Only use S3FileSystemStore for https endpoint

dgault · Apr 26, 2024 · 44d5622 · 44d5622
1 parent 141f8be
commit 44d5622
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Showing 2 changed files with 13 additions and 4 deletions.
diff --git a/src/loci/formats/S3FileSystemStore.java b/src/loci/formats/S3FileSystemStore.java
@@ -75,6 +75,7 @@ public class S3FileSystemStore implements Store {
 
     private Path root;
     AmazonS3 client;
+    public static final String ENDPPOINT_PROTOCOL= "https://";
     protected static final Logger LOGGER =
         LoggerFactory.getLogger(S3FileSystemStore.class);
 
@@ -97,7 +98,7 @@ public String getRoot() {
 
     private void setupClient() {
       String[] pathSplit = root.toString().split(File.separator);
-      String endpoint = "https://" + pathSplit[1] + File.separator;
+      String endpoint = "ENDPPOINT_PROTOCOL" + pathSplit[1] + File.separator;
       try {   
         client = AmazonS3ClientBuilder.standard()
           .withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(endpoint, "auto"))
@@ -179,7 +180,7 @@ public TreeSet<String> getGroupKeys() throws IOException {
      * @throws IOException
      */
     public TreeSet<String> getKeysEndingWith(String suffix) throws IOException {
-        return (TreeSet)Files.walk(this.root).filter((path) -> {
+        return (TreeSet<String>)Files.walk(this.root).filter((path) -> {
             return path.toString().endsWith(suffix);
         }).map((path) -> {
             return this.root.relativize(path).toString();

diff --git a/src/loci/formats/services/JZarrServiceImpl.java b/src/loci/formats/services/JZarrServiceImpl.java
@@ -1,5 +1,7 @@
 package loci.formats.services;
 
+import java.io.File;
+
 /*-
  * #%L
  * Implementation of Bio-Formats readers for the next-generation file formats
@@ -79,7 +81,13 @@ public class JZarrServiceImpl extends AbstractService
   public JZarrServiceImpl(String root) {
       checkClassDependency(com.bc.zarr.ZarrArray.class);
       if (root != null && (root.toLowerCase().contains("s3:") || root.toLowerCase().contains("s3."))) {
-        s3fs = new S3FileSystemStore(Paths.get(root));
+        String[] pathSplit = root.toString().split(File.separator);
+        if (!S3FileSystemStore.ENDPPOINT_PROTOCOL.contains(pathSplit[0].toLowerCase())) {
+          s3fs = new S3FileSystemStore(Paths.get(root));
+        }
+        else {
+          LOGGER.warn("Zarr Reader is not using S3FileSystemStore as this is currently for use with S3 configured with a https endpoint");
+        }
       }
   }
 
@@ -89,7 +97,7 @@ public void open(String file) throws IOException, FormatException {
     if (s3fs == null) {
       zarrArray = ZarrArray.open(file);
     }
-    else {      
+    else {
       s3fs.updateRoot(getZarrRoot(s3fs.getRoot()) + stripZarrRoot(file));
       zarrArray = ZarrArray.open(s3fs);
     }