Support ALT ID's (#1374)

* Add alt (#1362) * Init commit - add alt ID to data models Signed-off-by: Angelica Ochoa <[email protected]> * Support searching by alt ID in persistence and service layers Signed-off-by: Angelica Ochoa <[email protected]> --------- Signed-off-by: Angelica Ochoa <[email protected]> * Add request-reply handler for fetching samples by alt ID (#1363) * Add a message handler for alt ID * Create a mocked incoming request for the alt id test * Create a mocked outgoing request for the alt id test * Add test for the alt id handler * Rename 'altId' to 'altid' in the incoming mocked request to match IGO casing --------- Signed-off-by: Angelica Ochoa <[email protected]> Co-authored-by: Quan Nguyen <[email protected]>
mskcc · Jan 15, 2025 · b889029 · b889029
1 parent 9588cae
commit b889029
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Showing 12 changed files with 520 additions and 3 deletions.
diff --git a/model/src/main/java/org/mskcc/smile/model/SampleMetadata.java b/model/src/main/java/org/mskcc/smile/model/SampleMetadata.java
@@ -96,6 +96,7 @@ public SampleMetadata(IgoSampleManifest igoSampleManifest) throws JsonProcessing
         this.qcReports =  igoSampleManifest.getQcReports();
         this.libraries = igoSampleManifest.getLibraries();
         this.cmoSampleIdFields = igoSampleManifest.getCmoSampleIdFields();
+        addAdditionalProperty("altId", igoSampleManifest.getAltid());
     }
 
     /**
@@ -380,6 +381,10 @@ public void addAdditionalProperty(String property, String value) {
         this.additionalProperties.put(property, value);
     }
 
+    public String getAdditionalProperty(String property) {
+        return additionalProperties.get(property);
+    }
+
     public Status getStatus() {
         return status;
     }

diff --git a/model/src/main/java/org/mskcc/smile/model/igo/IgoSampleManifest.java b/model/src/main/java/org/mskcc/smile/model/igo/IgoSampleManifest.java
@@ -16,6 +16,7 @@ public class IgoSampleManifest {
     private String cmoPatientId;
     private String cmoSampleName;
     private String sampleName;
+    private String altid;
     private String baitSet;
     private String cfDNA2dBarcode;
     private String cmoInfoIgoId;
@@ -70,6 +71,14 @@ public void setSampleName(String sampleName) {
         this.sampleName = sampleName;
     }
 
+    public String getAltid() {
+        return altid;
+    }
+
+    public void setAltid(String altid) {
+        this.altid = altid;
+    }
+
     public String getBaitSet() {
         return baitSet;
     }

diff --git a/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmileSampleRepository.java b/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmileSampleRepository.java
@@ -27,13 +27,18 @@ public interface SmileSampleRepository extends Neo4jRepository<SmileSample, UUID
     SmileSample findSampleBySampleSmileId(@Param("smileSampleId") UUID smileSampleId);
 
     @Query("MATCH (s: Sample)-[:HAS_METADATA]->(sm: SampleMetadata {primaryId: $primaryId}) "
-            + "RETURN s")
+            + "RETURN DISTINCT s")
     SmileSample findSampleByPrimaryId(@Param("primaryId") String primaryId);
 
     @Query("MATCH (s: Sample)-[:HAS_METADATA]->(sm: SampleMetadata {cmoSampleName: $cmoSampleName}) "
-            + "RETURN s")
+            + "RETURN DISTINCT s")
     List<SmileSample> findSamplesByCmoSampleName(@Param("cmoSampleName") String cmoSampleName);
 
+    @Query("MATCH (s: Sample)-[:HAS_METADATA]->(sm: SampleMetadata) "
+            + "WHERE sm.additionalProperties CONTAINS $altId "
+            + "RETURN DISTINCT s")
+    List<SmileSample> findSamplesByAltId(@Param("altId") String altId);
+
     @Query("MATCH (s: Sample {smileSampleId: $smileSampleId})-[:HAS_METADATA]->(sm: SampleMetadata) "
             + "OPTIONAL MATCH (sm)-[hs:HAS_STATUS]->(ss: Status) "
             + "RETURN sm, hs, ss")

