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IRC log for #dataverse, 2015-03-31

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All times shown according to UTC.

Time S Nick Message
03:39 axfelix joined #dataverse
04:39 axfelix joined #dataverse
13:14 bencomp joined #dataverse
15:06 axfelix joined #dataverse
15:23 trobitaille joined #dataverse
15:24 trobitaille hi there! is anyone else around?
15:32 bencomp I am
15:32 bencomp trobitaille: ^^
15:32 bencomp I was going to see if pdurbin was around
15:33 pdurbin trobitaille: hi!
15:34 pdurbin trobitaille: I sent a link to https://github.com/dvn/swordpoc/issues/3 to my team this morning!
15:34 pdurbin a "dataverse importer" sounds good!
15:35 trobitaille great, thanks!
15:36 trobitaille basically I'm planning on writing a GUI dataverse importer for glue:
15:36 trobitaille http://glue-viz.org/
15:36 trobitaille (though it could maybe be used by other Python projects)
15:37 trobitaille I'm getting stuck pretty quickly at the moment with the client code
15:37 trobitaille see https://github.com/dvn/swordpoc/issues/4
15:37 pdurbin trobitaille: now I know why I know your name! I spun up some VMs for you when I was a FASRC.
15:37 trobitaille ah cool!
15:37 trobitaille thanks for that btw!
15:37 pdurbin heh. sure
15:38 pdurbin ok. so. that client. it's old code. hold on
15:38 trobitaille I'm not familiar with SWORD, hence the issues I'm running into - if you have any insight into the 403 error I'm seeing at the moment, let me know!
15:38 pdurbin jeffspies_ and I took that code and put it in a new repo
15:38 trobitaille ah I see
15:39 pdurbin this one: https://github.com/IQSS/dvn-client-python
15:39 pdurbin BUT!
15:39 pdurbin that code was forked again!
15:39 pdurbin hmm, several times, actually: https://github.com/IQSS/dvn-client-python/network/members
15:39 trobitaille hehe
15:40 pdurbin ok, so I would try https://github.com/rliebz/dvn-client-python/tree/4.0
15:40 pdurbin AND!
15:40 trobitaille ok, thanks!
15:40 pdurbin and please test against https://apitest.dataverse.org
15:40 pdurbin which is running Dataverse 4.0 rather than DVN 3.x.
15:40 trobitaille ok - I'll give it a shot
15:40 trobitaille thanks!
15:41 pdurbin sure!
15:41 pdurbin what we *really* want...
15:41 pdurbin is `pip install dataverse-client`
15:41 pdurbin trobitaille: if you can help us get there, please let me know! :)
15:41 trobitaille ok cool, I'll look into the codebase to see what's missing
15:42 trobitaille should be easy enough :)
15:42 trobitaille so in case I need to do any fixes, any pull requests should be done against https://github.com/rliebz/dvn-client-python/tree/4.0 ?
15:42 pdurbin jeffspies_: what do you think?
15:43 pdurbin probably!
15:43 pdurbin eventually I'd like it all to go into a repo under https://github.com/IQSS
15:43 pdurbin but we can cross that bridge later :)
15:43 pdurbin skay: isn't this exciting?! you were helping with this effort
15:44 skay what?
15:44 pdurbin skay: making `pip install dataverse-client` possible :)
15:45 skay thanks. I didn't do much but glad you are happy about it
15:45 skay future me thanks you
15:47 trobitaille hehe
15:47 trobitaille so at the moment it doesn't look like settings/local.py actually gets used?
15:47 skay pdurbin: but seriously, I haven't reviewed rliebz's code in a long time. he's changed it a lot.
15:48 skay pdurbin: is someone else reviewing it? no merges have gone to IQSS in a while
15:48 pdurbin skay: he's the only one using that code that I know of (which is fine)
15:49 trobitaille well, I'm trying now ;)
15:49 pdurbin trobitaille: I used Peter's code you found (the old, original code) but I haven't used Robert's.
