Fb cleanup (#78)

Author: labkey-adam

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

@@ -21,7 +21,7 @@
 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.services.ServiceRegistry;
 
@@ -70,7 +70,7 @@ 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 = LabKeyScriptEngineManager.get();
             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 = LabKeyScriptEngineManager.get();
             for (ExternalScriptEngineDefinition def : svc.getEngineDefinitions())
             {
                 if (RScriptEngineFactory.isRScriptEngine(def.getExtensions()))

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

@@ -33,7 +33,7 @@
 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 = LabKeyScriptEngineManager.get();
         for (ExternalScriptEngineDefinition def : svc.getEngineDefinitions())
         {
             if (def.getExtensions() != null && Arrays.stream(def.getExtensions()).anyMatch("pl"::equals))

jbrowse/src/org/labkey/jbrowse/view/browser.jsp

@@ -1,25 +1,25 @@
+<%
+/*
+ * Copyright (c) 2005-2014 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+%>
 <%@ page import="org.labkey.api.settings.AppProps" %>
 <%@ page import="org.labkey.api.util.PageFlowUtil" %>
 <%@ page import="org.labkey.jbrowse.JBrowseController" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.api.data.Container" %>
-<%
-    /*
-     * Copyright (c) 2005-2014 LabKey Corporation
-     *
-     * Licensed under the Apache License, Version 2.0 (the "License");
-     * you may not use this file except in compliance with the License.
-     * You may obtain a copy of the License at
-     *
-     *     http://www.apache.org/licenses/LICENSE-2.0
-     *
-     * Unless required by applicable law or agreed to in writing, software
-     * distributed under the License is distributed on an "AS IS" BASIS,
-     * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-     * See the License for the specific language governing permissions and
-     * limitations under the License.
-     */
-%>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 
 <%