#1137, add examined paths to HCS error message

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.0.6-SNAPSHOT</version>
+    <version>5.0.6</version>
 
     <!-- force javadoc generation to fetch errors:    -->
     <!-- mvn javadoc:javadoc | grep error -->

src/main/java/org/embl/mobie/command/open/OpenHCSDatasetCommand.java

@@ -33,6 +33,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.io.util.IOHelper;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.hcs.OMEXMLParser;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -50,8 +51,8 @@ public class OpenHCSDatasetCommand implements Command
 {
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
-	@Parameter ( label = "HCS Plate Directory" ) // , style = "directory"
-	public String hcsDirectory; // changed to String, because otherwise S3 addresses do not work
+	@Parameter ( label = "HCS Plate Directory", style = "directory")
+	public File hcsDirectory;
 
 	@Parameter ( label = "Relative Well Margin" )
 	public double wellMargin = 0.1;
@@ -84,7 +85,7 @@ public void run()
 
 		try
 		{
-			new MoBIE( hcsDirectory, new MoBIESettings(), wellMargin, siteMargin, voxelDimensions );
+			new MoBIE( MoBIEHelper.toURI( hcsDirectory ), new MoBIESettings(), wellMargin, siteMargin, voxelDimensions );
 		}
 		catch ( IOException e )
 		{

src/main/java/org/embl/mobie/lib/hcs/Plate.java

@@ -38,6 +38,7 @@
 import mpicbg.spim.data.sequence.FinalVoxelDimensions;
 import mpicbg.spim.data.sequence.VoxelDimensions;
 import net.imglib2.RandomAccessibleInterval;
+import net.thisptr.jackson.jq.internal.misc.Strings;
 import org.embl.mobie.io.ImageDataFormat;
 import org.embl.mobie.io.ImageDataOpener;
 import org.embl.mobie.io.imagedata.ImageData;
@@ -403,7 +404,13 @@ private HCSPattern determineHCSPattern( String hcsDirectory, List< String > path
 			}
 		}
 
-		throw new RuntimeException( "Could not determine HCSPattern for " + hcsDirectory );
+		ArrayList< String > messages = new ArrayList<>();
+		messages.add( "Could not determine HCSPattern for " + hcsDirectory );
+		messages.add( "Examined paths:" );
+		messages.addAll( paths );
+		String join = Strings.join( "\n", messages );
+
+		throw new RuntimeException( join );
 	}
 
 	public Set< Channel > getChannels()

src/test/java/develop/OpenOMEZarrHCSWithLabelsFromS3.java

@@ -31,6 +31,8 @@
 import net.imagej.ImageJ;
 import org.embl.mobie.command.open.OpenHCSDatasetCommand;
 
+import java.io.File;
+
 public class OpenOMEZarrHCSWithLabelsFromS3
 {
     public static void main( String[] args )
@@ -40,7 +42,7 @@ public static void main( String[] args )
 
         OpenHCSDatasetCommand command = new OpenHCSDatasetCommand();
         // Does this really have labels?
-        command.hcsDirectory = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0001A/2551.zarr";
+        command.hcsDirectory = new File("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0001A/2551.zarr");
         command.run();
     }
 }

src/test/java/develop/hcs/HCSInCarta.java

@@ -31,6 +31,8 @@
 import net.imagej.ImageJ;
 import org.embl.mobie.command.open.OpenHCSDatasetCommand;
 
+import java.io.File;
+
 public class HCSInCarta
 {
     public static void main( String[] args )
@@ -39,7 +41,8 @@ public static void main( String[] args )
         imageJ.ui().showUI();
 
         OpenHCSDatasetCommand command = new OpenHCSDatasetCommand();
-        command.hcsDirectory = "/Users/tischer/Downloads/timepoint0";
+        command.hcsDirectory = new File( "/Users/tischer/Downloads/timepoint0" );
+        //command.hcsDirectory = new File( "/Users/tischer/Downloads/demo_data/Sample_005/Sample_005_images_20240202_1659_30/00000000" );
         command.run();
     }
 }

src/test/java/issues/Issue1066.java

@@ -3,6 +3,8 @@
 import net.imagej.ImageJ;
 import org.embl.mobie.command.open.OpenHCSDatasetCommand;
 