diff --git a/service/src/main/java/org/mskcc/smile/service/RequestReplyHandlingService.java b/service/src/main/java/org/mskcc/smile/service/RequestReplyHandlingService.java
@@ -6,6 +6,7 @@ public interface RequestReplyHandlingService {
     void initialize(Gateway gateway) throws Exception;
     void patientSamplesHandler(String patientId, String replyTo) throws Exception;
     void samplesByCmoLabelHandler(String cmoLabel, String replyTo) throws Exception;
+    void samplesByAltIdHandler(String cmoLabel, String replyTo) throws Exception;
     void crdbMappingHandler(String inputId, String replyTo) throws Exception;
     void shutdown() throws Exception;
 }
diff --git a/service/src/main/java/org/mskcc/smile/service/SmileSampleService.java b/service/src/main/java/org/mskcc/smile/service/SmileSampleService.java
@@ -36,4 +36,5 @@ List<SmileSample> getSamplesByCategoryAndCmoPatientId(String cmoPatientId,
     Boolean sampleExistsByInputId(String primaryId);
     List<SmileSample> getSamplesByCohortId(String cohortId) throws Exception;
     List<SmileSample> getSamplesByCmoSampleName(String cmoSampleName) throws Exception;
+    List<SmileSample> getSamplesByAltId(String altId) throws Exception;
 }
diff --git a/service/src/main/java/org/mskcc/smile/service/impl/RequestReplyHandlingServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/RequestReplyHandlingServiceImpl.java
@@ -34,6 +34,9 @@ public class RequestReplyHandlingServiceImpl implements RequestReplyHandlingServ
     @Value("${request_reply.samples_by_cmo_label_topic}")
     private String SAMPLES_BY_CMO_LABEL_REQREPLY_TOPIC;
 
+    @Value("${request_reply.samples_by_alt_id_topic}")
+    private String SAMPLES_BY_ALT_ID_REQREPLY_TOPIC;
+
     @Value("${request_reply.crdb_mapping_topic}")
     private String CRDB_MAPPING_REQREPLY_TOPIC;
 
@@ -54,10 +57,13 @@ public class RequestReplyHandlingServiceImpl implements RequestReplyHandlingServ
         new LinkedBlockingQueue<ReplyInfo>();
     private static final BlockingQueue<ReplyInfo> samplesByCmoLabelReqReplyQueue =
         new LinkedBlockingQueue<ReplyInfo>();
+    private static final BlockingQueue<ReplyInfo> samplesByAltIdReqReplyQueue =
+        new LinkedBlockingQueue<ReplyInfo>();
     private static final BlockingQueue<ReplyInfo> crdbMappingReqReplyQueue =
         new LinkedBlockingQueue<ReplyInfo>();
     private static CountDownLatch patientSamplesHandlerShutdownLatch;
     private static CountDownLatch samplesByCmoLabelHandlerShutdownLatch;
+    private static CountDownLatch samplesByAltIdHandlerShutdownLatch;
     private static CountDownLatch crdbMappingHandlerShutdownLatch;
     private static Gateway messagingGateway;
 
@@ -160,6 +166,45 @@ public void run() {
         }
     }
 
+    private class SamplesByAltIdReqReplyHandler implements Runnable {
+
+        final Phaser phaser;
+        boolean interrupted = false;
+
+        SamplesByAltIdReqReplyHandler(Phaser phaser) {
+            this.phaser = phaser;
+        }
+
+        @Override
+        public void run() {
+            phaser.arrive();
+            while (true) {
+                try {
+                    // reply info request message contains cmo sample label
+                    ReplyInfo replyInfo = samplesByAltIdReqReplyQueue.poll(100, TimeUnit.MILLISECONDS);
+                    if (replyInfo != null) {
+                        List<SmileSample> matchingSamples =
+                                sampleService.getSamplesByAltId(replyInfo.getRequestMessage());
+                        List<SampleMetadata> sampleMetadataList = new ArrayList<>();
+                        for (SmileSample sample : matchingSamples) {
+                            sampleMetadataList.add(sample.getLatestSampleMetadata());
+                        }
+                        messagingGateway.replyPublish(replyInfo.getReplyTo(),
+                                mapper.writeValueAsString(sampleMetadataList));
+                    }
+                    if (interrupted && samplesByAltIdReqReplyQueue.isEmpty()) {
+                        break;
+                    }
+                } catch (InterruptedException e) {
+                    interrupted = true;
+                } catch (Exception e) {
+                    LOG.error("Error during request handling", e);
+                }
+            }
+            samplesByAltIdHandlerShutdownLatch.countDown();
+        }
+    }
+
     private class CrdbMappingReqReplyHandler implements Runnable {
 
         final Phaser phaser;
@@ -205,6 +250,7 @@ public void initialize(Gateway gateway) throws Exception {
             messagingGateway = gateway;
             setupPatientSamplesHandler(messagingGateway, this);
             setupSamplesByCmoLabelHandler(messagingGateway, this);
+            setupSamplesByAltIdHandler(messagingGateway, this);
             setupCrdbMappingHandler(messagingGateway, this);
             initializeRequestReplyHandlers();
             initialized = true;
@@ -239,6 +285,19 @@ public void samplesByCmoLabelHandler(String cmoLabel, String replyTo) throws Exc
         }
     }
 
+    @Override
+    public void samplesByAltIdHandler(String altId, String replyTo) throws Exception {
+        if (!initialized) {
+            throw new IllegalStateException("Message Handling Service has not been initialized");
+        }
+        if (!shutdownInitiated) {
+            samplesByAltIdReqReplyQueue.put(new ReplyInfo(altId, replyTo));
+        } else {
+            LOG.error("Shutdown initiated, not accepting alt ID req-reply: " + altId);
+            throw new IllegalStateException("Shutdown initiated, not handling any more alt IDs");
+        }
+    }
+
     @Override
     public void crdbMappingHandler(String inputId, String replyTo) throws Exception {
         if (!initialized) {
@@ -308,6 +367,28 @@ public void onMessage(Message msg, Object message) {
         });
     }
 
