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04:02 iqlogbot joined #dataverse
04:02 Topic for #dataverse is now Dataverse is open source research data repository software: http://dataverse.org | IRC Logs: http://irclog.iq.harvard.edu/dataverse/today | Who's who: https://docs.google.com/spreadsheets/d/16h3jv24usMGq18495C-JA-yNcQCKiKDa65MTraNDd7k/edit?usp=sharing
07:36 Virgile joined #dataverse
08:12 edipretoro joined #dataverse
08:13 edipretoro
Hi, I have a question: is there a way to delete a metadata block?
09:26 Thibbo joined #dataverse
09:26 Thibbo
Hello all!
09:29 poikilotherm2
Hi Thibbo
09:29 poikilotherm2
Hi edipretoro
09:30 Thibbo
I have a user who uploaded a wrong file. The dataset is deaccessioned but the files must be deleted from the server. I can't find a "clean" method to delete the file in the native api.
09:31 poikilotherm2
edipretoro: I'm not sure I get your question completely. If you meant if there is an option to unload a metadata block definition from a running instance: there isn't. But you can deactivate a block for a Dataverse collection.
09:32 poikilotherm2
Thibbo: where do you store the files?
09:32 Thibbo
local disk on 1 server
09:33 poikilotherm2
OK and the dataset has been deaccessioned because everything was wrong or just because of the file?
09:33 poikilotherm2
(There is an endpoint to replace a file)
09:34 poikilotherm2
(Also it does not delete the old files, as it creates a new version)
09:34 Thibbo
only 2 versions of dataset have been deaccessioned because of the file
09:34 Thibbo
the last version contains only metadatas
09:34 Thibbo
no files
09:35 Thibbo
I try the replace endpoint but it did not deleted file
09:37 poikilotherm2
Has the file already been published?
09:38 Thibbo
yes
09:38 poikilotherm2
OK. Then only superusers can delete the file.
09:40 Thibbo
I have the same issue as https://github.com/IQSS/dataverse/issues/6925
09:41 poikilotherm2
Oh. I see. I was just looking at the code. There is a command to delete a file, but it is not exposed as a REST endpoint.
09:41 poikilotherm2
(At least not as far as I see it)
09:41 poikilotherm2
You should be able to delete files via the UI
09:42 poikilotherm2
In case of published files this is restricted to superusers
09:42 poikilotherm2
Too bad there is such an error for deaccessioned datasets
09:43 poikilotherm2
Did you see the workaround Julian posted?
09:43 poikilotherm2
A workaround is to create the draft version another way, such as clicking Edit > Metadata then "Save Changes" (you don't have to make any changes), then delete the file(s).
09:47 edipretoro
poikilotherm2: Thanks for your answer! And yes, I was talking about unload completely a customized metadata block from a running instance
09:49 poikilotherm2
edipretoro: this is not possible due to the fact that there might exist metadata that uses the schema. It would be necessary to delete all of that before unloading. If you feel this is a necessity, please open an issue with a detailed use case.
09:50 edipretoro
that make sense, indeed
09:51 edipretoro
the only use case I have for the moment is related to tests we are conducting for now, so no real use case at the moment
09:52 Thibbo
poikilotherm2: it does not work :( (dataverse 4.20 here)
09:52 Thibbo
"The object [edu.harvard.iq.dvn.core.study.FileMetadata[id=89]] cannot be merged because it has changed or been deleted since it was last read. Class> edu.harvard.iq.dataverse.FileMetadata"
09:53 poikilotherm2
Oh, Julian posted that for Dataverse 5
09:53 poikilotherm2
Sorry
09:55 Thibbo
On my test server, I try to change file content directly on disk. There is not error but I'm not proud of me
10:06 Thibbo
I will try the workaround after upgrade to dataverse 5
10:11 Thibbo
thank you poikilotherm2. have a good day
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14:57 pdurbin
poikilotherm2: wow, thanks for answering questions all morning!
14:58 pdurbin
to all: the community call is starting soon: https://dataverse.org/community-calls
14:58 Virgile joined #dataverse
14:58 poikilotherm2
pdurbin: you're welcome. You seemed asleep :-P
14:59 poikilotherm2
I hope I gave the right answers and didn't overlook stuff :-D
15:14 pdurbin
I think so. For deaccessioned files, perhaps we should offer the option to delete the file from the file system (or S3 or whatever).
15:21 Virgile
Hello! That would be nice :)
16:31 pkiraly joined #dataverse
16:33 pdurbin
poikilotherm2: nice find: https://github.com/IQSS/dataverse/issues/6656#issuecomment-794085682
16:34 pkiraly
Hi! I just started working on a ticket. Created a new local branch from develop. `mvn clean install` get into stuck when it starts downloading a Payara dependency: microbean-microprofile-config-0.4.1.jar. Is it only for me, or did you also meet this issue?
