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01:23 JonathanNeal joined #dataverse
08:02 jri joined #dataverse
11:58 donsizemore joined #dataverse
12:53 dataverse-user joined #dataverse
12:57 dataverse-user
Hi,my dataverse is throwing the following message when I try to publish a dataset: Register/update file persistent identifiers workflow in progress – Publish workflow in progress
12:58 dataverse-user
I've been able to publish datasets without any problem before... Do you guy know what might be happening?
13:00 Zalabany joined #dataverse
13:02 donsizemore
@dataverse-user can you find the full error from glassfish's server.log?
13:03 dataverse-user
ok I'll check
13:03 Zalabany
Hello Dataverse people :), I was trying to deploy the Ansible playbook, the deploy stopped while the system was trying to start the glassfish service, with a time out error. any suggestions ?
13:13 donsizemore
@zalabany that too will likely be detailed in the glassfish server.log
13:13 Zalabany
from the Log file it seems something with the HTTP2/ addon
13:13 Zalabany
@donsizemore " at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$UpOneLevel.run(CurrentTaskFuture.java:762) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.ClassNotFoundException: org.glassfish.grizzly.npn.AlpnServerNegotiator
13:14 Zalabany
[Payara 5.201] [WARNING] [] [org.glassfish.grizzly.config.GenericGrizzlyListener] [tid: _ThreadID=17 _ThreadName=RunLevelControllerT$ Unable to construct HTTP /2 Addon
13:15 donsizemore
@zalabany what version of payara?
13:16 donsizemore
oh. 201, there it is
13:16 donsizemore
do you have the latest version of the role?
13:17 Zalabany
@donsizemore yes, just cloned the git repo today morning
13:18 donsizemore
@zalabany interesting. i've run the role multiple times this morning to test some other changes and haven't hit that error
13:19 Zalabany
Ummm, can it be port conflict issue ?
13:20 donsizemore
@zalabany i'm also waiting hopefully for https://github.com/payara/Payara/milestone/33 so i can do away with that SSL incompatibility.
13:20 donsizemore
@zalabany what ports are listening on your box?
13:22 Zalabany
tcp 0 0 0.0.0.0:22 0.0.0.0:* LISTEN 983/sshd tcp 0 0 127.0.0.1:631 0.0.0.0:* LISTEN 991/cupsd tcp 0 0 127.0.0.1:5432 0.0.0.0:* LISTEN 1043/postmaster tcp 0 0 127.0.0.1:25 0.0.0.0:* LISTEN 1212/master tcp 0 0 0.0.0.0:6311 0.0.0.0:* LISTEN 151
13:22 Zalabany
oh sorry,
13:24 donsizemore
https://github.com/payara/Payara/issues/3138
14:14 donsizemore
@pdurbin hey hey. i'm happy to host what you need, particularly if it's in AWS. i've got some spare wheeze-boxes in our datacenter but nothing's a spring chicken
14:15 pdurbin
donsizemore: thank you! Keeping everything more or less as-is for now sounds fine. We can modernize it later. :)
14:15 pdurbin
poikilotherm1: this is about the chat/irclog hosting I emailed you about.
14:16 pdurbin
Others are welcome to jump into this discussion as well, of course!
14:18 pdurbin
donsizemore: also, we have until Nov 30 so maybe we could start by simply listing some tasks under https://github.com/IQSS/chat.dataverse.org somewhere.
14:21 donsizemore
@pdurbin you don't understand the nature of my anxieties. all problems must be dealt with immediately.
14:21 pdurbin
I've noticed that about you. :)
14:21 pdurbin
It makes you very productive. :)
14:22 donsizemore
though i'm still waiting for an official centos8 AWS image
14:23 pdurbin
Actually, for iqlogbot Ubuntu is better.
14:23 donsizemore
but for now Jon says we can use Odum's AWS space, particularly for a low-resource instance such as IRC logging
14:25 pdurbin
I don't have a strong opinion about where it's hosted. I run iqlogbot (philbot, actually) on a $5 per month Ubuntu Digital Ocean droplet (along with other stuff) and it works fine. Low-resourse, like you say.
14:26 donsizemore
I would love a GDCC build environment
14:30 pdurbin
Instead of AWS?
14:34 donsizemore
depending on the number of VMs and CPU usage, on-prem can often be cheaper
14:34 donsizemore
and i've been meaning to finish standing up my XCP-NG cluster, so that'll be a good friday afternoon project
14:36 pdurbin
Huh. Xen was all the rage back in the day. I've lost track of it.
14:44 pdurbin
You know, one thing we might get out of this is emojis. Because we should probably install the latest version of The Lounge rather than Shout. More stability too, hopefully.
14:51 pdurbin
donsizemore: ok, I put the high level steps in this new doc: https://docs.google.com/document/d/15EYxey6T613DONznpu6QNe8YNBsp8io-SuonlRszshI/edit
17:15 dataverse-user94 joined #dataverse
17:16 dataverse-user94
Hi, can you guys please tell me what this message means?
17:16 dataverse-user94
Register/update file persistent identifiers workflow in progress – Publish workflow in progress
17:16 dataverse-user94
it's showing when I try to publish some datasets
17:17 dataverse-user94
This datasets had Handles in the past, but, we change the handles for dois using: curl -H "X-Dataverse-key: $API_TOKEN" -X POST http://$SERVER/api/datasets/$dataset-id/modifyRegistrationMetadata
17:18 pdurbin
dataverse-user94: I need to step out for a bit but please hang around.
17:18 dataverse-user94
Ok I'll wait, thanks
17:28 donsizemore
@pdurbin when you come back, let me know what size of what AWS instance you'll need for your irclog and i'll create it.
17:44 pdurbin
dataverse-user94: back. Let me look.
