Restore casing

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/RCommandWrapper.java

@@ -17,11 +17,10 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 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.services.ServiceRegistry;
 
@@ -70,7 +69,7 @@ private 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 = ServiceRegistry.get().getService(LabKeyScriptEngineManager.class);
+            LabkeyScriptEngineManager svc = ServiceRegistry.get().getService(LabkeyScriptEngineManager.class);
             for (ExternalScriptEngineDefinition def : svc.getEngineDefinitions())
             {
                 if (RScriptEngineFactory.isRScriptEngine(def.getExtensions()))

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

@@ -11,7 +11,7 @@
 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 = ServiceRegistry.get().getService(LabKeyScriptEngineManager.class);
+            LabkeyScriptEngineManager svc = ServiceRegistry.get().getService(LabkeyScriptEngineManager.class);
             for (ExternalScriptEngineDefinition def : svc.getEngineDefinitions())
             {
                 if (RScriptEngineFactory.isRScriptEngine(def.getExtensions()))

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

@@ -34,7 +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;
@@ -141,7 +141,7 @@ private boolean runScript(String scriptName, List<String> args) throws IOExcepti
 
     private String getPerlLocation()
     {
-        LabKeyScriptEngineManager svc = ServiceRegistry.get().getService(LabKeyScriptEngineManager.class);
+        LabkeyScriptEngineManager svc = ServiceRegistry.get().getService(LabkeyScriptEngineManager.class);
         for (ExternalScriptEngineDefinition def : svc.getEngineDefinitions())
         {
             if (def.getExtensions() != null && Arrays.stream(def.getExtensions()).anyMatch("pl"::equals))