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IRC log for #dataverse, 2015-08-12

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All times shown according to UTC.

Time S Nick Message
03:39 axfelix joined #dataverse
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14:01 pdurbin michbarsinai: I can't figure out how to test service beans: https://netbeans.org/kb/docs/javaee/javaee-entapp-junit.html
14:14 michbarsinai pdurbin: is that exercise not working?
14:15 pdurbin nope
14:17 michbarsinai All these containers are just too much magi
14:17 michbarsinai magic
14:21 pdurbin michbarsinai: but you wrote tests for some commands, right?
14:22 michbarsinai Yes. I'm passing a test command context, though.
14:22 pdurbin michbarsinai: which commands have tests?
14:23 michbarsinai MoveDataverseCommandTest.
14:23 pdurbin but we don't support moving dataverses
14:24 michbarsinai True. But that was more of a PoC for testing commands.
14:25 pdurbin well, I'm open to ideas about the best way to write tests for regressions
14:26 pdurbin that video yesterday really drove home the importance of testing: Agile Product Ownership in a Nutshell - https://www.youtube.com/watch?v=502ILHjX9EE https://dl.dropboxusercontent.com/u/1018963/Articles/PO-in-a-nutshell.png
14:26 michbarsinai That test can server as a good example for command logic. The embeddable GF in that tutorial is also an option, when it works.
14:32 pdurbin yeah
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15:06 pdurbin bencomp: maybe you can remind me to show this to Don: explain importance of AJP_ shib config · IQSS/dataverse@9ce6507 - https://github.com/IQSS/dataverse/commit/9ce6507
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15:20 bencomp pdurbin: I'm flattered, but how about an email? :)
15:22 pdurbin meh. he'll be back. I hate email :)
15:22 pdurbin bencomp: how's your shib testing going?
15:24 bencomp someone has to install and configure Shib on our test server and I don't get updates from that someone
15:25 pdurbin bummer
15:27 pdurbin michbarsinai: so easy! http://wiki.netbeans.org/MavenCodeCoverage . I just sent a screenshot about this.
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17:00 donsizemore pdurbin: i see your commit on the importance of AJP, and think it's wonderful! i eventually would've noticed it in the example, but was using our ID mgmt folks' XML
17:01 donsizemore bencomp: may we offer you a test server with shib and shell? happy to set one up and help how i can
17:02 pdurbin donsizemore: I'm glad you found that commit :)
17:04 pdurbin donsizemore: you can see the HTML version here: http://guides.dataverse.org/en/4.2/installation/shibboleth.html#shibboleth2-xml
17:14 donsizemore pdurbin: you just sent me looking for a 4.2 release announcement =)
17:15 pdurbin donsizemore: no, no, still a lot to do: https://github.com/IQSS/dataverse/milestones
17:22 donsizemore pdurbin: so... if my next task were to be a 3.6.2 => 4.x test upgrade, 4.0.1 would remain a good target? that's the one that's currently shibbolized
17:24 pdurbin donsizemore: I would target 4.1: https://github.com/IQSS/dataverse/releases/tag/v4.1
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17:29 donsizemore pdurbin: would the shib code have changed significantly to have me set up a 4.1 server for this test upgrade, or should I just take our shib test from 4.0.1 => 4.1?
17:30 pdurbin I would just upgrade from 4.0.1 to to 4.1 on the same server.
17:30 pdurbin I actually need to do this on https://apitest.dataverse.org
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17:36 pdurbin ok. done
17:37 pdurbin oddly, I got this: remote failure: Error occurred during deployment: Exception while deploying the app [dataverse-4.1] : Could not load any resource bundle by com.sun.org.apache.xerces.inter​nal.impl.msg.XMLSchemaMessages. Please see server.log for more details. Command deploy failed.
17:37 pdurbin but then I stopped and started glassfish and was able to deploy the new war file
17:38 pdurbin hmm, I need to update my solr schema and reindex too
17:38 pdurbin or else MyData doesn't work
17:44 pdurbin ok, done
17:46 pdurbin oh, and https://github.com/IQSS/dataverse/releases/download/v4.1/upgrade_v4.0.1_to_v4.1.sql
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17:51 pdurbin psql dvndb -f /tmp/upgrade_v4.0.1_to_v4.1.sql
17:51 pdurbin ok, should be all set
17:51 pdurbin donsizemore: so it's not too bad
18:22 donsizemore pdurbin: i undeployed, restarted glassfish, updated solr schema. but on deploying the 4.1 war i get a ton of SQL errors - * already exists
18:23 donsizemore pdurbin: however, the homepage shows 4.1 build 71 and shib still works =)
18:41 pdurbin donsizemore: that's glassfish trying to create tables that already exist
18:46 donsizemore pdurbin: that's what it looked like; now that you tell me that i'm happy
18:47 donsizemore so... what's the planning process for importing 3.6.2 files and DB into this 4.1 installation?
18:48 donsizemore pdurbin: note that it's shibbolized and will use a webdavfs/milton.io mount to store data directly into iRODS
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18:59 pdurbin donsizemore: I'm really not sure how we migrated files. Can you please ask via support@dataverse.org ?
19:12 donsizemore pdurbin: done. and thank you again for all your help
19:13 pdurbin donsizemore: oh sure
19:13 pdurbin donsizemore: I'm pretty excited you got Shibboleth working. Good job.
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19:22 donsizemore pdurbin: it was just the AJP_ prefix. i'm fairly new to Dataverse and hadn't worked with Shib since 2009 or so, so please forgive me spinning back up
