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Add mock data for new IGO fields (#134)
- updated smile-commons version - added mock data for new IGO fields Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>
1 parent 47d071b commit 07900be

7 files changed

+593
-1
lines changed

‎pom.xml‎

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@@ -32,7 +32,7 @@
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<smile_messaging_java.version>2.1.2.RELEASE</smile_messaging_java.version>
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<!-- smile commons centralized config properties -->
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<smile_commons.group>com.github.mskcc</smile_commons.group>
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<smile_commons.version>2.1.4.RELEASE</smile_commons.version>
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<smile_commons.version>2.1.5.RELEASE</smile_commons.version>
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</properties>
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<dependencies>

‎src/test/resources/data/lims_schema_update/mocked_request_igo_to_universal_schema.json‎

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{
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"smileRequestId": "86b34225-5ad1-4893-a371-c726f3fafc9d",
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"igoProjectId": "MOCKREQUEST1",
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"igoRequestId": "MOCKREQUEST1_B",
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"igoDeliveryDate": 1757388036044,
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"ilabRequestId": "IGO-658741",
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"genePanel": "GENESET101",
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"projectManagerName": "Bar, Foo",
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"piEmail": "request1pi@mskcc.org",
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"labHeadName": "Foo Bar",
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"labHeadEmail": "request1pi@mskcc.org",
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"investigatorName": "John Smith",
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"investigatorEmail": "NEWINVESTIGATOREMAIL@mskcc.org",
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"dataAnalystName": "Poin Dexter",
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"dataAnalystEmail": "dexterp@mskcc.org",
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"otherContactEmails": "dexterp@mskcc.org",
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"dataAccessEmails": "",
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"qcAccessEmails": "",
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"strand": null,
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"libraryType": null,
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"isCmoRequest": true,
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"bicAnalysis": false,
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"status": {
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"validationStatus": true,
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"validationReport": "{}"
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},
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"requestJson": "{\"ilabRequestId\":\"IGO-658741\",\"requestId\":\"MOCKREQUEST1_B\",\"projectId\":\"MOCKREQUEST1\",\"dataAccessEmails\":\"\",\"dataAnalystEmail\":\"dexterp@mskcc.org\",\"dataAnalystName\":\"Poin Dexter\",\"investigatorEmail\":\"NEWINVESTIGATOREMAIL@mskcc.org\",\"investigatorName\":\"John Smith\",\"labHeadEmail\":\"request1pi@mskcc.org\",\"labHeadName\":\"Foo Bar\",\"libraryType\":null,\"otherContactEmails\":\"dexterp@mskcc.org\",\"piEmail\":\"request1pi@mskcc.org\",\"projectManagerName\":\"Bar, Foo\",\"qcAccessEmails\":\"\",\"recipe\":\"GENESET101\",\"strand\":null,\"deliveryDate\":1757388036044,\"bicAnalysis\":false,\"isCmoRequest\":true,\"samples\":[{\"igoId\":\"MOCKREQUEST1_B_1\",\"cmoPatientId\":\"C-MP789JR\",\"cmoSampleName\":\"C-MP789JR-X001-d\",\"sampleName\":\"XXX002_P3_12345_L1\",\"altid\":null,\"baitSet\":\"GENESET101_BAITS\",\"cfDNA2dBarcode\":null,\"cmoInfoIgoId\":null,\"cmoSampleClass\":\"Primary\",\"collectionYear\":\"\",\"investigatorSampleId\":\"XXX002_P3_12345_L1\",\"oncoTreeCode\":\"CLL\",\"preservation\":\"Frozen\",\"sampleOrigin\":\"Tissue\",\"sex\":\"F\",\"species\":\"Human\",\"specimenType\":\"PDX\",\"tissueLocation\":\"\",\"tubeId\":\"\",\"tumorOrNormal\":\"UpdatedTumor\",\"igoComplete\":true,\"qcReports\":[],\"libraries\":[{\"barcodeId\":\"IDT29\",\"barcodeIndex\":\"ATTGAGGA\",\"libraryIgoId\":\"MOCKREQUEST1_B_1_1_1_1\",\"libraryVolume\":35.0,\"libraryConcentrationNgul\":34.8,\"dnaInputNg\":null,\"captureConcentrationNm\":\"11.49425287356322\",\"captureInputNg\":\"400.0\",\"captureName\":\"Pool-MOCKREQUEST1_B-Tube7_1\",\"runs\":[{\"runMode\":\"HiSeq High Output\",\"runId\":\"RUNID_0123\",\"flowCellId\":\"X5KL2KKAY\",\"readLength\":\"\",\"runDate\":\"2018-06-05\",\"flowCellLanes\":[5],\"fastqs\":[\"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R1_001.fastq.gz\",\"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R2_001.fastq.gz\"]}]}],\"cmoSampleIdFields\":{\"naToExtract\":\"\",\"sampleType\":\"Tissue\",\"normalizedPatientId\":\"MRN_REDACTED\",\"recipe\":\"GENESET101_BAITS\"},\"sampleStatus\":\"IGO sample status PASSED\"}],\"pooledNormals\":[]}",
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"pooledNormals": [],
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"samples": [
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{
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"smileSampleId": "c47ffd66-e724-4b7a-a665-c7e3d26d963e",
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"smilePatientId": "8594c785-56d9-4f35-b866-100c70f75223",
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"primaryId": "MOCKREQUEST1_B_1",
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"cmoPatientId": "C-MP789JR",
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"cmoSampleName": "C-MP789JR-X001-d",
