Modified igo updates handling and new smile-commons version (#796)

Signed-off-by: Divya Madala <[email protected]>

Signed-off-by: Divya Madala <[email protected]>

model/src/main/java/org/mskcc/smile/model/SmileRequest.java

@@ -396,6 +396,25 @@ public void updateRequestMetadataByMetadata(RequestMetadata requestMetadata)
         addRequestMetadata(requestMetadata);
     }
 
+    /**
+     * Updates by LIMS
+     * Update Metadata to only include accepted updates for a list of fields
+     * @param requestMetadata
+     * @throws JsonProcessingException
+     */
+    public void applyIgoRequestMetadataUpdates(RequestMetadata requestMetadata)
+            throws JsonProcessingException {
+        Map<String, Object> metadataMap =
+                mapper.readValue(requestMetadata.getRequestMetadataJson(), Map.class);
+
+        this.genePanel = resolveGenePanel(metadataMap);
+        this.strand = String.valueOf(metadataMap.get("strand"));
+        this.libraryType = String.valueOf(metadataMap.get("libraryType"));
+        this.isCmoRequest = Boolean.parseBoolean(String.valueOf(metadataMap.get("isCmoRequest")));
+        this.pooledNormals = mapper.convertValue(metadataMap.get("pooledNormals"), List.class);
+        addRequestMetadata(requestMetadata);
+    }
+
     /**
      * Resolves gene panel from recipe or genePanel sample json field.
      * @param metadataMap

model/src/main/java/org/mskcc/smile/model/SmileSample.java

@@ -154,6 +154,37 @@ public SampleMetadata getLatestSampleMetadata() throws ParseException {
         return null;
     }
 
+    /**
+     * Applies IGO LIMS updates for the following fields
+     * @param sampleMetadata
+     * @return
+     */
+    public void applyIgoLimsUpdates(SampleMetadata sampleMetadata) throws ParseException {
+        SampleMetadata latestSampleMetadata = getLatestSampleMetadata();
+
+        sampleMetadata.setId(null);
+        sampleMetadata.setCmoPatientId(latestSampleMetadata.getCmoPatientId());
+        sampleMetadata.setInvestigatorSampleId(latestSampleMetadata.getInvestigatorSampleId());
+        sampleMetadata.setInvestigatorSampleId(latestSampleMetadata.getInvestigatorSampleId());
+        sampleMetadata.setSampleName(latestSampleMetadata.getSampleName());
+        sampleMetadata.setCmoInfoIgoId(latestSampleMetadata.getCmoInfoIgoId());
+        sampleMetadata.setOncotreeCode(latestSampleMetadata.getOncotreeCode());
+        sampleMetadata.setCollectionYear(latestSampleMetadata.getCollectionYear());
+        sampleMetadata.setTubeId(latestSampleMetadata.getTubeId());
+        sampleMetadata.setSpecies(latestSampleMetadata.getSpecies());
+        sampleMetadata.setSex(latestSampleMetadata.getSex());
+        sampleMetadata.setTumorOrNormal(latestSampleMetadata.getTumorOrNormal());
+        sampleMetadata.setSampleType(latestSampleMetadata.getSampleType());
+        sampleMetadata.setPreservation(latestSampleMetadata.getPreservation());
+        sampleMetadata.setSampleClass(latestSampleMetadata.getSampleClass());
+        sampleMetadata.setSampleOrigin(latestSampleMetadata.getSampleOrigin());
+        sampleMetadata.setTissueLocation(latestSampleMetadata.getTissueLocation());
+        sampleMetadata.setGenePanel(latestSampleMetadata.getGenePanel());
+        sampleMetadata.setIgoComplete(latestSampleMetadata.getIgoComplete());
+
+        addSampleMetadata(sampleMetadata);
+    }
+
     public void updateSampleMetadata(SampleMetadata sampleMetadata) throws ParseException {
         sampleMetadata.setId(null);
         addSampleMetadata(sampleMetadata);

pom.xml

@@ -51,7 +51,7 @@
     <smile_messaging_java.version>1.3.6.RELEASE</smile_messaging_java.version>
     <!-- smile commons centralized config properties -->
     <smile_commons.group>com.github.mskcc</smile_commons.group>
-    <smile_commons.version>1.3.6.RELEASE</smile_commons.version>
+    <smile_commons.version>1.3.8.RELEASE</smile_commons.version>
     <!-- smile expected schema version -->
     <smile.schema_version>v2.2</smile.schema_version>
   </properties>

