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IRC log for #dataverse, 2019-06-04

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All times shown according to UTC.

Time S Nick Message
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10:49 pdurbin pkiraly: welcome back :)
10:52 pkiraly pdurbin: Thanks! Yesterday at Skype call you mention that an institution is working on a feature like this: if a user publish something in Dataverse, the data will be published as well in another archive.
10:53 pkiraly pdurbin: Thanks! Yesterday at Skype call you mentioned that an institution is working on a feature like this: if a user publish something in Dataverse, the data will be published as well in another archive.
11:02 pdurbin pkiraly: yes, Jim from QDR talked about it most recently here: https://groups.google.com/d/msg/dataverse-community/JHIfe2uqvkc/GjLbOfIZAwAJ
11:05 pdurbin and answered some questions from Janet in that thread
11:18 pkiraly pdurbin: thanks! I'll check it. We have a similar use case.
11:19 pdurbin ok
11:49 donsizemore joined #dataverse
11:55 pdurbin donsizemore: mornin'. If I'm Mr. Shib, what does that make you? :) Or are you the new Mr. Shib? I forget which season or reboot we're on. :)
12:02 pdurbin I'm asking because pkiraly just started a "user affiliation and Shibboleth" thread at https://groups.google.com/d/msg/dataverse-community/7FwrzfIQZfY/nHCsNSy3CQAJ
12:10 donsizemore i saw that, started googling a little bit but everybody's back from iasist this morning
12:11 donsizemore i could run it by our ID Mgmt guy here in central IT? he was pretty interested in federating shibboleth because usually UNC policy is UNC-only
12:15 pdurbin Ah, cool that they're back. That's ok. I have a good handle on what pkiraly wants. He doesn't run shib the way we do. The "affiliation" for our users probably make sense. I should go look at the user dashboard to see if it's there.
12:18 donsizemore affiliation looks good in odum's dashboard
12:18 pdurbin Yeah, at https://demo.dataverse.org/dashboard-users.xhtml when Authentication is Shibboleth I see reasonable values under Affiliation like Arizona State University and New York University.
12:18 donsizemore so, install docs. a year or two ago i asked about updating init vs. systemctl calls and we wanted to keep 6 commands, time to switch? i can make a PR if you want
12:18 pdurbin donsizemore: the difference is that you and I have hundreds of Shib IdPs.
12:19 pdurbin pkiraly only has one Shib IdP, I think
12:19 pdurbin donsizemore: on a related note, can you first please look at dan-drexel 's pull request? This: https://github.com/IQSS/dataverse/pull/5906
12:21 pdurbin it's sort of this init territory
12:23 donsizemore looks fine by me
12:24 pdurbin Huh. Ok, Oliver had a problem with it. Do you see his review? I wasn't following the discussion very closely yesterday.
12:25 donsizemore oliver's correct that i did manually kill solr in my last walk-through. i can edit the PR?
12:26 pdurbin I would suggest just making a new PR.
12:26 pdurbin If you want to get fancy, you could make a PR into dan-drexel's PR. :)
12:27 pdurbin That's what we do when contributors don't let us push to their forks.
12:43 donsizemore he wants to use service/systemctl in the first place
12:44 pdurbin I like `service` because it's what I learned in the 90s. :)
12:47 donsizemore p.s. on RHEL8: EPEL has been pushed to Oct 1
12:47 pdurbin What about CentOS 8? When is it expected?
12:47 donsizemore i started out calling /etc/init.d directly on solaris
12:48 donsizemore they're in "build loop 0" https://wiki.centos.org/About/Building_8
12:48 pdurbin Yeah, I was just thinking that maybe I started with init.d. It was a whlie ago. :)
12:49 pdurbin Ok, thanks. I guess I'll keep an eye on "release work".
12:51 donsizemore p.s. i set up a pydataverse job on jenkins.dataverse. it simply calls a 'python3 setup.py test'
12:51 pdurbin o.O
12:52 pdurbin Ah, it's waiting for the next webhook, I suppose. :) Thanks!
12:55 donsizemore we'll see about test reports two merges out
12:57 pdurbin Awesome. Want me to send webhooks from the R and Java client libraries?