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"sampleName": "XXX002_P3_12345_L1",
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"cmoInfoIgoId": null,
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"investigatorSampleId": "XXX002_P3_12345_L1",
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"importDate": "2026-01-08",
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"sampleType": "Primary",
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"oncotreeCode": "CLL",
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"collectionYear": "",
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"tubeId": "",
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"cfDNA2dBarcode": null,
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"species": "Human",
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"sex": "Female",
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"tumorOrNormal": "UpdatedTumor",
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"preservation": "Frozen",
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"sampleClass": "PDX",
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"sampleOrigin": "Tissue",
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"tissueLocation": "",
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"genePanel": "GENESET101_BAITS",
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"baitSet": "GENESET101_BAITS",
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"datasource": "igo",
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"igoComplete": true,
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"status": {
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"validationStatus": true,
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"validationReport": "{}"
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},
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"cmoSampleIdFields": {
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"naToExtract": "",
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"sampleType": "Tissue",
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"normalizedPatientId": "MRN_REDACTED",
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"recipe": "GENESET101_BAITS"
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},
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"qcReports": [],
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"libraries": [
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{
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"barcodeId": "IDT29",
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"barcodeIndex": "ATTGAGGA",
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"libraryIgoId": "MOCKREQUEST1_B_1_1_1_1",
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"libraryVolume": 35,
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"libraryConcentrationNgul": 34.8,
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"dnaInputNg": null,
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"captureConcentrationNm": "11.49425287356322",
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"captureInputNg": "400.0",
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"captureName": "Pool-MOCKREQUEST1_B-Tube7_1",
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"runs": [
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{
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"runMode": "HiSeq High Output",
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"runId": "RUNID_0123",
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"flowCellId": "X5KL2KKAY",
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"readLength": "",
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"runDate": "2018-06-05",
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"flowCellLanes": [
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5
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],
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"fastqs": [
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"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R1_001.fastq.gz",
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"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R2_001.fastq.gz"
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]
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}
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]
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}
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],
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"sampleAliases": [
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{
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"value": "MOCKREQUEST1_B_1",
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"namespace": "igoId"
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},
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{
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"value": "XXX002_P3_12345_L1",
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"namespace": "investigatorId"
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}
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],
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"patientAliases": [
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{
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"value": "C-MP789JR",
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"namespace": "cmoId"
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}
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],
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"additionalProperties": {
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"isCmoSample": "true",
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"igoSampleStatus": "IGO sample status PASSED",
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"altId": "ALT-908",
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"igoRequestId": "MOCKREQUEST1_B"
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}
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}
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]
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}

