chore: add platform-test workflow (#74)

* chore: add n5-aws-s3, n5-blosc dependencies
* test: fix macro test for windows
* pref: add uri validation
* pref: rm file:// prefix from uri
* test: uri validation

.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

@@ -1514,9 +1514,6 @@ 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);
+		}
+
+	}
+
 }