13:04 donsizemore shore
13:12 stefankasberger joined #dataverse
13:13 pdurbin stefankasberger: https://jenkins.dataverse.org/job/pyDataverse/ :)
13:13 pdurbin donsizemore: ok, and dataverse-metrics and dataverse-kubernetes?
13:14 stefankasberger @pdurbin: hi! i have a question regarding required fields of api metadata uploads. which attributes must be in the json for a dataset upload? which ones for a dataset? is there any documentation or file, where i could get this information from?
13:14 donsizemore dataverse-metrics sure. dataverse-kubernetes, fine but that will take more time
13:14 stefankasberger * dataverse instead of dataset for the first one.
13:15 pdurbin stefankasberger: there is a minimal JSON at http://guides.dataverse.org/en/4.14/_downloads/dataset-finch1.json via http://guides.dataverse.org/en/4.14/api/native-api.html#create-a-dataset-in-a-dataverse
13:16 pdurbin stefankasberger: and here's one for all the fields: https://github.com/IQSS/dataverse/blob/v4.14/scripts/api/data/dataset-create-new-all-default-fields.json
13:18 pdurbin donsizemore: ok. Added: https://github.com/IQSS/dataverse-client-java/settings/hooks
13:19 pdurbin donsizemore: and https://github.com/IQSS/dataverse-client-r/settings/hooks
13:19 donsizemore i have four hours of meetings today, so i'll cobble them into jenkins in the installment plan ;)
13:19 pdurbin donsizemore: and https://github.com/IQSS/dataverse-metrics/settings/hooks :)
13:20 pdurbin I guess I'll wait on dataverse-kubernetes :)
13:20 donsizemore jenkins.dataverse will need more engine power for that
13:20 pdurbin I'm probably forgetting some repos. But I'll be happy to eventually have https://jenkins.dataverse.org be a bit of a dashboard for Dataverse-related code. More engine power. Ok.
13:21 pdurbin donsizemore: should I be able to see pyDataverse somewhere in https://github.com/IQSS/dataverse-jenkins already?
13:22 pdurbin I can add an issue per repo if that would be helpful.
13:32 pdurbin larsks: any ideas on https://github.com/IQSS/dataverse/issues/5910 ? OpenStack/Swift storage question.
13:32 pdurbin stefankasberger: did those JSON files help? :)
13:32 pdurbin dan-drexel: thanks for pushing another commit to your pull request
13:33 larsks pdurbin: sounds a lot like the previous problem to me.
13:33 larsks If the workaround works (assign a default project to the user)...that would be a positive identification.
13:36 pdurbin larsks: ok, would you be able to add a comment about this? I don't know what I'm talking about. :)
13:39 larsks pdurbin:commented.
13:39 donsizemore joined #dataverse
13:40 pdurbin larsks: thanks! Is there an open issue on the JOSS side?
13:41 larsks Looks like https://github.com/javaswift/joss/issues/155
13:41 larsks That claims a PR was merge last July.
13:42 larsks Oh! No, merged 15 days ago.
13:42 larsks So very recent.
13:42 dan-drexel pdurbin: no problem!
13:44 pdurbin larsks: nice and ferrys is commenting over at https://github.com/javaswift/joss/pull/156 ... But did that pull request make it into a release yet, I wonder.
13:44 dan-drexel So I finished installing Dataverse, it told me it was installed ok, but I cant seem to reach it
13:44 dan-drexel It said I should have an instance running at http://129.25.170.214+:8080
13:44 dan-drexel However, that does not seem to work. Also that "+" in there seems odd?
13:44 pdurbin that + is very odd
13:45 pdurbin What do you see at http://129.25.170.214:8080/api/info/version ?
13:45 dan-drexel ohh I just looked back and I must had accidently put that + in there!
13:45 dan-drexel Nothing
13:46 pdurbin bah
13:46 dan-drexel Is it possible to fix that or do I need to do a fresh install?
13:46 pdurbin Well, it's nicer when the installation "just works" of course.
13:46 dan-drexel haha yep
13:47 dan-drexel It probably would have, if it wasent for me putting a random + on the ip
13:47 pdurbin I forget, did you say this is in VirtualBox?
13:47 dan-drexel Yep, I have it set to bridge the network adaptor and also have port 80 open on the host machine
13:47 pdurbin Are you familiar with Vagrant?
