Implement missing endpoints, add profile for integration B

hms-dbmi · Dec 14, 2023 · c184304 · c184304
1 parent ef3f480
commit c184304
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Showing 5 changed files with 79 additions and 14 deletions.
diff --git a/.../src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicProcessorController.java b/.../src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicProcessorController.java
@@ -4,10 +4,7 @@
 import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery;
 import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.bind.annotation.*;
 import reactor.core.publisher.Mono;
 
 import java.math.BigInteger;
@@ -26,7 +23,7 @@ public GenomicProcessorController(GenomicProcessor genomicProcessor) {
     }
 
     @PostMapping("/patients")
-    public Mono<BigInteger> queryForPatientMask(@RequestBody DistributableQuery distributableQuery) throws InterruptedException {
+    public Mono<BigInteger> queryForPatientMask(@RequestBody DistributableQuery distributableQuery) {
         return genomicProcessor.getPatientMask(distributableQuery);
     }
 
@@ -40,6 +37,16 @@ public List<String> getPatientIds() {
         return genomicProcessor.getPatientIds();
     }
 
+    @GetMapping("/info/columns")
+    public List<String> getInfoStoreColumns() {
+        return genomicProcessor.getInfoStoreColumns();
+    }
+
+    @GetMapping("/info/values")
+    public List<String> getInfoStoreValues(@RequestParam("conceptPath") String conceptPath) {
+        return genomicProcessor.getInfoStoreValues(conceptPath);
+    }
+
     @GetMapping("/info/meta")
     public List<InfoColumnMeta> getInfoMetadata() {
         return genomicProcessor.getInfoColumnMeta();

diff --git a/...g/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorConfig.java b/...g/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorConfig.java
@@ -9,6 +9,8 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
 
 @SpringBootApplication
 @PropertySource("classpath:application.properties")
@@ -26,6 +28,16 @@ public GenomicProcessor localGenomicProcessor() {
         return new GenomicProcessorNodeImpl(hpdsGenomicDataDirectory);
     }
 
+    @Bean(name = "localDistributedGenomicProcessor")
+    @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "localDistributed")
+    public GenomicProcessor localDistributedGenomicProcessor() {
+        //System.getProperty("HPDS_GENOMIC_DATA_DIRECTORY", "/opt/local/hpds/all/");
+        List<GenomicProcessor> processorNodes = IntStream.range(1, 22)
+                .mapToObj(i -> new GenomicProcessorNodeImpl(hpdsGenomicDataDirectory + "/" + i))
+                .collect(Collectors.toList());
+        return new GenomicProcessorParentImpl(processorNodes);
+    }
+
     @Bean(name = "remoteGenomicProcessor")
     @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "remote")
     public GenomicProcessor remoteGenomicProcessor() {

diff --git a/...ava/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClient.java b/...ava/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClient.java
@@ -21,6 +21,10 @@ public class GenomicProcessorRestClient implements GenomicProcessor {
 
     private final WebClient webClient;
 
+    private static final ParameterizedTypeReference<Collection<String>> VARIANT_LIST_TYPE_REFERENCE = new ParameterizedTypeReference<>(){};
+    private static final ParameterizedTypeReference<List<InfoColumnMeta>> INFO_COLUMNS_META_TYPE_REFERENCE = new ParameterizedTypeReference<>(){};
+    private static final ParameterizedTypeReference<List<String>> LIST_OF_STRING_TYPE_REFERENCE = new ParameterizedTypeReference<>(){};
+
     public GenomicProcessorRestClient(String serviceUrl) {
         this.webClient = WebClient.builder()
                 .baseUrl(serviceUrl)
@@ -41,16 +45,14 @@ public Mono<BigInteger> getPatientMask(DistributableQuery distributableQuery) {
 
     @Override
     public Set<Integer> patientMaskToPatientIdSet(BigInteger patientMask) {
-        return null;
+        throw new RuntimeException("Not Implemented");
     }
 
     @Override
     public BigInteger createMaskForPatientSet(Set<Integer> patientSubset) {
-        return null;
+        throw new RuntimeException("Not Implemented");
     }
 