service/src/main/java/org/mskcc/smile/service/SmileRequestService.java

@@ -16,10 +16,11 @@ public interface SmileRequestService {
     Boolean saveRequestMetadata(SmileRequest request);
     SmileRequest getSmileRequestById(String requestId) throws Exception;
     PublishedSmileRequest getPublishedSmileRequestById(String requestId) throws Exception;
-    Boolean updateRequestMetadata(RequestMetadata requestMetadata) throws Exception;
-    Boolean requestHasUpdates(SmileRequest existingRequest, SmileRequest request) throws Exception;
+    Boolean updateRequestMetadata(RequestMetadata requestMetadata, Boolean fromLims) throws Exception;
+    Boolean requestHasUpdates(SmileRequest existingRequest, SmileRequest request, Boolean fromLims)
+            throws Exception;
     Boolean requestHasMetadataUpdates(RequestMetadata existingRequestMetadata,
-            RequestMetadata requestMetadata) throws Exception;
+            RequestMetadata requestMetadata, Boolean fromLims) throws Exception;
     List<SmileSample> getRequestSamplesWithUpdates(SmileRequest request) throws Exception;
     List<RequestSummary> getRequestsByDate(String startDate, String endDate) throws Exception;
     List<RequestMetadata> getRequestMetadataHistory(String reqId);

service/src/main/java/org/mskcc/smile/service/SmileSampleService.java

@@ -11,7 +11,7 @@
 public interface SmileSampleService {
     SmileSample saveSmileSample(SmileSample smileSample) throws Exception;
     SmileSample fetchAndLoadPatientDetails(SmileSample smileSample) throws Exception;
-    Boolean updateSampleMetadata(SampleMetadata sampleMetadata) throws Exception;
+    Boolean updateSampleMetadata(SampleMetadata sampleMetadata, Boolean fromLims) throws Exception;
     List<SmileSample> getMatchedNormalsBySample(SmileSample smileSample)
             throws Exception;
     List<String> getPooledNormalsBySample(SmileSample smileSample) throws Exception;
@@ -20,7 +20,7 @@ List<SmileSample> getMatchedNormalsBySample(SmileSample smileSample)
     List<SmileSample> getResearchSamplesByRequestId(String requestId) throws Exception;
     List<SampleMetadata> getResearchSampleMetadataHistoryByIgoId(String igoId) throws Exception;
     Boolean sampleHasMetadataUpdates(SampleMetadata existingSampleMetadata,
-            SampleMetadata sampleMetadata, Boolean isResearchSample)
+            SampleMetadata sampleMetadata, Boolean isResearchSample, Boolean fromLims)
             throws Exception;
     PublishedSmileSample getPublishedSmileSample(UUID smileSampleId) throws Exception;
     List<PublishedSmileSample> getPublishedSmileSamplesByCmoPatientId(String cmoPatientId)

service/src/main/java/org/mskcc/smile/service/impl/ClinicalMessageHandlingServiceImpl.java

@@ -126,7 +126,7 @@ public void run() {
                                     mapper.writeValueAsString(smileSample));
                         } else if (sampleService.sampleHasMetadataUpdates(
                                 existingSample.getLatestSampleMetadata(),
-                                smileSample.getLatestSampleMetadata(), Boolean.FALSE)) {
+                                smileSample.getLatestSampleMetadata(), Boolean.FALSE, Boolean.FALSE)) {
                             LOG.info("Found updates for sample - persisting to database: "
                                     + smileSample.getPrimarySampleAlias());
                             existingSample.updateSampleMetadata(smileSample.getLatestSampleMetadata());
@@ -180,7 +180,7 @@ public void run() {
                                     mapper.writeValueAsString(smileSample));
                         } else if (sampleService.sampleHasMetadataUpdates(
                                 existingSample.getLatestSampleMetadata(),
-                                smileSample.getLatestSampleMetadata(), Boolean.FALSE)) {
+                                smileSample.getLatestSampleMetadata(), Boolean.FALSE, Boolean.FALSE)) {
                             LOG.info("Found updates for sample - persisting to database: "
                                     + smileSample.getPrimarySampleAlias());
                             existingSample.updateSampleMetadata(smileSample.getLatestSampleMetadata());

service/src/main/java/org/mskcc/smile/service/impl/RequestServiceImpl.java

@@ -172,17 +172,22 @@ public PublishedSmileRequest getPublishedSmileRequestById(String requestId) thro
     }
 
     @Override
-    public Boolean updateRequestMetadata(RequestMetadata requestMetadata) throws Exception {
+    public Boolean updateRequestMetadata(RequestMetadata requestMetadata, Boolean fromLims) throws Exception {
         SmileRequest existingRequest = getSmileRequestById(requestMetadata.getIgoRequestId());
         if (existingRequest == null) {
             LOG.error("Cannot persist updates to a request that does not already exist: "
                     + requestMetadata.getIgoRequestId());
             return Boolean.FALSE;
         }
-        // persist updates for request metadata if applicable
-        if (requestHasMetadataUpdates(existingRequest.getLatestRequestMetadata(), requestMetadata)) {
-            LOG.info("Persisting updates for request: " + existingRequest.getIgoRequestId());
-            existingRequest.updateRequestMetadataByMetadata(requestMetadata);
+        if (requestHasMetadataUpdates(existingRequest.getLatestRequestMetadata(),
+                requestMetadata, fromLims)) {
+            if (fromLims) {
+                LOG.info("Persisting igo property updates for request: " + existingRequest.getIgoRequestId());
+                existingRequest.applyIgoRequestMetadataUpdates(requestMetadata);
+            } else {
+                LOG.info("Persisting updates for request: " + existingRequest.getIgoRequestId());
+                existingRequest.updateRequestMetadataByMetadata(requestMetadata);
+            }
             saveRequestMetadata(existingRequest);
             return Boolean.TRUE;
         }
@@ -205,16 +210,28 @@ private Boolean timestampWithin24Hours(Date referenceTimestamp, Date newTimestam
     }
 
