Add test case for brca high severity data issue

hms-dbmi · Jan 17, 2024 · 8f00af0 · 8f00af0
1 parent e2cc488
commit 8f00af0
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Showing 3 changed files with 9 additions and 10 deletions.
diff --git a/genomic-processor/src/main/resources/application.properties b/genomic-processor/src/main/resources/application.properties
@@ -1,2 +1,2 @@
-hpds.genomicDataDirectory = /opt/local/hpds/orchestration/1040/20/all/
+hpds.genomicDataDirectory = /opt/local/hpds/phs0000946/17/
 server.port=8090
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
@@ -13,7 +13,6 @@
 import java.util.stream.IntStream;
 
 @SpringBootApplication
-@PropertySource("classpath:application.properties")
 public class GenomicProcessorConfig {
 
     @Value("${HPDS_GENOMIC_DATA_DIRECTORY:/opt/local/hpds/all/}")
@@ -29,7 +28,7 @@ public GenomicProcessor localGenomicProcessor() {
     @Bean(name = "localDistributedGenomicProcessor")
     @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "localDistributed")
     public GenomicProcessor localDistributedGenomicProcessor() {
-        List<GenomicProcessor> processorNodes = IntStream.range(1, 22)
+        List<GenomicProcessor> processorNodes = IntStream.range(1, 23)
                 .mapToObj(i -> new GenomicProcessorNodeImpl(hpdsGenomicDataDirectory + "/" + i + "/"))
                 .collect(Collectors.toList());
         return new GenomicProcessorParentImpl(processorNodes);

diff --git a/...edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java b/...edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java
@@ -11,6 +11,8 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
 
 public class GenomicProcessorRestClientTest {
 
@@ -24,15 +26,13 @@ public void simpleTest() {
         List<Query.VariantInfoFilter> variantInfoFilters = new ArrayList<>();
         Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter();
         variantInfoFilter.categoryVariantInfoFilters = Map.of(
-                "Gene_with_variant", new String[]{"FRG1FP"}
+                "Gene_with_variant", new String[]{"BRCA1"},
+                "Variant_consequence_calculated", new String[]{"splice_donor_variant"}
         );
-        Query.VariantInfoFilter variantInfoFilter2 = new Query.VariantInfoFilter();
-        variantInfoFilter2.categoryVariantInfoFilters = Map.of(
-                "Gene_with_variant", new String[]{"ACTG1P3"}
-        );
-        variantInfoFilters.add(variantInfoFilter2);
+        variantInfoFilters.add(variantInfoFilter);
         distributableQuery.setVariantInfoFilters(variantInfoFilters);
-        distributableQuery.setPatientIds(Set.of(1, 2, 3, 4, 5, 6, 7, 8, 9, 10));
+        Set<Integer> patientIds = IntStream.range(53000, 53635).boxed().collect(Collectors.toSet());
+        distributableQuery.setPatientIds(patientIds);
 
         BigInteger patientMaskForVariantInfoFilters = genomicProcessorRestClient.getPatientMask(distributableQuery).block();
         System.out.println(patientMaskForVariantInfoFilters);