Time
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Nick
Message
04:58 jri joined #dataverse
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05:18 Glodojo
I have been billed %21.34 by this site and I don't know what it is for. Please help
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12:18 donsizemore joined #dataverse
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14:11 pdurbin joined #dataverse
14:15 pdurbin
donsizemore poikilotherm: session chairs! Nice!
14:15 poikilotherm
Ah that reminds me that I have to answer to Danny
14:18 pdurbin
Do you two want comments on this doc?
14:32 poikilotherm
Ah gotta go, look after kids.
14:32 * poikilotherm
waves at all
14:38 pdurbin
donsizemore: I'm looking at https://github.com/IQSS/dataverse-jenkins/pull/32 and I could just click approve but I'm wondering about these jacoco.exec files.
14:39 donsizemore
@pdurbin one of them was getting created (by default) and as of @poikilotherm's 4024 jakarta branch merged it stopped appearing
14:40 donsizemore
@pdurbin so ansible no longer does a jacoco merge
14:41 pdurbin
Now only one jacoco.exec file appears, you're saying.
14:42 donsizemore
correct, the one under domain1/config/ disappeared on thursday
14:43 donsizemore
the remaining file is in /tmp/dataverse/target/
14:44 pdurbin
Ok. Approved. Thanks!
16:17 poikilotherm
donsizemore I keep feeding you with more work resulting from merging my breaking changes :-D
16:17 poikilotherm
I hope you don't mind ;-)
16:18 poikilotherm
BTW should we take the opportunity to upgrade JaCoCo?
16:54 donsizemore
@pdurbin didn't you fix the validation problem in pom.xml?
16:55 donsizemore
@poikilotherm I think the dependency re-org disabled integration tests but I'm not sure how
16:58 pdurbin
donsizemore: I kind of half fixed it. Do I need to fix it more?
16:59 donsizemore
@pdurbin NetBeans complains "cvc-elt.1: Cannot find the declaration of element 'project'. [2]"
16:59 donsizemore
@pdurbin we seem to be missing a doctype
17:01 pdurbin
donsizemore: I don't see it in my pom.xml. Want to do a quick call?
17:01 donsizemore
if you have a minute that would be great
17:02 pdurbin
bah, you're a single channel guest in slack
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17:51 donsizemore
@pdurbin I switched to Payara for a quick test. nada
17:53 pdurbin
bummer
17:53 * pdurbin
blames poikilotherm :)
17:53 donsizemore
I'll need to switch to payara anyway because some if not most of those changes aren't backwardly compatible
17:54 pdurbin
Yeah. Onward and upward. Leave the old and busted behind. :)
17:55 pdurbin
Oh, I watched Onward with the kids over the weekend. Cute movie.
18:02 poikilotherm
Yeah pdurbin just blame that random german guy from the internet :-P
18:04 donsizemore
@pdurbin i'm cribbing from https://github.com/payara/Payara/blob/master/nucleus/pom.xml
18:06 pdurbin
donsizemore: should we tell poikilotherm what happened?
18:07 poikilotherm
O.O
18:28 donsizemore
@poikilotherm java code coverage for integration tests seems to have dropped out with the jakarta merge
19:07 poikilotherm
Bummer
19:11 poikilotherm
Is that related to dataverse-ansible#32?
19:11 poikilotherm
Err... dataverse-jenkins#32
19:14 poikilotherm
Oh... Is this running on Payara already? Because things will break on GF...
19:14 poikilotherm
Is there an issue or logs to look at?
19:15 poikilotherm
Iiiiinnnnnppppuuuuuutttttt
19:25 donsizemore
it's on payara, i only modified dataverse-ansible because the jacoco.exec file stopped getting created
19:27 donsizemore
the exec file creation stopped after the jakarta branch merge; i wasn't sure about compatibility, in reading more i don't see nearly as many version specifications
19:28 donsizemore
I fleshed things out a bit but no dice: https://github.com/OdumInstitute/dataverse/commit/57ce6dad3ba1fc25c2f4f1cef7cc687af1acc598
19:31 pdurbin
Oh dear, poikilotherm died without input.
19:32 donsizemore
i was thinking he should be asleep by now? but i'm an early-to-bed type these days
19:33 pdurbin
Yeah, I'd be nagging kids to turn their lights out.
19:34 poikilotherm
TADA
19:35 poikilotherm
Just made C1 make her head rest on a pilow
19:35 poikilotherm
Pff "asleep". It's 21:35 over here. No sleep in sight yet
19:36 poikilotherm
Left construction site early today :-)
19:36 donsizemore
heh. i'm usually in bed by 1900 if i can help it
19:37 poikilotherm
Ha. In our new home, there will be a KNX automation system. I can switch off their lights without even leaving the couch
19:37 poikilotherm
donsizemore: WOW! Now that's early!
19:38 poikilotherm
Alright guys, how may I be of help with this?
19:43 donsizemore
eh, i'm just poking at things. the easiest test would be to try a reverted pom.xml but i hate to go backwards
19:44 donsizemore
i was wondering about jakarta compatibility, i've bumped the jacoco version to 0.8.6-SNAPSHOT
19:53 poikilotherm
To broaden the search possibilities: Jakarta EE 8 is just the same as Java EE 8. Only the name changed.
19:54 dataverse-user joined #dataverse
20:01 poikilotherm
I tend to forget... Where is that JaCoCo magic happening again?