19:24 donsizemore so, for now I've opened up our test dataverse to anyone to see how it treats shib accounts (which don't seem to show up in the permissions user/group list)
19:26 pdurbin donsizemore: you should be able to assign roles to shib accounts
19:28 donsizemore pdurbin: ah - i just don't see them until i assign them something.
19:30 pdurbin yeah
19:36 buckwheat joined #dataverse
19:36 buckwheat Hello All. Anyone up for a few install questions?
19:37 donsizemore i'm no expert but happy to help!
19:38 buckwheat Hi Don. I ran thru the install guide, the R setup was pretty badly documented but finally got all modules to install. My issue is the webapp is not displaying yet no issues in the glassfish logs
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19:39 donsizemore can you see it listening on the correct port? (blank screen in browser, or no connection?)
19:42 donsizemore you can also try an "asadmin list-applications" in glassfish/bin/ to ensure that it deployed
19:43 buckwheat Yes, java is listening on 8080 and 8081, along with several other ports. When i try to load the site at <hostname>:8080 oddly enough I get the index.html page in the docroot dir. the dvninstall placed a war in the autodeploy dir, and it does appear to deploy it.
19:44 buckwheat I ran asadmin list-applications, it returned : dataverse  <ejb, web> Command list-applications executed successfully.
19:45 pdurbin what does the index.html file have in it?
19:46 buckwheat guess you would call it the glassfish "welcome" page....Your server is now running  To replace this page, overwrite the file index.html in the document root folder of this server. The document root folder for this server is the docroot subdirectory of this server's domain directory.  To manage a server on the local host with the default administration port, go to the Administration Console.
19:48 pdurbin weird. I'd refresh the browser, undeploy and redeploy
19:49 buckwheat It does seem strange. I am a Tomcat guy, so getting a crash course in GF. Similar but NOT the same. Most likely its me misconfiguring something but not sure what at this point
19:50 buckwheat Not sure if it matters, but the TwoRavens/R app under Apache on port 80 is working but has no data to manipulate at this point
19:51 pdurbin buckwheat: one thing you could try is `vagrant up` - http://guides.dataverse.org/en/latest/developers/tools.html#vagrant
19:51 pdurbin more of a developer thing
19:56 pdurbin buckwheat: I don't mean to send you on a wild goose chase though.
19:56 buckwheat saw the vagrant setup but could not go that route. thanks anyway...
19:56 pdurbin buckwheat: have you already contacted support@dataverse.org ?
19:57 buckwheat not yet. spent a couple hours looking around and getting the feel for the apps footprint. dont like to waste time, but dont go calling for support without doing some work first. If no luck today will think on it tonight and reach out to some folks tomorrow.
19:59 buckwheat with stuff like this it usually turns out to be some arcane symlink is out of whack or a tiny but crucial bit of documentation is missing. Part of the fun....and madness ;)
19:59 pdurbin heh. sure
19:59 pdurbin I'd undeploy, stop glassfish, start glassfish, redeploy.
19:59 pdurbin tailing server.log the whole time
20:00 buckwheat have done that but will do again. tail -f is my buddy....until kill -9 takes over. Kidding....
20:01 pdurbin buckwheat: you could also ask in #glassfish. I hang out there too.
20:01 buckwheat just to make sure I understand the R and TwoRavens IS or IS NOT required to make this puppy work?
20:01 pdurbin right
20:02 buckwheat is that a you need it...or you dont need it?
20:02 pdurbin you don't need R or TwoRavens
20:02 pdurbin just Java, Glassfish, PostgreSQL, and Solr
20:03 buckwheat figures, that part works :) Also, solr is not running in GF but on port 8983...so is there a jetty embedded somewhere too?
20:03 pdurbin um. I just start Solr with `java -jar start.jar`
20:04 pdurbin yes, there is jetty embedded in solr
20:04 buckwheat must have missed that is the docs. I may have an old copy, will check with the folks who asked me to install this and make sure I have the latest
20:05 pdurbin buckwheat: sounds good. oh, maybe you can give us some feedback on making the installation guide better. bencomp and I have been working on a reorg: https://docs.google.com/document/d/1GLky44JbtCNhGuavLXGEP8WPNdjbyHNxalEGjR78MaA/edit?usp=sharing
20:07 buckwheat Be happy to....for one, the command to start solr is nowhere in my docs. will look again
20:09 pdurbin yeah: https://github.com/IQSS/dataverse/issues/2401
20:19 bencomp pdurbin: I'm not working, but congrats on the milestone of having 100 tests run on a build!
20:19 pdurbin bencomp: huh. thanks. better than 3.6 at least :)
20:19 pdurbin the netbeans/jacoco integration is nice
20:19 bencomp Netbeans says coverage is 4.36%
20:20 pdurbin yeah
20:21 bencomp still lots of test to write and code to clean up, so I'll leave you to it :)
20:21 pdurbin thanks. at the moment I'm playing a bit with https://github.com/mbosecke/pebble
20:22 bencomp while I play with Ansible as provisioner for Vagrant to see if I can use it to manage a personal VM
20:23 pdurbin cool
20:23 bencomp what are you looking to use it for?
20:23 bencomp Pebble I mean
20:23 pdurbin well, https://mozilla.github.io/nunjucks/ got added for MyData in 4.1
20:23 pdurbin but it's client side
20:27 pdurbin Pebble is server-side templating.
20:27 bencomp I see
20:28 bencomp but I'll see later
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| Channels | #dataverse index | Today | | Search | Google Search | Plain-Text | plain, newest first | summary

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.