Time
S
Nick
Message
00:57 donsizemore joined #dataverse
01:16 donsizemore
@pdurbin @pameyer if either of you get a minute i'd love a second pair of eyes at https://github.com/IQSS/dataverse-ansible/commit/1548325ec3ca585cb2c6752b537aab10c33d6f4c#diff-c298af2491e6cea8a8a97039e4e3f8a4R74
01:18 donsizemore
@pdurbin @pameyer i haven't quite entered "thrashing" regexp territory, but i haven't found the right incantation to make ansible-1.9 bump the jetty requestHeaderSize.
01:18 donsizemore
@pdurbin @pameyer newer ansible versions contain an xml module for this purpose, but that means we have to bump the source centos7/ansible image, and... maybe later.
01:55 * pdurbin
adds it to his todo list
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12:42 donsizemore joined #dataverse
12:43 donsizemore
@pdurbin i should note that the jetty.xml value should be the last snafu before dataverse-ansible will correctly install 4.9 and solr 7.3.0
13:26 pdurbin
donsizemore: great! To help do I first need to learn ansible?
13:26 donsizemore
@pdurbin no, it's just me whining about syntax compatibility
13:26 pdurbin
knikolla: can you please fact check my reply on this thread: https://groups.google.com/d/msg/dataverse-community/2gxiHT5B0xA/p0k8ebnYAQAJ ?
13:27 pdurbin
donsizemore: ok. If can help, please explain how. :)
13:28 donsizemore
@pdurbin I'm more interested in sussing out these "No such dataset: doi:10.5072/FK2/S3/HZJFNZ" errors I'm getting when I try to create a dataset on a 4.9 test box (and why I want to get dataverse-ansible up to 4.9)
13:34 pdurbin
What's the S3 for?
13:34 pdurbin
And is this a new installation? Or an upgrade?
13:35 pdurbin
You've got me wondering if the "strip shoulder from authority setting" update here is working properly: https://github.com/IQSS/dataverse/blob/v4.9/scripts/database/upgrades/upgrade_v4.8.6_to_v4.9.0.sql#L67
13:37 pdurbin
As of 4.9 the authority should only be "10.507" or whatever. No shoulder. And there's a new setting called :Shoulder. Please see https://github.com/IQSS/dataverse/blob/v4.9/scripts/api/setup-all.sh#L52
13:38 donsizemore
@pdurbin it's a dump of our production 4.8.6 imported to a test box, then upgraded
13:39 pdurbin
Ok. I'd examine your authority and shoulder.
13:39 pdurbin
but I'm no doctor
13:41 donsizemore
@pdurbin aha! i don't see that mentioned in the 4.9 upgrade instructions. let me poke.
13:41 pdurbin
Cool. If you're still stuck please email your server.log to support
13:44 donsizemore
@pdurbin OH... it wasn't your upgrade script. I have a "reset_configs" shell script I use to make a production dump not a production dump WRT certain settings. i bet this is all my fault.
13:48 donsizemore
@pdurbin it was a "me" problem! my reset script now resets the authority and the shoulder. thanks
13:49 donsizemore
@pdurbin and as you can see I've been checking out the instruments in Harvard's Memorial Church https://irss-dvn4-akiotest.irss.unc.edu/dataset.xhtml?persistentId=doi:10.5072/FK2DMUUHX
14:03 donsizemore
@pdurbin with your permission I'll gladly update the driver in PR #4721
14:04 pameyer joined #dataverse
14:06 pameyer
@donsizemore I'll see if I can take a look today
14:41 pdurbin
pameyer: thanks. I don't know ansible. Should probably learn some day.
15:04 dataverse-user joined #dataverse
15:04 dataverse-user
Hi, I am having an issue installing Dataverse
15:05 dataverse-user
The installer fails at step #6 deploying the WAR file
15:05 dataverse-user
I can copy and paste the error from the server.log file in glassfish if it helps
15:06 pameyer
hi dataverse-user: how are you installing?
15:07 dataverse-user
on a local machine
15:07 dataverse-user
solar , postgres DB are local as well
15:08 pameyer
interactive, non-interactive, ansible, docker?
15:09 dataverse-user
non interactive , just running ./install
15:09 donsizemoe joined #dataverse
15:09 dataverse-user
in the dvinstall folder
15:11 donsizemoe
@pdurbin i'm testing my commits to #4709... once i figure out why solr7 won't launch on my buildbox
15:11 pameyer
dataverse-user: what error is it giving you?
