Time
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Nick
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00:07 dataverse-user joined #dataverse
00:09 dataverse-user
Hello Dataverse Community, I am testing a local dataverse instance in my system. I got the test credential from http://doi.test.datacite.org Can anyone help me to configure my dataverse? I have tried my best with the website guideline but still something is preventing from dataset to be published.
00:20 dataverse-user
what is :myshoulder ?
00:34 pdurbin
dataverse-user: hi! I'm sorry to hear you're having trouble
00:35 pdurbin
dataverse-user: I just heard about a DataCite policy change at https://github.com/whole-tale/whole-tale/issues/49#issuecomment-438374085 but I haven't confirmed it myself.
00:37 pdurbin
dataverse-user: can you please open an issue about this at https://github.com/IQSS/dataverse/issues ?
02:12 jri joined #dataverse
07:42 dataverse-user joined #dataverse
07:42 dataverse-user
Can I create dataverse on root node with RESTAPIon demo.dataverse.org
07:42 dataverse-user
?
07:47 poikilotherm joined #dataverse
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07:59 jri joined #dataverse
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11:50 pdurbin
yes
13:01 poikilotherm
Hi pdurbin
13:02 poikilotherm
What do you think about ascii based graphics in the docs?
13:02 poikilotherm
Do you guys prefer real graphics?
13:03 poikilotherm
Or would it be ok to use things like sphinx extensions for rendering graphviz?
13:07 pdurbin_m joined #dataverse
13:07 pdurbin_m
poikilotherm: I like plantuml for diagrams. please see https://github.com/IQSS/dataverse/commit/02ef8683da06d91125a5f7e82d9b8568006b45d6#diff-a113b497c0000aefdd6cffd396399756
13:08 poikilotherm
Uhm... but you are rendering that separatly and use an image, right?
13:09 poikilotherm
I am talking about using sth like https://www.sphinx-doc.org/en/1.8/usage/extensions/graphviz.html
13:11 poikilotherm
(This is also possible for plantuml)
13:24 pdurbin_m
poikilotherm: as long as you don't require paid, proprietary tools, I'm cool with it.
13:26 donsizemore joined #dataverse
13:27 poikilotherm
Great :-)
13:27 poikilotherm
This is actually just an entry in conf.py and then you are ready to go :-)
13:27 poikilotherm
I like the option to have the graph right within the code and not to generate pictures in a separate step
13:28 * poikilotherm
is writing docs about dep management...
13:45 pdurbin
Sure, that sounds great. We've had people try to contribute images made in OmniGraffle but I don't want them in the guides for a variety of reasons such as that OmniGraffle is paid and proprietary. Your solution sounds just fine.
14:13 cdsp-rmo joined #dataverse
15:08 xarthisius
hi! If only have fileId and siteUrl, what's a good way to get basic info (title, size, etc)? /api/access/datafile/:persistentId/metadata/ddi ?
15:08 xarthisius
*If I
15:41 poikilotherm
Hey pdurbin, I am not yet finished, but if you are curios, have a look at https://github.com/IQSS/dataverse/pull/5289/commits/0990d83508d8d737bbdbe1abec2d0b8aab7ced64
15:41 poikilotherm
Still need to describe helpfull tools like mvn enforcer, etc
15:42 pameyer joined #dataverse
15:44 pameyer
graphiz is nice - not sure offhand if it'll need config changes to the system that builds the "official" docs
15:44 poikilotherm
Don't think so - it is part of sphinx since 0.6
15:45 poikilotherm
(But still handled as a "extension")
15:46 poikilotherm
Wow, that geotoolkit stuff is driving me nuts
15:46 poikilotherm
Travis builds failing because they are offline
15:46 poikilotherm
*grrr*
15:47 pameyer
huh - had assumed that graphviz needed other packages outside python/pip/etc. but it's useful enough that I usually have it installed
15:47 poikilotherm
Ah that might be correct!
15:48 poikilotherm
We'll see what happens - most certainly, if sphinx is installed from repos, graphviz has been a dependency anyway
15:49 poikilotherm
Alright guys, I gotta run... Kids are waiting...
15:49 pameyer
@poikilotherm have a good night
15:49 poikilotherm
Thx. Cu tomorrow :-)
15:53 pameyer
@xarthisius arbritrary file or special (tabular etc) file?
15:57 xarthisius
pameyer: whatever kind works with external tools (I assume it's only the latter for now)
15:58 pameyer
not an area of I've got a lot of experience, but it *looks* like api/access/datafile/{fileId}/metadata
16:00 pameyer
not sure what's in there though. I don't see anything in the native API - I believe the native dataset API gives info about files (name, size, etc); but that takes a dataset parameter, not file parameter
16:00 xarthisius
it gives me the same document as /metadata/ddi
16:01 xarthisius
yeah, when using /dataset API it's way easier
16:01 xarthisius
metadata doesn't have a size though, but it's easy to workaound
16:02 pameyer
seems slightly non-intuitive that the file API doesn't seem to have a generic GET method
16:02 xarthisius
my thought exactly :D
16:03 pameyer
pdurbin might have better ideas about it than me
16:04 xarthisius
ok, thanks for your help!
16:15 pdurbin
xarthisius: sorry, I was in a design meeting. And heading to a standup meeting, which is usually short.
17:05 pdurbin
xarthisius: back. Please take a look at https://dataverse.harvard.edu/api/search?q=entityId:3040230
17:06 pdurbin
That output will give you the citation of the dataset, file size in bytes, MD5, etc.
17:13 xarthisius
oh! and it's not XML ! Thank you!
17:21 pdurbin
xarthisius: sure, does it have everything you need?
