Restore original NT sequence location

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java

@@ -555,26 +555,13 @@ public File getOffsetsFile()
 
     private File getSequenceFileBaseDir(@Nullable File outDir, boolean create)
     {
-        if (outDir != null)
-        {
-            return outDir;
-        }
-
-        File baseDir = getBaseSequenceDir();
-        String digest = Crypt.MD5.digest(String.valueOf(getRowid()));
-
-        baseDir = FileUtil.appendName(baseDir, digest.substring(0,4));
-        baseDir = FileUtil.appendName(baseDir, digest.substring(4,8));
-        baseDir = FileUtil.appendName(baseDir, digest.substring(8,12));
-        baseDir = FileUtil.appendName(baseDir, digest.substring(12,20));
-        baseDir = FileUtil.appendName(baseDir, digest.substring(20,28));
-        baseDir = FileUtil.appendName(baseDir, digest.substring(28,32));
+        outDir = outDir == null ? getBaseSequenceDir() : outDir;
 
-        if (create)
+        if (create && !outDir.exists())
         {
-            baseDir.mkdirs();
+            outDir.mkdirs();
         }
 
-        return baseDir;
+        return outDir;
     }
 }

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

@@ -285,9 +285,14 @@ public static void doSequenceMigration(User u, Logger log, int maxSequences, @Nu
                 }
 
                 File legacyFile = legacyExpData.getFile();
-                if (!RefNtSequenceModel.BASE_DIRNAME.equals(legacyFile.getParentFile().getName()))
+                if (RefNtSequenceModel.BASE_DIRNAME.equals(legacyFile.getParentFile().getName()))
                 {
-                    // NOTE: this includes sequences imported to custom locations, such as refSequenceImport pipeline jobs
+                    continue;
+                }
+
+                if (!legacyFile.getPath().contains(RefNtSequenceModel.BASE_DIRNAME))
+                {
+                    // Includes sequences imported as pipeline jobs
                     continue;
                 }