15:49 skay I should probably step down as a member since I've not done anything in a while
15:49 trobitaille I guess one question is if I want to suggest changes, I would need to suggest it to his repository - but might be good to encourage him to merge his changes back into the main repo in IQSS so that I can also make pull requests there
15:49 pdurbin skay: you slacker ;)
15:50 skay pdurbin: I agree with trobitaille
15:50 pdurbin trobitaille: well, there *is* no main repo at IQSS yet :(
15:50 pdurbin but we totally want one
15:50 skay since no one is using the dvn-client-python master
15:50 skay pdurbin: what is https://github.com/IQSS/dvn-client-python
15:50 trobitaille but what about  https://github.com/IQSS/dvn-client-python
15:50 skay jinx!
15:50 trobitaille isn't that the main repo that the changes should be pushed back to?
15:50 skay :)
15:51 pdurbin skay: I'd like to rename it to dataverse-client-python anyway (drop the deprecated term "dvn" from the repo name)
15:51 pdurbin trobitaille: no. or at least I'd like to rename it, like I'm saying (drop "dvn")
15:51 skay pdurbin: rename it and merge in his changes and then trobitaille can work from there
15:51 trobitaille right - renaming is easy and doesn't break the forks btw
15:51 skay as can rleibtz
15:52 trobitaille the old URL will work for everyone too
15:52 trobitaille so renaming doesn't break anything
15:52 pdurbin trobitaille: true!
15:52 skay that will make bookkeeping a little easier
15:52 skay and then encourage rleibz to make merge requests often
15:53 trobitaille I wonder whether rlieibz's repo is in the middle of some changes because it mentions things about tokens in the readme but then that's not used in the actual code as far as I can tell
15:53 * skay is not saying anything non-obvious but only stating the usual
15:53 pdurbin trobitaille: he's preparing his code to work with Dataverse 4.0 (which is awesome of him)
15:54 trobitaille ok yes, that will be great
15:54 trobitaille it also looks like it may depend on some custom fork of sword2
15:54 trobitaille for now
15:54 pdurbin yeah, unfortunately
15:54 trobitaille not a problem
15:55 pdurbin trobitaille: we also have a new JSON-based API you can try
15:55 trobitaille I get the 403: forbidden error again though :-/
15:55 trobitaille oh, really?
15:55 pdurbin :)
15:55 trobitaille I would be much happier with a JSON api if there is one!
15:55 pdurbin for now it's called the "native" API: http://guides.dataverse.org/en/latest/api
15:55 trobitaille that has a good sound to it
15:55 skay oh, make a requests based wrapper around it
15:55 trobitaille yep
15:56 trobitaille that's what I was thinking
15:56 trobitaille ok, I'll try it out now
15:57 trobitaille what are the downsides compared to sword?
15:57 pdurbin it's new
15:57 * pdurbin thinks
15:57 pdurbin oh
15:58 pdurbin you can't upload files via the native api yet
15:58 pdurbin you'll have to use sword for that, for now
15:58 pdurbin trobitaille: I'm using the native API here: https://github.com/IQSS/dataverse/blob/master/scripts/deploy/apitest.dataverse.org/post
15:58 pdurbin which calls this script: https://github.com/IQSS/dataverse/blob/master/scripts/search/tests/create-all-and-test
15:59 pdurbin and you express a dataset in JSON like this: https://github.com/IQSS/dataverse/blob/master/scripts/search/tests/data/dataset-finch1.json
15:59 pdurbin the huge upside of the JSON API is that *all* metadata fields are available to you
15:59 pdurbin unlike sword where you only get a few
16:00 trobitaille that's pretty cool
16:03 trobitaille just one simple question, to make sure I understand right - I'm trying this JSON request:
16:03 trobitaille GET http://$SERVER/api/datasets/$id?key=$apiKey
16:04 trobitaille setting apikey to my API token
16:04 trobitaille but given a dataset, e.g.
16:04 trobitaille https://apitest.dataverse.org/dataset.xhtml?globalId=doi:10.5072/FK2/A4KFW8&versionId=33
16:04 trobitaille what is the ID - is it the full DOI?
