Merge 22.12 to develop

Author: labkey-teamcity

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java

@@ -258,7 +258,7 @@ public static void logModuleVersions(Logger log)
         log.debug("java.io.tmpDir: " + System.getProperty("java.io.tmpdir"));
         try
         {
-            File tmp = File.createTempFile("sa-tmp", "tmp");
+            File tmp = FileUtil.createTempFile("sa-tmp", "tmp");
             log.debug("temp file location: " + tmp.getParent());
             tmp.delete();
         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java

@@ -8,6 +8,7 @@
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
+import org.labkey.api.util.FileUtil;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
 
 import java.io.File;
@@ -34,7 +35,7 @@ public File sortGxf(File gxf, @Nullable File output) throws PipelineJobException
             if (output == null)
             {
                 getLogger().debug("file will sort sorted in place");
-                outputFile = File.createTempFile("gffread", ".txt");
+                outputFile = FileUtil.createTempFile("gffread", ".txt");
             }
             else
             {

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java

@@ -554,7 +554,7 @@ public void setUp()
             try
             {
                 //create input data
-                _input = File.createTempFile("barcodeTest", ".fastq");
+                _input = FileUtil.createTempFile("barcodeTest", ".fastq");
                 if (_input.exists())
                     _input.delete();
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java

@@ -541,7 +541,7 @@ public static Set<String> getContigsInVcf(File vcf) throws PipelineJobException
     {
         try
         {
-            File script = File.createTempFile("script", "sh");
+            File script = FileUtil.createTempFile("script", "sh");
             try (PrintWriter writer = PrintWriters.getPrintWriter(script))
             {
                 writer.println("#!/bin/bash");

SequenceAnalysis/src/org/labkey/sequenceanalysis/visualization/VariationChart.java

@@ -23,6 +23,7 @@
 import org.jfree.ui.RectangleEdge;
 import org.jfree.ui.TextAnchor;
 import org.json.old.JSONObject;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.writer.PrintWriters;
 import org.w3c.dom.DOMImplementation;
 import org.w3c.dom.Document;
@@ -311,7 +312,7 @@ private FeatureList readGff(String gff) throws IOException
         if (gff == null)
             return new FeatureList();
 
-        File f = File.createTempFile("variationChart", ".gff");
+        File f = FileUtil.createTempFile("variationChart", ".gff");
         try (PrintWriter writer = PrintWriters.getPrintWriter(f))
         {
             writer.write(gff);
@@ -354,7 +355,7 @@ public Map<String, Object> toSVG(List<JFreeChart> charts, int width, int height)
             i++;
         }
 
-        File output = File.createTempFile("sequenceGraph", ".svg");
+        File output = FileUtil.createTempFile("sequenceGraph", ".svg");
         try (BufferedWriter writer = new BufferedWriter(new FileWriter(output)))
         {
             generator.stream(writer);

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

@@ -184,7 +184,7 @@ protected List<Chunk> addAdditionalChunks(SequenceOutputHandler.JobContext ctx,
             //Add one more indentation to headers:
             try
             {
-                File updated = File.createTempFile("headerUpdate", ".md");
+                File updated = FileUtil.createTempFile("headerUpdate", ".md");
                 try (PrintWriter writer = PrintWriters.getPrintWriter(updated); BufferedReader reader = Readers.getReader(markdown))
                 {
                     String line;