Quote filenames and also ensure cached JB2 files lack spaces

Author: bbimber

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

@@ -55,12 +55,12 @@ public File sortGff(File input, @Nullable File output) throws PipelineJobExcepti
             writer.println("OUT_GFF='" + outputFile.getPath() + "'");
 
             String cat = inputIsGzip ? "zcat" : "cat";
-            writer.println(cat + " $GFF | awk '{ if ($1 ~ \"^#\" ) print $0; else exit; }' > $OUT_GFF");
-            writer.println("(" + cat  + " $GFF | grep -v '#' | grep -v \"Parent=\" | sort -V -t$'\\t' -k1,1 -k4,4n -k5,5n; " + cat + " $GFF | grep -v '#' | grep -e \"Parent=\" | sort -V -t$'\\t' -k1,1 -k4,4n -k5,5n)| sort -V -t$'\\t' -k1,1 -k4,4n -s >> $OUT_GFF");
+            writer.println(cat + " '$GFF' | awk '{ if ($1 ~ \"^#\" ) print $0; else exit; }' > '$OUT_GFF'");
+            writer.println("(" + cat  + " '$GFF' | grep -v '#' | grep -v \"Parent=\" | sort -V -t$'\\t' -k1,1 -k4,4n -k5,5n; " + cat + " '$GFF' | grep -v '#' | grep -e \"Parent=\" | sort -V -t$'\\t' -k1,1 -k4,4n -k5,5n)| sort -V -t$'\\t' -k1,1 -k4,4n -s >> '$OUT_GFF'");
 
             if (outputIsGzip)
             {
-                writer.println("bgzip -f $OUT_GFF");
+                writer.println("bgzip -f '$OUT_GFF'");
                 outputFile = new File(outputFile.getPath() + ".gz");
             }
         }
@@ -89,8 +89,8 @@ public File sortGtf(File input, @Nullable File output) throws PipelineJobExcepti
             writer.println("OUT_GTF='" + outputFile.getPath() + "'");
 
             String cat = inputIsGzip ? "zcat" : "cat";
-            writer.println(cat + " $GTF | awk '{ if ($1 ~ \"^#\" ) print $0; else exit; }' > $OUT_GTF");
-            writer.println(cat + " $GTF | grep -v '#' | awk -v OFS='\\t' ' {");
+            writer.println(cat + " '$GTF' | awk '{ if ($1 ~ \"^#\" ) print $0; else exit; }' > '$OUT_GTF'");
+            writer.println(cat + " '$GTF' | grep -v '#' | awk -v OFS='\\t' ' {");
             writer.println("so = 3");
             writer.println("if (tolower($3) == \"gene\")");
             writer.println("    so = 1");
@@ -100,11 +100,11 @@ public File sortGtf(File input, @Nullable File output) throws PipelineJobExcepti
             writer.println("    so = 3");
             writer.println("else if (tolower($3) == \"cds\")");
             writer.println("    so = 4");
-            writer.println("print so, $0 } ' | sort -V -t$'\\t' -k2,2 -k5,5n -k1,1n | cut -d$'\\t' -f2- >> $OUT_GTF");
+            writer.println("print so, $0 } ' | sort -V -t$'\\t' -k2,2 -k5,5n -k1,1n | cut -d$'\\t' -f2- >> '$OUT_GTF'");
 
             if (outputIsGzip)
             {
-                writer.println("bgzip -f $OUT_GTF");
+                writer.println("bgzip -f '$OUT_GTF'");
                 outputFile = new File(outputFile.getPath() + ".gz");
             }
         }

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -41,6 +41,7 @@
 import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.FileType;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Path;
@@ -860,7 +861,7 @@ public File getLocationOfProcessedTrack(boolean createDir)
             trackDir.mkdirs();
         }
 
-        return new File(trackDir, getSourceFileName() + (needsGzip() && !isGzipped() ? ".gz" : ""));
+        return new File(trackDir, FileUtil.makeLegalName(getSourceFileName()).replaceAll(" ", "_") + (needsGzip() && !isGzipped() ? ".gz" : ""));
     }
 
     protected String getSourceFileName()