Stream: troubleshooting

Topic: can't delete dataset

view this post on Zulip Guillermo Esteban Murillo Goussen (Sep 09 2024 at 15:18):

Hi everyone, I've just installed my first Dataverse. I'm trying to delete a dataset in Draft Status but it got stucked with the blue circule going round and round. The server log at payara doesnt show any messages related... or maybe they do...

[2024-09-09T08:56:10.603-0600] [Payara 6.2023.8] [WARNING] [] [edu.harvard.iq.dataverse.util.BundleUtil] [tid: _ThreadID=77 _ThreadName=http-thread-pool::http-listener-1(5)] [timeMillis: 1725893770603] [levelValue: 900] [[
Could not find key "notification.typeDescription.GLOBUSUPLOADCOMPLETEDWITHERRORS" in bundle file: ]]

[2024-09-09T08:56:10.603-0600] [Payara 6.2023.8] [WARNING] [] [edu.harvard.iq.dataverse.util.BundleUtil] [tid: _ThreadID=77 _ThreadName=http-thread-pool::http-listener-1(5)] [timeMillis: 1725893770603] [levelValue: 900] [[
Could not find key "notification.typeDescription.GLOBUSDOWNLOADCOMPLETED" in bundle file: ]]

[2024-09-09T08:56:10.603-0600] [Payara 6.2023.8] [WARNING] [] [edu.harvard.iq.dataverse.util.BundleUtil] [tid: _ThreadID=77 _ThreadName=http-thread-pool::http-listener-1(5)] [timeMillis: 1725893770603] [levelValue: 900] [[
Could not find key "notification.typeDescription.GLOBUSDOWNLOADCOMPLETEDWITHERRORS" in bundle file: ]]

image.png

Thanks for your help

view this post on Zulip Philip Durbin 🚀 (Sep 09 2024 at 16:08):

@Guillermo Esteban Murillo Goussen weird. Are you using Globus?

view this post on Zulip Guillermo Esteban Murillo Goussen (Sep 09 2024 at 16:19):

Hi @Philip Durbin 🐢 I guess no, I honestly dont know what Globus is

view this post on Zulip Philip Durbin 🚀 (Sep 09 2024 at 16:23):

Ha, ok, just checking! I saw it there in the log. Hmm. :thinking:

view this post on Zulip Philip Durbin 🚀 (Sep 09 2024 at 16:23):

What if you create a new draft and then delete it? Does that work?

view this post on Zulip Guillermo Esteban Murillo Goussen (Sep 10 2024 at 17:26):

I tried again but this came to the server log

[2024-09-10T10:57:33.678-0600] [Payara 6.2023.8] [WARNING] [] [org.glassfish.grizzly.http2.Http2Session] [tid: _ThreadID=76 _ThreadName=http-thread-pool::http-listener-1(4)] [timeMillis: 1725987453678] [levelValue: 900] [[

Unable to write GOAWAY.  Terminating session.

java.io.IOException: Connection reset by peer
    at java.base/sun.nio.ch.FileDispatcherImpl.write0(Native Method)
    at java.base/sun.nio.ch.SocketDispatcher.write(SocketDispatcher.java:62)
    at java.base/sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:132)
    at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:76)
    at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:53)....

[2024-09-10T11:03:24.266-0600] [Payara 6.2023.8] [INFO] [] [edu.harvard.iq.dataverse.dataset.DatasetUtil] [tid: _ThreadID=74 _ThreadName=http-thread-pool::http-listener-1(2)] [timeMillis: 1725987804266] [levelValue: 800] [[

Failed to delete dataset logo: /usr/local/payara6/glassfish/domains/domain1/files/20.500.14500/FK2/RGZEUU/dataset_logo_original]]

[2024-09-10T11:18:44.995-0600] [Payara 6.2023.8] [INFO] [] [edu.harvard.iq.dataverse.DataverseHeaderFragment] [tid: _ThreadID=75 _ThreadName=http-thread-pool::http-listener-1(3)] [timeMillis: 1725988724995] [levelValue: 800] [[

Sending user to = /dataverse.xhtml]]

[2024-09-10T11:21:39.695-0600] [Payara 6.2023.8] [INFO] [] [edu.harvard.iq.dataverse.dataset.DatasetUtil] [tid: _ThreadID=76 _ThreadName=http-thread-pool::http-listener-1(4)] [timeMillis: 1725988899695] [levelValue: 800] [[

Failed to delete dataset logo: /usr/local/payara6/glassfish/domains/domain1/files/20.500.14500/FK2/RGZEUU/dataset_logo_original]]

[2024-09-10T11:22:32.638-0600] [Payara 6.2023.8] [WARNING] [] [edu.harvard.iq.dataverse.HandlenetServiceBean] [tid: _ThreadID=77 _ThreadName=http-thread-pool::http-listener-1(5)] [timeMillis: 1725988952638] [levelValue: 900] [[

