Merge pull request #8 from tomburke-rse/fix_test_filechange

Fix test filechange

src/test/java/io/scif/labeling/LabelingIOTest.java

@@ -39,6 +39,7 @@
 import java.io.Reader;
 import java.lang.reflect.Type;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.List;
@@ -53,31 +54,37 @@
 import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 
+import org.junit.AfterClass;
 import org.junit.Assert;
-import org.junit.Before;
+import org.junit.BeforeClass;
 import org.junit.Test;
 import org.scijava.Context;
 
 public class LabelingIOTest {
 
-	Context context;
+	private static Context context;
 
-	@Before
-	public void beforeTests() {
+	@BeforeClass
+	public static void setUp() {
 		context = new Context();
 	}
 
+	@AfterClass
+	public static void tearDown() {
+		context.dispose();
+	}
+
 	@Test
 	public void testEquality() throws IOException {
 		final LabelingIOService labelingIOService = context.getService(
 			LabelingIOService.class);
 		final ImgLabeling<Integer, IntType> imgLabeling = labelingIOService.load(
 			"src/test/resources/labeling/labelSaveTestSimple", Integer.class,
 			IntType.class);
-		labelingIOService.save(imgLabeling,
-			"src/test/resources/labeling/example1_sav");
+		Path tempFile = mktemp();
+		labelingIOService.save(imgLabeling, tempFile.toString());
 		final ImgLabeling<Integer, IntType> imgLabeling2 = labelingIOService.load(
-			"src/test/resources/labeling/example1_sav", Integer.class, IntType.class);
+				tempFile.toString(), Integer.class, IntType.class);
 		Assert.assertEquals(imgLabeling.getMapping().getLabels(), imgLabeling2
 			.getMapping().getLabels());
 	}
@@ -88,9 +95,10 @@ public void testEquality2() throws IOException {
 			LabelingIOService.class);
 		final ImgLabeling<Integer, IntType> imgLabeling = labelingIOService.load(
 			"src/test/resources/labeling/test", Integer.class, IntType.class);
-		labelingIOService.save(imgLabeling, "src/test/resources/labeling/test2");
+		Path tempFile = mktemp();
+		labelingIOService.save(imgLabeling, tempFile.toString());
 		final ImgLabeling<Integer, IntType> imgLabeling2 = labelingIOService.load(
-			"src/test/resources/labeling/test2", Integer.class, IntType.class);
+				tempFile.toString(), Integer.class, IntType.class);
 		Assert.assertEquals(imgLabeling.getMapping().getLabels(), imgLabeling2
 			.getMapping().getLabels());
 	}
@@ -100,8 +108,7 @@ public void saveLabelingWithMetadataPrimitiveTest() throws IOException {
 		final ImgLabeling<Integer, UnsignedByteType> labeling =
 			getSimpleImgLabeling();
 		context.getService(LabelingIOService.class).saveWithMetaData(labeling,
-			new File("src/test/resources/labeling/labelSaveTestSimple.tif")
-				.getAbsolutePath(), new Example("a", 2.0, 1));
+				mktemp().toString(), new Example("a", 2.0, 1));
 	}
 
 	@Test
@@ -122,9 +129,8 @@ public void saveLabelingWithMetadataComplexTest() throws IOException {
 		final ImgLabeling<Example, IntType> labeling = getComplexImgLabeling();
 		final LabelingIOService labelingIOService = context.getService(
 			LabelingIOService.class);
-		labelingIOService.saveWithMetaData(labeling, new File(
-			"src/test/resources/labeling/labelSaveTestComplexMeta.tif")
-				.getAbsolutePath(), new Example("a", 2.0, 1));
+		labelingIOService.saveWithMetaData(labeling, mktemp().toString(),
+				new Example("a", 2.0, 1));
 	}
 
 	@Test
@@ -143,18 +149,6 @@ public void loadLabelingWithMetadataComplexWithCodecTest()
 			mapping.getMapping().getLabels());
 	}
 