‎src/test/resources/data/lims_schema_update/mocked_request_new_igo_schema.json‎

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{
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"projectId": "MOCKREQUEST1",
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"requestId": "MOCKREQUEST1_B",
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"ilabRequestId": "IGO-658741",
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"deliveryDate": 1757388036044,
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"recipe": "GENESET101",
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"projectManagerName": "Bar, Foo",
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"piEmail": "request1pi@mskcc.org",
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"labHeadName": "Foo Bar",
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"labHeadEmail": "request1pi@mskcc.org",
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"investigatorName": "John Smith",
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"investigatorEmail": "NEWINVESTIGATOREMAIL@mskcc.org",
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"dataAnalystName": "Poin Dexter",
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"dataAnalystEmail": "dexterp@mskcc.org",
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"otherContactEmails": "dexterp@mskcc.org",
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"dataAccessEmails": "",
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"qcAccessEmails": "",
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"isCmoRequest": true,
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"bicAnalysis": false,
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"samples": [
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{
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"cmoSampleName": "C-MP789JR-X001-d",
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"sampleName": "XXX002_P3_12345_L1",
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"altid": "ALT-908",
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"cmoSampleClass": "Primary",
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"oncoTreeCode": "CLL",
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"collectionYear": "",
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"tubeId": "",
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"qcReports": [],
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"libraries": [
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{
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"barcodeId": "IDT29",
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"barcodeIndex": "ATTGAGGA",
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"libraryIgoId": "MOCKREQUEST1_B_1_1_1_1",
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"libraryVolume": 35.0,
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"libraryConcentrationNgul": 34.8,
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"captureConcentrationNm": "11.49425287356322",
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"captureInputNg": "400.0",
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"captureName": "Pool-MOCKREQUEST1_B-Tube7_1",
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"runs": [
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{
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"runMode": "HiSeq High Output",
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"runId": "RUNID_0123",
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"flowCellId": "X5KL2KKAY",
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"readLength": "",
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"runDate": "2018-06-05",
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"flowCellLanes": [
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5
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],
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"fastqs": [
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"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R1_001.fastq.gz",
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"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R2_001.fastq.gz"
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]
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}
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]
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}
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],
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"cmoPatientId": "C-MP789JR",
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"igoId": "MOCKREQUEST1_B_1",
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"investigatorSampleId": "XXX002_P3_12345_L1",
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"species": "Human",
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"sex": "Female",
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"tumorOrNormal": "UpdatedTumor",
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"preservation": "Frozen",
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"specimenType": "PDX",
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"sampleOrigin": "Tissue",
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"tissueLocation": "",
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"baitSet": "GENESET101_BAITS",
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"igoComplete": true,
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"cmoSampleIdFields": {
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"naToExtract": "",
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"sampleType": "Tissue",
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"normalizedPatientId": "MRN_REDACTED",
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"recipe": "GENESET101_BAITS"
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},
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"status": {
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"validationStatus": true,
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"validationReport": "{}"
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},
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"sampleStatus": "IGO sample status PASSED"
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}],
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"pooledNormals": [
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"/FASTQ/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA/FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA_S23_R1_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA/FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA_S23_R2_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG_S86_R1_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG_S86_R2_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG_S147_R1_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG_S147_R2_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG_S196_R1_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG_S196_R2_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT/MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT_S61_R1_001.fastq.gz",
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"/FASTQ/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT/MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT_S61_R2_001.fastq.gz"
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],
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"projectId": "MOCKREQUEST1"
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}

‎src/test/resources/data/lims_schema_update/mocked_request_universal_schema_igo_data_changes.json‎

