Set gzip compression properly for zarr

Fixes #105.
constantinpape · Aug 5, 2019 · 9dab916 · 9dab916
1 parent 8ec2ff7
commit 9dab916
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Showing 2 changed files with 5 additions and 8 deletions.
diff --git a/include/z5/metadata.hxx b/include/z5/metadata.hxx
@@ -125,13 +125,13 @@ namespace z5 {
                 throw std::runtime_error("z5.DatasetMetadata.fromJsonZarr: wrong compressor for zarr format");
             }
 
-            if(zarrCompressorId == "zlib") {
-                compressionOptions["useZlib"] = true;
-            } else if (zarrCompressorId == "gzip") {
-                compressionOptions["useZlib"] = false;
-            }
             types::readZarrCompressionOptionsFromJson(compressor, compressionOpts,
                                                       compressionOptions);
+            // we need to do this after 'readZarrCompressionOptionsFromJson' is called,
+            // because otherwise this will be overriden
+            if (zarrCompressorId == "gzip") {
+                compressionOptions["useZlib"] = false;
+            }
         }
 
 

diff --git a/src/python/test/test_zarr.py b/src/python/test/test_zarr.py
@@ -62,7 +62,6 @@ def test_write_zarr_irregular(self):
     def test_read_zarr(self):
         from z5py.dataset import Dataset
         dtypes = list(Dataset._zarr_dtype_dict.values())
-        compressions = Dataset.compressors_zarr
         zarr_compressors = {'blosc': numcodecs.Blosc(),
                             'zlib': numcodecs.Zlib(),
                             'raw': None,
@@ -87,8 +86,6 @@ def test_read_zarr(self):
                 self.assertEqual(data.shape, out.shape)
                 self.assertTrue(np.allclose(data, out))
 
-    # zarr gzip compression is not working properly yet
-    @unittest.expectedFailure
     @unittest.skipUnless(HAVE_ZARR, 'Requires zarr package')
     def test_write_zarr(self):
         from z5py.dataset import Dataset