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Add 'igoComplete: false' to sample-level validation report (#55)
* Add 'igoComplete: false' to sample-level validation report * Add test * Update test function's comment * Fix typing of sampleMap
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263 changes: 263 additions & 0 deletions
263
src/test/resources/data/incoming_requests/mocked_request8_false_igo_complete.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,263 @@ | ||
| { | ||
| "requestId": "MOCKREQUEST1_B", | ||
| "recipe": "GENESET101_BAITS", | ||
| "projectManagerName": "Bar, Foo", | ||
| "piEmail": "[email protected]", | ||
| "labHeadName": "Foo Bar", | ||
| "labHeadEmail": "[email protected]", | ||
| "investigatorName": "John Smith", | ||
| "investigatorEmail": "[email protected]", | ||
| "dataAnalystName": "Poin Dexter", | ||
| "dataAnalystEmail": "[email protected]", | ||
| "otherContactEmails": "[email protected]", | ||
| "dataAccessEmails": "", | ||
| "qcAccessEmails": "", | ||
| "isCmoRequest": true, | ||
| "bicAnalysis": false, | ||
| "samples": [ | ||
| { | ||
| "cmoSampleName": "C-MP789JR-X001-d", | ||
| "sampleName": "XXX002_P3_12345_L1", | ||
| "cmoSampleClass": "Primary", | ||
| "oncoTreeCode": "CLL", | ||
| "collectionYear": "", | ||
| "tubeId": "", | ||
| "qcReports": [], | ||
| "libraries": [ | ||
| { | ||
| "barcodeId": "IDT29", | ||
| "barcodeIndex": "ATTGAGGA", | ||
| "libraryIgoId": "MOCKREQUEST1_B_1_1_1_1", | ||
| "libraryVolume": 35.0, | ||
| "libraryConcentrationNgul": 34.8, | ||
| "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" | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "cmoPatientId": "C-MP789JR", | ||
| "igoId": "MOCKREQUEST1_B_1", | ||
| "investigatorSampleId": "XXX002_P3_12345_L1", | ||
| "species": "Human", | ||
| "sex": "F", | ||
| "tumorOrNormal": "Tumor", | ||
| "preservation": "Frozen", | ||
| "specimenType": "PDX", | ||
| "sampleOrigin": "Tissue", | ||
| "tissueLocation": "", | ||
| "baitSet": "GENESET101_BAITS", | ||
| "igoComplete": false, | ||
| "cmoSampleIdFields": { | ||
| "naToExtract": "", | ||
| "sampleType": "Tissue", | ||
| "normalizedPatientId": "MRN_REDACTED", | ||
| "recipe": "GENESET101_BAITS" | ||
| } | ||
| }, | ||
| { | ||
| "cmoSampleName": "C-MP789JR-N001-d", | ||
| "sampleName": "01-0012345a", | ||
| "cmoSampleClass": "Normal", | ||
| "oncoTreeCode": "CLL", | ||
| "collectionYear": "", | ||
| "tubeId": "", | ||
| "qcReports": [], | ||
| "libraries": [ | ||
| { | ||
| "barcodeId": "TNG41", | ||
| "barcodeIndex": "CGACTGGA", | ||
| "libraryIgoId": "MOCKREQUEST1_B_2_1_1_1", | ||
| "libraryVolume": 35.0, | ||
| "libraryConcentrationNgul": 33.5, | ||
| "captureConcentrationNm": "5.074626865671642", | ||
| "captureInputNg": "170.0", | ||
| "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_01-0012345a_IGO_MOCKREQUEST1_B_2/01-0012345a_IGO_MOCKREQUEST1_B_2_S83_R2_001.fastq.gz", | ||
| "/FASTQ/Project_MOCKREQUEST1_B/Sample_01-0012345a_IGO_MOCKREQUEST1_B_2/01-0012345a_IGO_MOCKREQUEST1_B_2_S83_R1_001.fastq.gz" | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "cmoPatientId": "C-MP789JR", | ||
| "igoId": "MOCKREQUEST1_B_2", | ||
| "investigatorSampleId": "01-0012345a", | ||
| "species": "Human", | ||
| "sex": "F", | ||
| "tumorOrNormal": "Normal", | ||
| "preservation": "Frozen", | ||
| "specimenType": "Blood", | ||
| "sampleOrigin": "Whole Blood", | ||
| "tissueLocation": "", | ||
| "baitSet": "GENESET101_BAITS", | ||
| "igoComplete": false, | ||
| "cmoSampleIdFields": { | ||
| "naToExtract": "", | ||
| "sampleType": "Whole Blood", | ||
| "normalizedPatientId": "MRN_REDACTED", | ||
| "recipe": "GENESET101_BAITS" | ||
| } | ||
| }, | ||
| { | ||
| "cmoSampleName": "C-8DH24X-X001-d", | ||
| "sampleName": "XXX002_P1_12348a_R_43", | ||
| "cmoSampleClass": "Primary", | ||
| "oncoTreeCode": "COAD", | ||
| "collectionYear": "", | ||
| "tubeId": "", | ||
| "qcReports": [], | ||
| "libraries": [ | ||
| { | ||
| "barcodeId": "TNG53", | ||
| "barcodeIndex": "GCTCGGTA", | ||
| "libraryIgoId": "MOCKREQUEST1_B_3_1_1_1", | ||
