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Refactor label generator (#130)
* Refactored Label Generator - Added CmoLabelParts that is agnostic of sample data from IGO vs. updates from dashboard - Removes dependency on `model` layer of `smile-server` repo - Simplifies logic for label generation of incoming samples as part of a request and incoming sample updates from the dashboard - Cleaned up redundancies in label generation logic Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com> * Simplified logic for generating labels for IGO_NEW_REQUEST samples Main label generator method now also resolves which label to use if current sample being handled exists and has a label assigned. i.e., only labels with meaningful changes are kept Updated logic to bypass label generation step if there aren't any applicable updates to label-specific data fields. Added and updated unit tests for bypass check. Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com> * Simplified logic for sample label updates topic Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com> --------- Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>
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‎pom.xml‎

Lines changed: 6 additions & 9 deletions
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@@ -33,9 +33,6 @@
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<!-- smile commons centralized config properties -->
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<smile_commons.group>com.github.mskcc</smile_commons.group>
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<smile_commons.version>a661a7b9a81ae51cb761ae32a6444dd01fb1994d</smile_commons.version> <!-- this is 2.1.3.RELEASE -->
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<!-- smile server model module -->
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<smile_server.group>com.github.mskcc.smile-server</smile_server.group>
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<smile_server.version>2.1.37.RELEASE</smile_server.version>
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</properties>
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<dependencies>
@@ -51,12 +48,6 @@
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<artifactId>smile-commons</artifactId>
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<version>${smile_commons.version}</version>
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</dependency>
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<!-- smile server model -->
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<dependency>
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<groupId>${smile_server.group}</groupId>
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<artifactId>model</artifactId>
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<version>${smile_server.version}</version>
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</dependency>
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<!-- spring -->
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<dependency>
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<groupId>org.springframework</groupId>
@@ -94,6 +85,12 @@
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<artifactId>jsonassert</artifactId>
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<version>1.5.3</version>
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</dependency>
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<dependency>
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<groupId>commons-lang</groupId>
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<artifactId>commons-lang</artifactId>
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<version>2.6</version>
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<type>jar</type>
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</dependency>
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</dependencies>
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<build>

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

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@@ -2,31 +2,25 @@
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import com.fasterxml.jackson.core.JsonProcessingException;
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import java.util.List;
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import org.mskcc.smile.model.SampleMetadata;
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import org.mskcc.smile.model.Status;
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import org.mskcc.smile.model.igo.IgoSampleManifest;
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import java.util.Map;
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import org.mskcc.smile.service.util.CmoLabelParts;
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/**
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*
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* @author ochoaa
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*/
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public interface CmoLabelGeneratorService {
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String generateCmoSampleLabel(String requestId,
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IgoSampleManifest sampleManifest, List<SampleMetadata> existingPatientSamples,
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List<SampleMetadata> samplesByAltId);
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String generateCmoSampleLabel(SampleMetadata sample, List<SampleMetadata> existingPatientSamples,
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List<SampleMetadata> samplesByAltId);
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Status generateSampleStatus(String requestId, IgoSampleManifest sampleManifest,
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List<SampleMetadata> existingSamples, List<SampleMetadata> samplesByAltId)
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throws JsonProcessingException;
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Status generateSampleStatus(SampleMetadata sampleMetadata, List<SampleMetadata> existingSamples,
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List<SampleMetadata> samplesByAltId) throws JsonProcessingException;
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Boolean sampleHasLabelSpecificUpdates(CmoLabelParts sample,
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List<CmoLabelParts> existingPatientSamples) throws Exception;
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String generateCmoSampleLabel(CmoLabelParts sample, List<CmoLabelParts> existingPatientSamples,
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List<CmoLabelParts> samplesByAltId);
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Map<String, Object> generateSampleStatus(CmoLabelParts sample, List<CmoLabelParts> existingSamples,
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List<CmoLabelParts> samplesByAltId) throws JsonProcessingException;
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Boolean igoSampleRequiresLabelUpdate(String newCmoLabel, String existingCmoLabel);
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String resolveSampleTypeAbbreviation(String specimenTypeValue, String sampleOriginValue,
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String cmoSampleClassValue, String sampleTypeDetailedValue);
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String resolveSampleTypeAbbreviation(CmoLabelParts sample);
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String resolveSampleTypeAbbrevWithContext(String primaryId, String resolvedSampleTypeAbbrev,
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List<SampleMetadata> samplesByAltId);
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String generateValidationReport(String originalJson, String filteredJson, Boolean isSample)
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List<CmoLabelParts> samplesByAltId);
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String generateValidationReportLog(String originalJson, String filteredJson, Boolean isSample)
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throws JsonProcessingException;
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String incrementNucleicAcidCounter(String cmoLabel);
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String incrementSampleCounter(String cmoLabel);