Caught exception trying to process lookup request

HandleException (CANNOT_CONNECT_TO_SERVER) 86.111.195.107: java.net.SocketTimeoutException: Connect timed out
    at net.handle.hdllib.HandleResolver.sendRequestToService(HandleResolver.java:1087)
    at net.handle.hdllib.HandleResolver.getServiceInfoForNA(HandleResolver.java:693)
    at net.handle.hdllib.HandleResolver.getServiceInfo(HandleResolver.java:869)
    at net.handle.hdllib.HandleResolver.findLocalSites(HandleResolver.java:910)
    at net.handle.hdllib.HandleResolver.processRequestGlobally(HandleResolver.java:617)
    at net.handle.hdllib.HandleResolver.processRequest(HandleResolver.java:587)
    at net.handle.hdllib.HandleResolver.processRequest(HandleResolver.java:595)

Caused by: HandleException (CANNOT_CONNECT_TO_SERVER) 86.111.195.107: java.net.SocketTimeoutException: Connect timed out
    at net.handle.hdllib.HandleResolver.sendHttpOrHttpsRequest(HandleResolver.java:2783)
    at net.handle.hdllib.HandleResolver.sendHttpRequest(HandleResolver.java:2702)
    at net.handle.hdllib.HandleResolver.sendRequestToInterface(HandleResolver.java:2163)
    at net.handle.hdllib.HandleResolver.sendRequestToServerByProtocol(HandleResolver.java:1847)
    at net.handle.hdllib.HandleResolver.sendRequestToServerByProtocol(HandleResolver.java:1712)
    at net.handle.hdllib.HandleResolver.sendRequestToServerInSiteByProtocol(HandleResolver.java:1447)
    at net.handle.hdllib.HandleResolver.sendRequestToSite(HandleResolver.java:1425)
    at net.handle.hdllib.HappyEyeballsResolver.sendRequestToSiteViaProtocol(HappyEyeballsResolver.java:209)
    at net.handle.hdllib.HappyEyeballsResolver.sendRequestToSites(HappyEyeballsResolver.java:176)
    at net.handle.hdllib.HappyEyeballsResolver.sendRequestAndSetResponseOrPublicException(HappyEyeballsResolver.java:152)
    at net.handle.hdllib.HappyEyeballsResolver.run(HappyEyeballsResolver.java:93)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    ... 1 more

Caused by: java.net.SocketTimeoutException: Connect timed out

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 17:57):

Are you using Handles? What version of Dataverse is this, please? And in server.log to do you see any line numbers for Dataverse code? (I don't see any yet.) Maybe you could post more of server.log.

view this post on Zulip Guillermo Esteban Murillo Goussen (Sep 10 2024 at 18:09):

I am trying also to configure dataverse to use handles yes.

It is the latest version of Dataverse 6.3

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 18:12):

Do you want to go ahead and open an issue about this?

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 18:13):

(I'm still interested in seeing a line number from Dataverse, though, if possible.)

view this post on Zulip Guillermo Esteban Murillo Goussen (Sep 10 2024 at 18:32):

server.log

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 18:34):

at edu.harvard.iq.dataverse.DatasetPage.deleteDataset(DatasetPage.java:2922) Thanks!

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 18:36):

Huh, but https://github.com/IQSS/dataverse/blob/v6.3/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java#L2922 doesn't make sense. :thinking:

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 18:38):

OptimisticLockException. Interesting.

view this post on Zulip Guillermo Esteban Murillo Goussen (Sep 10 2024 at 18:40):

I really don't now whats the problem because it happens wether Im creating a dataset or deleting it. It always got stuck with the blue will spinning and then several minutes after... one of the datasets appears in draft status or the dataset desappears so the deleting worked but dont know when or how

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 18:42):

So strange. I assume you started with a FAKE DOI provider. If you switch back to that, does the problem go away?

view this post on Zulip Guillermo Esteban Murillo Goussen (Sep 10 2024 at 18:45):

I didnt configured the fake doi identifier, I started whith the handle configuration from the very top of the installation
How do I do that?
-Delete every jvm-option related to handle
-Delete the authority and the protocol
-Leave it like that or add jvm-optios for the fake id?

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 18:52):

Something like that. It may have changed recently. This is how I do it in Docker: https://github.com/IQSS/dataverse/blob/v6.3/docker-compose-dev.yml#L54-L59

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 18:53):

Really I'm just wondering if this is related to handles or not. :thinking:

view this post on Zulip Guillermo Esteban Murillo Goussen (Sep 10 2024 at 19:02):

I began with the handle configuration at the very begining.
When I tried to publish a dataset I got errors about the keys handle-passphrase or handle-dir not found.
I installed a handle server, followed the instructions, but then this errors appears I think they may be related

view this post on Zulip Philip Durbin 🚀 (Sep 10 2024 at 19:45):

Yeah, it sounds like there's a good chance it's related. Please do feel free to create an issue. And if you do, please upload that server.log file.

Last updated: Oct 30 2025 at 06:21 UTC