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IRC log for #dataverse, 2019-09-30

Connect via chat.dataverse.org to discuss Dataverse (dataverse.org, an open source web application for sharing, citing, analyzing, and preserving research data) with users and developers.

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All times shown according to UTC.

Time S Nick Message
07:25 poikilotherm joined #dataverse
07:47 corentin95 joined #dataverse
07:49 corentin95 Hi guys, hope you're all doing fine. I'm wondering if this is the good place to ask a question if I encounter a problem with dataverse after my installation
07:49 juancorr joined #dataverse
07:49 poikilotherm Good morning corentin95
07:50 poikilotherm IQSS people are all at sleep, but I can try to help you
07:50 corentin95 Thanks !
07:51 corentin95 So here is my problem : I installed dataverse on a kubernetes cluster. Everything seems to be all good. I can create a user. But when I connect using the user I just created, I land on the main webpage with this message : Not Authorized - You are not authorized to view this page.
07:52 poikilotherm Ah, then you do have reached out to the right guy. I'm the maintainer of dataverse-kubernetes
07:52 poikilotherm Did you use my repo or did you try your own stuff?
07:53 corentin95 I used the IQSS/dataverse-kubernetes repo
07:53 poikilotherm Nice :-)
07:53 poikilotherm What components did you choose?
07:54 poikilotherm Minikube? k3s? AWS? Kind?
07:54 poikilotherm (Lots of options out there)
07:55 corentin95 We have a cluster on Exoscale (Swiss cloud provider), this is where I deployed it using IQSS/dataverse-kubernetes/tree/master/k8s
07:56 poikilotherm Ok. What K8s version is Exoscale using?
07:57 corentin95 let me check that :-)
07:59 corentin95 v1.12.3
07:59 poikilotherm Ui. That might be a problem
07:59 poikilotherm I am testing all of this stuff on 1.14
08:00 poikilotherm I'd be happy to help debugging this.
08:00 poikilotherm Would you like me to take a look at your deployment?
08:01 corentin95 Yes sure !
08:01 poikilotherm Any chance you can grant me temporary access to take a look?
08:01 poikilotherm Would very much ease debugging ;-)
08:02 poikilotherm We can do a live video meeting to look at it together
08:02 corentin95 Yes I know ! :-) I'll have to ask my superior before due to security issue ...
08:03 poikilotherm Sure. I dunno which timezone you're in, but I'll be around for a few hours now.
08:03 poikilotherm Its 10:00 here.
08:04 corentin95 I'm glad to here that, same here !
08:04 poikilotherm Where are you from?
08:04 stefankasberger joined #dataverse
08:04 corentin95 Switzerland, french part
08:05 poikilotherm Ah, ok :-)
08:05 poikilotherm This is where I am now... https://www.openstreetmap.org/node/367648305
08:06 corentin95 That's a bit far away :-D
08:06 poikilotherm At least same timezone :-D
08:07 poikilotherm Phil Durbin from IQSS will be around in about 2 hours
08:07 poikilotherm He's an early bird
08:07 poikilotherm I'm sure he will love to hear more from what you guys are up to, etc
08:08 poikilotherm Pretty sure there is no swiss based installation on the map yet
08:08 poikilotherm He is always eager to see new repos on that map ;-)
08:09 corentin95 Great to hear ! :-)
08:09 corentin95 And yeah I'm fortunate it's the same timezone
08:11 corentin95 Unfortunatly I'm afraid I won't be able to grand you a temporary access for the moment :'(
08:13 poikilotherm Meh
08:14 poikilotherm Alright then.
08:14 poikilotherm How did you deploy?
08:14 poikilotherm kubectl apply -k ?
08:15 corentin95 Sorry...
08:15 corentin95 Yes
08:15 corentin95 I followed this workflow :
08:15 corentin95 https://camo.githubusercontent[…]d776f726b732e6d64
08:16 poikilotherm Hehehe. You should be aware that this is the internal workflow and normally hidden from you, as the jobs do all the hard work
08:17 corentin95 Hmmmm, so I should have deploy in a different way ?
08:17 poikilotherm That depends on what you actually did.
08:17 poikilotherm When you tried to do everything by yourself, there might be sth missing.
