shan (Jul 15 2024 at 07:24): shan (Jul 15 2024 at 07:24):Hi, we just set up the environments, and want to delete some data sets, but it seems that not all the data sets can be deleted, any ideas or guides on this?
Oliver Bertuch (Jul 15 2024 at 07:53):https://guides.dataverse.org/en/latest/user/dataset-management.html#dataset-versions
https://guides.dataverse.org/en/latest/user/dataset-management.html#dataset-deaccession
shan (Jul 15 2024 at 08:16):@Oliver Bertuch can I delete the dataset from dashboard? I didn't find the delete action in the dashboard. see below:
image.png
shan (Jul 15 2024 at 08:19):Meanwhile, Is it possible to delete the deaccessioned datasets?
Oliver Bertuch (Jul 15 2024 at 08:28):shan said:
Meanwhile, Is it possible to delete the deaccessioned datasets?
Nope. Underlying reasons: https://support.datacite.org/docs/doi-persistence#deactivate-a-doi
shan (Jul 15 2024 at 08:48):It is really complicated, Can I clear up all the dataverses and datasets in the system?
Oliver Bertuch (Jul 15 2024 at 08:50):Sure. Just drop the database and start over. Keep in mind that any datasets already registered for real at DataCite will have cost you money and you really should deaccession those DOIs.
Oliver Bertuch (Jul 15 2024 at 08:51):For experimental setups and learning, please use the fake PID provider. That way you don't spend money. Or, if you really need to test with DataCite, use their Test Fabrica (which is also for free and without risks)
shan (Jul 15 2024 at 08:57):Thanks, right now, we use the fake DOI, so it will not cost money :)
Philip Durbin 🚀 (Jul 15 2024 at 14:02):@shan you can delete datasets via API: https://guides.dataverse.org/en/6.3/api/native-api.html#delete-published-dataset
shan (Jul 19 2024 at 02:11):@Philip Durbin I drop the database through "psql -U dvnapp -c 'DROP DATABASE "dvndb"' template1", and restart domain, by "java -jar /usr/local/payara6/glassfish/lib/client/appserver-cli.jar start-domain", and when I open the webpage of http://datavserse.domain:8080, it only shows that
image.png
Do I need to create the dvndb database and tables by hand? where can I download the create schema?
shan (Jul 19 2024 at 07:31):@Philip Durbin I run the "python3 install.py", it did create the "dvndb" database, but no tables there, it is an empty database.
and still the webpage " http://datavserse.domain:8080" didn't show any login interface, it only shows payara is running, see blow:
image.png
Philip Durbin 🚀 (Jul 19 2024 at 13:04):It sounds like you're doing a refresh reinstall: https://guides.dataverse.org/en/6.3/installation/installation-main.html#fresh-reinstall
You've re-run install.py but all database tables are empty.
Perhaps the war file was not successfully deployed?
Can you please upload your server.log file?
shan (Jul 20 2024 at 02:13):@Philip Durbin
server.log
here is the log
shan (Jul 20 2024 at 02:30):@Philip Durbin The former log is based on "./asadmin restart-domains /home/dataverse/dataverse-6.2/target/dataverse-6.2.war", and the war file seems not deployed, I retried deploying the war file by "./asadmin deploy /home/dataverse/dataverse-6.2/target/dataverse-6.2.war", it seems the war file was deployed successfully, but the page is still not working properly when I go to " http://datavserse.domain:8080", here is the new server.log file
server.log
shan (Jul 20 2024 at 02:35):and I found the following error message in the server.log file, whether it is related to the issue?
shan (Jul 20 2024 at 02:35):[2024-07-20T10:31:54.969+0800] [Payara 6.2023.8] [SEVERE] [] [] [tid: _ThreadID=74 _ThreadName=RunLevelControllerThread-1721442678838] [timeMillis: 1721442714969] [levelValue: 1000] [[
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...]]
shan (Jul 20 2024 at 02:40):When I head to http://datavserse.domain:8080 I see "Page Not Found - The page you are looking for was not found."
shan (Jul 20 2024 at 02:41):BTW, The system installed on physical machine not on docker
shan (Jul 20 2024 at 02:46):[2024-07-20T10:20:21.176+0800] [Payara 6.2023.8] [WARNING] [] [javax.org.glassfish.persistence.org.glassfish.persistence.common] [tid: _ThreadID=191 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1721442021176] [levelValue: 900] [[
PER01000: Got SQLException executing statement "ALTER TABLE fileaccessrequests ADD CONSTRAINT FK_fileaccessrequests_DATAFILE_ID FOREIGN KEY (DATAFILE_ID) REFERENCES DVOBJECT (ID)": org.postgresql.util.PSQLException: ERROR: constraint "fk_fileaccessrequests_datafile_id" for relation "fileaccessrequests" already exists]]
Here is another error message in server.log
shan (Jul 20 2024 at 04:23):I reinstalled again, and it works now , but two error messages still appears: PER01000: Got SQLException executing statement "ALTER TABLE fileaccessrequests ADD CONSTRAINT FK_fileaccessrequests_DATAFILE_ID FOREIGN KEY (DATAFILE_ID) REFERENCES DVOBJECT (ID)": org.postgresql.util.PSQLException: ERROR: constraint "fk_fileaccessrequests_datafile_id" for relation "fileaccessrequests" already exists]]
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...]]
how can I handle this?
Philip Durbin 🚀 (Jul 22 2024 at 14:03):I'm pretty sure that error about fileaccessrequests is always there. It's confusing. Please feel free to open an issue about it. I don't think it does any harm.
I'm glad the reinstallation worked! Good job!
Last updated: Oct 30 2025 at 06:21 UTC