Time
S
Nick
Message
12:48 Virgile joined #dataverse
14:46 pdurbin joined #dataverse
14:47 pdurbin
Happy New Year!
16:58 bjonnh
Happy New Year!
17:02 pdurbin
How's it going, bjonnh?
17:02 bjonnh
good
17:02 bjonnh
working from home ;)
17:03 pdurbin
Same. It's getting a little old. :)
20:22 Sherry joined #dataverse
20:23 Sherry
Hello - question about a long ingest job.
20:23 pdurbin
Hey Sherry, please go ahead.
20:23 Sherry
Ingest was taking way too long. So I unlocked the dataset and now am trying to restart glass fish. Getting a time out when trying to stop.
20:25 pdurbin
Have you tried something like this? /usr/local/payara5/mq/bin/imqcmd -u admin query dst -t q -n DataverseIngest
20:26 pdurbin
That's from https://guides.dataverse.org/en/5.3/admin/troubleshooting.html#long-running-ingest-jobs-have-exhausted-system-resources
20:26 Sherry
No. haven't tried anything else - and we are still on glassfish.
20:26 pdurbin
Those commands will work on Glassfish too.
20:28 pdurbin
Sometimes Glassfish won't stop for me. I don't usually know why and end up killing it with kill -9. But since you mentioned ingest I'd suggest checking the queue with the command above.
20:29 Sherry
Ok, running now. I do not have permissions on our production server - so am relaying this to my sysadmin (via Slack).
20:29 pdurbin
Good thing Slack is back up. :)
20:31 Sherry
Prompting for password, Is the glassfish, or server password?
20:33 Sherry
Now getting this error - Is glassfish up???
20:33 Sherry
Querying the destination where: ------------------------------------ Destination Name Destination Type ------------------------------------ DataverseIngest Queue On the broker specified by: ------------------------- Host Primary Port ------------------------- localhost 7676 Jan 04, 2021 3:30:25 PM com.sun.messaging.jmq.jmsclient.ExceptionHandler throwConnectionException WARNING: [C4003]: Error occurred on connection creation [localhost:
20:33 Sherry41 joined #dataverse
20:34 Sherry41 left #dataverse
20:34 pdurbin
I assume it's the Glassfish password. But it sounds like the command won't work while Glassfish is unresponsive. You might need to kill it with kill -9.
20:36 nightowl313 joined #dataverse
20:36 Sherry
My sysadmin does not see the Glassfish process. , so maybe it finally stopped.
20:36 pdurbin
Phew.
20:37 Sherry
Any special "starting Glassfish, or just our usual way?
20:37 pdurbin
The usual way should be fine.
20:37 Sherry
She says she usually runs this command before star: rm -rf /usr/local/glassfish4/glassfish/domains/domain1/generated
20:38 pdurbin
Yep, I do that a lot too.
20:38 pdurbin
We document it in the guides.
20:41 nightowl313
hi all ... happy new year! got a quick (and probably dumb) question ... is it possible to run dataverse without generating persistent identifers? ie: can you just not set the doi and/or handle jvm options? I see this comment "By default Dataverse attempts to register DOIs for each dataset and file under a test authority, though you must apply for your own credentials as explained above." in the docs, so I'm assuming it automatically configure
20:44 pdurbin
nightowl313: I think you got cut off after "automatically configures" but no, you can't run Dataverse without PIDs. We get this question a lot. :)
20:45 donsizemore joined #dataverse
20:47 nightowl313
okay, thought so ... but we got a question about it ... thanks!
20:53 Sherry
Thanks @pdurbin. LibraData is back up. And I have set TabularIngestSizeLimit "low" so hopefully ingest won't get hung up.
20:56 pdurbin
Sherry: cool. As you may know, you can also set limits per file type. We keep RData extra low, I think.
21:07 pdurbin
donsizemore: so I watched What's Up Doc. Good movie Thanks. :)
21:08 donsizemore
it's extremely silly but one of my favorites =)
21:09 pdurbin
I believe the Simpsons paid homage to that glass pane bit.
21:11 pdurbin
nightowl313: here are a couple issues about "Make dataset DOI publication optional" https://github.com/IQSS/dataverse/issues/3652 and https://github.com/IQSS/dataverse/issues/6423
21:13 pdurbin
donsizemore: here it is: https://i.imgur.com/Gbaub92.gif
21:16 nightowl313
ah thanks! don't think we want to get into "creative breakage"! haha ... I think we will tell the person with the question about this (thinking of putting up a test dv site) to use handles instead of DOIs
21:18 donsizemore
@pdurbin that's very Simpsons =)
21:20 foobarbecue joined #dataverse
21:21 pdurbin
nightowl313: sure, Handles are supported.
21:59 pdurbin left #dataverse