08:17 corentin95 So, let me describe it to you
08:17 corentin95 Yes !
08:17 corentin95 I had to declare a storage class
08:19 corentin95 It was missing so the pvc was stuck in a pending state
08:19 corentin95 I also added an ingress to expose dataverse but I don't thing this is the problem here
08:20 corentin95 (It's exposed using traefik)
08:22 corentin95 So basically, I should have only run "kubectl apply -f ." ?
08:22 corentin95 And maybe add this ingress
08:22 poikilotherm Not -f, but -k. As I do not offer a helm chart or operator right now, people can use (builtin) kustomization
08:23 corentin95 Oups sorry, -k
08:23 corentin95 Should I try to redeploy that way ?
08:24 poikilotherm You could do so. Please keep in mind that you can create you own kustomization file with the necessary patch for that storage class.
08:24 poikilotherm You can even reference the repo remotely
08:25 poikilotherm There are a few options for patching in Kustomization. A working example for AWS storage class which might work as a template for you is in docs/aws-demo
08:27 corentin95 Okay, thanks ! I'm going to take a look right away and keep you updated :-)
08:27 poikilotherm We can still do a VC if you want with screen sharing.
08:27 poikilotherm Up to you.
08:28 poikilotherm And I would love you to open issues for what you think is missing
08:28 poikilotherm Or even PRs adding docs about what would have helped you
08:28 corentin95 Could be nice ! Don't want to bother you too much. In the first place I'm going to take a look on my own and I'll come back to you if I got any problems.
08:29 poikilotherm Okidoki :-)
08:29 corentin95 I'll do it once it's all fixed, be sure of that :-)
08:32 poikilotherm Thank you!
08:37 pdurbin_m joined #dataverse
08:37 pdurbin_m corentin95: have you published the root dataverse yet?
08:40 corentin95 Not sure ... How should I do that ?
08:41 poikilotherm http://guides.dataverse.org/en/latest/user/dataverse-management.html#publish-your-dataverse
08:42 poikilotherm Meh. A screenshot would be benefical for that part of the guide
08:47 corentin95 joined #dataverse
08:49 corentin95 I don't see any publish button ...
08:50 poikilotherm You need to be logged in as dataverseAdmin
08:50 poikilotherm (or other admin user)
08:50 poikilotherm Otherwise it's hidden
08:56 corentin95 Oh great !! That works :-D
08:58 pdurbin_m corentin95: fantastic :)
09:01 corentin95 I may have a couple of questions left...
09:02 * poikilotherm is all ears
09:04 corentin95 Oh no, sorry to bother you find the answer !
09:06 corentin95 Well, thank you very much for your help. I really appreciated  it ! You spare me many working hours. Thanks again :-)
09:07 poikilotherm Sure. Again: I'd love issues and feedback on dataverse-kubernetes
09:07 poikilotherm You might have seen my 4.16 milestone.
09:07 poikilotherm There are some things still left open
09:07 poikilotherm If you would like to help, go ahead.
09:07 poikilotherm It's Hacktoberfest :-)
09:08 poikilotherm https://hacktoberfest.digitalocean.com/
09:08 corentin95 Let me check that :-) I would gladly help if I can
09:09 pdurbin_m corentin95: you are also welcome to help with the Installation Guide. :)
09:12 corentin95 Oh actually, I might have a final question ...
09:14 corentin95 To allow a user to add a dataset for example, does he/her has to be a superuser ?
09:15 corentin95 Because when I'm logged as a user lambda, I can't that " + Add data " button ...
09:15 poikilotherm pdurbin_m that's a question for you :-D I out for lunch
09:15 poikilotherm I am
09:18 corentin95 Enjoy your meal :-)
09:21 pdurbin_m corentin95: please read http://guides.dataverse.org/en/4.16/installation/config.html#root-dataverse-permissions
09:22 corentin95 Oh yes, I just didn't find the "edit" all good now thanks :9
09:22 corentin95 :)
09:25 pdurbin_m Sure! The guides are in the main repo on GitHub if you'd like to open an issue or fix them up.
09:38 corentin95 I may open an issue about those storage class, I add to add them myself (no big deal) but just to let people know
09:40 pdurbin_m corentin95: please do!