16:06 trobitaille I tried doing https://apitest.dataverse.org/api/dataverses/root/contents?key=... and got a list of objects, with IDs, for example 178 or 7
16:06 trobitaille but if I use 178 or 7 in this call: http://$SERVER/api/datasets/$id?key=$apiKey - it says dataset not found
16:07 trobitaille (sorry, I know these are beginner questions, just trying to get a feel for the API but then should be able to figure out the rest)
16:20 pdurbin trobitaille: sorry, sorry, I wandered away. one sec
16:21 pdurbin trobitaille: the id is the database id of the dataset
16:22 pdurbin curl -s -X DELETE "http://localhost:8080/api/datasets/$FIRST_FINCH_DATASET_ID?key=$FINCHKEY"
16:22 pdurbin that's from https://github.com/IQSS/dataverse/blob/master/scripts/search/tests/delete-all-and-test
16:22 pdurbin FIRST_FINCH_DATASET_ID=`curl -s "http://localhost:8080/api/dataverses/finches/contents?key=$FINCHKEY" | jq '.data[0].id'`
16:22 pdurbin that's from https://github.com/IQSS/dataverse/blob/master/scripts/search/assumptions
16:23 pdurbin I sure hope this makes sense! :)
16:23 trobitaille right, that's what I was trying but was running into issues - take the following example (replacing with your API key)
16:23 trobitaille https://apitest.dataverse.org/api/dataverses/root/contents?key=$KEY
16:23 trobitaille I get the following output
16:23 trobitaille {"status":"OK","data":[{"type":"datavers​e","id":168,"title":"ad_db"},{"type":"da​taverse","id":178,"title":"Antislavery Petitions Test"},{"type":"dataverse","id":17,"title":"Robert​"},{"type":"dataverse","id":165,"title":"testINFSC​I"},{"type":"dataverse","id":7,"title":"Trees"}]}
16:23 trobitaille so let's say I want dataset 168
16:23 trobitaille I tried
16:23 trobitaille https://apitest.dataverse.org/api/datasets/168?key=$KEY
16:23 trobitaille but that fails
16:24 trobitaille {"status":"ERROR","message":"dataset not found"}
16:24 trobitaille maybe I'm making a silly mistake though
16:24 pdurbin trobitaille: that's because id 168 is a dataverse rather than a dataset.
16:24 trobitaille oh right
16:25 trobitaille ahhh
16:26 pdurbin I haven't used that "contents" endpoint much.
16:26 trobitaille so all ids are integers
16:26 trobitaille but some are IDs to dataverses and some to datasets
16:26 trobitaille ok cool
16:26 pdurbin trobitaille: under the covers dataverses, datasets, and datafiles share a common pool of IDs. Collectively we call them DvObjects.
16:26 trobitaille right, that makes sense - thanks!
16:27 trobitaille so one last question - how soon do you think it's likely the 'cfa' dataverse would be available using the JSON API?
16:27 trobitaille or should that already work?
16:29 pdurbin "real soon now" :)
16:29 pdurbin we're trying to ship 4.0
16:30 pdurbin and CfA will be migrated, of course
16:30 trobitaille ok
16:30 pdurbin will all the rest
16:30 pdurbin with* all the rest
16:30 trobitaille so do you have a specific ETA? (just very very very roughly - in the sense of days/weeks/months)
16:30 pdurbin less than months, hopefully!
16:31 pdurbin trobitaille: oh!
16:31 pdurbin actually, if you're nice to this server, you can play with CfA data here: https://dataverse-demo.iq.harvard.edu/dataverse/cfa
16:32 trobitaille ok, cool! that's all I need and I'll be nice to the server :)
16:32 pdurbin that server is primarily for GUI testing and the API code lags behind the code at https://apitest.dataverse.org
16:32 trobitaille if you notice too much activity, then please send me an email
16:32 pdurbin sure :)
16:33 pdurbin trobitaille: feel free to pull down some of that CfA data as JSON and upload it to the apitest server :)
16:34 trobitaille ok cool, will give it a try
16:34 pdurbin hmm
16:34 pdurbin you'll need a key, of course
16:34 pdurbin but you're getting used to that
16:34 pdurbin :)
16:34 trobitaille yep :)
16:35 trobitaille ah ha, seems to work
16:35 trobitaille thanks!
16:35 trobitaille off now
16:35 pdurbin bye! come by any time :)
16:36 trobitaille ok cool :) bye!
18:50 rliebz joined #dataverse
19:11 trobitaille joined #dataverse
19:12 trobitaille pdurbin - thanks for your help earlier! I have been playing around with the CfA dataverse on the demo server and have run into a strange issue
19:12 trobitaille this URL works: https://dataverse-demo.iq.harvard.edu/api/datasets/7/versions/1/metadata?key=...