17:47 pdurbin
dataverse-user94: to change from Handle to DOI I assume you used this instead: curl -H "X-Dataverse-key: $API_TOKEN" -X POST http://$SERVER/api/admin/$dataset-id/reregisterHDLToPID
17:49 pdurbin
dataverse-user94: like Don said, it would be good to see what errors appear in server.log. Perhaps you could click publish again and then email server.log to support
17:54 donsizemore joined #dataverse
18:06 dataverse-user94
that's the think ... we couldn't find anything about this in the server.log
18:06 pdurbin
hmm
18:06 dataverse-user94
and we can't even click on publish again ... the button is disabled
18:07 pdurbin
maybe there is a lock
18:07 dataverse-user94
then again this message is display as a "warning"
18:07 dataverse-user94
not as an error
18:09 pdurbin
dataverse-user94: you might want to check for a lock: http://guides.dataverse.org/en/4.20/api/native-api.html#dataset-locks
18:09 pdurbin
... because a lock with turn the publish button grey and unclickable
18:10 pdurbin
a lock will* turn the
18:13 dataverse-user94
Ok, i'm on it!
18:13 pdurbin
:)
18:36 donsizemore
@pdurbin as of https://github.com/IQSS/dataverse-ansible/commit/6e2f42597c115cc95e9e5a5790a7ab48c6879fa0 dataverse-ansible ensures openjdk 11 (or other) for payara, solr and maven
18:37 pdurbin
donsizemore: wow, and everything works? :)
18:37 donsizemore
@pdurbin pallinger is correct that 1.8 is currently required https://github.com/IQSS/dataverse/blob/develop/scripts/installer/install.py#L273
18:38 pdurbin
Hmm. I hadn't seen that sys.exit. Thanks.
18:38 dataverse-user94
@pdurbin sorry, i was grabbing some lunch but now i'm back ... I checked if my dataset was locked and this is the result of the CURL: {"status":"OK","data":[{"lockType":"pidRegister","date":"Fri Jun 12 13:35:18 COT 2020","user":"dataverseAdmin","message":"Adding File PIDs asynchronously"},{"lockType":"pidRegister","date":"Wed Jun 10 15:42:52 COT 2020","user":"julian.cortess","message":"Adding File PIDs asynchronously"}]}
18:38 donsizemore
@pdurbin the role currently calls artifacts from IQSS/dataverse. as you say it'd be good to request java version flexibility either via https://github.com/IQSS/dataverse/issues/4259 (or a new issue?)
18:40 donsizemore
@pdurbin in the Spirit of Small Chunks I'm tempted to open a new issue since #4259 has grown to be more about testing under newer JVMs
18:40 dataverse-user94
all i'm seeing is that dataverse is taking a while when I publish a dataset ... however that's happening now that I removed the class "disabled" from the button just to click it again
18:41 pdurbin
dataverse-user94: how many files are in this dataset?
18:44 pdurbin
From the message, it's trying to get a DOI for each file, which can be slow.
18:45 dataverse-user94
10+ files
18:46 pdurbin
That's not very many. On thing you can do is turn off the async registration of files.
18:50 Zalabany joined #dataverse
18:52 pdurbin
But I wouldn't want to tell you the wrong thing. I'm happy to keep chatting here but you should probably get a ticket started by emailing support
19:00 dataverse-user
ok will do
19:01 dataverse-user
thank you very much @pdurbin ... you helped me a lot!
19:01 pdurbin
I hope so.
19:01 pdurbin
I'll look for your ticket.
19:04 pdurbin
donsizemore: do you still want to talk about AWS instances?
19:04 donsizemore
@pdurbin if you think the requirements are that minimal i'll just pick one, maybe even free tier?
19:04 pdurbin
Sure!
19:18 donsizemore
@pdurbin java version Q: 1.8 is currently required. 11 is LTS. 14 is current.
19:18 donsizemore
@pdurbin 12 and 13 are already EOL. add check for 15 in antici... pation?
19:19 pdurbin
We're only ever going to run LTS versions of Java. 8, 11, whatever the next one is.
19:21 donsizemore
i'll check for 1.8, 11 and 14 for now. p.s. the EoA for openjdk 1.8 says "At Least May 2026" ?!?
19:22 pdurbin
Red Hat is going to support Java 8 for quite a long time, from what I understand.
19:22 donsizemore
:thumbsup:
19:37 donsizemore
@pdurbin hey, what's IQSS' public ipv4 space again?
19:37 pdurbin
buh, I don't know
19:38 pdurbin
but does it matter? we're all at home :)
19:38 donsizemore
@pdurbin for SSH for your IRC -log instance. I found 65.112.8.0/24 + whatever you want
19:39 pdurbin
Ah, ok. Makes sense.
19:40 donsizemore
"free tier eligible up to 30GB" — so i'm specifying 29
19:41 pdurbin
heh. ok
20:01 donsizemore
@pdurbin and pallinger is also correct... on Java 11 Payara indeed prompts for an asadmin password
20:02 pdurbin
but not on Java 8? weird
20:04 donsizemore
yup
20:08 donsizemore
@pdurbin so, current develop doesn't deploy on Java 11:
20:08 donsizemore
remote failure: A Mail resource named mail/notifyMailSession does not exist.
20:08 donsizemore
but that may be something I did or didn't do in testing.
20:08 donsizemore
now that I realize how long OpenJDK 1.8 is supported I'm less concerned
20:09 donsizemore
oh, wait. that wasn't a fatal error. we have a current develop on payara-5.201 with java 11
20:11 pdurbin
nice
20:11 pdurbin
notifyMailSession is something the installer sets up
20:30 donsizemore
there's my answer
20:36 pdurbin
good
20:53 pdurbin
Have a great weekend, everyone!
20:53 pdurbin left #dataverse
