Time
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Nick
Message
09:31 jri joined #dataverse
11:52 pdurbin joined #dataverse
12:27 poikilotherm joined #dataverse
14:20 donsizemore joined #dataverse
14:34 pdurbin
Happy New Year, everyone. :)
14:45 poikilotherm
Happy New Year :-)
15:26 pameyer joined #dataverse
16:05 pameyer
pdurbin: your RT still has the "we're off for the break" message in its autoresponder
16:08 pdurbin
pameyer: ah, thanks for the heads up. I just let people know.
16:10 pameyer
no problem - I'm still getting warmed up too ;)
16:11 pdurbin
We're already deep into a discussion about trusted remote storage agents.
16:11 pdurbin
donsizemore ^^
16:39 Mahsa joined #dataverse
16:39 Mahsa
Hi all and happy new year
16:40 Mahsa
Just a quick question regarding Dataverse 4.10 release
16:40 Mahsa
The large data support in 4.10 is independent of Data Capture Module, is this correct ?
16:42 pameyer
hi Mahsa - no, the large data support in 4.10 still uses DCM for uploads
16:43 Mahsa
I see, Thanks!
16:44 pameyer
you're welcome
16:45 Mahsa
We store our files on AWS S3. On the Big data support page of the website, it says: "Please note that S3 support for DCM is highly experimental"
16:45 Mahsa
Is the issue around downloading big data from S3 resolved in the new version ?
16:46 Mahsa
http://guides.dataverse.org/en/latest/developers/big-data-support.html
16:46 pameyer
the issues for downloading big data from S3 should be resolved in 4.10
16:46 Mahsa
Great, Thanks!
16:48 pameyer
I'm not sure if the guides have been updated for 4.10 or not yet
16:48 Mahsa
Yes, I was just checking that.
16:48 pmauduit95 joined #dataverse
16:48 pameyer
I'd tend to interpret "experimental" as roughly "try it on a staging site first, and keep an eye on it in early production"
16:48 pmauduit joined #dataverse
16:49 pameyer
as far as I'm aware, dcm/s3 isn't something that's being used in production yet
16:49 pmauduit
hello
16:49 pameyer
hi pmauduit
16:50 Mahsa
We only have a staging site at this time as we are still prototyping the system. But the guides seem to have been updated: http://guides.dataverse.org/en/4.10/developers/big-data-support.html
16:50 pmauduit
I am trying to create my own docker composition based on wildfly, and I have some issues trying to deploy the war into it
16:50 pameyer
Mahsa: great that you have a staging site available
16:51 Mahsa
Sure, I will give it a try and see how it goes, Thanks for your help/
16:51 pameyer
Mahsa: no problem - please feel free to ask if you hit more questions
16:52 pmauduit
I have seen that the official installation guide is mentioning glassfish, but I could not find any relevant docker images (official ones from oracle seem to refer to a private docker repository)
16:52 pameyer
pmauduit: poikilotherm might be one to ask about wildfly. glassfish is the only app server that's supported
16:53 pameyer
there's been a bunch of discussion of dockerizing dataverse, so it's still got some rough edges
16:53 pameyer
the approach I've always taking was to start with a stock os image, and add glassfish to it myself
16:54 pmauduit
ok, I'm also pretty new to J2EE environment, if glassfish is more relevant, then I'll go for it
16:55 pameyer
are you thinking about dev or production?
16:56 pmauduit
for now on, dev :-)
16:56 pameyer
dev wise; the `conf/docker-aio` directory in the dataverse repo should work out of the box. with the caveat that it's essentially "docker done exactly wrong"
16:57 pmauduit
ok, I'll have a look then ; my goal once I'd have a better idea of the big picture is to dockerize for production purposes at the end
16:58 pameyer
cool - there are other folks working on production dockerizing too
16:59 Mahsa
Thanks, I have another quick Q around updating citation metadata blocks. I have previously done metadata customization so I am a bit familiar with the process.