+import java.io.File;
+
 public class Issue1066
 {
     public static void main( String[] args )
@@ -17,7 +19,7 @@ public static void main( String[] args )
 
         // Open local HCS Plate
         // - does not open the labels...why?
-        command.hcsDirectory = "/Users/tischer/Downloads/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr";
+        command.hcsDirectory = new File( "/Users/tischer/Downloads/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr" );
         command.run();
     }
 }

src/test/java/org/embl/mobie/command/open/OpenOMEZarrHCSDatasetCommandTest.java

@@ -3,6 +3,8 @@
 import net.imagej.ImageJ;
 import org.junit.jupiter.api.Test;
 
+import java.io.File;
+
 class OpenOMEZarrHCSDatasetCommandTest
 {
     static { net.imagej.patcher.LegacyInjector.preinit(); }
@@ -13,7 +15,7 @@ public void test( )
         new ImageJ().ui().showUI(); // initialise SciJava Services
 
         final OpenHCSDatasetCommand command = new OpenHCSDatasetCommand();
-        command.hcsDirectory = "src/test/resources/single-plane-hcs.zarr";
+        command.hcsDirectory = new File( "src/test/resources/single-plane-hcs.zarr" );
         command.run();
 
         // TODO: add a test assertion for ensuring the the number of channels is correct.

src/test/java/projects/OpenLocalThomasMolDev.java

@@ -33,6 +33,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.open.OpenHCSDatasetCommand;
 
+import java.io.File;
 import java.io.IOException;
 
 public class OpenLocalThomasMolDev
@@ -43,7 +44,7 @@ public static void main( String[] args )
 		imageJ.ui().showUI();
 
 		OpenHCSDatasetCommand command = new OpenHCSDatasetCommand();
-		command.hcsDirectory = "/Users/tischer/Downloads/TBO-Test31-01-2024-10x-TL-DAPI_Plate_260/TimePoint_1";
+		command.hcsDirectory = new File( "/Users/tischer/Downloads/TBO-Test31-01-2024-10x-TL-DAPI_Plate_260/TimePoint_1" );
 		command.run();
 	}
 }

src/test/java/projects/colony_detection_anavo/OpenAnavoHCSData.java

@@ -31,13 +31,15 @@
 import net.imagej.ImageJ;
 import org.embl.mobie.command.open.OpenHCSDatasetCommand;
 
+import java.io.File;
+
 public class OpenAnavoHCSData
 {
     public static void main( String[] args )
     {
         new ImageJ().ui().showUI();
         final OpenHCSDatasetCommand command = new OpenHCSDatasetCommand();
-        command.hcsDirectory = "/Users/tischer/Desktop/moritz/U2OS_subset";
+        command.hcsDirectory = new File( "/Users/tischer/Desktop/moritz/U2OS_subset" );
         //command.hcsDirectory = "/Users/tischer/Desktop/moritz/CQ1_testfiles";
         command.run();
     }

src/test/java/projects/colony_detection_anavo/OpenAnavoHCSDataWithVoxelDimensions.java

@@ -39,7 +39,7 @@ public static void main( String[] args )
     {
         new ImageJ().ui().showUI();
         final OpenHCSDatasetCommand command = new OpenHCSDatasetCommand();
-        command.hcsDirectory = "/Users/tischer/Desktop/moritz/U2OS_subset";
+        command.hcsDirectory = new File( "/Users/tischer/Desktop/moritz/U2OS_subset" );
         command.voxelDimensionFetching = OpenHCSDatasetCommand.VoxelDimensionFetching.FromOMEXML;
         command.omeXML = new File("/Users/tischer/Desktop/moritz/MeasurementResult.ome.xml");
         command.run();