Allow Cohort sample list updates (#1212)

Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Jul 2, 2024 · 1efb394 · 1efb394
1 parent de5f044
commit 1efb394
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Showing 8 changed files with 120 additions and 20 deletions.
diff --git a/model/src/main/java/org/mskcc/smile/model/tempo/Cohort.java b/model/src/main/java/org/mskcc/smile/model/tempo/Cohort.java
@@ -1,9 +1,12 @@
 package org.mskcc.smile.model.tempo;
 
 import java.io.Serializable;
+import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import org.apache.commons.lang.builder.ToStringBuilder;
 import org.mskcc.smile.model.SmileSample;
 import org.mskcc.smile.model.tempo.json.CohortCompleteJson;
@@ -103,7 +106,7 @@ public void setCohortSamples(List<SmileSample> cohortSamples) {
 
     /**
      * Returns latest cohort complete data.
-     * @return
+     * @return CohortComplete
      */
     public CohortComplete getLatestCohortComplete() {
         if (cohortCompleteList != null && !cohortCompleteList.isEmpty()) {
@@ -116,6 +119,22 @@ public CohortComplete getLatestCohortComplete() {
         return null;
     }
 
+    /**
+     * Returns sample ids as set of strings.
+     * @return Set
+     * @throws ParseException
+     */
+    public Set<String> getCohortSamplePrimaryIds() throws ParseException {
+        if (cohortSamples == null) {
+            return new HashSet<>();
+        }
+        Set<String> sampleIds = new HashSet<>();
+        for (SmileSample sample : cohortSamples) {
+            sampleIds.add(sample.getPrimarySampleAlias());
+        }
+        return sampleIds;
+    }
+
     @Override
     public String toString() {
         return ToStringBuilder.reflectionToString(this);

diff --git a/service/src/main/java/org/mskcc/smile/service/CohortCompleteService.java b/service/src/main/java/org/mskcc/smile/service/CohortCompleteService.java
@@ -3,7 +3,6 @@
 import java.util.List;
 import java.util.Set;
 import org.mskcc.smile.model.tempo.Cohort;
-import org.mskcc.smile.model.tempo.CohortComplete;
 
 /**
  *
@@ -13,6 +12,8 @@ public interface CohortCompleteService {
     Cohort saveCohort(Cohort cohort, Set<String> samplePrimaryIds) throws Exception;
     Cohort getCohortByCohortId(String cohortId) throws Exception;
     List<Cohort> getCohortsBySamplePrimaryId(String primaryId) throws Exception;
-    Boolean hasUpdates(Cohort cohort, CohortComplete newCohortComplete) throws Exception;
+    Boolean hasUpdates(Cohort existingCohort, Cohort cohort) throws Exception;
+    Boolean hasCohortCompleteUpdates(Cohort existingCohort, Cohort cohort)
+            throws Exception;
     Cohort updateCohort(Cohort cohort) throws Exception;
 }
diff --git a/service/src/main/java/org/mskcc/smile/service/impl/CohortCompleteServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/CohortCompleteServiceImpl.java
@@ -10,7 +10,6 @@
 import org.mskcc.smile.commons.JsonComparator;
 import org.mskcc.smile.model.SmileSample;
 import org.mskcc.smile.model.tempo.Cohort;
-import org.mskcc.smile.model.tempo.CohortComplete;
 import org.mskcc.smile.persistence.neo4j.CohortCompleteRepository;
 import org.mskcc.smile.service.CohortCompleteService;
 import org.mskcc.smile.service.SmileSampleService;
@@ -87,10 +86,20 @@ public List<Cohort> getCohortsBySamplePrimaryId(String primaryId) throws Excepti
     }
 
     @Override
-    public Boolean hasUpdates(Cohort cohort, CohortComplete cohortComplete) throws Exception {
-        String existingCohortComplete = mapper.writeValueAsString(cohort.getLatestCohortComplete());
-        String currentCohortComplete = mapper.writeValueAsString(cohortComplete);
-        return !jsonComparator.isConsistentGenericComparison(existingCohortComplete, currentCohortComplete);
+    public Boolean hasUpdates(Cohort existingCohort, Cohort cohort) throws Exception {
+        // check cohort complete data for updates first
+        Boolean hasUpdates = hasCohortCompleteUpdates(existingCohort, cohort);
+        Set<String> newSamples = cohort.getCohortSamplePrimaryIds();
+        newSamples.removeAll(existingCohort.getCohortSamplePrimaryIds());
+        return (hasUpdates || !newSamples.isEmpty());
+    }
+
+    @Override
+    public Boolean hasCohortCompleteUpdates(Cohort existingCohort, Cohort cohort) throws Exception {
+        String existingCohortComplete = mapper.writeValueAsString(existingCohort.getLatestCohortComplete());
+        String currentCohortComplete = mapper.writeValueAsString(cohort.getLatestCohortComplete());
+        return !jsonComparator.isConsistentGenericComparison(existingCohortComplete,
+                currentCohortComplete);
     }
 
