From 2a084543503ac207850f06f23fedeb738b1b32bd Mon Sep 17 00:00:00 2001 From: ao508 <15623749+ao508@users.noreply.github.com> Date: Thu, 16 Mar 2023 12:43:18 -0700 Subject: [PATCH] Sample status bug fix (#908) - Add status to mock incoming request data Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com> --- .../smile/service/impl/SampleServiceImpl.java | 3 +- .../service/util/RequestDataFactory.java | 22 ++++- .../smile/service/util/SampleDataFactory.java | 10 ++- .../CorrectCmoPatientIdHandlerTest.java | 4 +- ...d_request1_all_samples_missing_fastqs.json | 16 ++++ ...mocked_request1_complete_tumor_normal.json | 16 ++++ ...mplete_tumor_normal_updated_libraries.json | 16 ++++ ...mocked_request1_sample_missing_fastqs.json | 16 ++++ ...equest1_updated_complete_tumor_normal.json | 16 ++++ ...ed_request1a_sample_type_abbreviation.json | 16 ++++ ...d_request1b_nucleic_acid_abbreviation.json | 16 ++++ .../mocked_request1c_missing_all_samples.json | 16 ++++ .../mocked_request1d_missing_few_samples.json | 16 ++++ .../mocked_request1e_null_string_baitset.json | 16 ++++ ...d_request2a_one_empty_sample_metadata.json | 4 + .../mocked_request2a_one_normal.json | 4 + .../mocked_request2b_missing_one_normal.json | 84 +++++++++++++++++++ .../mocked_request3_pooled_normals.json | 16 ++++ .../mocked_request4_null_or_empty_values.json | 16 ++++ .../mocked_request5_pt_multi_samples.json | 24 ++++++ .../mocked_request6_cmopt_after_swap.json | 16 ++++ .../mocked_request6_cmopt_swap.json | 16 ++++ 22 files changed, 370 insertions(+), 9 deletions(-) diff --git a/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java index 192c3957..6159476b 100644 --- a/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java +++ b/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java @@ -219,7 +219,8 @@ public Boolean updateSampleMetadata(SampleMetadata sampleMetadata, Boolean fromL } LOG.info("Persisting new sample to db: " + sampleMetadata.getPrimaryId()); SmileSample sample = SampleDataFactory.buildNewResearchSampleFromMetadata( - sampleMetadata.getIgoRequestId(), sampleMetadata, request.getIsCmoRequest()); + sampleMetadata.getIgoRequestId(), sampleMetadata, + request.getIsCmoRequest(), sampleMetadata.getStatus()); saveSmileSample(sample); createSampleRequestRelationship(sample.getSmileSampleId(), request.getSmileRequestId()); return Boolean.TRUE; diff --git a/service/src/main/java/org/mskcc/smile/service/util/RequestDataFactory.java b/service/src/main/java/org/mskcc/smile/service/util/RequestDataFactory.java index c394fce8..9d6443ce 100644 --- a/service/src/main/java/org/mskcc/smile/service/util/RequestDataFactory.java +++ b/service/src/main/java/org/mskcc/smile/service/util/RequestDataFactory.java @@ -6,6 +6,7 @@ import java.time.LocalDateTime; import java.time.format.DateTimeFormatter; import java.util.ArrayList; +import java.util.Arrays; import java.util.List; import java.util.Map; import org.mskcc.smile.model.RequestMetadata; @@ -54,15 +55,28 @@ public static RequestMetadata buildNewRequestMetadataFromMetadata(String request private static List extractSmileSamplesFromIgoResponse(Object message) throws JsonProcessingException { Map map = mapper.readValue(message.toString(), Map.class); - IgoSampleManifest[] samples = mapper.convertValue(map.get("samples"), - IgoSampleManifest[].class); + /// SAMPLE STATUS NOT GETTING SET HERE + List sampleManifests = + Arrays.asList(mapper.convertValue(map.get("samples"), + Object[].class)); String requestId = (String) map.get("requestId"); Boolean isCmoRequest = (Boolean) map.get("isCmoRequest"); List requestSamplesList = new ArrayList<>(); - for (IgoSampleManifest s: samples) { + for (Object s : sampleManifests) { + Map sampleMap = mapper.convertValue(s, Map.class); + Map sampleStatusMap = mapper.convertValue( + sampleMap.get("status"), Map.class); + Status sampleStatus = new Status(Boolean.valueOf( + sampleStatusMap.get("validationStatus").toString()), + sampleStatusMap.get("validationReport").toString()); + + IgoSampleManifest sampleManifest = mapper.convertValue(s, + IgoSampleManifest.class); SmileSample sample = SampleDataFactory - .buildNewResearchSampleFromMetadata(requestId, s, isCmoRequest); + .buildNewResearchSampleFromMetadata(requestId, + sampleManifest, isCmoRequest, sampleStatus); + requestSamplesList.add(sample); } return requestSamplesList; diff --git a/service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java b/service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java index d04ec10d..d6fca026 100644 --- a/service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java +++ b/service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java @@ -46,10 +46,11 @@ private static Map initDmpClinicalMetastasisValuesMap() { * @param requestId * @param sampleMetadata * @param isCmoRequest + * @param sampleStatus * @return SmileSample */ public static SmileSample buildNewResearchSampleFromMetadata(String requestId, - SampleMetadata sampleMetadata, Boolean isCmoRequest) { + SampleMetadata sampleMetadata, Boolean isCmoRequest, Status sampleStatus) { sampleMetadata.setIgoRequestId(requestId); if (sampleMetadata.getImportDate() == null) { sampleMetadata.setImportDate(LocalDateTime.now().format(DateTimeFormatter.ISO_LOCAL_DATE)); @@ -58,6 +59,7 @@ public static SmileSample buildNewResearchSampleFromMetadata(String requestId, if (isCmoRequest != null) { sampleMetadata.addAdditionalProperty("isCmoSample", Boolean.TRUE.toString()); } + sampleMetadata.setStatus(sampleStatus); SmileSample sample = new SmileSample(); sample.addSampleMetadata(sampleMetadata); @@ -80,13 +82,15 @@ public static SmileSample buildNewResearchSampleFromMetadata(String requestId, * @param requestId * @param igoSampleManifest * @param isCmoRequest + * @param sampleStatus * @return SmileSample * @throws JsonProcessingException */ public static SmileSample buildNewResearchSampleFromMetadata(String requestId, - IgoSampleManifest igoSampleManifest, Boolean isCmoRequest) throws JsonProcessingException { + IgoSampleManifest igoSampleManifest, Boolean isCmoRequest, Status sampleStatus) + throws JsonProcessingException { SampleMetadata sampleMetadata = new SampleMetadata(igoSampleManifest); - return buildNewResearchSampleFromMetadata(requestId, sampleMetadata, null); + return buildNewResearchSampleFromMetadata(requestId, sampleMetadata, null, sampleStatus); } /** diff --git a/service/src/test/java/org/mskcc/smile/service/CorrectCmoPatientIdHandlerTest.java b/service/src/test/java/org/mskcc/smile/service/CorrectCmoPatientIdHandlerTest.java index f161266a..21b196ce 100644 --- a/service/src/test/java/org/mskcc/smile/service/CorrectCmoPatientIdHandlerTest.java +++ b/service/src/test/java/org/mskcc/smile/service/CorrectCmoPatientIdHandlerTest.java @@ -61,7 +61,9 @@ public org.neo4j.ogm.config.Configuration configuration() { /** * Persists the Mock Request data to the test database. - * @throws Exception + * @param requestRepository + * @param sampleRepository + * @param patientRepository */ @Autowired public CorrectCmoPatientIdHandlerTest(SmileRequestRepository requestRepository, diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1_all_samples_missing_fastqs.json b/service/src/test/resources/data/incoming_requests/mocked_request1_all_samples_missing_fastqs.json index 919e486c..c3c2bc9d 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1_all_samples_missing_fastqs.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1_all_samples_missing_fastqs.json @@ -65,6 +65,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -105,6 +109,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -156,6 +164,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -208,6 +220,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1_complete_tumor_normal.json b/service/src/test/resources/data/incoming_requests/mocked_request1_complete_tumor_normal.json index 28c6c2de..1926dcb6 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1_complete_tumor_normal.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1_complete_tumor_normal.json @@ -68,6 +68,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1_complete_tumor_normal_updated_libraries.json b/service/src/test/resources/data/incoming_requests/mocked_request1_complete_tumor_normal_updated_libraries.json index 69b3f7fb..fc8b77cb 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1_complete_tumor_normal_updated_libraries.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1_complete_tumor_normal_updated_libraries.json @@ -68,6 +68,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1_sample_missing_fastqs.json b/service/src/test/resources/data/incoming_requests/mocked_request1_sample_missing_fastqs.json index 4c9d30e0..5a218669 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1_sample_missing_fastqs.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1_sample_missing_fastqs.json @@ -68,6 +68,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -174,6 +182,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -226,6 +238,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1_updated_complete_tumor_normal.json b/service/src/test/resources/data/incoming_requests/mocked_request1_updated_complete_tumor_normal.json index bfc29593..52a9da64 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1_updated_complete_tumor_normal.