refactor(test): move some test function around, use TempDir for tests

src/main/kotlin/org/janelia/saalfeldlab/util/n5/DatasetDiscovery.kt

@@ -1,7 +1,6 @@
 package org.janelia.saalfeldlab.util.n5
 
 import io.github.oshai.kotlinlogging.KotlinLogging
-import org.commonmark.internal.util.Parsing
 import org.janelia.saalfeldlab.n5.N5Reader
 import org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer
 import org.janelia.saalfeldlab.n5.universe.N5TreeNode
@@ -43,9 +42,7 @@ private val LOG = KotlinLogging.logger {  }
 @JvmOverloads
 internal fun discoverAndParseRecursive(n5Reader: N5Reader, initialGroup: String = "/", callback: (N5TreeNode) -> Unit = {}): N5TreeNode {
 	val discoverer = getDiscoverer(n5Reader)
-	println("\tParsing ${n5Reader.uri}")
 	return discoverer.discoverAndParseRecursive(initialGroup) {
-		println("\t\tDiscovered dataset ${it.path} with metadata ${it.metadata}")
 		callback(it)
 	}
 }

src/main/kotlin/org/janelia/saalfeldlab/util/n5/universe/N5FactoryWithCache.kt

@@ -9,6 +9,7 @@ import org.janelia.saalfeldlab.n5.N5Writer
 import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader
 import org.janelia.saalfeldlab.n5.universe.N5Factory
 import org.janelia.saalfeldlab.n5.universe.StorageFormat
+import org.janelia.saalfeldlab.paintera.serialization.GsonHelpers
 import java.net.URI
 
 class N5FactoryWithCache : N5Factory() {

src/test/java/org/janelia/saalfeldlab/util/n5/N5HelpersTest.java

@@ -3,6 +3,8 @@
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import net.imglib2.img.cell.CellGrid;
+import org.janelia.saalfeldlab.labels.blocks.LabelBlockLookup;
+import org.janelia.saalfeldlab.labels.blocks.LabelBlockLookupAdapter;
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.CompressionAdapter;
 import org.janelia.saalfeldlab.n5.DataType;
@@ -11,12 +13,16 @@
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.RawCompression;
 import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
+import org.janelia.saalfeldlab.paintera.Paintera;
+import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.lang.invoke.MethodHandles;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.stream.Collectors;
@@ -49,6 +55,14 @@ private static void assertDatasetAttributesEquals(final DatasetAttributes expect
 		assertEquals(gsonWithCompression.toJson(expected.getCompression()), gsonWithCompression.toJson(actual.getCompression()));
 	}
 
+	@BeforeAll
+	public static void setupN5Factory() {
+
+		final var builder = new GsonBuilder();
+		builder.registerTypeHierarchyAdapter(LabelBlockLookup.class, LabelBlockLookupAdapter.getJsonAdapter());
+		Paintera.getN5Factory().gsonBuilder(builder);
+	}
+
 	@Test
 	public void testAsCellGrid() {
 
@@ -66,9 +80,10 @@ public void testVolumetricDataGroup() {
 		assertEquals(group + "/" + N5Helpers.PAINTERA_DATA_DATASET, N5Helpers.volumetricDataGroup(group, true));
 	}
 
-	@Test public void testIsMultiscale() throws IOException {
+	@Test
+	public void testIsMultiscale(@TempDir Path tmp) throws IOException {
 
-		final N5Writer writer = N5TestUtil.fileSystemWriterAtTmpDir(!LOG.isDebugEnabled());
+		final N5Writer writer = Paintera.getN5Factory().newWriter(tmp.toAbsolutePath().toString());
 		final String group = "group";
 		writer.createGroup(group);
 
@@ -91,9 +106,9 @@ public void testVolumetricDataGroup() {
 	}
 
 	@Test
-	public void testListAndSortScaleDatasets() throws IOException {
+	public void testListAndSortScaleDatasets(@TempDir Path tmp) throws IOException {
 
-		final N5Writer writer = N5TestUtil.fileSystemWriterAtTmpDir(!LOG.isDebugEnabled());
+		final N5Writer writer = Paintera.getN5Factory().newWriter(tmp.toAbsolutePath().toString());
 		final String group = "group";
 		writer.createGroup(group);
 		writer.setAttribute(group, N5Helpers.MULTI_SCALE_KEY, true);
@@ -109,9 +124,9 @@ public void testListAndSortScaleDatasets() throws IOException {
 	}
 
 	@Test
-	public void testDiscoverDatasets() throws IOException {
+	public void testDiscoverDatasets(@TempDir Path tmp) throws IOException {
 
-		final N5Writer writer = N5TestUtil.fileSystemWriterAtTmpDir(!LOG.isDebugEnabled());
+		final N5Writer writer = Paintera.getN5Factory().newWriter(tmp.toAbsolutePath().toString());
 		final String group = "group";
 		writer.createGroup(group);
 		writer.setAttribute(group, N5Helpers.MULTI_SCALE_KEY, true);
@@ -134,9 +149,9 @@ public void testDiscoverDatasets() throws IOException {
 	}
 