-	@Test
-	public void t() throws IOException {
-		final GsonBuilder builder = new GsonBuilder();
-		final Reader reader = Files.newBufferedReader(Paths.get(
-			"src/test/resources/labeling/labelSaveTestComplexMeta.lbl.json"));
-		final Type labelingDataType =
-			new TypeToken<LabelingData<Example, Example>>()
-			{}.getType();
-		final LabelingData<Example, Example> labelingData = builder.create()
-			.fromJson(reader, labelingDataType);
-	}
-
 	private ImgLabeling<Integer, UnsignedByteType> getSimpleImgLabeling() {
 		final Integer[] values1 = new Integer[] { 42, 13 };
 		final Integer[] values2 = new Integer[] { 1 };
@@ -219,4 +213,9 @@ public int compareTo(final Example o) {
 		}
 	}
 
+	public static Path mktemp() throws IOException {
+		Path tempFile = Files.createTempFile(null, null);
+		tempFile.toFile().deleteOnExit();
+		return tempFile;
+	}
 }

src/test/java/io/scif/labeling/tutorials/E01_LoadLabeling.java

@@ -37,49 +37,47 @@
 import net.imglib2.roi.labeling.ImgLabeling;
 import net.imglib2.type.numeric.integer.IntType;
 
+import org.junit.AfterClass;
 import org.junit.Assert;
-import org.junit.Before;
+import org.junit.BeforeClass;
 import org.junit.Test;
 import org.scijava.Context;
 
 public class E01_LoadLabeling {
 
-	Context context;
+	private static Context context;
 
-	@Before
-	public void beforeTests() {
+	@BeforeClass
+	public static void setUp() {
 		context = new Context();
 	}
 
+	@AfterClass
+	public static void tearDown() {
+		context.dispose();
+	}
+
 	@Test
 	public void loadBasicLabeling() throws IOException {
-		// get the LabelingIO service from the context
-		final LabelingIOService labelingIOService = context.getService(
-			LabelingIOService.class);
-		// load a JSON file with IntType labels
-		// the container contains an ImgLabeling of that type as well as an optional
-		// sourcemap
-		// the sourcemap is a mapping of a source img to a list of labels that where
-		// contained in it and added to
-		// the ImgLabeling
-
-		final ImgLabeling<Integer, IntType> imgLabeling = labelingIOService.load(
-			"src/test/resources/labeling/labelSaveTestSimple.lbl.json", Integer.class,
-			IntType.class);
+		final LabelingIOService labelingIOService = context.service(LabelingIOService.class);
+		// Load a JSON file with IntType labels.
+		// The container contains an ImgLabeling of that type as well as an
+		// optional sourcemap. The sourcemap is a mapping of a source img to a
+		// list of labels that were contained in it and added to the ImgLabeling.
+		String inPath = "src/test/resources/labeling/labelSaveTestSimple.lbl.json";
+		final ImgLabeling<Integer, IntType> imgLabeling =
+			labelingIOService.load(inPath, Integer.class, IntType.class);
 		Assert.assertNotNull(imgLabeling);
 		Assert.assertNotNull(imgLabeling.getIndexImg());
 		Assert.assertFalse(imgLabeling.getMapping().getLabels().isEmpty());
-
 	}
 
 	@Test
 	public void loadClassBasedLabeling() throws IOException {
-		// get the LabelingIO service from the context
-		final LabelingIOService labelingIOService = context.getService(
-			LabelingIOService.class);
-		final Container<Example, Example, IntType> container = labelingIOService
-			.loadWithMetadata("src/test/resources/labeling/labelSaveTestComplex",
-				Example.class, Example.class, IntType.class);
+		final LabelingIOService labelingIOService = context.service(LabelingIOService.class);
+		final String inPath = "src/test/resources/labeling/labelSaveTestComplex";
+		final Container<Example, Example, IntType> container =
+			labelingIOService.loadWithMetadata(inPath, Example.class, Example.class, IntType.class);
 		final ImgLabeling<Example, IntType> mapping = container.getImgLabeling();
 		Assert.assertNotNull(mapping);
 	}

src/test/java/io/scif/labeling/tutorials/E02_SaveLabeling.java

@@ -34,6 +34,8 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -47,40 +49,40 @@
 import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 
-import org.junit.Before;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
 import org.junit.Test;
 import org.scijava.Context;
 
 public class E02_SaveLabeling {
 
-	Context context;
+	private static Context context;
 