-    private static final ParameterizedTypeReference<Collection<String>> VARIANT_LIST_TYPE_REFERENCE = new ParameterizedTypeReference<>(){};
-    private static final ParameterizedTypeReference<List<InfoColumnMeta>> INFO_COLUMNS_META_TYPE_REFERENCE = new ParameterizedTypeReference<>(){};
     @SuppressWarnings("unchecked")
     @Override
     public Mono<Collection<String>> getVariantList(DistributableQuery distributableQuery) {
@@ -65,10 +67,10 @@ public Mono<Collection<String>> getVariantList(DistributableQuery distributableQ
 
     @Override
     public List<String> getPatientIds() {
-        List result = webClient.get()
+        List<String> result = webClient.get()
                 .uri("/patients/ids")
                 .retrieve()
-                .bodyToMono(List.class)
+                .bodyToMono(LIST_OF_STRING_TYPE_REFERENCE)
                 .block();
         return result;
     }
@@ -80,12 +82,27 @@ public Optional<VariantMasks> getMasks(String path, VariantBucketHolder<VariantM
 
     @Override
     public List<String> getInfoStoreColumns() {
-        throw new RuntimeException("Not yet implemented");
+        List<String> result = webClient.get()
+                .uri(uriBuilder -> uriBuilder
+                        .path("/info/columns")
+                        .build())
+                .retrieve()
+                .bodyToMono(LIST_OF_STRING_TYPE_REFERENCE)
+                .block();
+        return result;
     }
 
     @Override
     public List<String> getInfoStoreValues(String conceptPath) {
-        throw new RuntimeException("Not Yet implemented");
+        List<String> result = webClient.get()
+                .uri(uriBuilder -> uriBuilder
+                        .path("/info/values")
+                        .queryParam("conceptPath", conceptPath)
+                        .build(conceptPath))
+                .retrieve()
+                .bodyToMono(LIST_OF_STRING_TYPE_REFERENCE)
+                .block();
+        return result;
     }
 
     @Override

diff --git a/...edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java b/...edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java
@@ -1,9 +1,10 @@
 package edu.harvard.hms.dbmi.avillach.hpds.processing.genomic;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
+import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta;
 import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query;
 import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery;
 import org.junit.jupiter.api.Test;
+import static org.junit.jupiter.api.Assertions.*;
 
 import java.math.BigInteger;
 import java.util.ArrayList;
@@ -36,4 +37,26 @@ public void simpleTest() {
         BigInteger patientMaskForVariantInfoFilters = genomicProcessorRestClient.getPatientMask(distributableQuery).block();
         System.out.println(patientMaskForVariantInfoFilters);
     }
+
+    @Test
+    public void getInfoStoreColumns() {
+        List<String> infoStoreColumns = genomicProcessorRestClient.getInfoStoreColumns();
+        assertTrue(infoStoreColumns.contains("Variant_consequence_calculated"));
+    }
+    @Test
+    public void getInfoStoreValues() {
+        List<String> infoStoreValues = genomicProcessorRestClient.getInfoStoreValues("Variant_consequence_calculated");
+        assertTrue(infoStoreValues.contains("inframe_deletion"));
+    }
+
+    @Test
+    public void getInfoColumnMeta() {
+        List<InfoColumnMeta> infoColumnMeta = genomicProcessorRestClient.getInfoColumnMeta();
+        for (InfoColumnMeta columnMeta : infoColumnMeta) {
+            if (columnMeta.getKey().equals("Variant_consequence_calculated")) {
+                return;
+            }
+        }
+        throw new RuntimeException("Variant_consequence_calculated not found in info column meta");
+    }
 }
diff --git a/service/src/main/resources/application-integrationB.properties b/service/src/main/resources/application-integrationB.properties
@@ -0,0 +1,6 @@
+SMALL_JOB_LIMIT = 100
+SMALL_TASK_THREADS = 1
+LARGE_TASK_THREADS = 1
+
+hpds.genomicProcessor.impl=localDistributed
+HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/