AWS updates

* Support custom, non-AWS, endpoint * Simplification of oAuth code * Remove custom S3Presigner code, this is now included in the SDK
igvteam · Jan 16, 2025 · 816c97e · 816c97e
1 parent e7bcd3e
commit 816c97e
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Showing 6 changed files with 294 additions and 401 deletions.
diff --git a/src/main/java/org/broad/igv/oauth/OAuthProvider.java b/src/main/java/org/broad/igv/oauth/OAuthProvider.java
@@ -230,24 +230,13 @@ public void fetchAccessToken(String authorizationCode) throws IOException {
                 fetchUserProfile(payload);
             }
 
-            if (authProvider != null && "Amazon".equals(authProvider)) {
-                // Get AWS credentials after getting relevant tokens
-                Credentials aws_credentials;
-                aws_credentials = AmazonUtils.GetCognitoAWSCredentials();
-
-                // Update S3 client with newly acquired token
-                AmazonUtils.updateS3Client(aws_credentials);
-            }
-
-
             // Notify UI that we are authz'd/authn'd
             if (isLoggedIn()) {
                 IGVEventBus.getInstance().post(new AuthStateEvent(true, this.authProvider, this.getCurrentUserName()));
             }
 
         } catch (Exception e) {
             log.error(e);
-            e.printStackTrace();
         }
     }
 
@@ -256,7 +245,7 @@ public void setAccessToken(String accessToken) {
     }
 
     /**
-     * Fetch a new access token from a refresh token.
+     * Fetch a new access token from a refresh token.  Unlike authorization, this is a synchronous operation
      *
      * @throws IOException
      */
@@ -293,18 +282,15 @@ private void refreshAccessToken() throws IOException {
             expirationTime = System.currentTimeMillis() + response.getAsJsonPrimitive("expires_in").getAsInt() * 1000;
         } else {
             // Refresh token has failed, reauthorize from scratch
-            reauthorize();
+            logout();
+            try {
+                openAuthorizationPage();
+            } catch (URISyntaxException e) {
+                e.printStackTrace();
+            }
         }
     }
 
-    private void reauthorize() throws IOException {
-        logout();
-        try {
-            openAuthorizationPage();
-        } catch (URISyntaxException e) {
-            e.printStackTrace();
-        }
-    }
 
     /**
      * Extract user information from the claim information
@@ -374,6 +360,15 @@ public void logout() {
         IGVEventBus.getInstance().post(new AuthStateEvent(false, this.authProvider, null));
     }
 
+    public JsonObject getAuthorizationResponse() {
+
+        if (response == null) {
+            // Go back to auth flow, not auth'd yet
+            checkLogin();
+            response = getResponse();
+        }
+        return response;
+    }
 
     /**
      * If not logged in, attempt to login
@@ -390,10 +385,10 @@ public synchronized void checkLogin() {
             }
 
         }
-        // wait until authentication successful or 1 minute -
+        // wait until authentication successful or 2 minutes -
         // dwm08
         int i = 0;
-        while (!isLoggedIn() && i < 600) {
+        while (!isLoggedIn() && i < 1200) {
             ++i;
             try {
                 Thread.sleep(100);

diff --git a/src/main/java/org/broad/igv/track/TrackLoader.java b/src/main/java/org/broad/igv/track/TrackLoader.java
@@ -120,11 +120,6 @@ public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadE
 
         final String path = locator.getPath().trim();
 
-        // Check if the AWS credentials are still valid. If not, re-login and renew pre-signed urls
-        if (AmazonUtils.isAwsS3Path(path)) {
-            AmazonUtils.checkLogin();
-        }
-
         log.info("Loading resource:  " + (locator.isDataURL() ? "<data url>" : path));
         try {
 

diff --git a/src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java b/src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java
@@ -109,9 +109,7 @@ private void loadUrls(List<String> inputs, List<String> indexes, boolean isHtsGe
         } else if (inputs.size() == 1 && SessionReader.isSessionFile(inputs.getFirst())) {
             // Session URL
             String url = inputs.getFirst();
-            if (url.startsWith("s3://")) {
-                checkAWSAccessbility(url);
-            }
+
             try {
                 LongRunningTask.submit(() -> this.igv.loadSession(url, null));
             } catch (Exception ex) {
@@ -186,29 +184,12 @@ private static boolean isHubURL(String input) {
 
     private static void checkURLs(List<String> urls) {
         for (String url : urls) {
-            if (url.startsWith("s3://")) {
-                checkAWSAccessbility(url);
-            } else if (url.startsWith("ftp://")) {
+             if (url.startsWith("ftp://")) {
                 MessageUtils.showMessage("FTP protocol is not supported");
             }
         }
     }
 
-    private static void checkAWSAccessbility(String url) {
-        try {
-            // If AWS support is active, check if objects are in accessible tiers via Load URL menu...
-            if (AmazonUtils.isAwsS3Path(url)) {
-                String bucket = AmazonUtils.getBucketFromS3URL(url);
-                String key = AmazonUtils.getKeyFromS3URL(url);
-                AmazonUtils.s3ObjectAccessResult res = isObjectAccessible(bucket, key);
-                if (!res.isObjectAvailable()) {
-                    MessageUtils.showErrorMessage(res.getErrorReason(), null);
-                }
-            }
-        } catch (NullPointerException npe) {
-            // User has not yet done Amazon->Login sequence
-            AmazonUtils.checkLogin();
-        }
-    }
+
 }