Failed to upload data after updating from 5.14 to 6.0

[Zhang Yue]

Dear Dataverse Community,

Yesterday I finished updating dataverse from 5.14 to 6.0 version. After following all steps in the README.md, I failed to upload some data in a existing dataset with certain message:  Error – Failed to add files to the dataset. Please try uploading the file(s) again. If you believe this is an error, please contact Root Support for assistance.. The server log is like this:

[2025-07-03T23:21:12.602+0000] [Payara 6.2023.8] [WARNING] [] [edu.harvard.iq.dataverse.ingest.IngestServiceBean] [tid: _ThreadID=115 _ThreadName=http-thread-pool::jk-connector(4)] [timeMillis: 1751584872602] [levelValue: 900] [[
  Failed to save the file, storage id 197d2981229-ca32a0e59064 (Failed to open local file file:///usr/local/payara6/glassfish/domains/domain1/files/10.82207/FK2/XCVOP2/197d2981229-ca32a0e59064 for writing.)]]

One hint: however, file 197d2981229-ca32a0e59064 exists in /usr/local/payara6/glassfish/domains/domain1/temp/ after uploading and before clicking "Save Changes" botton.

If anyone can help, please let me know

Best,

Yue

[Donald Sizemore II]

Hello,

Is your Payara service account (dataverse) able to write to that directory?

Don

painstakingly pecked on my iphone.

On Jul 3, 2025, at 19:31, Zhang Yue <yuezha...@gmail.com> wrote:

Dear Dataverse Community,

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[Zhang Yue]

Dear Don,

No, this problem happens not only under account dataverse but also other accounts.

Best,

Yue

[James Myers]

Yue,

Don is suggesting that the account running payara on your machine does not have write permissions to that directory. In the upgrade instructions, step 3 is

 

sudo chown -R dataverse /usr/local/payara6

 

If you missed that, or if payara is not being run by the “dataverse” unix user payara/Dataverse won’t be able to write directories and files under /usr/local/payara6/glassfish/domains/domain1/files (you can check which account is running Payara by running

 

ps -ef | grep payara

 

- the unix user running payara will be at the start of the response, e.g.

 

dataver+ 1572262       1  2 Jul03 ?        00:22:25 /usr/lib/jvm/java-21-openjdk-amd64/bin/java -cp /usr/local/payara6/glassfish/domains/domain1/lib/ext/*:/usr/local/payara-6.2025

 

Hope that helps,

--Jim

To view this discussion visit https://groups.google.com/d/msgid/dataverse-community/ba3d0eb9-cdb9-4458-bbb6-fd2f9ab0084cn%40googlegroups.com.

[Zhang Yue]

Dear Jim,

Thank you for correcting my misunderstanding. After I did this chown again now the data is successfully uploaded. (Strange is, in my history I have already set payara6 chown...)

Thank you all for your help.

Sincerely,

Yue