Update 5.5 -> 5.6 fails with both payara 5.2021.5 and 5.2021.10 #8376
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I haven't read line by line above but the line "URL invalid dvndbdvndb" might suggest a typo somewhere? |
I noticed this issue as well. But the setting in domain.xml is definitely correct and domain.xml was only copied together with the directory domain1. With our last updates glassfish/lib was never writable for the dataverse/payara user. What is the correct jar file for the ODBC driver? |
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If I understood #8064 correctly, it would probably help to install payara 5.2021.10 or higher and remove the contents of But I couldn't find such entries in domain.xml. Would this be a safe update path:
Which payara version would you currently recommend? Do I need a postgresql-x.y.z.jar in glassfish/lib? There is such a file in our running Payara instance, but not in the new Payara releases. I am not quite clear where this file comes from. I can't find anything about it in the Dataverse installation guide. Many thanks. |
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AFAIK, the recommendation is still 5.2021.5, moving to 5.2021.6 (.5 has a bug if you use asadmin set-log-levels). From my personal testing at various institutions, it looks like .8, .10, 5.2022.1 are all fine. The note about the lib/databases directory when going to 5.2021.8 or above relates only to the EJBTimers Dataverse uses. As with the osgi-cache and generated dirs, it appears that payara/Dataverse will end up recreating everything needed in those dirs at a restart. (The point of deleting the lib/databases dir is to remove EJBTimer info written in an older, incompatible db format.) At some point, the postgres driver file started being included in the war and no longer has to be added to glassfish/lib. In general, the release guide is the place for step-by-step instructions for upgrades with the install guide focusing on new installs. (If you find outdated info (like the doi password being in the clear), please send an issue/PR.) FWIW: My process for upgrading payara looks like yours (usually have a /usr/local/payara5 symbolic link that I redirect rather than moving payaras around) with the following additions:
chown to dataverse:
On one system, we also have the .aws directory (used for s3 stores) in a place where we have to copy/chown it as well. |
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Unfortunately, our next update attempt failed. With Payara 5.2021.6 we have the same problem as with 5.2021.10. Payara can be installed, but afterwards the deployment of Dataverse 5.6 fails. Apparently something has changed in the database access between 5.5 and 5.6. The server log shows: It looks to us like the URL (setURL) for database access is composed incorrectly. We have now looked through the old release notes again and found the following in version 5.3: In our case, it looks like this: Additionally in our domain.xml there are these two lines: Now when we want to run create-system-properties, we get the following message: What options do we have to set the database parameters correctly? |
Like @qqmyers pointed out, the "URL invalid" error and strange "dvndbdvndb" value are worrisome. When I run
Yes, I think these are important. It's strange to me that they aren't already defined for you. As you say, this was in the 5.3 release notes: https://github.com/IQSS/dataverse/releases/tag/v5.3 If I locally, I just ran So maybe you need to edit your domain.xml manually? Here are the db-related properties from my domain.xml: I hope this helps. Please do feel free to open a support ticket about this by emailing [email protected]. |
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Oh no. It should be |
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@lmaylein since you closed this, I assume you're all set! Great! 🎉 |
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@pdurbin Yes, at least on our test system the update has now worked without any problems. |
I have tried to update from 5.5 to 5.6 according to https://github.com/IQSS/dataverse/releases/tag/v5.6.
When I install payara version 5.2021.5 and copy domain1 to it, the start of payara fails:
At the next attempt with payara 5.2021.10 payara can be started, but afterwards the deploy of dataverse-5.6.war fails.
The directory glassfish/lib is writable for the dataverse/payara user.
Same, if I copy postgresql-42.2.2.jar (from our payara 5.2020.x installation) manually into glassfish/lib before.
server.log shows:
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