15:12 dataverse-user
This is the from server.log in glassfish:
15:12 dataverse-user
[2018-06-08T10:36:15.267-0400] [glassfish 4.1] [SEVERE] [NCLS-CORE-00026] [javax.enterprise.system.core] [tid: _ThreadID=45 _ThreadName=admin-listener(3)] [timeMillis: 1528468575267] [levelValue: 1000] [[
15:13 dataverse-user
Exception during lifecycle processing
15:13 dataverse-user
java.lang.RuntimeException: Cannot create scratch directory : /usr/local/glassfish4/glassfish/domains/domain1/generated/ejb/dataverse
15:13 dataverse-user
at org.glassfish.javaee.core.deployment.JavaEEDeployer.prepare(JavaEEDeployer.java:229)
15:14 dataverse-user
There is a big trace after this, do you want me top cpy it for you ?
15:14 dataverse-user
:q!
15:14 dataverse-user
Sorry, the last not was not meant for you :-)
15:20 dataverse-user joined #dataverse
15:20 dataverse-user
I am sorry I was just disconnected
15:20 pameyer
np - I was interrupted too
15:20 dataverse-user
I juts posted the error I get during dataverse installation
15:21 pameyer
yup - the "cannot create scratch directory" suggests to me that glassfish was installed as a different user than the user running the installer
15:21 pameyer
is it possible that the glassfish directory is owned by root, and the installer is running as non-root?
15:23 dataverse-user joined #dataverse
15:23 dataverse-user
I am back again. We have connection issues today
15:23 dataverse-user
I am the only user in the system though
15:24 dataverse-user
and I installed glassfish myself
15:24 dataverse-user
under my username
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15:24 pameyer
is glassfish also running under your username?
15:24 dataverse-user
yes
15:25 dataverse-user
Maybe I should ask you to clarify that
15:25 dataverse-user
I am new to glassfish
15:25 dataverse-user
I start glassfish under my username
15:25 dataverse-user
Is that what you mean ?
15:26 pameyer
ok - I'm wondering about the possibility that the glassfish server process is running under a different user account than the user that owns the /usr/local/glassfish4 directory. that would be one explaination for why the installer isn't able to create the directory
15:26 dataverse-user
I understand
15:26 pameyer
another possibility might be that a previous installer run failed, and the installer is trying to create a directory that already exists
15:27 dataverse-user
let me share with you what I think to see if we are on the same page
15:27 pameyer
if the directory exists, you could try removing it
15:27 pameyer
go for it
15:27 donsizemoe
@pdurbin dataverse 4.9 on current postgres driver =) http://irss-dls-buildbox:8080
15:28 donsizemoe
@pdurbin http://irss-dls-buildbox.irss.unc.edu:8080 even
15:28 donsizemoe
@pdurbin will tidy up PR after lunch
15:28 dataverse-user
The directories the glassfish are producing can not be written in/usr/local/glassfish becuase it needs admin privileges
15:28 dataverse-user
what if I change the line in the ./install file on step 6 and ass a sudo there ?
15:28 dataverse-user
Will this make any sense ?
15:28 dataverse-user
:-)
15:29 dataverse-user
The first link does not open
15:29 dataverse-user
the second one did open
15:30 pameyer
"admin privileges" suggests that ownership of the glassfish directory is root (or a system account)
15:30 dataverse-user
Or I change access to glassfish directory ?
15:30 dataverse-user
my user is root
15:31 dataverse-user
I am sorry but the second link timed out too
15:33 dataverse-user
Just one question, the glassfish user and password are admin by default
15:33 dataverse-user
is this correct ?
15:33 pameyer
by default, I don't think there's on OS account for glassfish.
15:34 jri_ joined #dataverse
15:34 pameyer
depends on the OS ; but I've never run across one that had one built-in
15:34 dataverse-user
Ok, I see
15:34 dataverse-user
So I will look into this and will get back whan I find sth
15:35 dataverse-user
Thanks for your help now
15:39 pdurbin
dataverse-user: hi! You're all set?
15:40 pdurbin
donsizemoe: cool, please just let me know when you're done tidying.
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17:39 donsizemore
@pdurbin i think #4709 is ready – though my lunch date came at an inopportune time for task interruption
17:53 pdurbin
donsizemore: cool, lemme take a look
17:55 pdurbin
Lemme see if Leonid is around.
17:55 * pdurbin
walks down the hall
18:17 pdurbin
donsizemore: he's at lunch but I'm wondering if we're deleting postgresql-42.1.4.jar should we also delete postgresql-8.4-703.jdbc4.jar, postgresql-9.0-802.jdbc4.jar etc through postgresql-9.4.1212.jar?
18:17 donsizemore
@pdurbin i'm intentionally leaving those for @pameyer =)
18:17 donsizemore
but i can pull them if you'd like
18:17 pdurbin
pameyer can dig them out of the git history ;)
18:18 donsizemore
you da boss
18:18 pdurbin
heh, no I'm fine with keeping them. whatever makes pameyer happy
18:18 pdurbin
donsizemore: where it is written about the compatibility? which jar to use?
18:18 donsizemore
the comments mention him specifically. then beneath: # for everybody else ...