19:13 trobitaille but this one doesn't: https://dataverse-demo.iq.harvard.edu/api/datasets/7/versions/1/files?key=...
19:13 trobitaille even though the guide said it should
19:13 trobitaille do you have any idea what the issue could be?
19:13 pdurbin doesn't work?
19:13 pdurbin what does the error say?
19:14 pdurbin oh oh oh
19:14 pdurbin files
19:14 pdurbin yeah, that's new
19:14 pdurbin remember how I said that server lags behind the other?
19:14 pdurbin actually...
19:14 pdurbin that "files" endpoint is so new I haven't even pushed it to the apitest server :(
19:15 pdurbin trobitaille: oh! and something else! I think I gave you the impression that all the JSON goodness is under the "native" API. This is not true. There is also JSON goodness under the Search API: http://guides.dataverse.org/en/latest/api/search.html
19:18 pdurbin rliebz: hi!
19:18 pdurbin rliebz: maybe your ears were burning!
19:20 rliebz pdurbin: I saw all the fun going on in the logs, so I thought I'd hop in
19:20 pdurbin isn't it fun? :)
19:22 * pdurbin loves this stuff
19:24 rliebz The time leading up to big releases is always exciting
19:24 pdurbin rliebz: hmm, you'd probably like a build on apitest too...
19:24 pdurbin rliebz: see how trobitaille is interested in the the "files" endpoint
19:24 pdurbin the new*
19:25 trobitaille no problem about files not being available yet! was just worried I was doing something silly
19:25 trobitaille :)
19:25 trobitaille I'll definitely try out the search API!
19:26 rliebz pdurbin: The files endpoint looks good so far. Is it able to take DOIs?
19:26 trobitaille For fun, I'm working on a mini-Python library that uses the JSON API
19:26 pdurbin cool. this little Android app proof of concept is built on the Search API: https://github.com/IQSS/dataverse-android
19:26 pdurbin rliebz: maybe I can run a build for you quick so you and trobitaille can check it out
19:27 pdurbin trobitaille: warning! this will drop the database so you'll need to create a new api key
19:27 trobitaille that's ok :)
19:27 trobitaille I'm used ito it now!
19:27 pdurbin trobitaille: it would be awesome if you and rliebz could collaborate on a common `pip install dataverse-client` thing
19:28 trobitaille right - I think there really are two approaches for the Python library, one via sword and one via JSON, so it depends which one you'd like to see as the main one, or if we should have both
19:28 trobitaille at the moment I'm just going to experiment with the JSON API
19:28 trobitaille happy to collaborate on making a joint thing
19:28 trobitaille once I have a better feel for it
19:28 rliebz pdurbin: If there's a way to access the new API with DOIs, or an endpoint to get dataset ID from DOI, I don't see any reason why https://github.com/rliebz/dvn-client-python/tree/4.0 can't include the other APIs as well
19:29 pdurbin rliebz: right. I think we should take your working code and add support for the native api
19:32 rliebz Absolutely. I've been holding off on merging it back into IQSS because my changes have virtually no backwards compatibility, but I'd be happy to put my changes into that or a different IQSS repo whenever
19:32 pdurbin rliebz: no one is using https://github.com/IQSS/dvn-client-python . you can force push to it
19:33 pdurbin skay: right?
19:34 skay pdurbin: yeah
19:34 rliebz pdurbin: We're currently using the master branch of my repo in OSF production, with 4.0 having the Dataverse 4.0 changes and some other improvements that I was planning on merging in after release
19:35 rliebz pdurbin: Any preference on IQSS/dvn-client-python?
19:35 pdurbin rliebz: let's drop "dvn" from the name
19:36 pdurbin and call it "dataverse"
19:36 pdurbin ok, I just kicked off a build: https://build.hmdc.harvard.edu:8443/job/apitest.dataverse.org-deploy/28/
19:36 pdurbin usually I test it first locally but I'm in a feature branch
19:39 pdurbin ok, https://apitest.dataverse.org looks normal for after a build
19:40 pdurbin and all the integration tests passed: https://build.hmdc.harvard.edu:8443/job/apitest.dataverse.org-apitester/27/
19:40 rliebz pdurbin: Thanks for building! I'll start working with the new endpoint shortly
19:40 pdurbin rliebz: lemme know if it works with DOIs. I don't even know!
