Time
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Message
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11:03 pdurbin
bencomp: I replied to your comment on docs and testing: https://github.com/IQSS/dataverse/issues/2648
11:05 bencomp
pdurbin: thanks, I noticed and am already working on a reply :)
11:07 pdurbin
bencomp: cool. I wonder if there's a better place to discuss it though. Maybe we should have a dataverse-dev mailing list.
11:09 pdurbin
bencomp: or maybe you could make a pull request for this: http://guides.dataverse.org/en/latest/developers/testing.html
11:56 bencomp
pdurbin: one needs requirements and a design to write tests
11:56 bencomp
could you ask someone to look at https://github.com/IQSS/dataverse/issues/2548 ?
12:04 pdurbin
bencomp: would you be willing to create an ordered list of issues you feel are important? This would be the "My Ranking" idea I wrote about at https://github.com/waffleio/waffle.io/issues/126#issuecomment-149087524
12:08 bencomp
pdurbin: are you asking me to manage the project? ;)
12:08 bencomp
I'm in a meeting now
12:13 pdurbin
bencomp: no. I'm asking you to tell us the order in which *you* think the issues should be worked on. I'd like to ask the same of everyone who has an interest the direction of Dataverse. But if you create your list, I can point to it as an example.
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13:44 bencomp
pdurbin: okay. I'll get back to this
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14:40 pdurbin
bencomp: thanks!
14:49 ata_t
Hi
14:58 pdurbin
ata_t: hi!
15:01 ata_t
Hey i am still trying to install dv
15:01 ata_t
:)
15:01 ata_t
I am running the install script in the 4.2
15:02 ata_t
up to setup.all script everything seems fine
15:02 ata_t
I think solr is ok as well as the solr check at the very beggining
15:02 ata_t
returns {"responseHeader":{"status":0,"QTime":10}}
15:03 pdurbin
ata_t: oh, right we chatted at http://irclog.iq.harvard.edu/dataverse/2015-10-01#i_25234
15:03 ata_t
yep :)
15:03 ata_t
when the setup the metadata blocks script is called
15:03 ata_t
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd "><html xmlns="http://www.w3.org/1999/xhtml "><head><title>GlassFish Server Open Source Edition 4.1 - Error report</title>
15:03 ata_t
I get an error
15:04 pdurbin
ata_t: are you seeing that html in a browser or in a terminal?
15:04 ata_t
terminal
15:05 ata_t
./setup-datasetfields.sh
15:05 ata_t
./setup-builtin-roles.sh
15:05 ata_t
./setup-identity-providers.sh
15:05 ata_t
all give similar results
15:11 ata_t
the error in the html is The requested resource is not available
15:11 ata_t
a full example is here:
15:11 ata_t
curl http://localhost:8080/api/admin/datasetfield/loadNAControlledVocabularyValue
15:11 ata_t
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd "><html xmlns="http://www.w3.org/1999/xhtml "><head><title>GlassFish Server Open Source Edition 4.1 - Error report</title><style type="text/css "><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family
15:14 pdurbin
ata_t: would you be able to "select all" the entire terminal session and put it in a file and attach it in an email it to support
15:14 ata_t
hmm sure was running screen may need to rerun it - a min
15:15 pdurbin
ata_t: if you could also attach your glassfish "server.log" it would be very helpful
15:17 ata_t
sure
15:26 pdurbin
ata_t: has the war file been deployed? When I run `/usr/local/glassfish4/glassfish/bin/asadmin list-applications` on https://apitest.dataverse.org it says "dataverse-4.2 <ejb, web>"
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15:27 ata_t
no
15:27 ata_t
[centos
15:27 ata_t
Nothing to list.
15:27 ata_t
No applications are deployed to this target server.
15:27 ata_t
Command list-applications executed successfully.
15:27 ata_t
[centos
15:27 pdurbin
that's no good
15:27 pdurbin
hopefully there will be something in server.log
15:28 pdurbin
bencomp: I just created the 4.2.1 branch but I'd like to touch base with you about the "default" branch at https://github.com/IQSS/dataverse
15:29 pdurbin
ata_t: if you feel like it, please go ahead and create an issue at https://github.com/IQSS/dataverse/issues that the installer should stop if the war file hasn't been deployed (and say so)
15:33 ata_t
:) yep sure
15:33 ata_t
I have the server log am sending an email now
15:33 pdurbin
ata_t: thanks!
15:46 pdurbin
ata_t: I'm seeing "Autodeploy failed : /usr/local/glassfish4/glassfish/domains/domain1/autodeploy/dataverse.war" but shouldn't it be "dataverse-4.2.war"?