     @Override

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
@@ -419,7 +419,8 @@ public SmileSample getDetailedSmileSample(SmileSample sample) throws Exception {
             sample.setTempo(tempo);
         } catch (IncorrectResultSizeDataAccessException e) {
             if (e.getActualSize() < 0) {
-                LOG.warn("There is no TEMPO data for sample: " + sample.getPrimarySampleAlias());
+                LOG.warn("There is no TEMPO data for sample: " + sample.getPrimarySampleAlias()
+                        + " - TEMPO data will not be set for sample.");
             } else {
                 StringBuilder b = new StringBuilder();
                 b.append("Error fetching TEMPO data for sample: ")

diff --git a/service/src/main/java/org/mskcc/smile/service/impl/TempoMessageHandlingServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/TempoMessageHandlingServiceImpl.java
@@ -3,11 +3,7 @@
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.nats.client.Message;
-import java.nio.charset.StandardCharsets;
 import java.util.AbstractMap;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
@@ -26,7 +22,6 @@
 import org.mskcc.smile.model.SmileSample;
 import org.mskcc.smile.model.tempo.BamComplete;
 import org.mskcc.smile.model.tempo.Cohort;
-import org.mskcc.smile.model.tempo.CohortComplete;
 import org.mskcc.smile.model.tempo.MafComplete;
 import org.mskcc.smile.model.tempo.QcComplete;
 import org.mskcc.smile.model.tempo.Tempo;
@@ -273,10 +268,18 @@ public void run() {
                             // compiles them into a set list of strings
                             cohortCompleteService.saveCohort(cohort, ccJson.getTumorNormalPairsAsSet());
                         } else if (cohortCompleteService.hasUpdates(existingCohort,
-                                cohort.getLatestCohortComplete())) {
+                                cohort)) {
                             LOG.info("Received updates for cohort: " + ccJson.getCohortId());
-                            existingCohort.addCohortComplete(cohort.getLatestCohortComplete());
-                            cohortCompleteService.updateCohort(existingCohort);
+                            if (cohortCompleteService.hasCohortCompleteUpdates(existingCohort, cohort)) {
+                                existingCohort.addCohortComplete(cohort.getLatestCohortComplete());
+                            }
+
+                            // new samples refer to samples that aren't yet linked to the given cohort
+                            Set<String> newSamples = ccJson.getTumorNormalPairsAsSet();
+                            newSamples.removeAll(existingCohort.getCohortSamplePrimaryIds());
+
+                            // persist updates to db
+                            cohortCompleteService.saveCohort(existingCohort, newSamples);
                         } else {
                             LOG.error("Cohort " + ccJson.getCohortId()
                                     + " already exists and no new updates were received.");

diff --git a/service/src/test/java/org/mskcc/smile/service/TempoServiceTest.java b/service/src/test/java/org/mskcc/smile/service/TempoServiceTest.java
@@ -4,6 +4,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import org.assertj.core.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.mskcc.smile.model.SmileRequest;
@@ -103,8 +104,16 @@ public void initializeMockDatabase() throws Exception {
         // mock request id: MOCKREQUEST1_B
         MockJsonTestData request1Data = mockDataUtils.mockedRequestJsonDataMap
                 .get("mockIncomingRequest1JsonDataWith2T2N");
-        SmileRequest request1 = RequestDataFactory.buildNewLimsRequestFromJson(request1Data.getJsonString());
+        SmileRequest request1 =
+                RequestDataFactory.buildNewLimsRequestFromJson(request1Data.getJsonString());
         requestService.saveRequest(request1);
+
+        // mock request id: 22022_BZ
+        MockJsonTestData request2bData = mockDataUtils.mockedRequestJsonDataMap
+                .get("mockIncomingRequest2bJsonDataMissing1N");
+        SmileRequest request2b =
+                RequestDataFactory.buildNewLimsRequestFromJson(request2bData.getJsonString());
+        requestService.saveRequest(request2b);
     }
 
     @Test
@@ -213,8 +222,7 @@ public void testUpdateCohortCompleteData() throws Exception {
         CohortCompleteJson ccJsonUpdate = getCohortEventData("mockCohortCompleteCCSPPPQQQQUpdated");
 
         Cohort updatedCohort = new Cohort(ccJsonUpdate);
-        CohortComplete updatedCohortComplete = updatedCohort.getLatestCohortComplete();
-        Boolean hasUpdates = cohortCompleteService.hasUpdates(cohort, updatedCohortComplete);
+        Boolean hasUpdates = cohortCompleteService.hasUpdates(cohort, updatedCohort);
         Assertions.assertThat(hasUpdates).isTrue();
     }
 