09:41 corentin95 had * I will :-)
09:45 pdurbin joined #dataverse
09:45 pdurbin ah, now I'm on a full sized keyboard :)
09:47 pdurbin corentin95: it's pretty cool that you're using Kubernetes. One thing you should be aware of is that dataverse-kubernetes is a community project (lead by poikilotherm). No one at IQSS has started using it yet. I'm not saying there's anything wrong with it. I'm just thinking of future emails to support@dataverse.org
09:51 pdurbin That said I have big dreams for dataverse-kubernetes for demo purposes. :)
09:58 poikilotherm Re
10:00 poikilotherm pdurbin are you doing anything special for that hot reloading of JSF components in Netbeans? Or is this working because of the exploded WAR?
10:01 poikilotherm I was looking for options to lower cycle times...
10:02 pdurbin Are you talking about before or after https://github.com/IQSS/dataverse/issues/6208 ? I can talk about a year ago or I can talk about now.
10:04 poikilotherm Dunno. It's not working from Netbeans anymore? Danny mentioned a workaround
10:04 poikilotherm I don't want to switch to Netbeans, but "know your options"
10:04 pdurbin The work around is to revert https://github.com/IQSS/dataverse/commit/5f99037 locally but not commit it. Not a great workaround.
10:05 pdurbin You're on intellij, right?
10:05 poikilotherm Aye
10:05 poikilotherm There is of course JDWP. But this is limited to classes and even with that limited to no scope or signature changes
10:06 poikilotherm There is HotSwap + DCEVM, but this seems like a stalled project
10:06 poikilotherm No updates for DCEVM anymore :-(
10:06 poikilotherm And there is JRebel
10:06 pdurbin Is there something like http://guides.dataverse.org/en/4.16/developers/tools.html#netbeans-connector-chrome-extension for intellij?
10:07 poikilotherm Hmm I dunno
10:07 poikilotherm Many people use LiveReload these dasys
10:07 pdurbin link?
10:07 poikilotherm http://livereload.com/
10:08 poikilotherm But you need support in the app for that
10:08 poikilotherm It's in Spring Boot for example
10:08 pdurbin this is what the Netbeans Connector Chrome Extension gives you
10:10 pdurbin hot reloading
10:10 poikilotherm Yeah
10:11 poikilotherm LiveReload uses a Firefox/Chrome/... plugin
10:11 poikilotherm Connecting to a server side that calls out for reload
10:11 poikilotherm Some projects (like Spring) integrated the server part in their dev tools
10:12 poikilotherm Looks like JRebel does it, too
10:14 pdurbin There's a nice podcast about JSF and related technologies: http://enterprisejavanews.com/episode-41-on-java-ee-guardians-jakarta-ee-vs-microprofile-jdk-13-and-javafx
10:16 poikilotherm Ui. 1:16. Going to listen to that while driving :-)
10:16 poikilotherm Thx for the suggestion
10:16 poikilotherm Reads promising
10:17 pdurbin Oh, and there's another UI thing I wanted to show you. One sec.
10:17 pdurbin Lightning Web Components: https://developer.salesforce.com/blogs/2018/12/introducing-lightning-web-components.html
10:18 pdurbin "Many features that required frameworks now come standard: you no longer need a proprietary component model, proprietary language extensions, proprietary modules, etc."
10:18 pdurbin "Lightning Web Components is the Salesforce implementation of that new breed of lightweight frameworks built on web standards."
10:19 poikilotherm :-)
10:20 pdurbin What do you think?
10:23 poikilotherm It's a pretty good idea to use Standards. I don't know how mature these are and how mature the implementations are. And I dunno if they are widespread enough. I remember to old days when IE did not support CSS transparency and you had to hack around that.
10:29 pdurbin Sure. I'm thinking about the future. Maybe five years out. For now I think we should probably use React.
10:29 poikilotherm My colleague Dirk know a lot about this...
10:29 poikilotherm He's using Vue for the open access monitor
10:30 pdurbin Ok, let's use Vue.
10:30 poikilotherm This is all frameworks anyway
10:30 pdurbin yeah
10:31 poikilotherm Setting up a project for such a transition is going to take a while.