-	@Before
-	public void beforeTests() {
+	@BeforeClass
+	public static void setUp() {
 		context = new Context();
 	}
 
+	@AfterClass
+	public static void tearDown() {
+		context.dispose();
+	}
+
 	@Test
 	public void saveLabelingTest() throws IOException {
-		final ImgLabeling<Integer, UnsignedByteType> labeling =
-			getSimpleImgLabeling();
-		// get the LabelingIO service from the context
-		final LabelingIOService labelingIOService = context.getService(
-			LabelingIOService.class);
-		labelingIOService.save(labeling, new File(
-			"src/test/resources/labeling/labelSaveTestSimple.tif").getAbsolutePath());
+		final ImgLabeling<Integer, UnsignedByteType> labeling = getSimpleImgLabeling();
+		Path outFile = Files.createTempFile(null, null);
+		final LabelingIOService labelingIOService = context.service(LabelingIOService.class);
+		labelingIOService.save(labeling, outFile.toString());
 
 	}
 
 	@Test
 	public void saveLabelingTest2() throws IOException {
 		final ImgLabeling<Example, IntType> labeling = getComplexImgLabeling();
-		// get the LabelingIO service from the context
-		final LabelingIOService labelingIOService = context.getService(
-			LabelingIOService.class);
-		labelingIOService.save(labeling, new File(
-			"src/test/resources/labeling/labelSaveTestComplex.tif")
-				.getAbsolutePath());
+		Path outFile = Files.createTempFile(null, null);
+		final LabelingIOService labelingIOService = context.service(LabelingIOService.class);
+		labelingIOService.save(labeling, outFile.toString());
 
 	}
 
@@ -102,12 +104,9 @@ public void saveLabelingWithMetaDataTest() throws IOException {
 
 		container.setMetadata(sources);
 
-		// get the LabelingIO service from the context
-		final LabelingIOService labelingIOService = context.getService(
-			LabelingIOService.class);
-		labelingIOService.saveWithMetaData(labeling, new File(
-			"src/test/resources/labeling/labelSaveTestSimpleMeta.tif")
-				.getAbsolutePath(), sources);
+		Path outFile = Files.createTempFile(null, null);
+		final LabelingIOService labelingIOService = context.service(LabelingIOService.class);
+		labelingIOService.saveWithMetaData(labeling, outFile.toString(), sources);
 
 	}
 

src/test/resources/labeling/labelSaveTestSimple.lbl.json

@@ -1 +1 @@
-{"version":3,"numSets":4,"numSources":1,"indexImg":"labelSaveTestSimple.tif","labelMapping":{},"labelSets":{"0":[],"1":[13,42],"2":[1],"3":[13,42,1]},"metadata":{"a":"a","b":2.0,"c":1}}
+{"version":3,"numSets":4,"numSources":1,"indexImg":"labelSaveTestSimple.tif","labelMapping":{},"labelSets":{"0":[],"1":[13,42],"2":[1],"3":[13,42,1]}}

src/test/resources/labeling/labelSaveTestSimpleMeta.lbl.json

@@ -1 +1 @@
-{"version":3,"numSets":4,"numSources":1,"indexImg":"labelSaveTestSimpleMeta.tif","labelSets":{"0":[],"1":[13,42],"2":[1],"3":[13,42,1]},"metadata":{"one":1,"two":2,"three":3}}
+{"version":3,"numSets":4,"numSources":1,"indexImg":"labelSaveTestSimpleMeta.tif","labelMapping":{},"labelSets":{"0":[],"1":[13,42],"2":[1],"3":[13,42,1]},"metadata":{"one":1,"two":2,"three":3}}