@@ -251,6 +259,32 @@ public void testNormalSampleTumorSampleTempoImportDefaults() throws Exception {
         Assertions.assertThat(tempoAfterSave3.getAccessLevel()).isNotBlank();
     }
 
+    @Test
+    public void testCohortSampleListUpdate() throws Exception {
+        CohortCompleteJson ccJson = getCohortEventData("mockCohortCompleteCCSPPPQQQQ");
+        cohortCompleteService.saveCohort(new Cohort(ccJson), ccJson.getTumorNormalPairsAsSet());
+        Cohort cohort = cohortCompleteService.getCohortByCohortId("CCS_PPPQQQQ");
+        Assertions.assertThat(cohort.getCohortSamplePrimaryIds().size()).isEqualTo(4);
+
+        CohortCompleteJson ccJsonUpdate =
+                getCohortEventData("mockCohortCompleteCCSPPPQQQQUpdatedSamplesOnly");
+        Assertions.assertThat(ccJsonUpdate.getTumorNormalPairsAsSet().size()).isEqualTo(6);
+
+        Cohort updatedCohort = new Cohort(ccJsonUpdate);
+        Boolean hasUpdates = cohortCompleteService.hasUpdates(cohort, updatedCohort);
+        Assertions.assertThat(hasUpdates).isTrue();
+
+        // verify there are 2 new samples getting added to the cohort
+        Set<String> newSamples = ccJsonUpdate.getTumorNormalPairsAsSet();
+        newSamples.removeAll(cohort.getCohortSamplePrimaryIds());
+        Assertions.assertThat(newSamples.size()).isEqualTo(2);
+
+        // save cohort and verify that it now has 6 samples instead of 4
+        cohortCompleteService.saveCohort(cohort, newSamples);
+        Cohort cohortAfterSave = cohortCompleteService.getCohortByCohortId("CCS_PPPQQQQ");
+        Assertions.assertThat(cohortAfterSave.getCohortSamplePrimaryIds().size()).isEqualTo(6);
+    }
+
     private CohortCompleteJson getCohortEventData(String dataIdentifier) throws JsonProcessingException {
         MockJsonTestData mockData = mockDataUtils.mockedTempoDataMap.get(dataIdentifier);
         CohortCompleteJson cohortCompleteData = mapper.readValue(mockData.getJsonString(),

diff --git a/service/src/test/resources/data/tempo/cohort_complete_CCS_PPPQQQQ_updated_samples_only.json b/service/src/test/resources/data/tempo/cohort_complete_CCS_PPPQQQQ_updated_samples_only.json
@@ -0,0 +1,32 @@
+{
+  "cohortId": "CCS_PPPQQQQ",
+  "date": "2022-11-12 21:59",
+  "type": "investigator",
+  "endUsers": [
+    "enduser1",
+    "enduser2",
+    "enduser3"
+  ],
+  "pmUsers": [
+    "pmuser1",
+    "pmuser2",
+    "pmuser3"
+  ],
+  "projectTitle": "A title",
+  "projectSubtitle": "A longer description",
+  "samples": [
+    {
+      "primaryId": "MOCKREQUEST1_B_1",
+      "normalPrimaryId": "MOCKREQUEST1_B_2"
+    },
+    {
+      "primaryId": "MOCKREQUEST1_B_3",
+      "normalPrimaryId": "MOCKREQUEST1_B_4"
+    },
+    {
+      "primaryId": "22022_BZ_15",
+      "normalPrimaryId": "22022_BZ_19"
+    }
+  ],
+  "status": "PASS"
+}
diff --git a/service/src/test/resources/data/tempo/mocked_tempo_data_details.txt b/service/src/test/resources/data/tempo/mocked_tempo_data_details.txt
@@ -16,3 +16,4 @@ mockMafCompleteSampleB3pass	tempo/maf_complete_MOCKREQUEST1_B_3_pass.json	Mocked
 mockCohortCompleteCCSPPPQQQQ	tempo/cohort_complete_CCS_PPPQQQQ.json	Mocked Cohort complete JSON with cohort ID CCS_PPPQQQQ. Has 4 samples associated with it.
 mockCohortCompleteCCSPPPQQQQ2	tempo/cohort_complete_CCS_PPPQQQQ_2.json	Mocked Cohort complete JSON with cohort ID CCS_PPPQQQQ_2. Has 2 samples associated with it.
 mockCohortCompleteCCSPPPQQQQUpdated	tempo/cohort_complete_CCS_PPPQQQQ_updated.json	Mocked updated Cohort complete JSON with cohort ID CCS_PPPQQQQ. Has 4 samples associated with it.
+mockCohortCompleteCCSPPPQQQQUpdatedSamplesOnly	tempo/cohort_complete_CCS_PPPQQQQ_updated_samples_only.json	Mocked updated Cohort complete JSON with cohort ID CCS_PPPQQQQ. Has 6 samples associated with it.