From 0b4cd4e86c808d1b8d3aa316e89dab75536fed31 Mon Sep 17 00:00:00 2001
From: Ezequiel Valencia <casualcucumber59@gmail.com>
Date: Tue, 3 Oct 2023 15:13:07 -0400
Subject: [PATCH] Light Refactor

Make the code slightly more clean, removing unused variables.
---
 .../org/vcell/vcellfiji/N5ImageHandler.java   | 27 ++-----------------
 .../java/org/vcell/vcellfiji/UI/VCellGUI.java |  6 -----
 .../vcell/vcellfiji/N5ImageHandlerTest.java   |  3 ---
 3 files changed, 2 insertions(+), 34 deletions(-)

diff --git a/src/main/java/org/vcell/vcellfiji/N5ImageHandler.java b/src/main/java/org/vcell/vcellfiji/N5ImageHandler.java
index 84cf8fe..d28d167 100644
--- a/src/main/java/org/vcell/vcellfiji/N5ImageHandler.java
+++ b/src/main/java/org/vcell/vcellfiji/N5ImageHandler.java
@@ -32,14 +32,6 @@
 import java.util.Arrays;
 import java.util.HashMap;
 
-// Command plugins
-/* TODO:
-     Security check for the S3Client builder, there seems to be an encrypted version of it and that should be checked
-     Test cases for handling all cases regarding
-
-
-
- */
 
 /*
     Able to open N5 files locally, display the datasets that can be chosen from it, and open the datasets within ImageJ.
@@ -112,9 +104,6 @@ public void displayN5Results(ArrayList<String> datasetList){
 
 
     public ImagePlus getImgPlusFromN5File(String selectedDataset, N5Reader n5Reader) throws IOException {
-//        N5CosemMetadataParser metadataParser = new N5CosemMetadataParser();
-//        CosemToImagePlus cosemToImagePlus = new CosemToImagePlus();
-
         // Theres definitly a better way to do this, I trie using a variable to change the cached cells first parameter type but it didn't seem to work :/
         switch (n5Reader.getDatasetAttributes(selectedDataset).getDataType()){
             case UINT8:
@@ -179,15 +168,7 @@ public void loadN5Dataset(String selectedDataset) throws IOException {
         }
     }
 
-    // https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/java-dg-region-selection.html
-    // Chain of handling region is what gets set by client builder
-    // AWS_REGION Environmental variable on computer
-    // The AWS default profile on the computer
-    // Use Amazon Elastic computing instance metadata to determine region
-        // Does this mean that region is only known for buckets hosted on Amazons servers? Is that why the error is thrown? Should I use the EC2 builder to find the region?
-    // Throw error
-
-    //Can make it so that our bucket links contain the region in it, making it significantly easier to determine it
+    //When creating client's try to make one for an Amazon link, otherwise use our custom url scheme
     public void createS3Client(String url, HashMap<String, String> credentials, HashMap<String, String> endpoint){
         AmazonS3ClientBuilder s3ClientBuilder = AmazonS3ClientBuilder.standard();
         URI uri = URI.create(url);
@@ -221,6 +202,7 @@ public void createS3Client(String url, HashMap<String, String> credentials, Hash
             return;
         }
 
+        //creds not null, but region is
         this.s3Client = s3ClientBuilder.withRegion(defaultRegion).build();
     }
 
@@ -246,9 +228,4 @@ public File getSelectedLocalFile() {
         return selectedLocalFile;
     }
 
-    public static void main(String[] args) {
-//        new N5ImageHandler().getS3N5DatasetList("s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5", null, null);
-        new N5ImageHandler().run();
-
-    }
 }
diff --git a/src/main/java/org/vcell/vcellfiji/UI/VCellGUI.java b/src/main/java/org/vcell/vcellfiji/UI/VCellGUI.java
index a4f74bb..eb5b40b 100644
--- a/src/main/java/org/vcell/vcellfiji/UI/VCellGUI.java
+++ b/src/main/java/org/vcell/vcellfiji/UI/VCellGUI.java
@@ -22,12 +22,6 @@ public class VCellGUI extends JFrame {
     public VCellGUI() {
         jFrame = this;
         localFileDialog = new JFileChooser();
-//        try {
-//            UIManager.setLookAndFeel("javax.swing.plaf.nimbus.NimbusLookAndFeel");
-//            SwingUtilities.updateComponentTreeUI(jFrame);
-//        } catch (Exception e) {
-//            throw new RuntimeException(e);
-//        }
 
 
         this.setTitle("VCell Manager");
diff --git a/src/test/java/org/vcell/vcellfiji/N5ImageHandlerTest.java b/src/test/java/org/vcell/vcellfiji/N5ImageHandlerTest.java
index 145fd9d..92f9a88 100644
--- a/src/test/java/org/vcell/vcellfiji/N5ImageHandlerTest.java
+++ b/src/test/java/org/vcell/vcellfiji/N5ImageHandlerTest.java
@@ -25,7 +25,6 @@
  */
 
 public class N5ImageHandlerTest {
-
     private final String n5FileName = "nfive/test_image.n5";
 
     private File getTestResourceFiles(String filePath){
@@ -66,8 +65,6 @@ public void testS3Client() throws IOException {
         credentials.put("AccessKey", "jj");
         credentials.put("SecretKey", "jj");
 
-        String testBucketName = "nfive";
-        final String s3KeyPath = "s3://" + testBucketName + "/test_image.n5";
         final String s3ProxyURL = "/" + this.n5FileName;
 
         N5ImageHandler n5ImageHandler = new N5ImageHandler();