20:03 donsizemore
most if it is specified in pom.xml, then there's offline instrumentation ansible
20:05 poikilotherm
Ah that offline instrumentation is what I can't find...
20:05 poikilotherm
BTW together with Jakarta came Primefaces 8
20:05 poikilotherm
Both changes where merged the same day
20:09 donsizemore
yes
20:09 donsizemore
and pom.xml had hard-coded jacoco to an older version
20:12 poikilotherm
It still has
20:12 poikilotherm
And as far as I can see, you are using the same version in the jacoco ansible tasks
20:13 jri joined #dataverse
20:14 donsizemore
i have a branch now. oh oh, i think i found it
20:15 pdurbin
poikilotherm: if you run `mvn package` you should find a nice report in target/site/jacoco/index.html ... a report of unit tests. Should be roughly 20% code coverage. But what broke recently is our report for API tests.
20:18 donsizemore
i think i found it
20:27 donsizemore
@pdurbin $ ls -al /usr/local/glassfish4/glassfish/domains/domain1/config/jacoco.exec =)
20:38 donsizemore
@pdurbin the solutions are always so simple.
20:39 oschoppe joined #dataverse
20:39 oschoppe
Hi all;
20:40 oschoppe
My web-based uploads fail and I do not know why
20:40 oschoppe
File the progress bar goes up to 100%, nothing happens afrerwards
20:40 oschoppe
*afterwards
20:41 oschoppe
If I click on "D", then I see an error message: "Upload unsuccessful (0: Network Error)."
20:41 oschoppe
*if I click on "Done"
20:42 oschoppe
This happen when I want to upload 135MB large ".pt" files (PyTorch deep learning models); it seems to work for small text files, though
20:42 oschoppe
Any idea why this could happen?
20:51 donsizemore
@oschoppe hell, can you look in your glassfish server.log?
20:51 donsizemore
@oschoppe make that HELLO! server.log will be in /usr/local/glassfish4/glassfish/domains/domain1/logs
20:52 oschoppe
Hi donsizemore, thanks for replying. I am new to this. What is the glassfish server log? Please note that I am using the web interface to upload my data
20:52 oschoppe
This worked well for my last dataset
20:52 jri joined #dataverse
20:54 donsizemore
Hello, I assumed you were running your own Dataverse installation. Is there a particular Dataverse instance you're trying to upload files into? You might contact their support.
20:55 oschoppe
I am just using https://dataverse.harvard.edu
20:56 oschoppe
On their support website, they linked this chat ;-)
20:56 pdurbin
lol, hell vs hello
20:56 pdurbin
oschoppe: howdy, thanks for using Harvard Dataverse
20:58 pdurbin
135 MB should work through the GUI but alternatives exist such as the DVUploader: http://guides.dataverse.org/en/4.20/user/dataset-management.html#command-line-dvuploader
20:59 pdurbin
Or if you're comfortable with curl: http://guides.dataverse.org/en/4.20/api/getting-started.html#uploading-files
20:59 oschoppe
Do you think it is a file size issue?
20:59 pdurbin
Well, you said small files work fine.
21:00 oschoppe
Are there any restrictions / known issues for some file formats?
21:00 pdurbin
No. There shouldn't be. Any file is fine.
21:00 pdurbin
The per file limit is 2.5 GB according to https://support.dataverse.harvard.edu/researchers
21:01 pdurbin
oschoppe: can you please tell me what you see at https://dataverse.harvard.edu/host.txt ?
21:01 oschoppe
dvn-cloud-app-2.lib.harvard.edu
21:02 pdurbin
thanks
21:03 oschoppe
I get the same issue with a 13MB file of a different format (Nifti, which saves 3D imaging data)
21:03 oschoppe
So far I only got it to work with a 4kb text file
21:03 pdurbin
yikes
21:03 pdurbin
very strange
21:03 oschoppe
I was able to upload those Nifti files for an earlier dataset
21:04 pdurbin
Does your 13 MB file upload ok to https://demo.dataverse.org ?
21:04 oschoppe
I'll give it a try
21:06 oschoppe
Nope, same "Upload unsuccessful (0: Network Error)." message
21:07 pdurbin
stranger still
21:08 pdurbin
oschoppe: can you please email support
21:08 oschoppe
Will do, thanks!
21:09 oschoppe
(tested in Firefox and Chrome, same issue)
21:09 pdurbin
Ok, I'm on dvn-cloud-app-1 and I'm trying to upload a file.
21:11 pdurbin
Seems like it took it, a 15 MB zip file. Desktop Goose if you must know. :)
21:12 oschoppe
Is there some kind of processing/verification of the file once uploaded? Maybe this process just takes very long or gets stuck?
21:13 oschoppe
Because the upload itself seems to work. Just after the upload nothing happens
21:13 pdurbin
Well, zip files are unzipped, Excel files and similar go through an "ingest" process.
21:13 oschoppe
The error message appears only if I click "Done", which I only do after waiting a bit after the upload completed
21:14 pdurbin
It sounds like you're doing everything right, even waiting to give the system a little time.
21:16 pdurbin
If you email that address, you should get a reply with a ticket number.
21:16 pdurbin
I'm asking in Slack but not hearing about any known issues.
21:17 pdurbin
Which doesn't mean there are no issues, of course. Are you comfortable with the command line? I mentioned a couple options above, curl and DVUploader.
22:42 pdurbin left #dataverse
