ALS-5905: Fix genomic configuration for HPDS with no genomic data

processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorConfig.java

@@ -70,4 +70,10 @@ public GenomicProcessor remoteGenomicProcessor(@Value("${hpds.genomicProcessor.r
         // todo: validate remote processors are valid
         return new GenomicProcessorParentImpl(genomicProcessors);
     }
+
+    @Bean
+    @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", matchIfMissing = true)
+    public GenomicProcessor noOpGenomicProcessor() {
+        return new GenomicProcessorNoOp();
+    }
 }

processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNoOp.java

@@ -0,0 +1,59 @@
+package edu.harvard.hms.dbmi.avillach.hpds.processing;
+
+import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta;
+import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMasks;
+import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder;
+import reactor.core.publisher.Mono;
+
+import java.math.BigInteger;
+import java.util.Collection;
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
+
+public class GenomicProcessorNoOp implements GenomicProcessor {
+    @Override
+    public Mono<BigInteger> getPatientMask(DistributableQuery distributableQuery) {
+        return null;
+    }
+
+    @Override
+    public Set<Integer> patientMaskToPatientIdSet(BigInteger patientMask) {
+        return null;
+    }
+
+    @Override
+    public BigInteger createMaskForPatientSet(Set<Integer> patientSubset) {
+        return null;
+    }
+
+    @Override
+    public Mono<Collection<String>> getVariantList(DistributableQuery distributableQuery) {
+        return null;
+    }
+
+    @Override
+    public List<String> getPatientIds() {
+        return null;
+    }
+
+    @Override
+    public Optional<VariantMasks> getMasks(String path, VariantBucketHolder<VariantMasks> variantMasksVariantBucketHolder) {
+        return Optional.empty();
+    }
+
+    @Override
+    public Set<String> getInfoStoreColumns() {
+        return null;
+    }
+
+    @Override
+    public Set<String> getInfoStoreValues(String conceptPath) {
+        return null;
+    }
+
+    @Override
+    public List<InfoColumnMeta> getInfoColumnMeta() {
+        return null;
+    }
+}

service/src/main/resources/application-open.properties

@@ -0,0 +1,3 @@
+SMALL_JOB_LIMIT = 100
+SMALL_TASK_THREADS = 1
+LARGE_TASK_THREADS = 1

service/src/main/resources/application.properties

@@ -1,12 +1,3 @@
 SMALL_JOB_LIMIT = 100
 SMALL_TASK_THREADS = 1
-LARGE_TASK_THREADS = 1
-
-#hpds.genomicProcessor.impl=local
-#HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/
-
-#hpds.genomicProcessor.impl=localDistributed
-#HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/phs0000946/
-
-hpds.genomicProcessor.impl=remote
-hpds.genomicProcessor.remoteHosts=http://localhost:8090/,http://localhost:8091/
+LARGE_TASK_THREADS = 1