Add ParallelWorkerTests

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/ParallelWorkerTests.java

@@ -0,0 +1,83 @@
+package org.monarchinitiative.exomiser.core.analysis;
+
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import org.monarchinitiative.exomiser.core.genome.*;
+import org.monarchinitiative.exomiser.core.model.VariantEvaluation;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.nio.file.Path;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ForkJoinPool;
+import java.util.concurrent.ForkJoinWorkerThread;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.IntStream;
+import java.util.stream.Stream;
+
+/**
+ * Playground/notebook for parallel execution
+ */
+@Disabled
+public class ParallelWorkerTests {
+
+    private static final Logger logger = LoggerFactory.getLogger(ParallelWorkerTests.class);
+    final GenomeAnalysisService genomeAnalysisService = TestFactory.buildDefaultHg19GenomeAnalysisService();
+
+    @Test
+    void paprllelStreamForkJoinSubclass() throws InterruptedException {
+        ForkJoinPool pool = new ForkJoinPool(4, ExomiserForkJoinThread::new, null, false);
+        try (Stream<String> stream = IntStream.range(1, 10000).parallel().mapToObj(String::valueOf).peek(x -> logger.info("{}", x))){
+            var result= pool.submit(stream::toList).get();
+            result.stream().limit(10).forEach(System.out::println);
+        } catch (ExecutionException e) {
+            throw new RuntimeException(e);
+        }
+        pool.shutdownNow();
+    }
+
+    @Test
+    void testVcfReadForkJoinPool() throws InterruptedException {
+//        Thread.sleep(3000);
+        VariantFactory variantFactory = new VariantFactoryImpl(genomeAnalysisService.getVariantAnnotator(), new VcfFileReader(Path.of("src/test/resources/Pfeiffer.vcf")));
+        ForkJoinPool pool = new ForkJoinPool(4, exomiserThreadFactory, null, false);
+        try (
+                Stream<VariantEvaluation> variantStream = variantFactory.createVariantEvaluations()
+                        .parallel()
+                        .peek(var -> logger.info("{}", var))) {
+            var result= pool.submit(variantStream::toList).join();
+        } finally {
+            pool.shutdown();
+        }
+    }
+
+    private static final ForkJoinPool.ForkJoinWorkerThreadFactory exomiserThreadFactory = new ForkJoinPool.ForkJoinWorkerThreadFactory() {
+        private final AtomicInteger workerNumber = new AtomicInteger(1);
+        @Override
+        public ForkJoinWorkerThread newThread(ForkJoinPool pool) {
+            return new ForkJoinWorkerThread(pool) {
+                @Override
+                protected void onStart() {
+                    super.onStart();
+                    setName("Exomiser-work-" + workerNumber.getAndIncrement());
+                }
+            };
+        }
+    };
+
+    static class ExomiserForkJoinThread extends ForkJoinWorkerThread {
+
+        private static final AtomicInteger count = new AtomicInteger(0);
+
+        /**
+         * Creates a ForkJoinWorkerThread operating in the given pool.
+         *
+         * @param pool the pool this thread works in
+         * @throws NullPointerException if pool is null
+         */
+        protected ExomiserForkJoinThread(ForkJoinPool pool) {
+            super(pool);
+            setName("Exomiser-work-" + count.incrementAndGet());
+        }
+    }
+}