17:55 xarthisius
pdurbin: yup
17:55 pdurbin
nice
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18:54 pameyer
@donsizemore - am I remembering correctly that you've done some looking at running dataverse with selinux?
19:00 pdurbin
pameyer: it should work, mostly, I think: http://guides.dataverse.org/en/4.9.4/developers/selinux.html :)
19:10 donsizemore
@pameyer i'm a "disable selinux except where disallowed" grey-beard
19:35 pameyer
me too - but every so often I get reminded to take a look at it
19:39 pameyer
pdurbin: thanks, I'd either missed that or forgotten it. I'll give in another look
19:43 pdurbin
sure, ymmv
19:50 xarthisius
pdurbin: I suddenly started to get 500 for https://dataverse.harvard.edu/api/access/datafile/:persistentId/metadata/ddi?persistentId=doi:10.7910/DVN/TJCLKP/BTRTVA
19:51 xarthisius
did I break something?
19:56 pdurbin
huh. HTTP /1.1 503 Service Unavailable
19:57 * xarthisius
ducks and covers
19:58 pdurbin
I'm getting 503 here too: https://demo.dataverse.org//api/access/datafile/:persistentId/metadata/ddi?persistentId=doi:10.5072/FK2/YO8HPX/B73FC7
19:59 pdurbin
NullPointerException
20:00 pdurbin
xarthisius: please feel free to create an issue at https://github.com/IQSS/dataverse/issues
20:00 xarthisius
oh I see the reason
20:01 xarthisius
I selected file that's not a tab
20:01 xarthisius
for https://dataverse.harvard.edu/api/access/datafile/:persistentId/metadata/ddi?persistentId=doi:10.7910/DVN/TJCLKP/JKTORG
20:01 xarthisius
it works just fine
20:01 xarthisius
I gotta run, but I'll file an issue when I get back
20:02 pdurbin
xarthisius: thanks!
20:56 pdurbin
xarthisius: check this out: https://medium.com/codeocean/new-jupyterlab-based-capsule-page-d618f34bc636
21:09 poikilotherm joined #dataverse
21:11 poikilotherm
Hey guys :-) Found some spare time to work on dev stuff...
21:11 pdurbin
poikilotherm: what about the kids?!
21:11 poikilotherm
They went to bed about 2,5h ago... ;-)
21:11 pdurbin
wow, great
21:12 poikilotherm
Oh, thats a ".", not a ","
21:13 poikilotherm
pdurbin: Do you think the doc guys might be happy to get more work? I have https://github.com/IQSS/dataverse/pull/5289/commits/2760fadc2db1e217fd45725136a57532e07460b8 for them to look at... :-D
21:14 poikilotherm
Maybe we can start an iteration on this even before talking with Matthew and Gustavo? (Matthew wrote they're gonna catch up ASAP)
21:16 pdurbin
poikilotherm: the only way stuff gets looked at is if there's a pull request. So you should feel free to make one.
21:16 poikilotherm
Sry, had a bad typo and needed to force push... https://github.com/IQSS/dataverse/pull/5289/commits/b5c12b65461ae063804107debb84612de21e819b
21:16 poikilotherm
This already is a PR
21:17 poikilotherm
But I entitled it with WIP
21:17 poikilotherm
Because the rest of the house keeping is not ready / finished discussing
21:17 pdurbin
Gotcha.
21:17 poikilotherm
But I think the doc part should be ok as is
21:18 pdurbin
Well, we love small chunks.
21:18 pdurbin
You could make it into two issues.
21:18 pdurbin
and two pull requests.
21:19 poikilotherm
Ok recently this is primarily targeting issue https://github.com/IQSS/dataverse/issues/5274 plus some minor stuff
21:19 poikilotherm
I could just rename the PR and give it a go :-D
21:20 poikilotherm
Then https://github.com/IQSS/dataverse/issues/5288 can have a new PR
21:20 poikilotherm
If there is more input for this
21:30 pdurbin
Sounds fine. Another way you could try getting dev input is by emailing https://groups.google.com/forum/#!forum/dataverse-dev
21:30 pdurbin
But pull requests are an excellent way to get attention as well. :)
21:31 poikilotherm
Ok, will rename it right away.
21:37 poikilotherm
Done :-)
21:49 poikilotherm
pdurbin: can you trigger a review?
21:49 poikilotherm
(Or even review yourself?)
21:49 pdurbin
poikilotherm: sorry, I stepped away. Which number should I drag to code review?
21:50 poikilotherm
The PR is 5289 and the issue is 5274
21:50 pdurbin
done!
21:50 poikilotherm
Thx!!!
21:51 pdurbin
If we need to install something for `make html` to continue working, please edit doc/sphinx-guides/source/developers/documentation.rst and say so.
21:52 poikilotherm
Now I will sit down in patience, tamp a pipe and wait for reviewers to appear on the sea of code
21:53 poikilotherm
I don't think so - most certainly graphviz is installed anyway
21:55 poikilotherm
Ah it could be needed on some dev machines...
21:55 poikilotherm
Better drop a note in there...
21:55 * poikilotherm
will force push after adding
22:02 poikilotherm
Ok, this seems to be tricky...
22:03 poikilotherm
You need to have the dot executable on the path, but this is painfull on windows
22:03 poikilotherm
the worst thing that will happen is a warning that dot cannotbe found an no image will appear
22:05 pameyer
windows seems to have the unfortunate tendency of not being compatiable with anything
22:10 poikilotherm
Alright, added a small note on GraphViz to the mentioned file
22:48 pdurbin
poikilotherm: thanks!
