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IRC log for #dataverse, 2019-02-05

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All times shown according to UTC.

Time S Nick Message
07:28 juancorr joined #dataverse
07:42 jri joined #dataverse
08:33 MrK joined #dataverse
09:31 pdurbin joined #dataverse
09:43 pdurbin Open Science Days just started: https://twitter.com/philipdurbin/status/1092713842772246528
09:53 dataverse-user joined #dataverse
09:54 dataverse-user hello can someone help with it-related issue in a dataverse installation?
09:54 pdurbin dataverse-user: I'm at a conference but I can try. What's up? :)
09:56 dataverse-user thank you so much in advance :) i am trying to publish an empty dataset in dataverse but i keep getting "error this dataverse was not able to be published. If you believe..." so on
09:57 dataverse-user may i send the error.log contents in here? i believe this is fqdn problem in domain.xml and i already tried some solutions but i cant get it to work :(
09:58 pdurbin I would be happy to see the log but can you please email it to support@dataverse.org?
09:58 dataverse-user of course, i will do so now
09:58 pdurbin Thanks. Are you using DOIs or Handles?
09:59 dataverse-user no we still havent configured any DOIs. Im not sure about Handles though
09:59 dataverse-user but pretty much this is a fresh installation of the latest version
10:00 pdurbin Are you just testing? You could try the "FAKE" DOI providers developers use.
10:00 pdurbin Please see http://guides.dataverse.org/en/4.10.1/developers/dev-environment.html#configure-your-development-environment-for-publishing
10:00 pdurbin curl http://localhost:8080/api/admin/settings/:DoiProvider -X PUT -d FAKE
10:02 dataverse-user i just mailed the error logs, i will now look the urls you posted here, thank you so much
10:03 pdurbin Thanks, I see some logs in https://help.hmdc.harvard.edu/Ticket/Display.html?id=272093
10:04 dataverse-user yes thiis is my assigned id
10:05 dataverse-user before installing in a live server, i tried installing the dataverse in a local machine for testing purposes and i did not faced this issue :(
10:05 pdurbin Unexpected Exception calling  publish dataverse command
10:05 pdurbin edu.harvard.iq.dataverse.engine.co​mmand.exception.CommandException: Command edu.harvard.iq.dataverse.engine.co​mmand.impl.PublishDataverseCommand@7386410f failed: null
10:05 pdurbin Caused by: org.apache.solr.client.solrj.impl.H​ttpSolrClient$RemoteSolrException: Error from server at http://localhost:8983/solr/collection1: Expected mime type application/octet-stream but got text/html.
10:06 pdurbin It seems like you're having problems with Solr.
10:06 dataverse-user so its a solr issue?
10:06 pdurbin I think so.
10:06 pdurbin You could try reinstalling Solr.
10:07 dataverse-user will it affect the dataverse installation if i reinstall solr?
10:08 pdurbin No. You can reindex Dataverse when you're done reinstalling Solr.
10:09 dataverse-user ok i will try now
10:09 pdurbin Please see http://guides.dataverse.org/en/4.10.1/admin/solr-search-index.html#full-reindex
10:10 dataverse-user thank you sir
10:11 pdurbin sure
10:12 pdurbin I was confused at first. I thought you were having trouble publishing a dataset. It looks like you're having trouble publishing a dataverse.
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11:22 dataverse-user hello?
11:22 pdurbin dataverse-user: hi!
11:22 dataverse-user i reinstalled solr as you suggested and problem still persists :(
11:23 dataverse-user Error – Command edu.harvard.iq.dataverse.engine.command​.impl.FinalizeDatasetPublicationCommand@7dfb767f failed: null If you believe this is an error
11:24 pdurbin What if you curl http://localhost:8983/solr/collection1/schema/fields ?
11:25 pdurbin Do you get JSON out?
11:25 dataverse-user no its more like jquery
11:25 pdurbin with output like "dvObjectType" etc
11:26 pdurbin Ok, it sounds like there's still something wrong with your Solr installation.
11:26 dataverse-user i run all these commands as solr user, right?