15:47 ata_t
the war file in the 4.2 installer is
15:47 ata_t
dataverse.war
15:48 ata_t
and when it is copied under
15:48 ata_t
ls /usr/local/glassfish4/glassfish/domains/domain1/autodeploy/
15:48 ata_t
bundles dataverse.war dataverse.war_deployFailed
15:49 pdurbin
ok. thanks
15:49 ata_t
it is copied as dataverse.war
15:49 pdurbin
"UnknownHostException" is troubling. This is a potential fix (/etc/hosts): http://stackoverflow.com/questions/21817809/glassfish-exception-during-deployment-project-with-stateful-ejb/21850873#21850873
15:50 pdurbin
ata_t: your goal would be to make sure that UnknownHostException doesn't appear in server.log
15:50 ata_t
for me cat /etc/hosts
15:50 ata_t
127.0.0.1 localhost localhost.localdomain localhost4 localhost4.localdomain4
15:50 ata_t
::1 localhost localhost.localdomain localhost6 localhost6.localdomain6
15:50 ata_t
ok let me check
15:57 pdurbin
ata_t: meanwhile, thanks for opening that issue. I just left a comment: installer script is not stopping if the war file hasn't been deployed (and it does not say so) · Issue #2660 · IQSS/dataverse - https://github.com/IQSS/dataverse/issues/2660
15:58 pdurbin
axfelix: we're co-authors! :) The Code4Lib Journal – Open Journal Systems and Dataverse Integration– Helping Journals to Upgrade Data Publication for Reusable Research - http://journal.code4lib.org/articles/10989
15:58 pdurbin
ata_t: thanks for opening https://help.hmdc.harvard.edu/Ticket/Display.html?id=228619 too
15:59 ata_t
np
15:59 ata_t
I am having issues in dropping the dvndb database
15:59 ata_t
psql -U dvnapp -c 'DROP DATABASE "dvndb"' template1
15:59 ata_t
ERROR: database "dvndb" is being accessed by other users
15:59 ata_t
DETAIL: There are 8 other session(s) using the database.
15:59 ata_t
any suggestions?
16:00 ata_t
I applied the host fix and wanted to test it so I was using the commands in the rebuild script: https://github.com/IQSS/dataverse/blob/4.3/scripts/deploy/apitest.dataverse.org/rebuild
16:04 pdurbin
ata_t: I can only assume those 8 sessions are from glassfish. But why would glassfish have those open connections to posgres if the war file isn't deployed?
16:09 pdurbin
postgres*
16:14 ata_t
well :)
16:15 ata_t
I don't know
16:15 ata_t
should I stop solr or sth?
16:15 ata_t
to get past this
16:15 ata_t
I did call the undeploy
16:16 ata_t
but ofc it did not
16:16 ata_t
since there is nothing deployed
16:17 ata_t
"/usr/local/glassfish4/glassfish/bin/asadmin undeploy dataverse-4.0"
16:17 ata_t
remote failure: Application dataverse-4.0 is not deployed on this target [server]
16:17 ata_t
Command undeploy failed.
16:18 ata_t
"/usr/local/glassfish4/glassfish/bin/asadmin undeploy dataverse"
16:18 ata_t
remote failure: Application dataverse-4.0 is not deployed on this target [server]
16:18 ata_t
Command undeploy failed.
16:18 pdurbin
I assume `asadmin list-applications` still doesn't show anything deployed
16:18 ata_t
"/usr/local/glassfish4/glassfish/bin/asadmin list-applications"
16:18 ata_t
Nothing to list.
16:19 ata_t
No applications are deployed to this target server.
16:19 ata_t
Command list-applications executed successfully.
16:19 ata_t
yep
16:19 pdurbin
ok
16:19 pdurbin
well, if you stop glassfish I bet you'll be able to delete that database
16:19 pdurbin
ata_t: I'll bet you a dollar
16:20 ata_t
:)
16:20 ata_t
:) you'd have it
16:20 ata_t
I think
16:20 ata_t
ps -ef | grep glassfish
16:20 ata_t
centos 1933 20587 0 15:13 pts/3 00:00:00 emacs glassfish-setup.sh
16:20 ata_t
root 2991 1 2 15:20 pts/1 00:01:37 /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/bin/java -cp /usr/local/glassfish4/glassfish/modules/glassfish.jar -XX:+UnlockDiagnosticVMOptions -XX:PermSize=256m -XX:MaxPermSize=512m -XX:NewRatio=2 -Xmx5981m -client -javaagent:/usr/local/glassfish4/glassfish/lib/monitor/flashlight-agent.jar -Ddataverse.files.directory=/usr/local/glassfish4/glassfish/domains/domain1/files -Dfelix.fileinstall.disableConfigSav
16:21 ata_t
sudo kill -9 2991
16:21 ata_t
[centos
16:21 ata_t
DROP DATABASE
16:21 pdurbin
sweet
16:24 pdurbin
bencomp: I decided to leave you a comment about my thoughts on the "default" branch: https://github.com/IQSS/dataverse/pull/2423#issuecomment-149621920
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16:26 ata_t
after fixing the /etc/hosts
16:26 ata_t
"/usr/local/glassfish4/glassfish/bin/asadmin list-applications"
16:26 ata_t
dataverse <ejb, web>
16:26 ata_t
Command list-applications executed successfully.
16:26 ata_t
I am waiting for the setup.all script to run now
16:26 ata_t
a question why there is a sleep for 3M?
16:28 pdurbin
ata_t: great! sounds like you should vote up http://stackoverflow.com/questions/21817809/glassfish-exception-during-deployment-project-with-stateful-ejb/21850873#21850873 ! :)
16:29 pdurbin
ata_t: here's why I think the sleep is there: https://github.com/IQSS/dataverse/issues/2660#issuecomment-149614358
16:44 bencomp
pdurbin: hope my comment on 2648, https://github.com/IQSS/dataverse/issues/2648#issuecomment-149626051 , helps
16:44 bencomp
time to go home
16:44 pdurbin
bencomp: it does. I already commented on your comment :)
16:44 pdurbin
thanks!
16:54 pdurbin
ata_t: does that make sense? the sleep is there to provide time for the war file to deploy after it has been copied to the "autodeploy" directory.
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agarnett: garnett so many nicks for you :)
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