Schema v1.0

Schema v1.0

This schema closely resembles the JSON schema delivered by the IGO LIMS get-request-samples and get-sample-manifest endpoints. The difference here is that the get-request-samples endpoint provides a simplified list of sample details in the request "samples" JSON field.

Simplified Sample Details

 . . . ,

  "samples": [
    {
      "igoComplete": true,
      "igoSampleId": "string",
      "investigatorSampleId": "string"
    }
  ],

 . . . 

Instead of this list of simplified sample details, the schema used for SMILE replaces this with a list of Sample Manifest JSONs, therefore packaging all request metadata and sample metadata in a single JSON. The resulting schema is shown below.

Combined Request & Request Samples JSON schema for SMILE.

{
  "bicAnalysis": true,
  "dataAccessEmails": "string",
  "dataAnalystEmail": "string",
  "dataAnalystName": "string",
  "deliveryDate": 0,
  "investigatorEmail": "string",
  "investigatorName": "string",
  "isCmoRequest": true,
  "labHeadEmail": "string",
  "labHeadName": "string",
  "libraryType": "string",
  "otherContactEmails": "string",
  "piEmail": "string",
  "pooledNormals": [
    "string"
  ],
  "projectManagerName": "string",
  "qcAccessEmails": "string",
  "recipe": "string",
  "requestId": "string",
  "samples": [
  {
    "baitSet": "string",
    "cfDNA2dBarcode": "string",
    "cmoInfoIgoId": "string",
    "cmoPatientId": "string",
    "cmoSampleClass": "string",
    "cmoSampleIdFields": {
      "naToExtract": "string",
      "normalizedPatientId": "string",
      "recipe": "string",
      "sampleType": "string"
    },
    "cmoSampleName": "string",
    "collectionYear": "string",
    "igoId": "string",
    "investigatorSampleId": "string",
    "libraries": [
      {
        "barcodeId": "string",
        "barcodeIndex": "string",
        "captureConcentrationNm": "string",
        "captureInputNg": "string",
        "captureName": "string",
        "dnaInputNg": 0,
        "libraryConcentrationNgul": 0,
        "libraryIgoId": "string",
        "libraryVolume": 0,
        "runs": [
          {
            "fastqs": [
              "string"
            ],
            "flowCellId": "string",
            "flowCellLanes": [
              0
            ],
            "readLength": "string",
            "runDate": "string",
            "runId": "string",
            "runMode": "string"
          }
        ]
      }
    ],
    "oncoTreeCode": "string",
    "preservation": "string",
    "qcReports": [
      {
        "IGORecommendation": "string",
        "comments": "string",
        "investigatorDecision": "string",
        "qcReportType": "DNA"
      }
    ],
    "sampleName": "string",
    "sampleOrigin": "string",
    "sex": "string",
    "species": "string",
    "specimenType": "string",
    "tissueLocation": "string",
    "tubeId": "string",
    "tumorOrNormal": "string"
  }
  . . . 
  ],
  "strand": "string"
}

---

Request JSON schema from IGO LIMS:

{
  "bicAnalysis": true,
  "dataAccessEmails": "string",
  "dataAnalystEmail": "string",
  "dataAnalystName": "string",
  "deliveryDate": 0,
  "investigatorEmail": "string",
  "investigatorName": "string",
  "isCmoRequest": true,
  "labHeadEmail": "string",
  "labHeadName": "string",
  "libraryType": "string",
  "otherContactEmails": "string",
  "piEmail": "string",
  "pooledNormals": [
    "string"
  ],
  "projectManagerName": "string",
  "qcAccessEmails": "string",
  "recipe": "string",
  "requestId": "string",
  "samples": [
    {
      "igoComplete": true,
      "igoSampleId": "string",
      "investigatorSampleId": "string"
    }
  ],
  "strand": "string"
}

Sample Manifest JSON schema from IGO LIMS:

[
  {
    "baitSet": "string",
    "cfDNA2dBarcode": "string",
    "cmoInfoIgoId": "string",
    "cmoPatientId": "string",
    "cmoSampleClass": "string",
    "cmoSampleIdFields": {
      "naToExtract": "string",
      "normalizedPatientId": "string",
      "recipe": "string",
      "sampleType": "string"
    },
    "cmoSampleName": "string",
    "collectionYear": "string",
    "igoId": "string",
    "investigatorSampleId": "string",
    "libraries": [
      {
        "barcodeId": "string",
        "barcodeIndex": "string",
        "captureConcentrationNm": "string",
        "captureInputNg": "string",
        "captureName": "string",
        "dnaInputNg": 0,
        "libraryConcentrationNgul": 0,
        "libraryIgoId": "string",
        "libraryVolume": 0,
        "runs": [
          {
            "fastqs": [
              "string"
            ],
            "flowCellId": "string",
            "flowCellLanes": [
              0
            ],
            "readLength": "string",
            "runDate": "string",
            "runId": "string",
            "runMode": "string"
          }
        ]
      }
    ],
    "oncoTreeCode": "string",
    "preservation": "string",
    "qcReports": [
      {
        "IGORecommendation": "string",
        "comments": "string",
        "investigatorDecision": "string",
        "qcReportType": "DNA"
      }
    ],
    "sampleName": "string",
    "sampleOrigin": "string",
    "sex": "string",
    "species": "string",
    "specimenType": "string",
    "tissueLocation": "string",
    "tubeId": "string",
    "tumorOrNormal": "string"
  }
]