11:26 dataverse-user not root
11:27 pdurbin If it's easier to just use root for now, please go ahead. :)
11:28 dataverse-user curl http://localhost:8080/api/admin/index {"status":"OK","data":{"availablePa​rtitionIds":[0],"args":{"numPartiti​ons":1,"partitionIdToProcess":[solr@sodanet ekke]$ curl http://localhost:8983/solr/collection1/schema/fields <html> <head> <meta http-equiv="Content-Type" content="text/html;charset=utf-8"/> <title>Error 404 Not Found</title> </head> <body><h2>HTTP ERROR 404</h2> <p>Problem accessing /solr/collection1/schema/fields. Reason
11:28 dataverse-user this is the output
11:28 dataverse-user i followed step by step the instructions, even increased the file size
11:29 pdurbin Did you do this step? bin/solr create_core -c collection1 -d server/solr/collection1/conf/
11:30 dataverse-user i think i did but i will sudo this again as solr now
11:30 pdurbin Ok. You're following http://guides.dataverse.org/en/4.10.1/installation/prerequisites.html#solr right?
11:32 dataverse-user was following this to now
11:32 dataverse-user http://guides.dataverse.org/en/4.10.1/installation/prerequisites.html#solr
11:32 pdurbin ok, good
11:32 pdurbin I'm wondering if "collection1" is missing.
11:33 dataverse-user it gives me sudo: bin/solr: command not found
11:34 pdurbin I usually do this
11:34 pdurbin sudo -i
11:34 pdurbin to become root
11:34 dataverse-user and without sudo it gives me bash bin/solr permission denied
11:34 pdurbin then
11:34 pdurbin su - solr
11:34 pdurbin to become the solr user
11:34 dataverse-user ok let me try again and sorry for the troubles i cause you :(
11:35 pdurbin no worries, out documentation could probably be improved
11:35 pdurbin our*
11:36 dataverse-user bash: bin/solr: no such file or directory
11:37 dataverse-user with sudo -i, then su - solr
11:38 pdurbin did you cd? cd /usr/local/solr/solr-7.3.0
11:39 dataverse-user silly me, multiple error gave me a headache :)
11:39 dataverse-user new error now, ERROR: Error CREATEing SolrCore 'collection1': Unable to create core [collection1] Caused by: Content is not allowed in prolog.
11:40 pdurbin Hmm, are the schema.xml and solrconfig.xml files ok? Valid XML?
11:40 dataverse-user these were auto configed during solr installation, right?
11:41 pdurbin No, you have to copy them into place.
11:41 pdurbin cp /tmp/dvinstall/schema.xml /usr/local/solr/solr-7.3.0/s​erver/solr/collection1/conf
11:41 pdurbin for example
11:42 dataverse-user will try now, so schema.xml is in dvinstall what about solrconfig.xml location?
11:43 pdurbin both should be in dvinstall.zip
11:56 dataverse-user there is no collection1 dir inside ‘/usr/local/solr/solr-7.3.0/server/solr'
11:56 dataverse-user only one dir called configsets
11:58 dataverse-user actually, these: configsets  README.txt  solr.xml  zoo.cfg
12:00 dataverse-user so it is as you first wondered, "collection1" is missing
12:00 pdurbin Did you do this step? cp -r server/solr/configsets/_default server/solr/collection1
12:01 dataverse-user do i perform this from anywhere?
12:02 pdurbin no, first cd solr-7.3.0
12:02 pdurbin But you need to do all these steps in the right order.
12:07 dataverse-user ok, i will again stop the process and start all over, how can i do a clean uninstall of solr?
12:48 andrewSC joined #dataverse
12:57 dataverse-user thank you pdurbin, my problem is fixed :) sorry for any inconvenience
13:05 pdurbin dataverse-user: no problem. I'm glad you fixed it!
13:35 donsizemore joined #dataverse
15:53 pameyer joined #dataverse
15:54 pameyer donsizemore: knock, knock
16:03 jri joined #dataverse
19:04 donsizemore joined #dataverse
19:09 donsizemore @pameyer who's there?
19:19 pameyer @donsizemore I heard a bird mentioning docker-aio...
19:28 Julio-Chaves joined #dataverse
19:29 donsizemore indeedily. i have what i /would/ want to work in a Dockerfile that calls dataverse-ansible using an external group_vars file, but... Docker and init systems
19:29 Julio-Chaves Hello ! I'm configuring shibboleth to connect to adfs, but the "Institutional Login" button does not appear at home screen, even after restart shibd and httpd. I thought you folks would give an ideia.
19:30 donsizemore @julio-chaves hello =) did you perform http://guides.dataverse.org/en/latest/installation/shibboleth.html#add-the-shibboleth-authentication-provider-to-dataverse
19:31 Julio-Chaves looking into...
