chore: add platform-test workflow

.github/workflows/platform-test.yml

@@ -0,0 +1,44 @@
+name: test
+
+on:
+ push:
+ branches:
+ - master
+ tags:
+ - "*-[0-9]+.*"
+ pull_request:
+ branches:
+ - master
+ workflow_dispatch:
+
+jobs:
+ build:
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest]
+ runs-on: ${{ matrix.os }}
+
+ steps:
+ - uses: actions/checkout@v2
+ - name: Setup Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: '3.10'
+ - name: Install blosc (Windows)
+ if: matrix.os == 'windows-latest'
+ run: |
+ pip install blosc --no-input --target src/test/resources
+ mv src/test/resources/bin/* src/test/resources
+ - name: Install blosc (Ubuntu)
+ if: matrix.os == 'ubuntu-latest'
+ run: |
+ pip install blosc --no-input --target src/test/resources
+ mv src/test/resources/lib64/* src/test/resources
+ - name: Set up Java
+ uses: actions/setup-java@v2
+ with:
+ java-version: '8'
+ distribution: 'zulu'
+ cache: 'maven'
+ - name: Maven Test
+ run: mvn -B clean test --file pom.xml

pom.xml

@@ -11,7 +11,7 @@
 
  <groupId>org.janelia.saalfeldlab</groupId>
  <artifactId>n5-ij</artifactId>
- <version>4.1.3-SNAPSHOT</version>
+ <version>4.1.2-SNAPSHOT</version>
 
  <name>N5 ImageJ Bindings</name>
  <description>ImageJ convenience layer for N5</description>
@@ -86,10 +86,12 @@
  <releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
  <n5.version>3.2.0</n5.version>
+ <n5-aws-s3.version>4.1.2</n5-aws-s3.version>
+ <n5-blosc.version>1.1.1</n5-blosc.version>
+ <n5-google-cloud.version>4.1.0</n5-google-cloud.version>
  <n5-hdf5.version>2.2.0</n5-hdf5.version>
  <n5-imglib2.version>7.0.0</n5-imglib2.version>
- <n5-google-cloud.version>4.1.0</n5-google-cloud.version>
- <n5-universe.version>1.4.2</n5-universe.version>
+ <n5-universe.version>1.4.3-SNAPSHOT</n5-universe.version>
  <n5-zarr.version>1.3.1</n5-zarr.version>
  <n5-zstandard.version>1.0.2</n5-zstandard.version>
  </properties>

src/main/java/org/janelia/saalfeldlab/n5/ij/N5Importer.java

@@ -27,7 +27,9 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URI;
 import java.net.URISyntaxException;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -62,6 +64,7 @@
 import org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
 import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
+import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadataParser;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMultiScaleMetadata;
@@ -108,6 +111,7 @@
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.type.numeric.real.DoubleType;
 import net.imglib2.type.numeric.real.FloatType;
+import net.imglib2.util.Pair;
 import net.imglib2.util.Util;
 import net.imglib2.view.Views;
 
@@ -855,11 +859,17 @@ public N5Reader apply(final String n5UriOrPath) {
  if (n5UriOrPath == null || n5UriOrPath.isEmpty())
  return null;
 
-
- String rootPath = null ;
+ String rootPath = null;
  if (n5UriOrPath.contains("?")) {
+
  try {
- rootPath = new N5URI(n5UriOrPath).getContainerPath();
+ // need to strip off storage format for n5uri to correctly remove query;
+ final Pair<StorageFormat, URI> fmtUri = N5Factory.StorageFormat.parseUri(n5UriOrPath);
+ final StorageFormat format = fmtUri.getA();
+
+ final N5URI n5uri = from(fmtUri.getB().toString());
+ // add the format prefix back if it was present
+ rootPath = format == null ? n5uri.getContainerPath() : format.toString().toLowerCase() + ":" + n5uri.getContainerPath();
  } catch (URISyntaxException e) {}
  }
 
