Time
S
Nick
Message
07:10 jri joined #dataverse
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08:17 stefankasberger joined #dataverse
08:36 poikilotherm joined #dataverse
10:44 pdurbin joined #dataverse
10:55 pdurbin
poikilotherm: good morning. You said you'd like me to look at the docs at https://github.com/IQSS/dataverse-kubernetes ?
10:55 poikilotherm
Yeah, that would be great :-)
10:56 poikilotherm
More feedback from people not as involved as I am is always a good idea... ;-)
11:00 pdurbin
poikilotherm: do you want me to add something to the top to say that the effort is community supported?
11:00 poikilotherm
Hmm that might be a good idea to mention this in the README :-D
11:01 poikilotherm
Sure, go ahead
11:04 pdurbin
Here you go: https://github.com/IQSS/dataverse-kubernetes/pull/53
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11:08 poikilotherm
Should I wait till you find more things to be changed?
11:09 pdurbin
It's up to you.
11:12 pdurbin
Oh, I got my Jupyter Notebook working. So now you can see that same plot of number of messages in this channel per month (it's growing!) it the nice previer GitHub has: https://github.com/pdurbin/dataverse-irc-metrics/blob/824d10cb3ca4f290505777820b31ddec3023bafc/index.ipynb
11:13 poikilotherm
Nice!
11:13 pdurbin
And if you go to https://github.com/pdurbin/dataverse-irc-metrics and click "launch binder" you can change the code or add additional plots or whatever.
11:15 poikilotherm
Looks pretty cool :-)
11:17 pdurbin
I think it should be possible to put that code and data in Dataverse and launch the Jupyter Notebook in Whole Tale from the Explore button.
11:18 poikilotherm
Looks like Binder is building a Docker container for you
11:18 poikilotherm
Takes some time to build
11:19 pdurbin
Yes, exactly. You can also play with it locally with https://github.com/jupyter/repo2docker
11:20 pdurbin
Actually, if you feel like it, you could pile on to https://github.com/jupyter/repo2docker/issues/444
11:22 poikilotherm
Man, this is still building...
11:22 poikilotherm
Looks like it is building R from scratch
11:25 pdurbin
Yeah, it's much faster with Ubuntu packages like r-cran-dplyr but while these packages work fine on my Ubuntu 18.04 server, they produce errors in mybinder (which also runs Ubuntu 18.04). I mentioned this at https://gitter.im/jupyterhub/binder/archives/2019/05/17?at=5cdf07bf879f4478c797cd7b
11:26 pdurbin
Oh, and the conversation continues at https://gitter.im/jupyterhub/binder/archives/2019/05/18
11:51 Richard_Valdivia joined #dataverse
12:39 pdurbin
Richard_Valdivia: hi! I recognize your name from your question about configuring Handles instead of DOIs: https://groups.google.com/d/msg/dataverse-community/FheyKhxDXYY/dhj-fvhPBgAJ
12:40 donsizemore joined #dataverse
13:18 pdurbin
donsizemore: mornin'. How many million things have I asked you for? I've lost track. :)
13:19 pdurbin
stefankasberger: hi, did you get a chance to read Jim's message at https://groups.google.com/d/msg/dataverse-community/07h0Ca-Ai1I/19U7Xlt7AwAJ about bagit and OAI_ORE?
13:20 donsizemore
@pdurbin ida know (remember family circus?) — was just looking at a switch for configurable pem location
13:20 pdurbin
perfect
13:20 donsizemore
@pdurbin and don't look now, but tests also fail on a VM identical to phoenix on current develop
13:21 pdurbin
hmm, but https://jenkins.dataverse.org is still sunny :)
13:22 donsizemore
@pdurbin i was waiting until i had them working to enable them
13:24 pdurbin
That's fine but if you expose the failures and the server.log I can try to help.
13:24 donsizemore
@pdurbin i gotta dig through the errors. on jenkins.dataverse.org running out of my home directory it didn't even build the warfile
13:25 pdurbin
bah
13:26 pdurbin
oh, Richard_Valdivia and I were chatting and he knows your boss :)
13:34 stefankasberger
yes, will answer later. sounds good.
13:35 Richard_Valdivia
@pdurbin Yes, we try to config Handle in the last month. But as we can not do it, we return to version 4.4 that does not have the obligation to have DOI or Handle.
13:35 Richard_Valdivia
But we will solve this in a future (I hope)... :)
13:40 Richard_Valdivia
donsizemore: hello!!! your boss make an exclent presentation here... :)
13:46 donsizemore
@Richard_Valdivia excellent, i'm glad to hear!
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15:07 donsizemore
@pdurbin i'll finish up the EC2 stuff hopefully during a meeting this afternoon, then i'm about to embark down end-to-end MD5 verification from Dataverse to iRODS off-site
16:16 pdurbin
Richard_Valdivia: I don't understand what you're saying about Dataverse 4.4. Can you please explain more?
16:16 pdurbin
stefankasberger: thanks, no rush. I just wanted to make sure you saw it. :)
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18:20 donsizemore
@pdurbin any reports of flyway going wonky in develop?
18:24 pdurbin
donsizemore: nope. Are you seeing issues?
18:26 donsizemore
@pdurbin i just did running the EC2-create script. lemme get this PR in and i'll test more
18:29 pdurbin
sounds great, thanks!
19:27 donsizemore joined #dataverse
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19:27 donsizemore
@pdurbin yup, develop breaks in both EC2 and dataverse-ansible: "remote failure: Error occurred during deployment: Exception while loading the app : javax.ejb.CreateException: Initialization failed for Singleton StartupFlywayMigrator. Please see server.log for more details.", "stderr_lines": ["remote failure: Error occurred during deployment: Exception while loading the app : javax.ejb.CreateException: Initialization failed for Singleto
19:28 pdurbin
huh.