13:47 dan-drexel No
13:48 pdurbin It might be worth trying Vagrant. Please see http://guides.dataverse.org/en/4.14/installation/prep.html#vagrant-for-testing-only
13:49 pdurbin You already have VirtualBox installed so you're halfway there: http://guides.dataverse.org/en/4.14/developers/tools.html#vagrant :)
13:49 pdurbin Oh, are you on Windows?
13:49 dan-drexel Yep
13:50 dan-drexel Interesting, I could give that a shot
13:50 pdurbin Please just watch out for this: On Windows if you see an error like /usr/bin/perl^M: bad interpreter you might need to run dos2unix on the installation scripts.
13:50 pdurbin I'm a little worried it won't work for you very well on Windows.
13:50 dan-drexel But I also cloned the VM before installing, so I can just try running the install script again
13:51 dan-drexel I might also try Vagrant anyways too, it looks like something that is worth learning
13:51 pdurbin Yeah, Vagrant is useful. How about Ansible? Have you ever heard of it or used it?
13:51 dan-drexel Nope, have never heard of that either
13:55 pdurbin Ansible is really nice and donsizemore maintains https://github.com/IQSS/dataverse-ansible . Does that README make sense? You could spin up a fresh CentOS 7 VM in Vagrant, install Ansible on it with yum, and try the steps in the README. But you would need to look out fo https://github.com/IQSS/dataverse-ansible/issues/68 so I would suggest yum install
13:55 pdurbin https://releases.ansible.com/ansible/rpm/release/epel-7-x86_64/ansible-2.7.9-1.el7.ans.noarch.rpm
13:58 dan-drexel Ohh wow, that does look usefull! Yes I will definitly give that a try later on today for sure!
13:59 pdurbin Cool. I use it all the time to spin up Dataverse on EC2. That's another option if you have an AWS account.
14:00 pdurbin I use the script at http://guides.dataverse.org/en/4.14/developers/deployment.html#deploying-dataverse-to-amazon-web-services-aws
14:09 pdurbin donsizemore: I'm about to cut a dataverse-metrics release. When you see what's coming at https://github.com/IQSS/dataverse-metrics/compare/v0.2.4...master do you think it should be v0.2.5 or v0.3.0? pkiraly you might be interested in this too.
14:10 donsizemore @pdurbin mmm. is it a major feature? 0.2.5 might be fine
14:12 pdurbin Not a major feature but now it reaches out to GitHub APIs, which is different.
14:13 pdurbin To pull down contributors to GitHub repos. As a metric.
14:15 donsizemore your call
14:26 dan-drexel ehh reinstalled (this time w/o screwing up the ip) and still cant get it to work... 129.25.171.39:8080/api/info/version goes nowhere
14:44 pdurbin_m joined #dataverse
14:45 pdurbin_m dan-drexel: bummer. Did you try with Ansible?
14:46 dan-drexel I'm actually working on trying Ansible right now
14:47 pdurbin_m great
14:49 poikilotherm joined #dataverse
14:50 poikilotherm A pleasent morning dear dataveristas
14:50 jri joined #dataverse
14:55 pdurbin_m poikilotherm: hi! Can you please try https://github.com/IQSS/dataverse/pull/5908 ?
14:56 * poikilotherm goes looking
14:56 poikilotherm Ah, that one
14:56 poikilotherm Did you see Steves last comment on changing the element instead?
14:57 poikilotherm https://github.com/IQSS/dataverse/issues/4172#issuecomment-498446352
15:00 donsizemore @pdurbin r client segfaults on ubuntu18/r-3.4.4
15:05 pdurbin_m poikilotherm: yes but the root dataverse is not always root. On the demo site it's demo.
15:05 pdurbin_m donsizemore: sadness
15:06 poikilotherm Can we replace this with a call to lookup the root dataverse for a sane default?
15:06 pdurbin_m donsizemore: should I create an issue per repo to capture the config in dataverse-jenkins?
15:07 pdurbin_m poikilotherm: you don't like my pull request? :) Why not? :)
15:07 poikilotherm I am hesitating to switch the behaviour.