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1_updated_complete_tumor_normal.json @@ -68,6 +68,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1a_sample_type_abbreviation.json b/service/src/test/resources/data/incoming_requests/mocked_request1a_sample_type_abbreviation.json index 796b9b89..e258261c 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1a_sample_type_abbreviation.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1a_sample_type_abbreviation.json @@ -68,6 +68,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "XenograftDerivedCellLine" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Exosome" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "testingNormalizedPatientIdvalue", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1b_nucleic_acid_abbreviation.json b/service/src/test/resources/data/incoming_requests/mocked_request1b_nucleic_acid_abbreviation.json index 62f01e1a..69c5da89 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1b_nucleic_acid_abbreviation.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1b_nucleic_acid_abbreviation.json @@ -68,6 +68,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1c_missing_all_samples.json b/service/src/test/resources/data/incoming_requests/mocked_request1c_missing_all_samples.json index 072380a1..84bb8b30 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1c_missing_all_samples.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1c_missing_all_samples.json @@ -68,6 +68,10 @@ "recipe": null, "normalizedPatientId": "wrongValue", "sampleType": "wrongValue" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "recipe": null, "normalizedPatientId": "wrongValue", "sampleType": "wrongValue" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "recipe": "", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "wrongValue" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "sampleType": null, "normalizedPatientId": "wrongValue", "recipe": "" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1d_missing_few_samples.json b/service/src/test/resources/data/incoming_requests/mocked_request1d_missing_few_samples.json index 7f8eec6b..fcffd7d7 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1d_missing_few_samples.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1d_missing_few_samples.json @@ -68,6 +68,10 @@ "recipe": "", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "", "sampleType": null + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "recipe": "GENESET101_BAITS", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request1e_null_string_baitset.json b/service/src/test/resources/data/incoming_requests/mocked_request1e_null_string_baitset.json index 7304271c..beddf66f 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request1e_null_string_baitset.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request1e_null_string_baitset.json @@ -68,6 +68,10 @@ "recipe": "null", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "recipe": "null", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "recipe": "null", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "PDX" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "recipe": "null", "normalizedPatientId": "testingNormalizedPatientIdvalue", "sampleType": "Blood" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request2a_one_empty_sample_metadata.json b/service/src/test/resources/data/incoming_requests/mocked_request2a_one_empty_sample_metadata.json index 85dc6329..16ee6294 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request2a_one_empty_sample_metadata.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request2a_one_empty_sample_metadata.json @@ -66,6 +66,10 @@ "recipe": "", "normalizedPatientId": "", "sampleType": "" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request2a_one_normal.json b/service/src/test/resources/data/incoming_requests/mocked_request2a_one_normal.json index 1130076d..fb605f5f 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request2a_one_normal.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request2a_one_normal.json @@ -77,6 +77,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request2b_missing_one_normal.json b/service/src/test/resources/data/incoming_requests/mocked_request2b_missing_one_normal.json index d2ad84c7..a782be92 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request2b_missing_one_normal.