Merge discvr-22.11 to develop

Author: bbimber

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

@@ -21,7 +21,7 @@
 import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.reports.ExternalScriptEngineDefinition;
 import org.labkey.api.reports.LabKeyScriptEngineManager;
-import org.labkey.api.reports.report.r.RScriptEngineFactory;
+import org.labkey.api.reports.RScriptEngineFactory;
 import org.labkey.api.services.ServiceRegistry;
 
 import java.io.File;

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

@@ -7,6 +7,7 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
@@ -137,7 +138,7 @@ private void verifySequenceDataPresent(Logger log)
     {
         log.info("verifying sequence data files present");
         TableInfo ti = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_READ_DATA);
-        TableSelector ts = new TableSelector(ti);
+        TableSelector ts = new TableSelector(ti, null, new Sort("container"));
 
         log.info("Inspecting ReadData");
         List<ReadDataImpl> readDatas = ts.getArrayList(ReadDataImpl.class);
@@ -202,13 +203,13 @@ else if (!d.getFile().exists())
         //also check analyses
         log.info("Inspecting Analyses");
         TableInfo analysesTable = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_ANALYSES);
-        TableSelector tsAnalyses = new TableSelector(analysesTable);
+        TableSelector tsAnalyses = new TableSelector(analysesTable, null, new Sort("container"));
         List<AnalysisModelImpl> analyses = tsAnalyses.getArrayList(AnalysisModelImpl.class);
         i = 0;
         for (AnalysisModelImpl m : analyses)
         {
             i++;
-            if (i % 500 == 0)
+            if (i % 1000 == 0)
             {
                 log.info("analysis " + i + " of " + analyses.size() + ". Current container: " + ContainerManager.getForId(m.getContainer()).getPath());
             }

singlecell/src/org/labkey/singlecell/pipeline/singlecell/NormalizeAndScale.java

@@ -51,7 +51,7 @@ public Provider()
                     }}, false),
                     SeuratToolParameter.create("nVariableFeatures", "# Variable Features", "Controls the number of variable features that will be used. This only applies to the standard NormalizeData/ScaleData pipeline, not SCTransform", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, null),
+                    }}, 3000),
                     SeuratToolParameter.create("scoreCellCycle", "Score Cell Cycle?", "If checked, ScoreCellCycle will be run to compute Phase, which is stored in meta.data. If a field named Phase already exists, this will be skipped", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true),