Merge pull request #56 from chris-allan/layout-version-3

Update expected layout version from 2 to 3
glencoesoftware · Apr 12, 2021 · 07759de · 07759de
2 parents f227a45 + 379127a
commit 07759de
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diff --git a/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java b/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
@@ -258,7 +258,7 @@ private Path getMetadataFile() {
    * @return Path representing the expected OME-XML metadata file
    */
   private Path getOMEXMLFile() {
-    return getZarr().resolve(OMEXML_FILE);
+    return getZarr().resolve("OME").resolve(OMEXML_FILE);
   }
 
   /**
@@ -584,7 +584,7 @@ public void initialize()
     if (layoutVersion == null) {
       LOG.warn("Layout version not recorded; may be unsupported");
     }
-    else if (layoutVersion != 2) {
+    else if (layoutVersion != 3) {
       throw new FormatException("Unsupported version: " + layoutVersion);
     }
 

diff --git a/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java b/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java
@@ -68,7 +68,8 @@ void assertBioFormats2Raw(String...additionalArgs) throws IOException {
       converter = new Converter();
       CommandLine.call(converter, args.toArray(new String[]{}));
       Assert.assertTrue(Files.exists(output.resolve(".zattrs")));
-      Assert.assertTrue(Files.exists(output.resolve("METADATA.ome.xml")));
+      Assert.assertTrue(Files.exists(
+        output.resolve("OME").resolve("METADATA.ome.xml")));
     }
     catch (RuntimeException rt) {
       throw rt;