Merge pull request #87 from melissalinkert/move-ome-xml

Move METADATA.ome.xml under data.zarr
glencoesoftware · Mar 12, 2021 · c705515 · c705515
2 parents ef70e17 + 3bcdb44
commit c705515
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Showing 2 changed files with 10 additions and 8 deletions.
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -510,10 +510,11 @@ public void convert()
         String xml = getService().getOMEXML(meta);
 
         // write the original OME-XML to a file
-        if (!Files.exists(outputPath)) {
-          Files.createDirectories(outputPath);
+        Path metadataPath = outputPath.resolve(pyramidName);
+        if (!Files.exists(metadataPath)) {
+          Files.createDirectories(metadataPath);
         }
-        Path omexmlFile = outputPath.resolve(METADATA_FILE);
+        Path omexmlFile = metadataPath.resolve(METADATA_FILE);
         Files.write(omexmlFile, xml.getBytes(Constants.ENCODING));
       }
       catch (ServiceException se) {

diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -85,8 +85,9 @@ void assertTool(String...additionalArgs) throws IOException {
     try {
       converter = new Converter();
       CommandLine.call(converter, args.toArray(new String[]{}));
-      assertTrue(Files.exists(output.resolve("data.zarr")));
-      assertTrue(Files.exists(output.resolve("METADATA.ome.xml")));
+      Path zarr = output.resolve("data.zarr");
+      assertTrue(Files.exists(zarr));
+      assertTrue(Files.exists(zarr.resolve("METADATA.ome.xml")));
     }
     catch (RuntimeException rt) {
       throw rt;
@@ -684,7 +685,7 @@ public void testOriginalMetadata() throws Exception {
 
     input = fake(null, null, originalMetadata);
     assertTool();
-    Path omexml = output.resolve("METADATA.ome.xml");
+    Path omexml = output.resolve("data.zarr").resolve("METADATA.ome.xml");
     StringBuilder xml = new StringBuilder();
     Files.lines(omexml).forEach(v -> xml.append(v));
 
@@ -798,8 +799,8 @@ public void testHCSMetadata() throws IOException {
     ZarrGroup z = ZarrGroup.open(root);
 
     // check valid group layout
-    // .zattrs (Plate), .zgroup (Plate) and 2 rows
-    assertEquals(4, Files.list(root).toArray().length);
+    // METADATA.ome.xml, .zattrs (Plate), .zgroup (Plate) and 2 rows
+    assertEquals(5, Files.list(root).toArray().length);
     for (int row=0; row<2; row++) {
       Path rowPath = root.resolve(Integer.toString(row));
       // .zgroup (Row) and 3 columns