15:07 poikilotherm No testing in place, who know what might break by this
15:08 poikilotherm It is a global change :-/
15:08 jri_ joined #dataverse
15:09 pdurbin_m I tested it a little bit. :)
15:11 poikilotherm For me its hard to tell if this is sufficient. My gut feeling tells me to be carefull with this
15:18 donsizemore let me poke at client-r for a bit
15:18 donsizemore metrics and pyDataverse are happy
15:20 donsizemore @pdurbin i can just create an issue per repo. java client tests fail against demo.dataverse.org; r client segfaults
15:20 stefankasberger @pdurbin: yes, json files helped. thanks!
15:21 poikilotherm pdurbin: I just send an email to our translation service. We'll see how this goes.
15:21 poikilotherm s/send/sent/
15:32 pdurbin stefankasberger: great
15:33 pdurbin poikilotherm: fingers crossed!
15:33 pdurbin donsizemore: I'm happy to create the issues if you want. Please just let me know either way.
15:35 donsizemore i have error messages to include =)
15:36 pdurbin donsizemore: ok, please feel free then. :)
15:37 dan-drexel joined #dataverse
15:37 dan-drexel so I just tried the vagrant version, and I get a page that says "Custom "site is unavailable" 503 page."
15:40 dan-drexel Ohh it said build failure'
15:40 dan-drexel Failed to execute goal org.apache.maven.plugins:mave​n-surefire-plugin:2.22.0:test (default-test) on project dataverse: There are test failures.
15:41 pdurbin dan-drexel: hmm, but no test failures on the "develop" branch at https://travis-ci.org/IQSS/dataverse
15:42 pdurbin It shouldn't be this hard to install Dataverse. :(
15:43 dan-drexel Haha yep agreed. But i'm new to linux servers, so it could be me
15:43 dan-drexel You should had seen me try to install CKAN lol
15:43 pdurbin Heh, did you get CKAN installed? Do you like it?
15:44 dan-drexel Nope. But I also had my father-in-law who is a data engineering director try to install it too, after 5 hours he gave up
15:44 dan-drexel I did however get DKAN running
15:45 dan-drexel It was ok, but I was not a huge fan of it
15:46 dan-drexel so how do I run dos2unix on the install script?
15:46 poikilotherm dan-drexel: you could try to switch to tag v4.14 and retry with vagrant
15:46 poikilotherm There might be issues with develop we don't know of on Windows
15:46 dan-drexel Ahh I see
15:46 pdurbin I have the card of a DKAN developer on my desk. I met him at LibrePlanet the other week. :)
15:47 poikilotherm Or, if you are feeling lucky, you can try minikube on Windoze and give dataverse-kubernetes a whirl :-D
15:47 pdurbin dan-drexel: the Dataverse vagrant environment will skip building the war file if it's already in "target" so you *could* download the 4.14 release war file and put it on disk in "target".
15:47 poikilotherm I haven't tried that yet, but would be interesting
15:48 pdurbin dan-drexel: or like poikilotherm, try minikube. It would be good to have a data point from Windows. :)
15:50 dan-drexel Ok, trying the v14.4 branch now
15:57 pdurbin poikilotherm: I was thinking. I don't know what your chat requirements are. I know IRC is old but I'm happy enough with it. We've been using since before Slack existed. :) How do you feel about creating issues over at https://github.com/IQSS/chat.dataverse.org/issues that capture problems that would be solved by switching to (or adding) something else?
15:57 poikilotherm Sounds like a plan
15:57 poikilotherm Working on #5906 right now
16:03 dan-drexel How do I do the dos2unix thing?
16:04 pdurbin dan-drexel: you'd have to do it from within the Vagrant VM running CentOS.
16:05 dan-drexel So after the install is done, I go into the VM right
16:05 dan-drexel and then what do I run dos2unix on?
16:06 pdurbin dan-drexel: actually, instead of that it would be better to clone the dataverse repo from within the Vagrant VM.
16:06 dan-drexel where should I clone it to?
16:07 dan-drexel And also what does it use for the logins when it makes the vm?
16:08 pdurbin the community call is starting: https://groups.google.com/d/msg/dataverse-community/CMXGyy6IhJI/e6tilK7GCQAJ
16:08 pdurbin andrewSC bjonnh bricas_ dan-drexel donsizemore juancorr pkiraly pmauduit poikilotherm stefankasberger ^^
16:10 poikilotherm Sry, I'm out. No headset around
16:10 dan-drexel me too :/
16:18 poikilotherm I'm outta here, going to construction site :-)
16:18 poikilotherm See you guys around
16:21 pdurbin dan-drexel: sorry, I'm multitasking not very well. I think you should try dataverse-ansible rather than Vagrant, to be honest.
