Avoid logging error for SequenceAnalysisMaintenanceTask when run on windows machines

Author: bbimber

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

@@ -324,7 +324,14 @@ private void processContainer(Container c, Logger log) throws IOException, Pipel
                         File gzi = new File(fasta.getPath() + ".gz.gzi");
                         if (!gzi.exists())
                         {
-                            new FastaIndexer(log).execute(gz);
+                            if (SystemUtils.IS_OS_WINDOWS)
+                            {
+                                log.warn("Cannot index gzipped FASTA on windows: " + fasta.getPath());
+                            }
+                            else
+                            {
+                                new FastaIndexer(log).execute(gz);
+                            }
                         }
 
                         expectedChildren.add(fasta.getName() + ".gz");

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

@@ -119,7 +119,7 @@ public String getPrimaryExtension()
     public static long getLineCount(File f) throws PipelineJobException
     {
         FileType gz = new FileType(".gz");
-        try (InputStream is = gz.isType(f) ? new GZIPInputStream(new FileInputStream(f)) : new FileInputStream(f);BufferedReader reader = new BufferedReader(new InputStreamReader(is, StringUtilsLabKey.DEFAULT_CHARSET));)
+        try (InputStream is = gz.isType(f) ? new GZIPInputStream(new FileInputStream(f)) : new FileInputStream(f); BufferedReader reader = new BufferedReader(new InputStreamReader(is, StringUtilsLabKey.DEFAULT_CHARSET));)
         {
             long i = 0;
             while (reader.readLine() != null)
@@ -228,7 +228,7 @@ public static void writeFastaRecord(Writer writer, String header, String sequenc
         if (sequence != null)
         {
             int len = sequence.length();
-            for (int i=0; i<len; i+=lineLength)
+            for (int i = 0; i < len; i += lineLength)
             {
                 writer.write(sequence.substring(i, Math.min(len, i + lineLength)) + "\n");
             }
@@ -627,4 +627,19 @@ else if (FILETYPE.cram.getFileType().isType(bamOrCram))
 
         throw new IllegalArgumentException("Must provide either a .bam or .cram file");
     }
-}
+
+    public static @Nullable File resolveUnderPath(String fn)
+    {
+        String path = System.getenv("PATH");
+        for (String dir : path.split(File.pathSeparator))
+        {
+            File toTest = new File(dir, fn);
+            if (toTest.exists())
+            {
+                return toTest;
+            }
+        }
+
+        return null;
+    }
+}