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

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@@ -1,13 +1,13 @@
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package org.mskcc.smile.service;
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import java.util.List;
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import java.util.Map;
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import org.mskcc.cmo.messaging.Gateway;
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import org.mskcc.smile.model.SampleMetadata;
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public interface MessageHandlingService {
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void initialize(Gateway gateway) throws Exception;
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void cmoLabelGeneratorHandler(String requestJson) throws Exception;
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void cmoPromotedLabelHandler(String requestJson) throws Exception;
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void cmoSampleLabelUpdateHandler(List<SampleMetadata> sampleMetadataList) throws Exception;
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void cmoSampleLabelUpdateHandler(List<Map<String, Object>> sampleMetadataList) throws Exception;
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void shutdown() throws Exception;
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}

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

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

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

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@@ -4,8 +4,8 @@
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import io.nats.client.Message;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Map;
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import java.util.concurrent.BlockingQueue;
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import java.util.concurrent.CountDownLatch;
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import java.util.concurrent.ExecutorService;
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import org.apache.commons.logging.LogFactory;
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import org.mskcc.cmo.messaging.Gateway;
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import org.mskcc.cmo.messaging.MessageConsumer;
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import org.mskcc.smile.model.SampleMetadata;
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import org.mskcc.smile.service.CmoLabelGeneratorService;
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import org.mskcc.smile.service.RequestReplyHandlingService;
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import org.mskcc.smile.service.util.CmoLabelParts;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Value;
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import org.springframework.stereotype.Service;
@@ -93,14 +93,15 @@ public void run() {
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// reply info request message contains cmo patient id
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ReplyInfo replyInfo = cmoLabelGeneratorReqReplyQueue.poll(100, TimeUnit.MILLISECONDS);
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if (replyInfo != null) {
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SampleMetadata sample = mapper.readValue(replyInfo.getRequestMessage(),
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SampleMetadata.class);
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List<SampleMetadata> existingPatientSamples
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= getExistingPatientSamples(sample.getCmoPatientId());
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List<SampleMetadata> samplesByAltId
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= getSamplesByAltId(sample.getAdditionalProperty("altId"));
96+
Map<String, Object> sample = mapper.readValue(replyInfo.getRequestMessage(),
97+
Map.class);
98+
CmoLabelParts sampleLabelParts = new CmoLabelParts(sample, null);
99+
List<CmoLabelParts> existingPatientSamples
100+
= getExistingPatientSamples(sampleLabelParts.getCmoPatientId());
101+
List<CmoLabelParts> samplesByAltId
102+
= getSamplesByAltId(sampleLabelParts.getAltId());
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String updatedCmoSampleLabel =
103-
cmoLabelGeneratorService.generateCmoSampleLabel(sample,
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cmoLabelGeneratorService.generateCmoSampleLabel(sampleLabelParts,
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existingPatientSamples, samplesByAltId);
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//log replied to the message
@@ -120,22 +121,32 @@ public void run() {
120121
}
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}
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private List<SampleMetadata> getExistingPatientSamples(String cmoPatientId) throws Exception {
124+
private List<CmoLabelParts> getExistingPatientSamples(String cmoPatientId) throws Exception {
124125
Message reply = messagingGateway.request(PATIENT_SAMPLES_REQUEST_TOPIC,
125126
cmoPatientId);
126-
SampleMetadata[] ptSamples = mapper.readValue(
127+
List<Object> sampleObjectList = mapper.readValue(
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new String(reply.getData(), StandardCharsets.UTF_8),
128-
SampleMetadata[].class);
129-
return new ArrayList<>(Arrays.asList(ptSamples));
129+
List.class);
130+
List<CmoLabelParts> ptSamples = new ArrayList<>();
131+
for (Object s : sampleObjectList) {
132+
Map<String, Object> sm = mapper.convertValue(s, Map.class);
133+
ptSamples.add(new CmoLabelParts(sm, null));
134+
}
135+
return ptSamples;
130136
}
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132-
private List<SampleMetadata> getSamplesByAltId(String altId) throws Exception {
138+
private List<CmoLabelParts> getSamplesByAltId(String altId) throws Exception {
133139
Message reply = messagingGateway.request(SAMPLES_BY_ALT_ID_REQREPLY_TOPIC,
134140
altId);
135-
SampleMetadata[] samplesByAltId = mapper.readValue(
141+
List<Object> sampleObjectList = mapper.readValue(
136142
new String(reply.getData(), StandardCharsets.UTF_8),
137-
SampleMetadata[].class);
138-
return new ArrayList<>(Arrays.asList(samplesByAltId));
143+
List.class);
144+
List<CmoLabelParts> samplesByAltId = new ArrayList<>();
145+
for (Object s : sampleObjectList) {
146+
Map<String, Object> sm = mapper.convertValue(s, Map.class);
147+
samplesByAltId.add(new CmoLabelParts(sm, null));
148+
}
149+
return samplesByAltId;
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}
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@Override

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