19:28 pdurbin
let me see when I last ran the tests on phoenx
19:28 pdurbin
phoenix*
19:28 donsizemore
server.log bonks at javax.ejb.EJBException: javax.ejb.CreateException: Initialization failed for Singleton StartupFlywayMigrator
19:29 donsizemore
Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateException: Migration V4.14.0.1__5822-export-var-meta.sql failed ---------------------------------------------------- SQL State : 42701 Error Code : 0 Message : ERROR: column "postquestion" of relation "variablemetadata" already exists Location : db/migration/V4.14.0.1__5822-export-var-meta.sql
19:30 pdurbin
phoenix was passing as of 771b8b but stuff has been merged since then
19:31 * pdurbin
clicks "build now" for phoenix
19:35 pdurbin
https://github.com/IQSS/dataverse/pull/5833/files looks good to me. I'm not sure why you're seeing that. I'll report back what phoenix says.
19:37 pdurbin
uh oh, deployment on phoenix failed as well: https://build.hmdc.harvard.edu:8443/job/phoenix.dataverse.org-deploy-develop/407/console
19:37 pdurbin
Message : ERROR: column "postquestion" of relation "variablemetadata" already exists
19:37 pdurbin
Location : db/migration/V4.14.0.1__5822-export-var-meta.sql (/usr/local/glassfish4/glassfish/domains/domain1/applications/dataverse/WEB-INF/classes/db/migration/V4.14.0.1__5822-export-var-meta.sql)
19:38 pdurbin
donsizemore: would you like to create an issue? :)
19:38 donsizemore
i'm happy to. all i know is what i can glean from server log though
19:39 pdurbin
The stuff you're gleaning is the same stuff I'm seeing.
19:40 donsizemore
opening per instruction ;)
19:41 pdurbin
thank you!
19:44 rigelk joined #dataverse
19:52 pdurbin
donsizemore: thanks for opening https://github.com/IQSS/dataverse/issues/5862 ... I just left a comment.
19:53 pdurbin
rigelk: hi! You must have seen my invitation to join us here over at https://chat.indieweb.org/social/2019-05-20 :)
19:54 rigelk
hi pdurbin and hi all
19:54 rigelk
thanks for the invitation
19:56 rigelk
I have read through both documents and I have come to the same conclusions regarding the potential benefits of using ActivityPub for corpora dissemination
19:57 pdurbin
Cool. I'm pinging the guy who wrote them (Michael) but he is many timezones ahead of me. :)
19:57 rigelk
one thing comes to mind though: clients compatible with Mastodon are specific to Mastodon's own API . Implementing ActivityPub won't give us de-facto compatibility with Mastodon clients.
19:58 rigelk
but I guess that's something to bring tomorrow :)
20:00 pdurbin
Right, in https://librelounge.org/episodes/episode-20-activitypub-part-3.html I was just hearing that Mastodon has it's own API . It sounds like there's the spec but then there are conventions that are being agreed upon outside the spec. :)
20:01 rigelk
pdurbin: I'm UTC +1, so I'll have time to discuss with Michael tomorrow if he reaches out before the call
20:02 pdurbin
ok, I think he's utc+3 or so :)
20:02 rigelk
indeed. There is the spec and its various implementations (dialects). But when we talk about the Mastodon API it is just to talk about the REST API of Mastodon, unrelated to ActivityPub.
20:03 rigelk
The spec talks about a potential use of ActivityPub as a client-server exchange protocol, but so far no major implementation uses it… (that I have heard of)
20:03 pdurbin
We recently implemented Make Data Count support in Dataverse and I was surprised how disconnected the spec was from what we actually needed to do. :)
20:07 rigelk
I didn't know about Make Data Count, but I'm not surprised :) making specifications is hard, and in the case of ActivityPub I would even say it is more of a framework to build on than a specification.
20:08 pdurbin
Sure. And I don't mean to be overly critical of anyone's spec. It does seem super hard and I've only read specs and implemented stuff (SWORD is another one). I've never written one. :)
20:09 pdurbin
While you're here, would you like to tell us about your project?
20:09 rigelk
same here
20:09 rigelk
anyway that also leaves us some leeway to build specific dialects like we plan to with OLKi (and Dataverse I hope)
20:14 rigelk
sure. I'm co-maintainer of the PeerTube project, and currently developing OLKi, an self-hostable open source platform that aims to help discuss and curate scientific corpora from the fediverse. It is part of a larger project at http://www.loria.fr/en/
20:15 pdurbin
Nice, can you please link to the OLKi code?
20:16 rigelk
the platform project is at https://olki.loria.fr/platform/ - the code at https://framagit.org/synalp/olki/olki
20:16 rigelk
it only started two months ago though, so don't expect much yet :)
20:16 pdurbin
heh, no worries and thanks
20:16 pdurbin
and I've heard of PeerTube, very cool
20:21 rigelk
the best thing is the interaction of PeerTube with the rest of the fediverse, just by using ActivityPub (or rather, allowing comments about a video to be made via textual ActivityPub dialects). But videos are disseminated via their own ActivityPub dialect.
20:23 rigelk
I hope we can make something similar with scientific data and activities. That would be cool :)
20:23 pdurbin
absolutely :)
20:28 pdurbin
Sorry, I'm trying to push one more commit before I jump on my bike and head home. And it's about to rain. :)
20:28 rigelk
it is a bit late here - I'll see you tomorrow for the call. In the meantime, feel free to ping me here
20:29 pdurbin
sounds good! thanks for dropping by!
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