Sample status bug fix (#908)

- Add status to mock incoming request data Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Mar 16, 2023 · 2a08454 · 2a08454
1 parent 403ebcd
commit 2a08454
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Showing 22 changed files with 370 additions and 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
@@ -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
@@ -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<SmileSample> extractSmileSamplesFromIgoResponse(Object message)
             throws JsonProcessingException {
         Map<String, Object> map = mapper.readValue(message.toString(), Map.class);
-        IgoSampleManifest[] samples = mapper.convertValue(map.get("samples"),
-                IgoSampleManifest[].class);
+        /// SAMPLE STATUS NOT GETTING SET HERE
+        List<Object> sampleManifests =
+                Arrays.asList(mapper.convertValue(map.get("samples"),
+                        Object[].class));
         String requestId = (String) map.get("requestId");
         Boolean isCmoRequest = (Boolean) map.get("isCmoRequest");
 
         List<SmileSample> requestSamplesList = new ArrayList<>();
-        for (IgoSampleManifest s: samples) {
+        for (Object s : sampleManifests) {
+            Map<String, Object> sampleMap = mapper.convertValue(s, Map.class);
+            Map<String, Object> 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
@@ -46,10 +46,11 @@ private static Map<Integer, String> 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
@@ -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/...src/test/resources/data/incoming_requests/mocked_request1_all_samples_missing_fastqs.json b/...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
@@ -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/...urces/data/incoming_requests/mocked_request1_complete_tumor_normal_updated_libraries.json b/...urces/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
@@ -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/.../test/resources/data/incoming_requests/mocked_request1_updated_complete_tumor_normal.json b/.../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/.../src/test/resources/data/incoming_requests/mocked_request1a_sample_type_abbreviation.json b/.../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": "{}"
       }
     }
   ],