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{
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"smileRequestId": "86b34225-5ad1-4893-a371-c726f3fafc9d",
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"igoProjectId": "MOCKREQUEST1",
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"igoRequestId": "MOCKREQUEST1_B",
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"igoDeliveryDate": 1757388036044,
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"ilabRequestId": "IGO-999999",
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"genePanel": "GENESET101",
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"projectManagerName": "Bar, Foo",
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"piEmail": "request1pi@mskcc.org",
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"labHeadName": "Foo Bar",
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"labHeadEmail": "request1pi@mskcc.org",
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"investigatorName": "John Smith",
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"investigatorEmail": "NEWINVESTIGATOREMAIL@mskcc.org",
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"dataAnalystName": "Poin Dexter",
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"dataAnalystEmail": "dexterp@mskcc.org",
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"otherContactEmails": "dexterp@mskcc.org",
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"dataAccessEmails": "",
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"qcAccessEmails": "",
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"strand": null,
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"libraryType": null,
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"isCmoRequest": true,
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"bicAnalysis": false,
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"status": {
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"validationStatus": true,
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"validationReport": "{}"
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},
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"requestJson": "{\"ilabRequestId\":\"IGO-658741\",\"requestId\":\"MOCKREQUEST1_B\",\"projectId\":\"MOCKREQUEST1\",\"dataAccessEmails\":\"\",\"dataAnalystEmail\":\"dexterp@mskcc.org\",\"dataAnalystName\":\"Poin Dexter\",\"investigatorEmail\":\"NEWINVESTIGATOREMAIL@mskcc.org\",\"investigatorName\":\"John Smith\",\"labHeadEmail\":\"request1pi@mskcc.org\",\"labHeadName\":\"Foo Bar\",\"libraryType\":null,\"otherContactEmails\":\"dexterp@mskcc.org\",\"piEmail\":\"request1pi@mskcc.org\",\"projectManagerName\":\"Bar, Foo\",\"qcAccessEmails\":\"\",\"recipe\":\"GENESET101\",\"strand\":null,\"deliveryDate\":1757388036044,\"bicAnalysis\":false,\"isCmoRequest\":true,\"samples\":[{\"igoId\":\"MOCKREQUEST1_B_1\",\"cmoPatientId\":\"C-MP789JR\",\"cmoSampleName\":\"C-MP789JR-X001-d\",\"sampleName\":\"XXX002_P3_12345_L1\",\"altid\":null,\"baitSet\":\"GENESET101_BAITS\",\"cfDNA2dBarcode\":null,\"cmoInfoIgoId\":null,\"cmoSampleClass\":\"Primary\",\"collectionYear\":\"\",\"investigatorSampleId\":\"XXX002_P3_12345_L1\",\"oncoTreeCode\":\"CLL\",\"preservation\":\"Frozen\",\"sampleOrigin\":\"Tissue\",\"sex\":\"F\",\"species\":\"Human\",\"specimenType\":\"PDX\",\"tissueLocation\":\"\",\"tubeId\":\"\",\"tumorOrNormal\":\"UpdatedTumor\",\"igoComplete\":true,\"qcReports\":[],\"libraries\":[{\"barcodeId\":\"IDT29\",\"barcodeIndex\":\"ATTGAGGA\",\"libraryIgoId\":\"MOCKREQUEST1_B_1_1_1_1\",\"libraryVolume\":35.0,\"libraryConcentrationNgul\":34.8,\"dnaInputNg\":null,\"captureConcentrationNm\":\"11.49425287356322\",\"captureInputNg\":\"400.0\",\"captureName\":\"Pool-MOCKREQUEST1_B-Tube7_1\",\"runs\":[{\"runMode\":\"HiSeq High Output\",\"runId\":\"RUNID_0123\",\"flowCellId\":\"X5KL2KKAY\",\"readLength\":\"\",\"runDate\":\"2018-06-05\",\"flowCellLanes\":[5],\"fastqs\":[\"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R1_001.fastq.gz\",\"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R2_001.fastq.gz\"]}]}],\"cmoSampleIdFields\":{\"naToExtract\":\"\",\"sampleType\":\"Tissue\",\"normalizedPatientId\":\"MRN_REDACTED\",\"recipe\":\"GENESET101_BAITS\"},\"sampleStatus\":\"IGO sample status PASSED\"}],\"pooledNormals\":[]}",
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"pooledNormals": [],
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"samples": [
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{
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"smileSampleId": "c47ffd66-e724-4b7a-a665-c7e3d26d963e",
32+
"smilePatientId": "8594c785-56d9-4f35-b866-100c70f75223",
33+
"primaryId": "MOCKREQUEST1_B_1",
34+
"cmoPatientId": "C-MP789JR",
35+
"cmoSampleName": "C-MP789JR-X001-d",
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"sampleName": "XXX002_P3_12345_L1",
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"cmoInfoIgoId": null,
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"investigatorSampleId": "XXX002_P3_12345_L1",
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"importDate": "2026-01-08",
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"sampleType": "Primary",
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"oncotreeCode": "CLL",
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"collectionYear": "",
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"tubeId": "",
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"cfDNA2dBarcode": null,
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"species": "Human",
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"sex": "Female",
47+
"tumorOrNormal": "UpdatedTumor",
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"preservation": "Frozen",
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"sampleClass": "PDX",
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"sampleOrigin": "Tissue",
51+
"tissueLocation": "",
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"genePanel": "GENESET101_BAITS",
53+
"baitSet": "GENESET101_BAITS",
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"datasource": "igo",
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"igoComplete": true,
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"status": {
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"validationStatus": true,
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"validationReport": "{}"
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},
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"cmoSampleIdFields": {
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"naToExtract": "DNA",
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"sampleType": "Tissue",
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"normalizedPatientId": "MRN_REDACTED",
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"recipe": "GENESET101_BAITS"
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},
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"qcReports": [],
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"libraries": [
68+
{
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"barcodeId": "IDT29",
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"barcodeIndex": "ATTGAGGA",
71+
"libraryIgoId": "MOCKREQUEST1_B_1_1_1_1",
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"libraryVolume": 35,
73+
"libraryConcentrationNgul": 34.8,
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"dnaInputNg": null,
75+
"captureConcentrationNm": "11.49425287356322",
76+
"captureInputNg": "400.0",
77+
"captureName": "Pool-MOCKREQUEST1_B-Tube7_1",
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"runs": [
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{
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"runMode": "HiSeq High Output",
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"runId": "RUNID_0123",
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"flowCellId": "X5KL2KKAY",
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"readLength": "",
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"runDate": "2018-06-05",
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"flowCellLanes": [
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5
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],
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"fastqs": [
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"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R1_001.fastq.gz",
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"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R2_001.fastq.gz"
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]
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}
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]
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}
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],
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"sampleAliases": [
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{
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"value": "MOCKREQUEST1_B_1",
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"namespace": "igoId"
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},
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{
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"value": "XXX002_P3_12345_L1",
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"namespace": "investigatorId"
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}
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],
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"patientAliases": [
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{
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"value": "C-MP789JR",
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"namespace": "cmoId"
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}
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],
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"additionalProperties": {
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"isCmoSample": "true",
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"igoSampleStatus": "IGO sample status PASSED",
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"altId": "ALT-908",
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"igoRequestId": "MOCKREQUEST1_B"
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}
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}
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]
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}

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