 	@Test
-	public void testGetDatasetAttributes() throws IOException {
+	public void testGetDatasetAttributes(@TempDir Path tmp) throws IOException {
 
-		final N5Writer writer = N5TestUtil.fileSystemWriterAtTmpDir(!LOG.isDebugEnabled());
+		final N5Writer writer = Paintera.getN5Factory().newWriter(tmp.toAbsolutePath().toString());
 		final DatasetAttributes attributes = new DatasetAttributes(new long[]{1}, new int[]{1}, DataType.UINT8, new GzipCompression());
 
 		// single scale

src/test/java/org/janelia/saalfeldlab/util/n5/N5TypesTest.java

@@ -1,5 +1,6 @@
 package org.janelia.saalfeldlab.util.n5;
 
+import com.google.gson.GsonBuilder;
 import net.imglib2.type.numeric.integer.ByteType;
 import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.type.numeric.integer.LongType;
@@ -10,12 +11,19 @@
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.type.numeric.real.DoubleType;
 import net.imglib2.type.numeric.real.FloatType;
+import org.janelia.saalfeldlab.labels.blocks.LabelBlockLookup;
+import org.janelia.saalfeldlab.labels.blocks.LabelBlockLookupAdapter;
 import org.janelia.saalfeldlab.n5.DataType;
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.RawCompression;
+import org.janelia.saalfeldlab.paintera.Paintera;
+import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
 
 import java.io.IOException;
+import java.nio.file.Path;
 import java.util.HashSet;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -27,6 +35,14 @@
 
 public class N5TypesTest {
 
+	@BeforeAll
+	public static void setupN5Factory() {
+
+		final var builder = new GsonBuilder();
+		builder.registerTypeHierarchyAdapter(LabelBlockLookup.class, LabelBlockLookupAdapter.getJsonAdapter());
+		Paintera.getN5Factory().gsonBuilder(builder);
+	}
+
 	@Test
 	public void testAndLogIsIntegerType() {
 
@@ -48,9 +64,9 @@ public void testAndLogIsIntegerType() {
 	}
 
 	@Test
-	public void testIsLabelMultisetType() throws IOException {
+	public void testIsLabelMultisetType(@TempDir Path tmp) throws IOException {
 
-		final N5Writer writer = N5TestUtil.fileSystemWriterAtTmpDir();
+		final N5Writer writer = Paintera.getN5Factory().newWriter(tmp.toAbsolutePath().toString());
 
 		final String noMultisetGroup = "no-multiset-group";
 		final String multisetGroup = "multiset-group";
@@ -67,10 +83,13 @@ public void testIsLabelMultisetType() throws IOException {
 		final String multisetGroupMultiscale = "multiset-group-multiscale";
 		writer.createGroup(noMultisetGroupMultiscale);
 		writer.createGroup(multisetGroupMultiscale);
-		writer.createDataset(noMultisetGroupMultiscale + "/s0", N5TestUtil.defaultAttributes());
-		writer.createDataset(noMultisetGroupMultiscale + "/s1", N5TestUtil.defaultAttributes());
-		writer.createDataset(multisetGroupMultiscale + "/s0", N5TestUtil.defaultAttributes());
-		writer.createDataset(multisetGroupMultiscale + "/s1", N5TestUtil.defaultAttributes());
+
+		final DatasetAttributes defaultAttributes = new DatasetAttributes(new long[]{1}, new int[]{1}, DataType.UINT8, new RawCompression());
+
+		writer.createDataset(noMultisetGroupMultiscale + "/s0", defaultAttributes);
+		writer.createDataset(noMultisetGroupMultiscale + "/s1", defaultAttributes);
+		writer.createDataset(multisetGroupMultiscale + "/s0", defaultAttributes);
+		writer.createDataset(multisetGroupMultiscale + "/s1", defaultAttributes);
 		writer.setAttribute(noMultisetGroupMultiscale + "/s0", N5Helpers.LABEL_MULTISETTYPE_KEY, false);
 		writer.setAttribute(multisetGroupMultiscale + "/s0", N5Helpers.LABEL_MULTISETTYPE_KEY, true);
 		assertFalse(N5Types.isLabelMultisetType(writer, noMultisetGroupMultiscale));
@@ -107,9 +126,9 @@ public void testMaxForType() {
 	}
 
 	@Test
-	public void testGetDataType() throws IOException {
+	public void testGetDataType(@TempDir Path tmp) throws IOException {
 
-		final N5Writer writer = N5TestUtil.fileSystemWriterAtTmpDir();
+		final N5Writer writer = Paintera.getN5Factory().newWriter(tmp.toAbsolutePath().toString());
 		for (final DataType t : DataType.values()) {
 			writer.createDataset(t.toString(), new long[]{1}, new int[]{1}, t, new RawCompression());
 			assertEquals(t, N5Types.getDataType(writer, t.toString()));