17:00 pdurbin I say this because that Ansible code gets run way more often than the Vagrant code.
17:10 dan-drexel Sorry got pulled out for a meeting. I'll give ansible a try
17:10 pdurbin cool
17:21 pdurbin donsizemore: I went for a dot release: https://github.com/IQSS/dataverse-metrics/releases/tag/v0.2.5
17:22 pdurbin If you could deploy the latest to https://dataverse.org/metrics and set month_filter_enabled to true and add github_repos (just the main repo), it would be appreciated! Also, is IRC the best way to ask for this stuff? :)
17:25 donsizemore @pdurbin IRC is fine. I just upgraded, let me make those changes
17:26 pdurbin \o/
17:27 pdurbin I wonder if I should backup the config file you're using to https://github.com/IQSS/dataverse.org ... or somewhere. It's pretty easy to keep the "diff" from the sample in my head right now but who knows in the future. :)
17:29 donsizemore @pdurbin i don't think it holds any state secrets
17:31 pdurbin definitely not :)
17:31 dan-drexel @pdurbin - this is the first time i'll run ansible,  what do I need for these vairiables? ansible-playbook -i <inventory file> [-u <user>] [-b] [-K] -e @<group_vars_file> [-v] dataverse.pb
17:32 pdurbin dan-drexel: I think it's in the README
17:32 dan-drexel but it's not
17:32 pdurbin oh, you're right :)
17:32 dan-drexel Haha, I also tried google as well
17:33 pdurbin let's look at what the script use puts for those flags
17:33 pdurbin the script I use
17:33 pdurbin ansible-playbook -v -i dataverse/inventory dataverse/dataverse.pb --connection=local $GVARG
17:34 pdurbin that's from https://github.com/IQSS/dataverse/blob/653b7b29caa05b111b95f718849e3c5f424f8a9d/scripts/installer/ec2-create-instance.sh#L138
17:35 pdurbin I think instead of $GVARG you'll want to somehow reference a main.yml file.
17:36 dan-drexel I see, so does this look right: ansible-playbook -v -i dataverse/inventory dataverse/dataverse.pb /dataverse/defaults/main.yml
17:36 donsizemore @dan-drexel if you're just testing, you can do a "vagrant up" in the dataverse-ansible directory and come up with a vanilla (temporary) dataverse
17:37 dan-drexel I think should prob remove that leading slash: ansible-playbook -v -i dataverse/inventory dataverse/dataverse.pb dataverse/defaults/main.yml
17:38 dan-drexel @donsizemore I tried vagrant and had some issues, @pdurbing reccomended I try using ansible on a vm
17:38 pdurbin donsizemore: he's ssh'ed into a VirtualBox VM running CentOS that I don't believe was spun up using Vagrant. He needs to add -e right?
17:39 donsizemore @dan-drexel did you use the Vagrantfile from the dataverse repo, or the dataverse-ansible?
17:39 dan-drexel @pdurbin - that's right, except i'm using cockpit to access the terminal not ssh
17:39 pdurbin I don't know what cockpit is but ok.
17:39 pdurbin donsizemore: he hasn't used Vagrant before.
17:40 donsizemore @pdurbin yes, -e with a yml file
17:40 dan-drexel @donsizemore - I tried using the vagrant file in Vagrant, but had some issues, so I am trying ansible
17:41 dan-drexel @pdurbin @donsizemore: does this look right? ansible-playbook -v -i dataverse/inventory dataverse/dataverse.pb -e dataverse/defaults/main.yml
17:41 donsizemore @dan-drexel there are two vagrant files. one comes in the dataverse repo, one comes with dataverse-ansible
17:42 dan-drexel @donsizemore I see, I think I used the one in the dataverse repo
17:42 pdurbin I think you want to cd into the directory you cloned and then run this: ansible-playbook -v -i inventory dataverse.pb -e defaults/main.yml
17:42 donsizemore @pdurbin eh? eh? https://dataversemetrics.odum.unc.edu/dataverse-metrics/
17:43 pdurbin donsizemore: looks perfect! Thanks!
