URL I get the following:
"A server error occurred. Please contact the administrator." in the browser and in the terminal:

File "/usr/local/lib/python3.8/dist-packages/backports/zoneinfo/_common.py", line 27, in load_tzdata
    raise ZoneInfoNotFoundError(f"No time zone found with key {key}")
backports.zoneinfo._common.ZoneInfoNotFoundError: 'No time zone found with key UTC'

Error uploading file

The export option to BCO Repository is not working

Screenshot 2023-07-18 at 11 25 51 AM

The URL being submitted is this:
Request URL: http://localhost:8000/export_to_bco_db?bco_url=http%3A%2F%2Flocalhost%3A8081%2F&prefix=BCO&owner_group=bco_drafters&user_token=07801a1a4cdbf1945e22ac8439f1db27fe813f7a

Screenshot 2023-07-18 at 11 26 34 AM

Description Domain

  • pipeline_steps.[int].step_number should be an INT
  • for Prerequisites, input, and output the URI is the only required field in pipeline_steps

Provenance domain validation

  • Extra Contribution object added upon upload
  • Extra Review object added upon upload
  • derived_from is not a required field

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