Update default for JBrowse lucene cores

Author: bbimber

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

@@ -425,8 +425,7 @@ public void getOrphanFilesForContainer(Container c, User u, Set<File> orphanFile
                     @Override
                     public boolean accept(File pathname)
                     {
-                        //50mb
-                        return (pathname.length() >= 5e7);
+                        return (pathname.length() >= 5e3);
                     }
                 });
 

jbrowse/resources/module.xml

@@ -0,0 +1,15 @@
+<module xmlns="http://labkey.org/moduleProperties/xml/">
+    <properties>
+        <propertyDescriptor name="JBrowseLuceneCores">
+            <canSetPerContainer>false</canSetPerContainer>
+            <defaultValue>1</defaultValue>
+            <description>The number of cores to allow for lucene searches</description>
+            <editPermissions>
+                <permission>ADMIN</permission>
+            </editPermissions>
+        </propertyDescriptor>
+    </properties>
+    <clientDependencies>
+
+    </clientDependencies>
+</module>

jbrowse/src/org/labkey/jbrowse/JBrowseServiceImpl.java

@@ -1,11 +1,13 @@
 package org.labkey.jbrowse;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
@@ -17,7 +19,9 @@
 import org.labkey.api.jbrowse.JBrowseFieldCustomizer;
 import org.labkey.api.jbrowse.JBrowseFieldDescriptor;
 import org.labkey.api.jbrowse.JBrowseService;
+import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.module.ModuleProperty;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineService;
@@ -436,7 +440,23 @@ public boolean isAvailable(Container c)
         }
     }
 
+    private static final String JBrowseLuceneCoresProp = "JBrowseLuceneCores";
+
     public int getCoresForLuceneSearches() {
-        return Runtime.getRuntime().availableProcessors();
+        Module m = ModuleLoader.getInstance().getModule(JBrowseModule.NAME);
+        ModuleProperty mp = m.getModuleProperties().get(JBrowseLuceneCoresProp);
+        String nCores = StringUtils.trimToNull(mp.getEffectiveValue(ContainerManager.getRoot()));
+        if (nCores == null)
+        {
+            return 1;
+        }
+        else if (!NumberUtils.isCreatable(nCores))
+        {
+            _log.error("Improper value for " + JBrowseLuceneCoresProp + ": " + nCores);
+        }
+
+        Number n = NumberUtils.createNumber(nCores);
+
+        return n.intValue();
     }
 }