Fix Tests and Refactor

Fixed the test cases that where failing with the new method for retrieving S3 objects. Also refactored the ImageJ plugin somewhat.
virtualcell · Oct 31, 2023 · cbe8146 · cbe8146
1 parent 0ae67b4
commit cbe8146
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Showing 2 changed files with 25 additions and 30 deletions.
diff --git a/src/main/java/org/vcell/vcellfiji/N5ImageHandler.java b/src/main/java/org/vcell/vcellfiji/N5ImageHandler.java
@@ -174,17 +174,32 @@ public void loadN5Dataset(String selectedDataset) throws IOException {
     public void createS3Client(String url, HashMap<String, String> credentials, HashMap<String, String> endpoint){
         AmazonS3ClientBuilder s3ClientBuilder = AmazonS3ClientBuilder.standard();
         URI uri = URI.create(url);
-        String defaultRegion = "site2-low";
+
+        if(credentials != null){
+            s3ClientBuilder.withCredentials(new AWSStaticCredentialsProvider(new BasicAWSCredentials(credentials.get("AccessKey"), credentials.get("SecretKey"))));
+        }
 
         // believe that it's a s3 URL
         try{
             AmazonS3URI s3URI = new AmazonS3URI(uri);
             this.s3ObjectKey = s3URI.getKey();
             this.bucketName = s3URI.getBucket();
-            defaultRegion = s3URI.getRegion();
             if(s3URI.isPathStyle()){
                 s3ClientBuilder.withPathStyleAccessEnabled(true);
             }
+            if(endpoint != null){
+                s3ClientBuilder.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(endpoint.get("Endpoint"), endpoint.get("Region")));
+                this.s3Client = s3ClientBuilder.build();
+                return;
+            }
+            // if nothing is given, default user and return so that code after if statement does not execute
+            if(endpoint == null && credentials == null){
+                this.s3Client = AmazonS3ClientBuilder.standard().withRegion(s3URI.getRegion()).withCredentials(new AWSStaticCredentialsProvider(new AnonymousAWSCredentials())).build();
+                return;
+            }
+            //creds not null, but region is
+            this.s3Client = s3ClientBuilder.withRegion(s3URI.getRegion()).build();
+            return;
         }
         // otherwise assume it is one of our URLs
         // http://vcell:8000/bucket/object/object2
@@ -193,30 +208,10 @@ public void createS3Client(String url, HashMap<String, String> credentials, Hash
             this.s3ObjectKey = pathSubStrings[2];
             this.bucketName = pathSubStrings[1];
             s3ClientBuilder.withPathStyleAccessEnabled(true);
-            s3ClientBuilder.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(uri.getScheme() + "://" + uri.getAuthority(), defaultRegion));
-            if(credentials != null){
-                s3ClientBuilder.withCredentials(new AWSStaticCredentialsProvider(new BasicAWSCredentials(credentials.get("AccessKey"), credentials.get("SecretKey"))));
-            }
-            this.s3Client = s3ClientBuilder.build();
-            return;
-        }
-
-        if(credentials != null){
-            s3ClientBuilder.withCredentials(new AWSStaticCredentialsProvider(new BasicAWSCredentials(credentials.get("AccessKey"), credentials.get("SecretKey"))));
-        }
-        if(endpoint != null){
-            s3ClientBuilder.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(endpoint.get("Endpoint"), endpoint.get("Region")));
+            s3ClientBuilder.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(uri.getScheme() + "://" + uri.getAuthority(), "site2-low"));
             this.s3Client = s3ClientBuilder.build();
             return;
         }
-        // if nothing is given, default user and return so that code after if statement does not execute
-        if(endpoint == null && credentials == null){
-            this.s3Client = AmazonS3ClientBuilder.standard().withRegion(defaultRegion).withCredentials(new AWSStaticCredentialsProvider(new AnonymousAWSCredentials())).build();
-            return;
-        }
-
-        //creds not null, but region is
-        this.s3Client = s3ClientBuilder.withRegion(defaultRegion).build();
     }
 
 

diff --git a/src/test/java/org/vcell/vcellfiji/N5ImageHandlerTest.java b/src/test/java/org/vcell/vcellfiji/N5ImageHandlerTest.java
@@ -65,22 +65,22 @@ public void testS3Client() throws IOException {
         credentials.put("AccessKey", "jj");
         credentials.put("SecretKey", "jj");
 
-        final String s3ProxyURL = "/" + this.n5FileName;
+        final String s3ProxyURI = "http://localhost:4000/" + this.n5FileName;
 
         N5ImageHandler n5ImageHandler = new N5ImageHandler();
 
         // Environment variables are set in github actions VM
 
-//        n5ImageHandler.createS3Client(s3ProxyURL, null, null);
-//        this.remoteN5ImgPlusTests(n5ImageHandler);
+        n5ImageHandler.createS3Client(s3ProxyURI, null, null);
+        this.remoteN5ImgPlusTests(n5ImageHandler);
 
-        n5ImageHandler.createS3Client(s3ProxyURL, null, s3Endpoint);
+        n5ImageHandler.createS3Client(s3ProxyURI, null, s3Endpoint);
         this.remoteN5ImgPlusTests(n5ImageHandler);
 
-//        n5ImageHandler.createS3Client(s3ProxyURL, credentials, null);
-//        this.remoteN5ImgPlusTests(n5ImageHandler);
+        n5ImageHandler.createS3Client(s3ProxyURI, credentials, null);
+        this.remoteN5ImgPlusTests(n5ImageHandler);
 
-        n5ImageHandler.createS3Client(s3ProxyURL, credentials, s3Endpoint);
+        n5ImageHandler.createS3Client(s3ProxyURI, credentials, s3Endpoint);
         this.remoteN5ImgPlusTests(n5ImageHandler);
     }