17:44 donsizemore @dan-drexel if you're just testing, you can 'cd' into your dataverse-ansible repo copy and run 'vagrant up' there?
17:45 dan-drexel I get this: ERROR! the role 'dataverse' was not found in /root/dataverse/roles:/root​/dataverse:/root/dataverse                                                                                                                                                                                                                                                                                                                                      The e
17:45 dan-drexel @donsizemore I'll try that - I was having issues related to the fact I have vagrant on a windows machine
17:46 dan-drexel @donsizemore do you know how to do the dos2unix that fixes the /usr/bin/perl^M: bad interpreter issue?
17:49 pdurbin donsizemore: he's on Windows
17:49 pdurbin Oh, dan-drexel just said that. :)
17:51 donsizemore @dan-drexel unless you're wed to Windows, I think you could save yourself a world of hurt by trying this in a Linux VM
17:54 dan-drexel @donsizemore ok, I'll see if I can get vagrant running ina  linux vm
18:04 donsizemore @dan-drexel excellent =) vagrant is useful for repeated testing, though you _could_ leave it running for a while
18:46 pdurbin donsizemore: when you're ready, let's circle back to "updating init vs. systemctl calls and we wanted to keep 6 commands, time to switch" because I forget what we wanted. :)
19:52 donsizemore joined #dataverse
19:57 donsizemore @pdurbin certainly, i was just asking about standardizing in the prereqs and other docs?
19:58 pdurbin Is the idea to drop tips on configuring CentOS 6? To just explain the modern way?
19:59 donsizemore @pdurbin 'service x start' works fine in either case, but to enable you need both chkconfig and systemctl examples
20:00 donsizemore @pdurbin i think for a new installation you might safely settle on systemctl these days unless you want to retain backwards compatibility
20:00 pdurbin I want what you want, I think. :)
20:01 donsizemore a chocolate milkshake?
20:01 pdurbin mmmmm
20:01 pdurbin Do others have opinions on this. I think Oliver is still hacking on that page.
20:02 pdurbin I think I'd like to prioritize getting the api test suite running from new Jenkins. :)
20:02 stefankasberger joined #dataverse
20:04 donsizemore i can do that
20:04 pdurbin And I guess I was thinking of standing up jenkins2 or something and trying to get it installed for the first time. To mirror your setup. I'd like the whole thing to be reproducible.
20:04 donsizemore it's just an RPM at this point. and you can import the config.xml from the repo
20:04 pdurbin Or I can try to help you troubleshoot docker-aio or whatever. Or we can use EC2 instead.
20:05 donsizemore i'd love to see if you get the same results on similar hardware/os/etc.
20:05 pdurbin Is a "medium" enough?
20:05 pdurbin that's what the ec2 create script spins up
20:05 donsizemore the current jenkins box has 2 cores and 8 gb of ram
20:06 pdurbin SIZE='t2.medium'
20:06 pdurbin Ok. And running CentOS 7?
20:08 pdurbin a t2.large gives 8GB RAM and 2 core according to https://aws.amazon.com/ec2/instance-types/t2/
20:08 pdurbin cores*
20:10 donsizemore perfect. yes centos7
20:12 pdurbin oh, that's right in the README. centos 7
20:13 pdurbin donsizemore: I might need help with how to use https://github.com/geerlingguy/ansible-role-jenkins
20:15 pdurbin Do I just clone this thing and use master somehow?
20:27 pdurbin huh, there's something called ansible-galaxy
20:32 pdurbin Welcome to Jenkins! http://ec2-35-153-208-116.compute-1.amazonaws.com:8080 \o/
20:38 pdurbin Don, I just left a comment at https://github.com/IQSS/dataverse-jenkins/issues/1#issuecomment-498834306
20:39 pdurbin and terminated that t2.large
21:00 dan-drexel joined #dataverse
21:01 dan-drexel @pdurbin - is it actually possible to run virtualbox on ubuntu which is already inside a vm? I get this error vt-x is not available (verr_vmx_no_vmx) ubuntu 18.04 virtualbox
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21:34 donsizemore @pdurbin PR submitted =)
21:40 pdurbin donsizemore: thanks!
21:41 pdurbin dan-drexel: I was a little worried about this idea of a VirtualBox spun up by Vagrant inside a VirtualBox spun up on Windows.
21:47 iqlogbot joined #dataverse
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