@@ -877,6 +887,42 @@ public N5Reader apply(final String n5UriOrPath) {
  }
  }
 
+ /**
+ * Generate an {@link N5URI} from a String.
+ *
+ * @param uriOrPath
+ * a string representation of a uri or a path string.
+ * @return the {@link N5URI}
+ */
+ private static N5URI from(final String uriOrPath) {
+
+ try {
+ return new N5URI(new URI(uriOrPath));
+ } catch (Throwable ignore) {}
+
+ try {
+ final String[] split = uriOrPath.split("\\?");
+ final URI tmp = Paths.get(split[0]).toUri();
+ if (split.length == 1)
+ return new N5URI(tmp);
+ else {
+ StringBuffer buildUri = new StringBuffer();
+ buildUri.append(tmp.toString());
+ buildUri.append("?");
+ for (int i = 1; i < split.length; i++)
+ buildUri.append(split[i]);
+
+ return new N5URI(new URI(buildUri.toString()));
+ }
+ } catch (Throwable ignore) {}
+
+ try {
+ return new N5URI(N5URI.encodeAsUri(uriOrPath));
+ } catch (URISyntaxException e) {
+ throw new N5Exception(e);
+ }
+ }
+
  private static String upToLastExtension(final String path) {
 
  final int i = path.lastIndexOf('.');

src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java

@@ -1487,9 +1487,6 @@ private static class DetailedOverwriteWarningDialog extends JDialog {
  public DetailedOverwriteWarningDialog(final Frame parent, final String root, final String dataset) {
  super(parent,"WARNING", true);
  initComponents(root, dataset);
- final Dimension dims = new Dimension(600, 250);
- setSize(dims);
- setPreferredSize(dims);
  setResizable(false);
  setLocationRelativeTo(null);
  }

src/main/java/org/janelia/saalfeldlab/n5/ui/DatasetSelectorDialog.java

@@ -50,13 +50,13 @@
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JFileChooser;
+import javax.swing.JFormattedTextField.AbstractFormatter;
 import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTabbedPane;
-import javax.swing.JTextField;
 import javax.swing.JTree;
 import javax.swing.ScrollPaneConstants;
 import javax.swing.SwingUtilities;
@@ -72,7 +72,11 @@
 import java.awt.GridBagLayout;
 import java.awt.Insets;
 import java.io.File;
+import java.net.URI;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.text.Collator;
+import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
@@ -105,7 +109,7 @@ public class DatasetSelectorDialog {
 
  private JFrame dialog;
 
- private JTextField containerPathText;
+ private ImprovedFormattedTextField containerPathText;
 
  private JCheckBox virtualBox;
 
@@ -366,8 +370,7 @@ private JFrame buildDialog() {
  tabs.addTab("Metadata Translation", translationPanel.buildPanel());
  tabs.addTab("Translation Result", translationResultPanel.buildPanel());
 
- containerPathText = new JTextField();
- containerPathText.setText(initialContainerPath);
+ containerPathText = new ImprovedFormattedTextField(new UriValidator(), initialContainerPath);
  containerPathText.setPreferredSize(new Dimension(frameSizeX / 3, containerPathText.getPreferredSize().height));
  containerPathText.addActionListener(e -> openContainer(n5Fun, () -> getN5RootPath(), pathFun));
 
@@ -934,4 +937,38 @@ private static boolean pathsEqual(final String a, final String b) {
  return normalDatasetName(a, "/").equals(normalDatasetName(b, "/"));
  }
 
+ protected static class UriValidator extends AbstractFormatter {
+
+ private static final long serialVersionUID = 6765664180035018335L;
+
+ @Override
+ public Object stringToValue(String input) throws ParseException {
+
+ if (input == null || input.isEmpty())
+ return null;
+
+ try {
+ final URI uri = new URI(input);
+ if (uri.isAbsolute())
+ return uri;
+ } catch (Throwable ignore) {}
+
+ try {
+ return Paths.get(input).toUri();
+ } catch (Throwable ignore) {}
+
+ throw new ParseException("input " + input + " not a valid URI", 0);
+ }
+
+ @Override
+ public String valueToString(Object arg) throws ParseException {
+
+ if( arg instanceof URI )
+ return ((URI)arg).toString().replaceFirst("^file://", "");
+ else
+ throw new ParseException("input " + arg + " not a valid URI", 0);
+ }
+
+ }
+
 }