     @Override
-    public Boolean requestHasUpdates(SmileRequest existingRequest, SmileRequest request) throws Exception {
-        return !(jsonComparator.isConsistent(mapper.writeValueAsString(existingRequest),
-                mapper.writeValueAsString(request)));
+    public Boolean requestHasUpdates(SmileRequest existingRequest, SmileRequest request,
+            Boolean fromLims) throws Exception {
+        if (fromLims) {
+            return !jsonComparator.isConsistentByIgoProperties(mapper.writeValueAsString(existingRequest),
+                    mapper.writeValueAsString(request));
+        }
+        return !jsonComparator.isConsistent(mapper.writeValueAsString(existingRequest),
+                mapper.writeValueAsString(request));
     }
 
     @Override
     public Boolean requestHasMetadataUpdates(RequestMetadata existingRequestMetadata,
-            RequestMetadata requestMetadata) throws Exception {
-        return !(jsonComparator.isConsistent(existingRequestMetadata.getRequestMetadataJson(),
-                requestMetadata.getRequestMetadataJson()));
+            RequestMetadata requestMetadata, Boolean fromLims) throws Exception {
+        // if request is  from LIMS, look for updates by igo properties
+        if (fromLims) {
+            return !jsonComparator.isConsistentByIgoProperties(
+                    existingRequestMetadata.getRequestMetadataJson(),
+                    requestMetadata.getRequestMetadataJson());
+        }
+        // if request is not from LIMS, look for updates by all properties
+        return !jsonComparator.isConsistent(existingRequestMetadata.getRequestMetadataJson(),
+                requestMetadata.getRequestMetadataJson());
     }
 
     @Override
@@ -230,7 +247,7 @@ public List<SmileSample> getRequestSamplesWithUpdates(SmileRequest request) thro
             }
             Boolean sampleHasUpdates =
                     sampleService.sampleHasMetadataUpdates(existingSample.getLatestSampleMetadata(),
-                    sample.getLatestSampleMetadata(), Boolean.TRUE);
+                    sample.getLatestSampleMetadata(), Boolean.TRUE, Boolean.FALSE);
             if (sampleHasUpdates) {
                 existingSample.updateSampleMetadata(sample.getLatestSampleMetadata());
                 updatedSamples.add(existingSample);

service/src/main/java/org/mskcc/smile/service/impl/ResearchMessageHandlingServiceImpl.java

@@ -127,9 +127,13 @@ public void run() {
                         } else {
                             // request-service and sample-service methods will check for updates and persist
                             // them if applicable (including patient swapping)
-                            requestService.updateRequestMetadata(request.getLatestRequestMetadata());
+                            // Boolean arg in updateRequestMetadata refers to fromLims
+                            requestService.updateRequestMetadata(request.getLatestRequestMetadata(),
+                                    Boolean.TRUE);
                             for (SmileSample sample : request.getSmileSampleList()) {
-                                sampleService.saveSmileSample(sample);
+                                // Boolean arg in updateSampleMetadata refers to fromLims
+                                sampleService.updateSampleMetadata(sample.getLatestSampleMetadata(),
+                                        Boolean.TRUE);
                                 sampleService.createSampleRequestRelationship(sample.getSmileSampleId(),
                                         existingRequest.getSmileRequestId());
                             }
@@ -180,7 +184,8 @@ public void run() {
                 try {
                     RequestMetadata requestMetadata = requestUpdateQueue.poll(100, TimeUnit.MILLISECONDS);
                     if (requestMetadata != null) {
-                        if (requestService.updateRequestMetadata(requestMetadata)) {
+                        // Boolean arg in updateRequestMetadata refers to fromLims
+                        if (requestService.updateRequestMetadata(requestMetadata, Boolean.FALSE)) {
                             LOG.info("Publishing Request-level Metadata updates "
                                     + "to " + CMO_REQUEST_UPDATE_TOPIC);
                             SmileRequest existingRequest =
@@ -222,7 +227,8 @@ public void run() {
                     SampleMetadata sampleMetadata = researchSampleUpdateQueue.poll(
                             100, TimeUnit.MILLISECONDS);
                     if (sampleMetadata != null) {
-                        if (sampleService.updateSampleMetadata(sampleMetadata)) {
+                        // Boolean arg in updateSampleMetadata refers to fromLims
+                        if (sampleService.updateSampleMetadata(sampleMetadata, Boolean.FALSE)) {
                             SmileSample existingSample = sampleService.getResearchSampleByRequestAndIgoId(
                                     sampleMetadata.getIgoRequestId(), sampleMetadata.getPrimaryId());
                             LOG.info("Publishing sample-level metadata history for research sample: "