Karma 2.3+ upload source file fails with NullPointerException on macOS 10.14.6

Question

Karma 2.3+ upload source file fails with NullPointerException on macOS 10.14.6

cbutcosk opened this issue 4 years ago · comments

Describe the bug
On macOS 10.14.6 with Karma releases for 2.3+, uploading a file in the web UI fails with a NullPointerException in the logs and no indication of failure in the web UI. Happened for me in JDK 12 and 1.8, but did not occur in Karma 2.2 with either JDK. Occurs in both one-click and source installs.

To Reproduce
Steps to reproduce the behavior:

Open Karma (or mvn jetty:run within karma-web/)
Click on "Import / From File"
Choose any file (used a minimal CSV, but issue is common to any file upload AFAICT) and upload
Select file type (CSV) and hit "Next"

Expected behavior
The file preview / dialect modal should pop up.

Desktop (please complete the following information):

OS: macOS 10.14.6
Browser: Chrome (85.0.4183.83) and Safari (13.1.2)

Additional context
The workaround I've used thus far is to manually copying the uploaded file to $KARMA_USER_HOME/user-uploaded-files and then reattempt the file upload.

Relevant log / trace section is here:

[INFO] Started Jetty Server
INFO [2020-09-09 09:51:42,635] (ModelLearningGraph->->136): loading the alignment graph ...
INFO [2020-09-09 09:51:42,648] (ModelLearningGraph->->144): loading is done!
INFO [2020-09-09 09:51:42,648] (ModelLearningGraph->->147): number of nodes: 0
INFO [2020-09-09 09:51:42,649] (ModelLearningGraph->->148): number of links: 0
ERROR [2020-09-09 09:51:50,820] (FileUtil->downloadFileFromHTTPRequest->104): Error encountered while uploading file
java.lang.NullPointerException
at edu.isi.karma.util.FileUtil.downloadFileFromHTTPRequest(FileUtil.java:94)
at edu.isi.karma.controller.command.importdata.ImportCSVFileCommandFactory.createCommand(ImportCSVFileCommandFactory.java:44)
at edu.isi.karma.webserver.ExecutionController.getCommand(ExecutionController.java:117)
at edu.isi.karma.webserver.RequestController.doPost(RequestController.java:85)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder$NotAsyncServlet.service(ServletHolder.java:1386)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:755)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1617)
at org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter.doFilter(WebSocketUpgradeFilter.java:226)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1604)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:545)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:590)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1610)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1300)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:485)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1580)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1215)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:221)
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:146)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.Server.handle(Server.java:500)
at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:383)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:547)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:375)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:273)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103)
at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:117)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:336)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:313)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:171)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:129)
at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:375)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:806)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:938)
at java.base/java.lang.Thread.run(Thread.java:835)
ERROR [2020-09-09 09:51:50,830] (CSVImportPreviewUpdate->generateJson->175): File not found!
java.io.FileNotFoundException: /Users/incharge/karma/user-uploaded-files/BRAN.csv (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:213)
at java.base/java.io.FileInputStream.(FileInputStream.java:155)
at edu.isi.karma.controller.update.CSVImportPreviewUpdate.generateJson(CSVImportPreviewUpdate.java:119)
at edu.isi.karma.controller.update.UpdateContainer.generateJson(UpdateContainer.java:87)
at edu.isi.karma.controller.update.UpdateContainer.generateJson(UpdateContainer.java:120)
at edu.isi.karma.webserver.RequestController.doPost(RequestController.java:90)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder$NotAsyncServlet.service(ServletHolder.java:1386)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:755)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1617)
at org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter.doFilter(WebSocketUpgradeFilter.java:226)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1604)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:545)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:590)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1610)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1300)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:485)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1580)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1215)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:221)
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:146)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.Server.handle(Server.java:500)
at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:383)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:547)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:375)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:273)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103)
at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:117)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:336)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:313)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:171)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:129)
at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:375)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:806)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:938)
at java.base/java.lang.Thread.run(Thread.java:835)

Rutuja Manoj Rane · Answer 1 · Tue Oct 06 2020 09:05:28 GMT+0800 (China Standard Time)

Fixed in the development branch: https://github.com/usc-isi-i2/Web-Karma/tree/development
If you still face this problem, please reopen this issue.

James Birmingham · Answer 2 · Sat Dec 05 2020 01:25:58 GMT+0800 (China Standard Time)

This is also an issue on Windows.

I would say this issue alone warrants a release, the last two releases are effectively broken.