17:00 pmauduit
for now, I've got the jdni to postgresql configured correctly, but it fails with the jndi / jms definitions
17:00 Mahsa
But when I tried to change the Subject filed in the citation metadata block to optional from mandatory, it did not seem to work.
17:01 pameyer
Mahsa: I thought that Subject was already mandatory in the citation block
17:01 Mahsa
yes, it is
17:01 pameyer
pmauduit: jndi/jms is a bit outside my expertise
17:01 Mahsa
But I tried to make it optional and update the block, but it did not work. Do you think this could be done ?
17:03 pameyer
Mahsa: unfortunately, I don't believe so. the closest I was able to get was to remove all but one subject, hide the field, and auto-select if there was only a single subject
17:03 pameyer
dataverse has hardcoded assumptions that some blocks exist, and I'm pretty sure subject is one of them
17:04 Mahsa
That is what I thought, so if I change the subject Dataset fields and keep everything else (ordering, vale, etc) the same, this would not cause any issues , right ?
17:04 pmauduit
I've got this error in my logs:
17:04 pmauduit
"WFLYCTL0412: Required services that are not installed:" => [
17:04 pmauduit
"jboss.naming.context.java.module.dataverse.dataverse.env.jboss.jms.IngestQueueConnectionFactory",
17:04 pmauduit
"jboss.naming.context.java.module.dataverse.dataverse.env.jboss.jms.DataverseIngest"
17:04 pmauduit
],
17:06 pameyer
Mahsa: I'm not sure - I don't think I understand what you meant
17:06 pmauduit
I could find the classes in the sources, and found that the jndi names for the jms queues are configured via annotations, so I created / adapted the code so that it can be resolved, but it seems the problem is elsewhere
17:06 Mahsa
I mean, changing for instance "Agriculture" in the subject to another value.
17:07 Mahsa
I mean changing the text of the Data fields
17:07 Mahsa
for subject
17:07 pameyer
ah - now I understand. I'm still not sure :( but I don't know of anything it would break
17:08 Mahsa
I hope so, I will test it out. Thanks again.
17:39 pdurbin
pmauduit: hi! As pameyer said poikilotherm was thinking about trying Dataverse on Wildfly ( http://irclog.iq.harvard.edu/dataverse/2018-11-19#i_79498 ) but I definitely don't expect it to "just work".
17:45 pdurbin
Mahsa: if you're considering changing "citation.tsv" (which has the "Subject" field) please note this warning: "Generally speaking it is safer to create your own custom metadata block rather than editing metadata blocks that ship with Dataverse, because changes to these blocks may be made in future releases of Dataverse." http://guides.dataverse.org/en/4.10/admin/metadatacustomization.html#introduction
17:48 Mahsa
Thanks for sharing this. That is a good point but since subject is mandatory and can not become optional, we need to update the datasetfields for subject regardless since they don't apply to us.
17:48 Mahsa
The good news is that I just updated the citation.tsv with edited text fields and it seems to be working fine.
17:54 pdurbin
Mahsa: ok, but please be warned that step 6 in the Dataverse 4.10 release notes is "Update citation metadata block" ( https://github.com/IQSS/dataverse/releases/tag/v4.10 ) so you will probably lose your changes. If you are willing, please open a new issue describing the need you have.
18:04 Mahsa
Thanks, yes, I noticed that this morning. We will have to remember to update the citation.tsv file if the new release makes any modifications on that. My changes are as simple as changing the text of the fields for subjects.
18:06 Mahsa
I doubt if this could cause complications in future.Am I right to assume that ?
18:10 pdurbin
Mahsa: you should probably get an official answer by emailing support
18:12 Mahsa
Sure, I will email the support team about that.
18:14 pdurbin
Mahsa: thanks. And again, please consider opening a GitHub issue describing the need you have, the reason you are editing citation.tsv in the first place.
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