Merge pull request #65 from chris-allan/symlink-check

Handle symlink as the root directory (Fixes #62)
glencoesoftware · Jun 28, 2021 · 602ae48 · 602ae48
2 parents f97ecc4 + eb6760f
commit 602ae48
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Showing 3 changed files with 32 additions and 8 deletions.
diff --git a/build.gradle b/build.gradle
@@ -39,6 +39,7 @@ dependencies {
     // be careful here, this is a newer version of org.json:json than formats-gpl uses
     implementation 'org.json:json:20190722'
     testImplementation 'junit:junit:4.12'
+    testImplementation 'org.apache.commons:commons-lang3:3.12.0'
     testImplementation 'com.glencoesoftware:bioformats2raw:0.3.0-SNAPSHOT'
 }
 

diff --git a/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java b/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
@@ -212,6 +212,8 @@ public static void main(String[] args) {
 
   @Override
   public Void call() throws Exception {
+    // Resolve symlinks
+    inputDirectory = inputDirectory.toRealPath();
     if (printVersion) {
       printVersion();
       return null;

diff --git a/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java b/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java
@@ -40,7 +40,9 @@
 import picocli.CommandLine;
 import picocli.CommandLine.ExecutionException;
 
+import org.apache.commons.lang3.SystemUtils;
 import org.junit.Assert;
+import org.junit.Assume;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
@@ -241,14 +243,7 @@ Object getPlane(ImageReader reader, int planeIndex) throws Exception {
         reader.isLittleEndian());
   }
 
-  /**
-   * Test defaults.
-   */
-  @Test
-  public void testDefaults() throws Exception {
-    input = fake();
-    assertBioFormats2Raw();
-    assertTool();
+  private void assertDefaults() throws Exception {
     ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0");
     Assert.assertTrue(series0.getNested());
     // Also ensure we're using the latest .zarray metadata
@@ -268,6 +263,32 @@ public void testDefaults() throws Exception {
    * Test defaults.
    */
   @Test
+  public void testDefaults() throws Exception {
+    input = fake();
+    assertBioFormats2Raw();
+    assertTool();
+    assertDefaults();
+  }
+
+  /**
+   * Test symlink as the root.
+   */
+  @Test
+  public void testSymlinkAsRoot() throws Exception {
+    Assume.assumeTrue(SystemUtils.IS_OS_LINUX);
+    input = fake();
+    assertBioFormats2Raw();
+    Path notASymlink = output.resolveSibling(output.getFileName() + ".old");
+    Files.move(output, notASymlink);
+    Files.createSymbolicLink(output, notASymlink);
+    assertTool();
+    assertDefaults();
+  }
+
+  /**
+   * Test series count check.
+   */
+  @Test
   public void testSeriesCountCheck() throws Exception {
     input = fake();
     assertBioFormats2Raw();