10:31 pdurbin yeah
10:31 poikilotherm It's also likely that the project itself will take some time
10:31 poikilotherm So maybe that's enough time to have sufficient support for things out in the wild?
10:31 pdurbin JSF -> React/Vue -> Web Components
10:31 poikilotherm So a transition to web components now might be a good idea
10:31 pdurbin yeah
10:32 poikilotherm I'm pretty sure this will take at least half a year to get this into the pipeline, funding etc. Coding for a year. That's a lot of water running down the rivers
10:33 poikilotherm And maybe you will simple have to say "we only support browsers XXX"
10:33 poikilotherm And no IE9, IE11, ...
10:33 pdurbin sure, evergreen browsers only
10:34 poikilotherm Everybody is welcome to write its own UI for older systems
10:34 poikilotherm There is a well defined API
10:34 pdurbin yeah
10:35 pdurbin Dataverse can have multiple UIs. Just like Jenkins.
10:35 pdurbin Kito is into Web Components. You'll hear him talk about them in that podcast above.
10:38 jri joined #dataverse
11:09 yoh joined #dataverse
11:29 yoh joined #dataverse
12:03 dataverse-user joined #dataverse
12:03 dataverse-user hi for all
12:04 dataverse-user i have a little error with worldmap, when I try to configure that
12:04 dataverse-user error "gis_data_info" not available
12:04 dataverse-user Sorry! This request is not from a Dataverse registered to use the WorldMap.  This dataverse url was not recognized: http://research-data.urosario.edu.co/file.xhtml?fileId=15&version=1.0
12:10 pdurbin_m joined #dataverse
12:11 pdurbin_m dataverse-user: hi! Please see DATAVERSE_SERVER_URL at https://github.com/IQSS/geoconnect/blob/master/heroku_setup.md#configure-additional-settings
12:14 corentin95 joined #dataverse
12:47 pdurbin dataverse-user: still there?
13:15 pdurbin poikilotherm: I just heard about another Web Components framework called ui5 ( https://github.com/SAP/ui5-webcomponents ) at http://adambien.blog/roller/abien/entry/sap_odata_opensource_and_apache (airhacks #55 at http://airhacks.fm )
13:16 pdurbin Which one sounds more promising? Lightning Web Components or UI5 Web Components?
13:22 poikilotherm I have absolutely no idea :-D
13:22 poikilotherm Let me listen to the podcasts first, ok?
13:22 pdurbin sure, sounds good, but it's only mentioned in passing :)
13:24 pdurbin the more interesting part of that episode is https://olingo.apache.org
13:26 poikilotherm Oh, ODATA
13:26 poikilotherm open-access-monitor has been using it.
13:26 pdurbin yeah?
13:26 poikilotherm But not from Apache
13:26 poikilotherm It was an MS implementation in C#
13:27 poikilotherm And IIRC they quited using it because they switched to MongoDB as datastore
13:28 pdurbin on the podcast they made it sound like you code the front end to ODATA
13:29 donsizemore joined #dataverse
13:37 pdurbin donsizemore: mornin'. I just opened https://github.com/scholarsportal/Dataverse-Data-Curation-Tool/issues/8
13:57 pdurbin poikilotherm: almost time for the call, right?
13:57 poikilotherm Yeah
14:00 * poikilotherm waits for the meeting to start...
14:00 pdurbin "The meeting will begin when Dataverse Team arrives"
14:01 pdurbin Here's how to connect if anyone here is interested: https://github.com/IQSS/dataverse/pull/6192#issuecomment-534830250
14:01 poikilotherm "Now approaching sector 6, anomalous materials"
14:06 donsizemore @pdurbin oh, i was just going to add it back in once localeCode arrived in release
14:07 pdurbin donsizemore: cool
14:07 pdurbin poikilotherm: should we just take notes here?
14:08 pdurbin "what type of microsoft logins are supported?"
14:08 dataverse-user pdurbin yes im here
14:10 pdurbin alemania
14:10 pdurbin "suggested vocabularies"
14:11 dataverse-user joined #dataverse
14:12 pdurbin dataverse-user: hi! poikilotherm and I are on a call right now. For another 45 minutes or so.