19:31 ashaw joined #dataverse
19:32 pameyer @donsizemore - I believe there's a fake-systemd type thing that can be used within docuer
19:32 pameyer s/docuer/docker/g
19:33 donsizemore @pameyer well, i enabled it per instructions, but... it mounts /sys/fs/cgroup from an Ubuntu host to a CentOS image, and... ew.
19:34 donsizemore @pameyer i'm all for fake everything, though.
19:34 pameyer @donsizemore that is ugly.  would I be guessing correctly that you're thinking of using docker to test dataveres-ansible?
19:36 donsizemore @pameyer i made an equally urgly Dockerfile for the prototype TRSA (just uses on H2 database with a hard-coded password, but the real one will talk to Dataverse instead)
19:37 Julio-Chaves @donsizemore Thank you, it showed up.
19:37 donsizemore @pameyer I just want a corresponding Dockerfile that can deploy a particular branch of a Dataverse fork, so now I'm keenly interested in your TTY investigation from last month
19:37 pameyer @Julio-Chaves glad that did the trick
19:38 pameyer @donsizemore my idea that the TTY change was related to centos version turned out to be a bust.  when I reverted it, it behaved the same
19:39 ashaw hi all - I have a question related to the MyData API..is it possible to specify a query param for a search term?  i want to be able to search the datasets by search term -- similar to the web interface
19:39 donsizemore @pameyer i'm always happy to blame docker, systemd and/or ipv6
19:40 ashaw since all of the datasets are unpublished, I can't use the Search API
19:40 pameyer @donsizemore - I'd be happy to know which to blame for this case.
19:41 pameyer @donsizemore - is your goal to end up with an image, or do you need a straight dockerfile build?
19:41 donsizemore @ashaw to the best of my knowledge, solr populates the web interface.
19:42 donsizemore @pameyer just an example that folks can pull and evaluate. any stab I've taken got me to about 98%, as one does
19:44 pameyer @ashaw if I'm remembering correctly, the mydata api is somewhat undocumented (there should be an issue for that).  have you looked into using the search API with a user token?
19:44 donsizemore @pameyer I was just searching the docs for it =)
19:45 pameyer mydata is using a javascript port of jinja2, but that port has some of its own APIs - I don't remember what they're called, or if the "make them documented" issue was resolved or not
19:47 ashaw I have not tried the search API with a user token..anything special I need to do?
19:48 pameyer @ashaw you need to put the API token in the X-Dataverse-key header
19:50 pameyer @donsizemore - it's possible that starting glassfish and commiting the image would make things happy-ish.  uglier than they already are, if such a thing is possible
19:50 pameyer I'll give it a shot
19:51 ashaw thanks will give that a try
19:52 pameyer @asahw - I took a quick look at the search API docs to check the syntax for that header, and it looks like I was wrong
19:53 pameyer it mentions that it's published only :( so I pointed you towards a blind alley
19:54 pameyer @donsizemore - it looks like the docker commit trick does work.
20:01 pameyer about to head into a meeting; will be back in a bit
20:04 jri joined #dataverse
20:13 ashaw thanks all for the help. i resorted to the old trick of just typing my search terms in the search box and printing results: )
20:19 Julio-Chaves Hey folks, we did the configurations to work with adfs through shibboleth, but now we are seeing an error after type user and password: "opensaml::FatalProfileException" , "Unable to establish security of incoming assertion". Somebody already saw this error?
20:25 donsizemore @julio-chaves the guy who probably knows the most about ADFS and Shib just went to a meeting, but Googling says "This error usually indicates a cookie or active login error (Shib does not like multiple users signed into the same browser at the same time). To resolve this issue, please clear your browser's cookies and cache"
20:46 Julio-Chaves Yes we did this. We think that this issue may be related with the certificate, which will be properly configured tomorrow. Thanks.
20:53 pameyer @Julio-Chaves - which log is that error coming from?
20:56 pameyer @donsizemore - expanding a little about the "docker commit" stuff.  I started docker-aio as usual, connected to the container and manually started glassfish (with dataverse already in there).  `docker commit $container_name $new_image_name` to create a new image
20:57 pameyer `docker run -d -p 8081:80 $new_image_name` , wait for it to be healthy, and had a running installed dataverse
20:57 donsizemore @pameyer it ain't ugly if it works. i'll tinker with that
20:57 pameyer $new_image_name can be pushed/pulled to wherever
20:57 donsizemore @pameyer we just want an easily stood-up example
20:57 pameyer @donsizemore - that should do the trick then
23:04 jri joined #dataverse
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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.