Schema v2.3 - mskcc/smile-server GitHub Wiki

Changes from v2.2:

Request-level and sample-level metadata changes:

Added status to request metadata and sample metadata to capture validation status (true/false where true = passed validation) and store validation report information.

Status JSON schema:

status is captured at the request-level and for every individual sample in a given request

  "status": {
    "validationReport": "string",
    "validationStatus": true
  }

Description:

• validationStatus : Boolean indicator for whether a sample or request passed or failed validation
• validationReport : A string representation of a JSON containing information regarding any failed validation checks. If validationStatus = true then validationReport is expected to be empty.

---

JSON Schema

{
  "bicAnalysis": true,
  "dataAccessEmails": "string",
  "dataAnalystEmail": "string",
  "dataAnalystName": "string",
  "genePanel": "string",
  "igoProjectId": "string",
  "igoRequestId": "string",
  "investigatorEmail": "string",
  "investigatorName": "string",
  "isCmoRequest": true,
  "labHeadEmail": "string",
  "labHeadName": "string",
  "libraryType": "string",
  "otherContactEmails": "string",
  "piEmail": "string",
  "pooledNormals": [
    "string"
  ],
  "projectManagerName": "string",
  "qcAccessEmails": "string",
  "requestJson": "string",
  "samples": [
    {
      "additionalProperties": {},
      "baitSet": "string",
      "cfDNA2dBarcode": "string",
      "cmoInfoIgoId": "string",
      "cmoPatientId": "string",
      "cmoSampleIdFields": {},
      "cmoSampleName": "string",
      "collectionYear": "string",
      "datasource": "string",
      "genePanel": "string",
      "igoComplete": true,
      "importDate": "string",
      "investigatorSampleId": "string",
      "libraries": [
        {
          "barcodeId": "string",
          "barcodeIndex": "string",
          "captureConcentrationNm": "string",
          "captureInputNg": "string",
          "captureName": "string",
          "dnaInputNg": 0,
          "libraryConcentrationNgul": 0,
          "libraryIgoId": "string",
          "libraryVolume": 0,
          "numFastQs": 0,
          "runs": [
            {
              "fastqs": [
                "string"
              ],
              "flowCellId": "string",
              "flowCellLanes": [
                0
              ],
              "readLength": "string",
              "runDate": "string",
              "runId": "string",
              "runMode": "string"
            }
          ]
        }
      ],
      "oncotreeCode": "string",
      "patientAliases": [
        {
          "namespace": "string",
          "value": "string"
        }
      ],
      "preservation": "string",
      "primaryId": "string",
      "qcReports": [
        {
          "IGORecommendation": "string",
          "comments": "string",
          "investigatorDecision": "string",
          "qcReportType": "DNA"
        }
      ],
      "sampleAliases": [
        {
          "namespace": "string",
          "value": "string"
        }
      ],
      "sampleClass": "string",
      "sampleName": "string",
      "sampleOrigin": "string",
      "sampleType": "string",
      "sex": "string",
      "smilePatientId": "string",
      "smileSampleId": "string",
      "species": "string",
      "status": {
        "validationReport": "string",
        "validationStatus": true
      },
      "tissueLocation": "string",
      "tubeId": "string",
      "tumorOrNormal": "string"
    }
  ],
  "smileRequestId": "string",
  "status": {
    "validationReport": "string",
    "validationStatus": true
  },
  "strand": "string"
}