18:19 pameyer
huh - when did I get tagged with the historical legacy of jdbc drivers? ;)
18:19 donsizemore
oh, about 10:30
18:21 pdurbin
donsizemore: does that make sense? Where does it say that this "42" jar works with old versions of postgres?
18:21 donsizemore
on the URL in the comment. should be backwards-compatible to 8.2
18:22 pdurbin
I'll go look for the comment.
18:23 donsizemore
whoops on the "about" page: https://jdbc.postgresql.org/about/about.html "The current version of the driver should be compatible with PostgreSQL 8.2 and higher"
18:23 pdurbin
gotcha and the comment at https://github.com/IQSS/dataverse/issues/3789#issuecomment-395748885
18:24 pdurbin
Ok. Kevin asked so I'll include this in a new comment.
18:24 pdurbin
pameyer: now you've got me confused about if you want those old jars or not? With your blessing, donsizemore can `git rm` them and remove your name from the install script.
18:26 pdurbin
pameyer: here's where he added "keeping this for pete": https://github.com/IQSS/dataverse/commit/92d7e98
18:32 donsizemore
@pdurbin p.s. I believe dataverse-ansible is good to go with 4.9 and solr-7.3.0
18:32 pdurbin
donsizemore: nice! Reason enough to have Jamie re-try?
18:33 pameyer
pdurbin donsizemore - taking a look momentarilly
18:33 donsizemore
@pdurbin she didn't really answer pete's question about the state of glassfish during the hang
18:37 pdurbin
Yeah. Well, I'll let her know it's been updated to 4.9 at least.
18:38 pameyer
ah - now I'm remembering. there was a point where I made sure the makefile put all the jdbc drivers into dvinstall.zip
18:38 pameyer
so I'm ok with taking them out
18:39 pdurbin
donsizemore: make: *** No rule to make target `pgdriver/postgresql-42.1.4.jar', needed by `dvinstall/pgdriver'. Stop.
18:39 donsizemore
@pameyer i'll take out the old jars, the commented-out versions and the version-checking code?
18:39 pameyer
but it's a reminder that we should update the makefile too ;)
18:40 pameyer
@donsizemore sounds reasonable to me
18:40 donsizemore
yeah, i didn't find a standard URL we could use... so filename coordination will be an ugly necessity
18:40 pdurbin
donsizemore: can you please try cd scripts/installer && make clean && make?
18:41 pdurbin
And please see also http://guides.dataverse.org/en/4.9/developers/making-releases.html#make-artifacts-available-for-download
18:41 donsizemore
@pdurbin i just fixed the makefile, in the short-term
18:41 pdurbin
donsizemore: ok, but you haven't pushed yet have you? I'm on 59a7104 syntax tweak
18:42 donsizemore
no, i'm cleaning out the comments and old jarfiles
18:42 pdurbin
sweet
18:42 donsizemore
then hopefully margaritas by the pool
18:42 pdurbin
well earned
18:42 donsizemore
i presented at the iRODS UGM yesterday. most terrifying presentation-to-friends i've done
18:44 pameyer
I'm reminded of the mvn / make dependency resolution thing
18:46 donsizemore
@pdurbin pushed
18:47 donsizemore
(and reading the artifact page now)
18:48 pdurbin
donsizemore: I'm still getthing this: make: *** No rule to make target `pgdriver/postgresql-8.4-703.jdbc4.jar', needed by `dvinstall/pgdriver'. Stop.
18:48 donsizemore
whoops. my mind's at the pool
18:51 donsizemore
@pdurbin how 'bout now
18:54 pameyer
5714450cd6c14ea09aa15bab4360b29a69078177 make works for me
18:54 pdurbin
donsizemore: "Done!" Time for the pool.
18:54 donsizemore
ima tell 'em you said it was okay!
18:56 pdurbin
you tell 'em
18:57 donsizemore
y'all have a great weekend. and see you wednesday!
18:57 pdurbin
you too! thanks, Don!
19:00 pameyer
donsizemore - enjoy the pool ;)
19:02 pameyer
pdurbin: good news, I can fix 4528. bad news, it requires hard-coding the version string in yet another place. any thoughts?
19:11 pdurbin
I'd rather not hard code the version string in another place. I'm annoyed that we have to update it twice in Sphinx for every release. Ideally it would only be in one place: pom.xml
19:13 pameyer
whoops - you want to delete the PR, or should I?
19:14 pameyer
I'd think it would be easier to have a file with just the version that maven/sphinx/anything else could use, rather than having other tools digging into xml
19:15 pdurbin
and somehow include the version from the file into pom.xml?
19:16 pameyer
something like that
19:16 pameyer
not sure how/if it's something maven supports, haven't dug into it recently
19:18 pdurbin
no idea, sorry
19:19 pameyer
np - not top of the list ;)
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21:14 pdurbin
Have a good weekend, everyone!
21:14 pdurbin left #dataverse
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