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request2b_missing_one_normal.json @@ -80,6 +80,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -147,6 +151,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -214,6 +222,10 @@ "sampleType": "", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -248,6 +260,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -315,6 +331,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -382,6 +402,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -449,6 +473,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -516,6 +544,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -583,6 +615,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -650,6 +686,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -717,6 +757,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -784,6 +828,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -851,6 +899,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -918,6 +970,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -985,6 +1041,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -1052,6 +1112,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -1119,6 +1183,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -1186,6 +1254,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -1253,6 +1325,10 @@ "sampleType": "Buffy Coat", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -1320,6 +1396,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -1387,6 +1467,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request3_pooled_normals.json b/service/src/test/resources/data/incoming_requests/mocked_request3_pooled_normals.json index d5f8fda9..609756bc 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request3_pooled_normals.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request3_pooled_normals.json @@ -75,6 +75,10 @@ "sampleType": "Sorted Cells", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -137,6 +141,10 @@ "sampleType": "Sorted Cells", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -199,6 +207,10 @@ "sampleType": "Sorted Cells", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -261,6 +273,10 @@ "sampleType": "Sorted Cells", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request4_null_or_empty_values.json b/service/src/test/resources/data/incoming_requests/mocked_request4_null_or_empty_values.json index 65c14e22..a6ef38ed 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request4_null_or_empty_values.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request4_null_or_empty_values.json @@ -68,6 +68,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request5_pt_multi_samples.json b/service/src/test/resources/data/incoming_requests/mocked_request5_pt_multi_samples.json index 278ec2a6..ee3efd8d 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request5_pt_multi_samples.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request5_pt_multi_samples.json @@ -69,6 +69,10 @@ "sampleType": "Plasma", "normalizedPatientId": "MRN_REDACTED", "recipe": "null" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "sampleType": "Plasma", "normalizedPatientId": "MRN_REDACTED", "recipe": "null" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -177,6 +185,10 @@ "sampleType": "Plasma", "normalizedPatientId": "MRN_REDACTED", "recipe": "null" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -231,6 +243,10 @@ "sampleType": "Plasma", "normalizedPatientId": "MRN_REDACTED", "recipe": "null" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -285,6 +301,10 @@ "sampleType": "Plasma", "normalizedPatientId": "MRN_REDACTED", "recipe": "null" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -339,6 +359,10 @@ "sampleType": "Plasma", "normalizedPatientId": "MRN_REDACTED", "recipe": "null" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request6_cmopt_after_swap.json b/service/src/test/resources/data/incoming_requests/mocked_request6_cmopt_after_swap.json index 012bab66..de188c06 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request6_cmopt_after_swap.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request6_cmopt_after_swap.json @@ -68,6 +68,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ], diff --git a/service/src/test/resources/data/incoming_requests/mocked_request6_cmopt_swap.json b/service/src/test/resources/data/incoming_requests/mocked_request6_cmopt_swap.json index 9a8084ab..6d0b9fa0 100644 --- a/service/src/test/resources/data/incoming_requests/mocked_request6_cmopt_swap.json +++ b/service/src/test/resources/data/incoming_requests/mocked_request6_cmopt_swap.json @@ -68,6 +68,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -123,6 +127,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -178,6 +186,10 @@ "sampleType": "Tissue", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } }, { @@ -233,6 +245,10 @@ "sampleType": "Whole Blood", "normalizedPatientId": "MRN_REDACTED", "recipe": "GENESET101_BAITS" + }, + "status": { + "validationStatus": true, + "validationReport": "{}" } } ],