URL Query Only

Before the table would open results based upon the saved JSON attribute "saved file name", but now it does it on the URL query variable "DataSetName"
virtualcell · Mar 26, 2024 · 7e8749e · 7e8749e
1 parent ae97a10
commit 7e8749e
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Showing 3 changed files with 23 additions and 13 deletions.
diff --git a/view-simulation-results/pom.xml b/view-simulation-results/pom.xml
@@ -137,14 +137,14 @@
         <dependency>
             <groupId>org.janelia.saalfeldlab</groupId>
             <artifactId>n5-imglib2</artifactId>
-            <version>7.0.0</version>
+            <version>6.0.0</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/org.janelia.saalfeldlab/n5-aws-s3 -->
         <dependency>
             <groupId>org.janelia.saalfeldlab</groupId>
             <artifactId>n5-aws-s3</artifactId>
-            <version>4.0.1</version>
+            <version>4.0.0</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/org.janelia.saalfeldlab/n5-universe -->
@@ -161,6 +161,13 @@
             <version>1.2.0</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/org.janelia.saalfeldlab/n5-ij -->
+        <dependency>
+            <groupId>org.janelia.saalfeldlab</groupId>
+            <artifactId>n5-ij</artifactId>
+            <version>4.0.0</version>
+        </dependency>
+
 
 
 

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/SimResultsLoader.java b/view-simulation-results/src/main/java/org/vcell/N5/SimResultsLoader.java
@@ -7,20 +7,25 @@
 import com.amazonaws.services.s3.AmazonS3;
 import com.amazonaws.services.s3.AmazonS3ClientBuilder;
 import com.amazonaws.services.s3.AmazonS3URI;
+import com.google.gson.GsonBuilder;
 import ij.ImagePlus;
 import net.imglib2.cache.img.CachedCellImg;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.type.numeric.real.DoubleType;
 import org.janelia.saalfeldlab.n5.N5FSReader;
+import org.janelia.saalfeldlab.n5.N5KeyValueReader;
 import org.janelia.saalfeldlab.n5.N5Reader;
+import org.janelia.saalfeldlab.n5.ij.N5IJUtils;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+import org.janelia.saalfeldlab.n5.s3.AmazonS3KeyValueAccess;
 import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader;
 
 import java.io.File;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.net.URI;
 import java.net.URLDecoder;
+import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -32,6 +37,7 @@ public class SimResultsLoader {
     private String s3ObjectKey;
     private URI uri;
     private String dataSetChosen;
+    private String uriSafeDataSetChosen;
 
     public SimResultsLoader(){
 
@@ -90,7 +96,7 @@ public void createS3Client(){
         createS3Client(uri.toString(), null, null);
     }
     public void createS3Client(HashMap<String, String> credentials, HashMap<String, String> endpoint){createS3Client(uri.toString(), credentials, endpoint);}
-    public ArrayList<String> getS3N5DatasetList(){
+    public ArrayList<String> getS3N5DatasetList() throws IOException {
 
         // used as a flag to tell that remote access is occurring, and that there is no local files
         try(N5AmazonS3Reader n5AmazonS3Reader = new N5AmazonS3Reader(this.s3Client, this.bucketName)) {
@@ -122,27 +128,26 @@ public ImagePlus getImgPlusFromLocalN5File() throws IOException {
     }
 
     public ImagePlus getImgPlusFromN5File() throws IOException {
-        return getImgPlusFromN5File(dataSetChosen);
-    }
-
-    public ImagePlus getImgPlusFromN5File(String selectedDataset) throws IOException {
+//        AmazonS3KeyValueAccess amazonS3KeyValueAccess = new AmazonS3KeyValueAccess(s3Client, bucketName, false);
+//        N5KeyValueReader n5KeyValueReader = new N5KeyValueReader(amazonS3KeyValueAccess, s3ObjectKey, new GsonBuilder(), true);
         N5AmazonS3Reader n5AmazonS3Reader = new N5AmazonS3Reader(s3Client, bucketName, "/" + s3ObjectKey);
-        return ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>) N5Utils.open(n5AmazonS3Reader, selectedDataset), selectedDataset);
+        return ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>) N5Utils.open(n5AmazonS3Reader, dataSetChosen), dataSetChosen);
     }
 
     public void setURI(URI uri){
         this.uri = uri;
         if(!(uri.getQuery() == null)){
-            dataSetChosen = uri.getQuery().split("=")[1]; // query should be "dataSetName=name", thus splitting it by = and getting the second entry gives the name
+            uriSafeDataSetChosen = uri.getQuery().split("=")[1]; // query should be "dataSetName=name", thus splitting it by = and getting the second entry gives the name
             try {
-                dataSetChosen = URLDecoder.decode(dataSetChosen, "UTF-8");
+                dataSetChosen = URLDecoder.decode(uriSafeDataSetChosen, "UTF-8");
             } catch (UnsupportedEncodingException e) {
                 throw new RuntimeException(e);
             }
         }
     }
 
-    public void setDataSetChosen(String dataSetChosen){
+    public void setDataSetChosen(String dataSetChosen) throws UnsupportedEncodingException {
         this.dataSetChosen = dataSetChosen;
+        uriSafeDataSetChosen = URLEncoder.encode(dataSetChosen, "UTF-8");
     }
 }
diff --git a/view-simulation-results/src/main/java/org/vcell/N5/UI/N5ExportTable.java b/view-simulation-results/src/main/java/org/vcell/N5/UI/N5ExportTable.java
@@ -274,9 +274,7 @@ public void actionPerformed(ActionEvent e) {
             ArrayList<SimResultsLoader> filesToOpen = new ArrayList<>();
             for(int row: exportListTable.getSelectedRows()){
                 String uri = n5ExportTableModel.getRowData(row).uri;
-                String datasetName = n5ExportTableModel.getRowData(row).savedFileName;
                 SimResultsLoader simResultsLoader = new SimResultsLoader(uri);
-                simResultsLoader.setDataSetChosen(datasetName);
                 filesToOpen.add(simResultsLoader);
             }
             openN5FileDataset(filesToOpen, openInMemory.isSelected());