| "libraryVolume": 35.0, | ||
| "libraryConcentrationNgul": 35.2, | ||
| "captureConcentrationNm": "11.363636363636363", | ||
| "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_P1_12348a_R_43_IGO_MOCKREQUEST1_B_3/XXX002_P1_12348a_R_43_IGO_MOCKREQUEST1_B_3_S84_R1_001.fastq.gz", | ||
| "/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P1_12348a_R_43_IGO_MOCKREQUEST1_B_3/XXX002_P1_12348a_R_43_IGO_MOCKREQUEST1_B_3_S84_R2_001.fastq.gz" | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "cmoPatientId": "C-8DH24X", | ||
| "igoId": "MOCKREQUEST1_B_3", | ||
| "investigatorSampleId": "XXX002_P1_12348a_R_43", | ||
| "species": "Human", | ||
| "sex": "M", | ||
| "tumorOrNormal": "Tumor", | ||
| "preservation": "Frozen", | ||
| "specimenType": "PDX", | ||
| "sampleOrigin": "Tissue", | ||
| "tissueLocation": "", | ||
| "baitSet": "GENESET101_BAITS", | ||
| "igoComplete": true, | ||
| "cmoSampleIdFields": { | ||
| "naToExtract": "", | ||
| "sampleType": "Tissue", | ||
| "normalizedPatientId": "MRN_REDACTED", | ||
| "recipe": "GENESET101_BAITS" | ||
| } | ||
| }, | ||
| { | ||
| "cmoSampleName": "C-8DH24X-N001-d", | ||
| "sampleName": "01-XXXXXXXa", | ||
| "cmoSampleClass": "Normal", | ||
| "oncoTreeCode": "COAD", | ||
| "collectionYear": "", | ||
| "tubeId": "", | ||
| "qcReports": [], | ||
| "libraries": [ | ||
| { | ||
| "barcodeId": "TNG65", | ||
| "barcodeIndex": "TGGAACAA", | ||
| "libraryIgoId": "MOCKREQUEST1_B_4_1_1_1", | ||
| "libraryVolume": 35.0, | ||
| "libraryConcentrationNgul": 34.1, | ||
| "captureConcentrationNm": "4.9853372434017595", | ||
| "captureInputNg": "170.0", | ||
| "captureName": "Pool-MOCKREQUEST1_B-Tube7_1", | ||
| "runs": [ | ||
| { | ||
| "runMode": "HiSeq High Output", | ||
| "runId": "RUNID_0123", | ||
| "flowCellId": "X5KL2KKAY", | ||
| "readLength": "", | ||
| "runDate": "2018-06-05", | ||
| "flowCellLanes": [ | ||
| 5 | ||
| ], | ||
| "fastqs": [] | ||
| }, | ||
| { | ||
| "runMode": "HiSeq High Output", | ||
| "runId": "RUNID_0123", | ||
| "flowCellId": "X5KL2KKAY", | ||
| "readLength": "", | ||
| "runDate": "2018-06-05", | ||
| "flowCellLanes": [ | ||
| 5 | ||
| ], | ||
| "fastqs": [ | ||
| "/FASTQ/Project_MOCKREQUEST1_B/Sample_01-XXXXXXXa_IGO_MOCKREQUEST1_B_4/01-XXXXXXXa_IGO_MOCKREQUEST1_B_4_S85_R1_001.fastq.gz", | ||
| "/FASTQ/Project_MOCKREQUEST1_B/Sample_01-XXXXXXXa_IGO_MOCKREQUEST1_B_4/01-XXXXXXXa_IGO_MOCKREQUEST1_B_4_S85_R2_001.fastq.gz" | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "cmoPatientId": "C-8DH24X", | ||
| "igoId": "MOCKREQUEST1_B_4", | ||
| "investigatorSampleId": "01-XXXXXXXa", | ||
| "species": "Human", | ||
| "sex": "M", | ||
| "tumorOrNormal": "Normal", | ||
| "preservation": "Frozen", | ||
| "specimenType": "Blood", | ||
| "sampleOrigin": "Whole Blood", | ||
| "tissueLocation": "", | ||
| "baitSet": "GENESET101_BAITS", | ||
| "igoComplete": true, | ||
| "cmoSampleIdFields": { | ||
| "naToExtract": "", | ||
| "sampleType": "Whole Blood", | ||
| "normalizedPatientId": "MRN_REDACTED", | ||
| "recipe": "GENESET101_BAITS" | ||
| } | ||
| } | ||
| ], | ||
| "pooledNormals": [ | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA/FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA_S23_R1_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA/FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA_S23_R2_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG_S86_R1_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG_S86_R2_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG_S147_R1_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG_S147_R2_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG_S196_R1_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG_S196_R2_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT/MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT_S61_R1_001.fastq.gz", | ||
| "/FASTQ/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT/MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT_S61_R2_001.fastq.gz" | ||
| ], | ||
| "projectId": "MOCKREQUEST1" | ||
| } |
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