14:12 dataverse-user excuseme, i lost connection
14:13 pdurbin dataverse-user: you are probably suffering from this bug: https://github.com/IQSS/chat.dataverse.org/issues/3 . Not your fault. You might want to try http://webchat.freenode.net/?channels=#dataverse instead.
14:14 pdurbin poikilotherm: https://datatest.servehttp.com
14:15 hblancoca joined #dataverse
14:15 hblancoca hi
14:17 hblancoca "error "gis_data_info" not available" "Sorry! This request is not from a Dataverse registered to use the WorldMap" i believe that my dataverse research-datageo.urosario.edu.co is not registeded
14:22 dataverse-user joined #dataverse
14:23 poikilotherm pdurbin: I will have to leave in ~20min to pick up kids...
14:24 pdurbin poikilotherm: sounds like the tested with "microsoft live" accounts and whatever one calls the microsoft accounts for an institution. Two kinds of accounts.
14:24 poikilotherm Right.
14:25 poikilotherm You will only have local AD accounts available with an Azure AD setup that is linked with the local one.
14:25 poikilotherm As the docs say ;-)
14:55 pdurbin dataverse-user: ok, the call is over. Sorry about that. Still here? :)
15:29 xarthisius pdurbin: can I ask you a favor? Could you change WT ext tool manifest on dev2.dataverse.org to point to https://girder.local.wholetale.org/api/v1/integration/dataverse ?
15:30 xarthisius also siteUrl being returned now is https://ec2-184-73-31-204.compute-1.amazonaws.com which is midly inconvienient. Could it match FQDN of the site (dev2.dataverse.org)  ?
15:31 jri joined #dataverse
15:32 jri_ joined #dataverse
15:33 jri joined #dataverse
15:44 pdurbin xarthisius: sure! I'm in a meeting right now but will fix it up soon.
15:46 xarthisius thanks!
16:32 pdurbin xarthisius: can you please give this a try? https://dev2.dataverse.org/dataset.xhtml?persistentId=doi:10.5072/FK2/VKI4P5
18:05 donsizemore @pdurbin does https://github.com/IQSS/dataverse-ansible/issues/113 sound robust enough to move API test suiting into jenkins? terminate all instances tagged say jenkins_delete_me with cron
18:06 pdurbin let me look at https://github.com/IQSS/dataverse-ansible/compare/113_support_ec2_tags
18:07 pdurbin looks like a nice generic solution, good work
18:15 donsizemore well, it's a 'for now' kind of thing.
18:15 pdurbin sure
18:15 pdurbin steady progress :)
18:16 pdurbin bit by bit we'll get there
18:25 nightowl joined #dataverse
18:27 nightowl hi all...I'm trying to install dataverse in AWS. Seems everything is geared for starting with MAC. However, I am a Windows user. Can I create the EC2 instance manually and then use the "dataverse-ansible" script/instructions to install?
18:27 nightowl referring to this specifically: http://guides.dataverse.org/en/latest/developers/deployment.html
18:31 pdurbin nightowl: yeah, we're very Mac and Linux oriented when it comes to dev. Sorry. You can absolutely spin up an EC2 instance (or Google or Azure or whatever) any way you know how and then follow the "quickstart" I added to the dataverse-ansible README.
18:33 nightowl it looks like it is creating security groups, key pairs, choosing the CentOS 7 AMI, t2.medium, and installing a few dependencies...right? I think we would like to use our own security groups and key pairs anyway. Thanks for the response! New to Dataverse and AWS! I think I need to get a MAC!
18:34 pdurbin Heh. Macs are nice! I use Linux at home. :)
18:35 pdurbin nightowl: if you're successful I might ask you to make a pull request to make the dataverse-ansible option more prominent at http://guides.dataverse.org/en/4.16/installation/prep.html#choose-your-own-installation-adventure
18:35 pdurbin donsizemore: Leonid keeps gushing about how much he loves dataverse-ansible.
18:36 nightowl I will do so. Thanks for the response...this is a great support option!
18:36 nightowl I tried using the dataverse-ansible on a local VM and it crashed...I couldn't figure out where...I assume it is specific to AWS?
