Merge develop to discvr-20.11

Author: bbimber

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/build.yml

@@ -0,0 +1,19 @@
+name: Build DISCVR
+on:
+  push:
+  pull_request:
+jobs:
+  build-modules:
+    # See: https://help.github.com/en/actions/reference/contexts-and-expression-syntax-for-github-actions#github-context
+    # https://help.github.com/en/actions/configuring-and-managing-workflows/using-environment-variables#default-environment-variables
+    if: github.repository == 'BimberLab/DiscvrLabKeyModules'
+    runs-on: ubuntu-latest
+    steps:
+      - name: "Build DISCVR"
+        uses: bimberlabinternal/DevOps/githubActions/discvr-build@master
+        with:
+          artifactory_user: ${{secrets.artifactory_user}}
+          artifactory_password: ${{secrets.artifactory_password}}
+          # NOTE: permissions are limited on the default secrets.GITHUB_TOKEN, including updating workflows, so use a personal access token
+          github_token: ${{ secrets.PAT }}
+

.travis.yml

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

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/RCommandWrapper.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/SequencePipelineServiceImpl.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))