Can SMILE samples be searched by outdated CMO sample names? - CONFIRMED YES

Example in dev server:

Sample primary ID: 08944_B_1 Historical CMO label: C-MP76JR-X001-d New label after submitting an update to the metadata: C-MP76JR-G001-d07

Latest metadata fetched

curl -X GET --header 'Accept: application/json' 'http://smile-dev.mskcc.org:3000/sampleById/C-MP76JR-X001-d'

response

{
  "smileSampleId": "8e615e05-31f1-4a86-8c73-ae1b6a5240b9",
  "smilePatientId": "fc37b5c9-7f6c-41b5-918f-6c0d10d15774",
  "primaryId": "08944_B_1",
  "cmoPatientId": "C-MP76JR",
  "cmoSampleName": "C-MP76JR-G001-d07",
  "sampleName": "LTG002_P3_17096_L1",
  "cmoInfoIgoId": null,
  "investigatorSampleId": "LTG002_P3_17096_L1",
  "importDate": "2024-06-11",
  "sampleType": "Tumor",
  "oncotreeCode": "SCLC",
  "collectionYear": "",
  "tubeId": "",
  "cfDNA2dBarcode": null,
  "species": "Human",
  "sex": "F",
  "tumorOrNormal": "Tumor",
  "preservation": "Frozen",
  "sampleClass": "Organoid",
  "sampleOrigin": "Tissue",
  "tissueLocation": "",
  "genePanel": "IMPACT468",
  "baitSet": "IMPACT468_BAITS",
  "datasource": "igo",
  "igoComplete": true,
  "status": {
    "validationStatus": true,
    "validationReport": "{}"
  },
  "cmoSampleIdFields": {
    "naToExtract": "",
    "normalizedPatientId": "ALLAJV_HCISCLC002",
    "sampleType": "DNA",
    "recipe": "IMPACT468"
  },
  "qcReports": [],
  "libraries": [
    {
      "barcodeId": null,
      "barcodeIndex": null,
      "libraryIgoId": "08944_B_1_1_1_1",
      "libraryVolume": 35,
      "libraryConcentrationNgul": 34.8,
      "dnaInputNg": null,
      "captureConcentrationNm": "11.49425287356322",
      "captureInputNg": "400.0",
      "captureName": "Pool-08944_B-Tube7_1",
      "runs": [
        {
          "runMode": "HiSeq High Output",
          "runId": "PITT_0319",
          "flowCellId": "H3MV7BBXY",
          "readLength": "",
          "runDate": "2019-02-11",
          "flowCellLanes": [
            5
          ],
          "fastqs": [
            "/igo/delivery/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG002_P3_17096_L1_IGO_08944_B_1/LTG002_P3_17096_L1_IGO_08944_B_1_S82_R1_001.fastq.gz",
            "/igo/delivery/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG002_P3_17096_L1_IGO_08944_B_1/LTG002_P3_17096_L1_IGO_08944_B_1_S82_R2_001.fastq.gz"
          ]
        }
      ]
    }
  ],
  "sampleAliases": [
    {
      "value": "08944_B_1",
      "namespace": "igoId"
    },
    {
      "value": "LTG002_P3_17096_L1",
      "namespace": "investigatorId"
    }
  ],
  "patientAliases": [
    {
      "value": "C-MP76JR",
      "namespace": "cmoId"
    }
  ],
  "additionalProperties": {
    "igoRequestId": "08944_B",
    "isCmoSample": "true"
  }
}

NOTE: Response does NOT have historical ID. Response only returns the latest metadata.

If historical data is needed then maybe we can add a param to this webservice call to return history.

mskcc / smile-server

Can SMILE samples be searched by outdated CMO sample names? - CONFIRMED YES #1178