+    private void setupSamplesByAltIdHandler(Gateway gateway,
+            RequestReplyHandlingServiceImpl requestReplyHandlingServiceImpl)
+            throws Exception {
+        gateway.replySub(SAMPLES_BY_ALT_ID_REQREPLY_TOPIC, new MessageConsumer() {
+            @Override
+            public void onMessage(Message msg, Object message) {
+                LOG.info("Received message on topic: " + SAMPLES_BY_ALT_ID_REQREPLY_TOPIC);
+                try {
+                    if (StringUtils.isBlank(new String(msg.getData()))) {
+                        LOG.error("Expected an alt ID but message received is empty: " + msg
+                                + " - message will not be added to request-reply queue");
+                    } else {
+                        requestReplyHandlingServiceImpl.samplesByAltIdHandler(
+                                new String(msg.getData()), msg.getReplyTo());
+                    }
+                } catch (Exception e) {
+                    e.printStackTrace();
+                }
+            }
+        });
+    }
+
     private void setupCrdbMappingHandler(Gateway gateway,
             RequestReplyHandlingServiceImpl requestReplyHandlingServiceImpl)
             throws Exception {
@@ -344,6 +425,15 @@ private void initializeRequestReplyHandlers() throws Exception {
         }
         samplesByCmoLabelPhaser.arriveAndAwaitAdvance();
 
+        samplesByAltIdHandlerShutdownLatch = new CountDownLatch(NUM_NEW_REQUEST_HANDLERS);
+        final Phaser samplesByAltIdPhaser = new Phaser();
+        samplesByAltIdPhaser.register();
+        for (int lc = 0; lc < NUM_NEW_REQUEST_HANDLERS; lc++) {
+            samplesByAltIdPhaser.register();
+            exec.execute(new SamplesByAltIdReqReplyHandler(samplesByAltIdPhaser));
+        }
+        samplesByAltIdPhaser.arriveAndAwaitAdvance();
+
         crdbMappingHandlerShutdownLatch = new CountDownLatch(NUM_NEW_REQUEST_HANDLERS);
         final Phaser crdbMappingPhaser = new Phaser();
         crdbMappingPhaser.register();

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
@@ -501,4 +501,26 @@ public List<SmileSample> getSamplesByCmoSampleName(String cmoSampleName) throws
         }
         return toReturn;
     }
+
+    @Override
+    public List<SmileSample> getSamplesByAltId(String altId) throws Exception {
+        // alt id is stored in the sample metadata 'additionalProperties' map which
+        // is stored in the database as a string so the query needs to specify the
+        // altId property name as well: "altId":"<altId>"
+        String altIdSearchTerm = new StringBuilder("\"altId\":\"")
+                .append(altId)
+                .append("\"").toString();
+
+        List<SmileSample> samples = sampleRepository.findSamplesByAltId(altIdSearchTerm);
+        if  (samples == null) {
+            return new ArrayList<>();
+        }
+
+        List<SmileSample> toReturn = new ArrayList<>();
+        for (SmileSample s : samples) {
+            SmileSample detailedSample = getSmileSample(s.getSmileSampleId());
+            toReturn.add(detailedSample);
+        }
+        return toReturn;
+    }
 }
diff --git a/service/src/test/java/org/mskcc/smile/service/SampleServiceTest.java b/service/src/test/java/org/mskcc/smile/service/SampleServiceTest.java
@@ -158,6 +158,12 @@ public void initializeMockDatabase() throws Exception {
         SmileRequest request8 = RequestDataFactory.buildNewLimsRequestFromJson(request8Data.getJsonString());
         requestService.saveRequest(request8);
 
+        // mock request id: MOCKREQUEST9_D
+        MockJsonTestData request9Data = mockDataUtils.mockedRequestJsonDataMap
+                .get("mockIncomingRequest9DupAltIds");
+        SmileRequest request9 = RequestDataFactory.buildNewLimsRequestFromJson(request9Data.getJsonString());
+        requestService.saveRequest(request9);
+
         //persist all mocked clinical data
         for (MockJsonTestData mockJsonTestData : mockDataUtils.mockedDmpMetadataMap.values()) {
             DmpSampleMetadata dmpSample = mapper.readValue(mockJsonTestData.getJsonString(),
@@ -713,5 +719,12 @@ public void testDuplicateCmoSampleLabels() throws Exception {
         List<SmileSample> samplesMatchingLabels = sampleService.getSamplesByCmoSampleName(cmoLabel);
         Assertions.assertEquals(2, samplesMatchingLabels.size());
     }
-}
 
+    @Test
+    @Order(24)
+    public void testDuplicateAltIds() throws Exception {
+        String altId = "AB9-ABC";
+        List<SmileSample> samplesMatchingAltIds = sampleService.getSamplesByAltId(altId);
+        Assertions.assertEquals(2, samplesMatchingAltIds.size());
+    }
+}