Use correct method for list deserialization

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java

@@ -6,6 +6,7 @@
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.collections.IntHashMap;
+import org.labkey.api.collections.LongArrayList;
 import org.labkey.api.collections.LongHashMap;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
@@ -28,6 +29,7 @@
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -319,6 +321,7 @@ public void testSerializeWithMap() throws Exception
             js1._cachedObjects.put("cachedInt", 1);
             js1._cachedObjects.put("cachedString", "foo");
             js1._cachedObjects.put("cachedLong", 2L);
+            js1._cachedObjects.put("cachedListLong", new LongArrayList(Arrays.asList(1L, 2L)));
 
             LongHashMap<Long> longMap = new LongHashMap<>();
             longMap.put(1L, 2L);
@@ -349,10 +352,15 @@ public void testSerializeWithMap() throws Exception
             assertEquals("Object not serialized with correct key type", Integer.class, serializedMap.keySet().iterator().next().getClass());
             assertNotNull("Map keys not serialized properly", serializedMap.get(1));
 
-            LongHashMap<Long> serializedLongMap = (LongHashMap<Long>)deserialized.getCachedObject("cachedLongMap", LongHashMap.class);
+            LongHashMap<Long> serializedLongMap = deserialized.getCachedObject("cachedLongMap", LongHashMap.class);
             assertEquals("LongMap not serialized properly", 1, serializedLongMap.size());
             assertEquals("Object not serialized with correct key type", Long.class, serializedLongMap.keySet().iterator().next().getClass());
             assertNotNull("LongMap keys not serialized properly", serializedLongMap.get(1L));
+
+            List<Long> serializedListLong = deserialized.getCachedObject("cachedListLong", mapper.getTypeFactory().constructType(LongArrayList.class));
+            assertEquals("List<Long> not serialized properly", 2, serializedListLong.size());
+            assertNotNull("List<Long> values not serialized properly", serializedListLong.get(1));
+            assertNotNull("List<Long> values not serialized properly", serializedListLong.get(2));
         }
 
         @Test

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java

@@ -5,6 +5,7 @@
 import htsjdk.variant.vcf.VCFHeader;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.collections.LongArrayList;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
@@ -81,7 +82,7 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Seque
                 throw new IllegalStateException("No samples found in VCF file");
             }
 
-            ArrayList<Long> toCache = new ArrayList<>();
+            ArrayList<Long> toCache = new LongArrayList();
             Container targetContainer = getPipelineCtx().getJob().getContainer().isWorkbookOrTab() ? getPipelineCtx().getJob().getContainer().getParent() : getPipelineCtx().getJob().getContainer();
             TableInfo outputFiles = QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_OUTPUTFILES);
             for (String sample : samples)
@@ -110,7 +111,7 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Seque
 
     private List<File> getCachedBams() throws PipelineJobException
     {
-        List<Long> cachedFiles = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructCollectionType(List.class, Long.class));
+        List<Long> cachedFiles = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructType(LongArrayList.class));
 
         return cachedFiles.stream().map(x -> getPipelineCtx().getSequenceSupport().getCachedData(x)).toList();
     }