Merge discvr-20.11 to develop

Author: bbimber

.github/workflows/sync-repos.yml

@@ -29,4 +29,4 @@ jobs:
           source_repo: "labkey/DiscvrLabKeyModules"
           source_branch: "develop"
           destination_branch: "develop"
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ secrets.PAT }}

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://api.travis-ci.com/BimberLab/DiscvrLabKeyModules.svg)](https://travis-ci.com/BimberLab/DiscvrLabKeyModules)
+![Build DISCVR](https://github.com/BimberLab/DiscvrLabKeyModules/workflows/Build%20DISCVR/badge.svg)
 
 ## Overview
 

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()))

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java

@@ -72,13 +72,13 @@ public Provider()
                     ToolParameterDescriptor.create(OUTPUT_GENBANK, "Create Genbank Output", "If selected, this will output a genbank file summarizing amplicons and primers", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true),
-                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--insert-type"), "insertType", "Insert Type", "The type of insert to detect.", "ldk-simplecombo", new JSONObject(){{
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--insert-name"), "insertType", "Insert Type", "The type of insert to detect.", "ldk-simplecombo", new JSONObject(){{
                         put("storeValues", "PiggyBac;Lentivirus");
                         put("allowBlank", false);
                     }}, "PiggyBac"),
                     ToolParameterDescriptor.create(DESIGN_PRIMERS, "Design Primers", "If selected, Primer3 will be used to design primers to flank integration sites", "checkbox", new JSONObject(){{
-                        put("checked", true);
-                    }}, true),
+                        put("checked", false);
+                    }}, false),
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--reads-to-output"), "readsToOutput", "Reads To Output Per Site", "If this is non-zero, up to this many reads per integration site will be written to a FASTA file.  This can serve as a way to verify the actual junction border.", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
                     }}, null),

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))