Fix build

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequencePipelineServiceImpl.java

@@ -4,14 +4,14 @@
 import htsjdk.samtools.ValidationStringency;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.reports.ExternalScriptEngineDefinition;
-import org.labkey.api.reports.LabKeyScriptEngineManager;
+import org.labkey.api.reports.LabkeyScriptEngineManager;
 import org.labkey.api.reports.RScriptEngineFactory;
 import org.labkey.api.sequenceanalysis.SequenceOutputFile;
 import org.labkey.api.sequenceanalysis.model.Readset;
@@ -426,7 +426,7 @@ public String inferRPath(Logger log)
         //preferentially use R config setup in scripting props.  only works if running locally.
         if (PipelineJobService.get().getLocationType() == PipelineJobService.LocationType.WebServer)
         {
-            LabKeyScriptEngineManager svc = LabKeyScriptEngineManager.get();
+            LabkeyScriptEngineManager svc = ServiceRegistry.get().getService(LabkeyScriptEngineManager.class);
             for (ExternalScriptEngineDefinition def : svc.getEngineDefinitions())
             {
                 if (RScriptEngineFactory.isRScriptEngine(def.getExtensions()))

jbrowse/src/org/labkey/jbrowse/JBrowseRoot.java

@@ -4,12 +4,13 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.SystemUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
+import org.labkey.api.assay.AssayFileWriter;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.CompareType;
@@ -33,7 +34,7 @@
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.reader.Readers;
 import org.labkey.api.reports.ExternalScriptEngineDefinition;
-import org.labkey.api.reports.LabKeyScriptEngineManager;
+import org.labkey.api.reports.LabkeyScriptEngineManager;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.sequenceanalysis.RefNtSequenceModel;
@@ -42,7 +43,6 @@
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
 import org.labkey.api.services.ServiceRegistry;
-import org.labkey.api.assay.AssayFileWriter;
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.GUID;
@@ -141,7 +141,7 @@ private boolean runScript(String scriptName, List<String> args) throws IOExcepti
 
     private String getPerlLocation()
     {
-        LabKeyScriptEngineManager svc = LabKeyScriptEngineManager.get();
+        LabkeyScriptEngineManager svc = ServiceRegistry.get().getService(LabkeyScriptEngineManager.class);
         for (ExternalScriptEngineDefinition def : svc.getEngineDefinitions())
         {
             if (def.getExtensions() != null && Arrays.stream(def.getExtensions()).anyMatch("pl"::equals))