19:41 rliebz pdurbin: I don't have permission to force push to https://github.com/IQSS/dvn-client-python
19:41 pdurbin rliebz: hmm. ok. can you please remind me to fix this later?
19:42 rliebz pdurbin: Will do
19:43 pdurbin rliebz: should I just fork your repo into the new name?
19:43 bencomp joined #dataverse
19:46 trobitaille pdurbin: just to check, the new build you are mentioning is just on the apitest server so far, but not the https://dataverse-demo.iq.harvard.edu server, right? (so I shouldn't expect /files to work yet)
19:48 pdurbin trobitaille: correct. https://dataverse-demo.iq.harvard.edu tracks this branch: https://github.com/IQSS/dataverse/tree/beta
19:48 pdurbin https://apitest.dataverse.org shows the date and commit in the lower right: v. 4.0 Beta build 28 (apitest), 2015-03-31, commit 95c3ca2
19:49 trobitaille ah great, thanks for the info
19:49 pdurbin oh sure
19:53 trobitaille ok, and just to also check, /files does not yet work on apitest? https://apitest.dataverse.org/api/datasets/10/files?key=... returns a page not found - this is also expected at this point?
19:54 pdurbin trobitaille: honestly, I haven't even tried it. rliebz might know :)
19:54 trobitaille ok cool - no worries!
19:54 trobitaille will try playing around with other aspects for now
19:54 pdurbin cool
19:54 pdurbin I'd take a look but I'm working on a feature: https://github.com/IQSS/dataverse/issues/90
19:55 trobitaille that's ok, there's no rush anyway :)
19:55 trobitaille before I open a feature request, is there a way for a program script to automatically fetch a token, kind of oauth-style?
19:56 trobitaille i.e. it would open the user's browser, get them to log in, then retrieve the token automatically
19:56 pdurbin trobitaille: when you create a user using the API the token comes back in the response
19:56 rliebz I've gotten /files to work on apitest, but not with DOI
19:56 pdurbin trobitaille: check out createUser at https://github.com/IQSS/dataverse-apitester/blob/master/src/test/java/org/dataverse/apitester/sword/SwordTest.java
19:56 pdurbin apiToken = jsonPath.get("data.apiToken");
19:56 trobitaille ok - and what if the user already exists and uses  a new tool?
19:57 rliebz +1 to fetching API tokens
19:57 pdurbin heh
19:57 trobitaille rliebz: is there something wrong with this URL? https://apitest.dataverse.org/api/datasets/10/files?key=
19:57 pdurbin trobitaille: not sure what you mean about already exists
19:58 trobitaille so let's say I have a user account (which I do), now I open up a tool, say glue
19:58 trobitaille I want glue to be able to access things on dataverse as me
19:58 pdurbin sure
19:58 trobitaille so then it would have a 'log in to dataverse' option
19:59 trobitaille is there a login mechanism that will then return the API key?
19:59 pdurbin nope. you have to use the GUI to find your API token
19:59 rliebz trobitaille: I assume you left off the key because you didn't want us to see it. If not that, I'd say 1) Verify that the object with ID #10 is in fact a dataset, and 2)  try specifying a version
19:59 pdurbin trobitaille: feel free to open an issue at https://github.com/IQSS/dataverse/issues about this though
19:59 trobitaille rliebz - yes, left off the key
19:59 rliebz trobitaille: For reference, I used: http://apitest.dataverse.org/api/datasets/18/versions/:latest/files?key=...
20:00 trobitaille pdurbin - ok, will do, bsasically I think that the users should never have to see an API key
20:00 trobitaille so it could just be a new JSON endpoint with POST over https - given user and password, return token - that would be enough
20:00 pdurbin ok
20:01 pdurbin rliebz: the reminds me. Are you aware that we're talking about disabling login via SWORD for Dataverse 4.0?
20:01 pdurbin you should expect an email about this, probably today
20:01 pdurbin axfelix: heads up!
20:01 pdurbin er
20:01 pdurbin login via *PASSWORD* I meant to say
20:01 pdurbin requiring API tokens
20:01 trobitaille rliebz - specifying the version works, thanks!
20:02 rliebz pdurbin: We have already made the switch to API tokens, so that isn't a problem
20:03 pdurbin rliebz: but you'll need to transition your users...