18:37 pdurbin No, it should work fine in Vagrant, for example.
18:38 pdurbin There's a Vagrantfile in there.
18:38 nightowl oh I was just running it in a virtualbox VM...not with Vagrant
18:48 jri joined #dataverse
18:54 donsizemore @pdurbin it's looking like RHEL8/CentOS8 will require Postgres-10+
18:55 pdurbin donsizemore: ok, in https://github.com/IQSS/dataverse/issues I don't see an issue for Postgres 10 support. Do you mind creating one?
18:57 donsizemore well, either that or the postgres repos can provide an older python-psycopg2 module, but i don't see them putting much work into postgres-9.6 under rhel/centos8
18:58 pdurbin what version does AWS RDS support?
18:59 donsizemore @pdurbin i think you're good https://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/CHAP_PostgreSQL.html#PostgreSQL.Concepts
19:00 pdurbin I see a lot of 10.x. Good. Thanks.
19:02 donsizemore and i have dataverse deploying on centos8 now
19:02 pdurbin nice!
19:02 pdurbin I always call you our pioneer. :)
19:02 donsizemore it's compiled/intended with postgresql10 so i don't think they'll backport those libraries for earlier versions
19:02 * pdurbin hands donsizemore a coonskin cap
19:03 donsizemore doniel boone? i heard he took every afternoon off for tin cup libations
19:03 pdurbin oh dear, my mom says we're related to him
19:04 donsizemore you missed my intentional misspelling ;)
19:04 pdurbin heh, so I did
19:05 donsizemore so... ima leave the role defaults at 9.6, and i'll update the README to note that at present RHEL/CentOS8 and Postgres < 10 are mutually exclusive
19:06 donsizemore p.s. if you can approve my dataverse-ansible pull request, tiny though it may be, i can start switching jenkins.dataverse.org over to running tests in EC2
19:07 Alejandra joined #dataverse
19:08 pdurbin I'll just merge it if that's ok.
19:09 GeraFp joined #dataverse
19:09 pdurbin GeraFp: hi!
19:10 donsizemore @pdurbin excellent. i may take a mental health trip to the gym, then i'll start on jenkins
19:11 pdurbin donsizemore: do it. I went this morning. Merged!
19:11 donsizemore @pdurbin i'll open the issue about PG10+ support. they can use dataverse-ansible to test ;)
19:11 pdurbin Alejandra: hi!
19:12 GeraFp Hi all!! :D Good Afternoon.
19:12 Alejandra @pdurbin Hi!
19:13 pdurbin It was a pleasure chatting with you this morning. :)
19:13 pdurbin donsizemore: these are the folks who are starting to use our spin up scripts and dataverse-ansible. :)
19:15 donsizemore hello =)
19:35 pdurbin And they've got some great stuff in the works: https://github.com/IQSS/dataverse/issues/6154 and https://github.com/IQSS/dataverse/issues/6155 and https://github.com/IQSS/dataverse/issues/6156 :)
19:49 pdurbin xarthisius: huh, the siteUrl is still wrong on dev2. I'm bringing it down to hack on it some more.
20:03 pdurbin oh, duh, I had siteUrl in domain.xml twice
20:05 pdurbin xarthisius: ok, please try again: https://dev2.dataverse.org/dataset.xhtml?persistentId=doi:10.5072/FK2/VKI4P5
20:05 xarthisius pdurbin: perfect! thank you!
20:06 pdurbin does it work? :) or... are you unblocked at least? :)
20:09 xarthisius it works, we'll be using it to test https://github.com/whole-tale/girder_wholetale/pull/352
20:09 xarthisius as soon as I add description :)
20:13 pdurbin great!
20:13 pdurbin What did you decided to to with regard to docs? Are you going to ship manifest files at both leves? File and dataset?
20:13 pdurbin to do*
20:20 xarthisius I think we're more interested in dataset level, so we'll focus on that. API will support any combination of fileId, filePid, datasetPid, datasetId though
20:22 pdurbin ok, sounds fine
20:22 pdurbin Thanks for providing Dataverse's first explore tool at the dataset level!
20:29 xarthisius yw! :)
21:01 pdurbin I'm feeling a Dataverse 4.17 release soon.

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