16:35 pkiraly
stuck precisely means that mvn starts waiting and after 15 minutes I killed it.
16:36 pdurbin
Huh. I haven't seen this. I always do `package` instead of `install` but I don't think it matters.
16:38 pdurbin
poikilotherm2: is this on topic for #ig-devops in Slack?
16:38 pdurbin
pkiraly's problem, I mean
16:39 pkiraly
I gave it a try, it seems the same result: waiting...
16:39 pdurbin
I think it's working fine in Jenkins.
16:41 poikilotherm2
Thx pdurbin. Was triggered by @donsizemore request this morning. The hunt was on.
16:41 pdurbin
With Jenkins we build the war file on a freshly spun up CentOS box. pkiraly: are you on Linux? I'm on a Mac.
16:42 poikilotherm2
pkiraly: IIRC that microbean is a test dependency I added.
16:42 pkiraly
pdurbin, I use Ubuntu Linux
16:42 pdurbin
poikilotherm2: did you break pkiraly's dev environment? 😄
16:43 pkiraly
poikilotherm2, do I understand correctly that you investigate it?
16:45 poikilotherm2
Well that dependency is on MVN central
16:45 poikilotherm2
https://mvnrepository.com/artifact/org.microbean/microbean-microprofile-config/0.4.1
16:46 poikilotherm2
So maybe they have some troubles right now
16:46 poikilotherm2
pdurbin: you are not experiencing this because it's very likely you already have this cached locally
16:47 pkiraly
poikilotherm2, These jars are downloaded from raw.github.com instead of a proper Maven repository
16:47 pkiraly
the rest of the jars returns a proper 301 redirection, which this one returns 404
16:47 poikilotherm2
No, that shouldn't happen. It's likely that Maven tries to go through the different repos we configured
16:47 poikilotherm2
Of course :-D
16:48 poikilotherm2
But Maven should continue with the next repo then
16:48 poikilotherm2
It's not a Payara dependency
16:49 pkiraly
The maven message is exactly this: "Downloading from payara-patched-externals: https://raw.github.com/payara/Payara_PatchedProjects/master/org/microbean/microbean-microprofile-config/0.4.1/microbean-microprofile-config-0.4.1.jar "
16:49 poikilotherm2
Yeah, that's Maven trying to reach packages.
16:50 poikilotherm2
That's fine, we added that repo for the Payara patched deps
16:50 poikilotherm2
But if it's not found, it should skip to the next repo
16:50 poikilotherm2
Maybe Github has a hickup and does quit the connection or whatever
16:51 poikilotherm2
You might try changing the repo order in pom.xml
16:51 poikilotherm2
Or comment it out for a second
16:54 pkiraly
I'll try it. However the problem is, that when I try to open the repo in the IDE , intellij first tries to fetch dependencies, then create the standard project stucture, so this issue blocks me to open the project in IntelliJ
16:55 poikilotherm2
Using IDEA here, too. If the deps are cached locally, you should be good to go.
16:55 pkiraly
I know, but in this case it is not cached locally
16:56 poikilotherm2
Yeah. So comment it out, do a biuld from cmdline to cache the deps and go go go hacking :-D
16:58 poikilotherm2
Folks I'm outta here for today. Lots of digging, now proceeding to construction site. See y'all (will read any maybe answer from my mobile)
16:59 pdurbin
If we can comment out the dependency, does that mean we don't need it? :)
17:04 poikilotherm2
Comment out the repo, not the deps. You can't live without, it's used in tests
17:04 pdurbin
Don't worry, I understand. I'm just playing with you. :)
17:05 poikilotherm2
Pkiraly can we talk about your ideas for the Solr managed schema later?
17:05 poikilotherm2
I need to solve my chicken egg problem for k8s and that might be a way to go
17:06 poikilotherm2
Pdurbin don't look now, but I almost have the dv 5 containers ready, building them from maven
17:06 poikilotherm2
(there is a draft pr if you're curious)
17:06 pdurbin
nice!
17:07 pdurbin
upgrading from 4.20?
17:07 poikilotherm2
Right away to 5.3/4
17:08 pdurbin
Heh. "v4.20-with-fzj-features"
17:09 poikilotherm2
Oh. It's not running in our repo...
17:10 poikilotherm2
Testing locally
17:11 pdurbin
yep, but I assume you're looking forward to upgrading prod
17:12 pkiraly
poikilotherm2, sure. Tomorrow is OK for you?
17:14 poikilotherm2
Pkiraly Sounds good. Reach out via Slack?
17:16 poikilotherm2
Pdurbin yeah... I do :-D
17:16 pdurbin
no more glassfish
17:16 poikilotherm2
We want all the goodies
17:16 poikilotherm2
🤑
17:16 pkiraly
poikilotherm2, OK
17:17 poikilotherm2
<pkiraly "oliver, OK"> Great
17:17 pkiraly
I'll ping you
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