20:03 rliebz pdurbin: I assume you still accept basic auth using the api token as a username though, right?
20:03 pdurbin rliebz: correct
20:03 rliebz trobitaille: No problem!
20:04 rliebz pdurbin: We will need to transition our users, but we were already planning on doing that for the security benefits and access to the new API, if needed. In that sense, having an endpoint to get from username/password to API token via the API would make it seamless.
20:08 trobitaille FYi I just opened a feature request for the username/pass -> api token endpoing here: https://github.com/IQSS/dataverse/issues/1818
20:11 axfelix hrm, good to know
20:11 axfelix I think this is probably acceptable given the changes we've made to the plugin to support API keys
20:11 axfelix but still, nice to be able to tell people
20:13 trobitaille Once I have the metadata about a given file, is there a way to actually retrieve the file? For example:
20:13 trobitaille {'data': [{'datafile': {'contentType': 'image/png',                         'description': '',                         'filename': '%2Fusr%2Flocal%2Fglassfish4%2Fglassfish%​2Fdomains%2Fdomain1%2Ffiles%2F10.5072%2FF​K2%2FIOOAJF%2F14c7157584b-15f561a376ee',                         'id': 12,                         'md5': '0386269a5acb2c57b4eade587ff4db64',                         'name': 'trees.png',                         'ori
20:13 trobitaille oops - formatting messed up
20:13 trobitaille but that's the returned JSON
20:13 trobitaille it has filename, path on computer, etc. but not clear how to retrieve it?
20:16 trobitaille (or maybe there is no way for now?)
20:19 rliebz trobitaille: Like this? http://guides.dataverse.org/en/latest/api/dataaccess.html#basic-file-access
20:19 trobitaille ah, perfect
20:19 trobitaille sorry, was looking for it in the wrong page
20:20 trobitaille thanks for all the help!
20:20 trobitaille I should be all set now :)
20:23 pdurbin rliebz: I'm glad you're on board with the security benefits
20:24 pdurbin trobitaille: thanks for opening that ticket!
20:24 pdurbin axfelix: glad it's acceptable! your users are mostly journals so there should be fewer of them
20:24 axfelix yeah, and anyone who's pointing at a 4.0 instance is already encouraged to do an API handsake
20:34 trobitaille thanks everyone for your help - off now, but will be back in touch soon once I've made progress
20:35 pdurbin we'll be here :)
20:45 pdurbin rliebz and axfelix: I'm getting some feedback on that new ticket about retrieving the API token: http://irclog.greptilian.com/rest/2015-03-31#i_106173
21:06 rliebz pdurbin: I'm off for the time being. Thanks for the help today!
21:41 bencomp pdurbin: I should have asked earlier today, but what happened to the "final" milestone? with the number of issues still increasing, is there a plan for the release?
21:57 pdurbin bencomp: I'm coding as fast as I can.
21:57 pdurbin No bugs! ;)
21:57 bencomp wasn't planning on adding new ones right now
21:58 bencomp :)
21:58 pdurbin If debugging is the process of removing bugs then programming must be the process of adding them.
21:58 * bencomp is preparing for meeting with users who are anxious to start using Dataverse 4
21:59 bencomp is that another way of saying "stay away from the code"?
22:04 pdurbin heh
22:04 pdurbin no! pull requests welcome!
22:06 pdurbin bencomp: I'm very glad to hear people excited (or is it just anxious?) to use Dataverse 4.
22:10 bencomp pdurbin: I guess that should be more excited than anxious :P
22:12 bencomp but as we might need to change things in our service offerings (e.g. more control at each institution), I'm a little anxious too ;)
22:13 pdurbin bencomp: ah, so you're looking forward to the new permissions model
22:16 bencomp definitely
22:17 bencomp there's a lot I'm looking forward to in v4
22:17 pdurbin yeah
22:17 pdurbin I hope people like it. :)
22:27 pdurbin bencomp: speaking of code, I'm curious if you've tried lombok: http://irclog.greptilian.com/sourcefu/2015-03-31#i_106137
22:29 bencomp no, I haven't
22:30 * pdurbin has heard good things
22:31 bencomp had to stop thinking about how I broke my Jenkins jobs by upgrading plugins and server core because the project ended
22:31 bencomp will look at lombok later
23:02 pdurbin jenkins is great when it's not broken

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