Interface not responding + NullPointerException after compiling from source

Question

Interface not responding + NullPointerException after compiling from source

SirkoS opened this issue 3 years ago · comments

Describe the bug

After following the instructions here to install Karma from the sources (and working my way around some gaps in the documentation) I was able to run karma-web locally.

When uploading a small sample CSV, the interface just doesn't do anything. The popup to define CSV-parameters never shows up.

To Reproduce

Compile and run karma-web:

git clone https://github.com/usc-isi-i2/Web-Karma.git --depth=1 /karma
cd /karma
mvn clean install
cd /karma/karma-web
mvn jetty:run

Access the webinterface and upload a sample CSV like this

a,b
1,2

Expected behavior
I see the CSV configuration popup and can continue.

Actual behavior
Web interface does not do anything, but shows an error in the JavaScript console (Firefox - Chrome showing something similar):

Uncaught TypeError: can't access property "fileName", data.elements[0] is undefined
    show http://xx.xx.xx.xx:8080/js/fileImport.js?v2.2:378
    done http://xx.xx.xx.xx:8080/js/fileImport.js?v2.2:113
    jQuery 8
fileImport.js:378:19

Looking at the output of the server itself, I see the following two error messages:

ERROR [2021-05-29 11:58:58,469] (FileUtil->downloadFileFromHTTPRequest->106): Error encountered while uploading file
java.lang.NullPointerException
        at edu.isi.karma.util.FileUtil.downloadFileFromHTTPRequest(FileUtil.java:96)
        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$Runner.run(QueuedThreadPool.java:938)
        at java.base/java.lang.Thread.run(Thread.java:829)
ERROR [2021-05-29 11:58:58,471] (CSVImportPreviewUpdate->generateJson->175): File not found!
java.io.FileNotFoundException: /xx/karma/user-uploaded-files/_test.csv (No such file or directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        at edu.isi.karma.controller.update.CSVImportPreviewUpdate.generateJson(CSVImportPreviewUpdate.java:119)
        at edu.isi.karma.controller.update.UpdateContainer.generateJson(UpdateContainer.java:87)
        at edu.isi.karma.controller.update.UpdateContainer.generateJson(UpdateContainer.java:120)
        at edu.isi.karma.webserver.RequestController.doPost(RequestController.java:90)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
        at org.eclipse.jetty.servlet.ServletHolder$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:829)

Desktop (please complete the following information):

OS: Debian 10
Browser Firefox 89, Chrome 90
openjdk 11.0.11 2021-04-20

Additional context
I tried to track down the error and it seems the following line in karma-common/src/main/java/edu/isi/karma/util/FileUtil.java:93 is not accounting for all eventualities:

                    	if (!t.getStoreLocation().renameTo(uploadedFile))

after changing that to

                    	if ( (t.getStoreLocation() == null) || (!t.getStoreLocation().renameTo(uploadedFile)) )

I can upload the file and progress to the following steps

Bidisha010496 · Answer 1 · Sun Oct 31 2021 07:35:13 GMT+0800 (China Standard Time)

Hi, there has been a recent release of the codebase. Can you please check and confirm if you are still facing this issue with the new version?