Hi @adina ,
Thanks a lot!
You understand the setup correctly
The permission denied error seems to be specific to the drop/remove operation, we have not experienced saving problems.
When creating super- and subdatasets, we typically always run git config core.sharedrepository world
, but the team member who created this particular subdataset may have forgotten, I am not sure. Interestingly, when trying to run that command in this particular subdataset now, I unexpectedly get a fatal: not in a git directory
error, contrary to running this in the superdataset. Hence, something may be wrong here, but there is a .git and .datalad dir inside.
The superdataset and its subdataset have also been succesfully pushed to GIN before, but I already removed the gin sibling for this sub-f dataset since I wanted to remove it from the local superdataset.
Here is the output from the first suggestion for drop
u0027997@gbw-s-labgas01:/data/proj_bitter-reward/firstlevel$ datalad -f json_pp drop --reckless availability
{
âactionâ: âdropâ,
âmessageâ: [
ânothing to drop from %sâ,
â/data/proj_bitter-reward/firstlevelâ
],
âpathâ: â/data/proj_bitter-reward/firstlevelâ,
ârefdsâ: â/data/proj_bitter-reward/firstlevelâ,
âstatusâ: ânotneededâ,
âtypeâ: âdirectoryâ
}
âŚand here the second one
u0027997@gbw-s-labgas01:/data/proj_bitter-reward/firstlevel$ datalad -l debug drop --reckless availability
[DEBUG ] Command line args 1st pass for DataLad 0.17.9. Parsed: Namespace() Unparsed: [âdropâ, âârecklessâ, âavailabilityâ]
[DEBUG ] Building doc for <class âdatalad.core.local.status.Statusâ>
[DEBUG ] Building doc for <class âdatalad.distributed.drop.Dropâ>
[DEBUG ] Parsing known args among [â/opt/anaconda3/bin/dataladâ, â-lâ, âdebugâ, âdropâ, âârecklessâ, âavailabilityâ]
[DEBUG ] Determined class of decorated function: <class âdatalad.distributed.drop.Dropâ>
[DEBUG ] Resolved dataset to drop: /data/proj_bitter-reward/firstlevel
[DEBUG ] Run [âgitâ, âconfigâ, â-zâ, â-lâ, ââshow-originâ] (protocol_class=StdOutErrCapture) (cwd=/data/proj_bitter-reward/firstlevel)
[DEBUG ] Finished [âgitâ, âconfigâ, â-zâ, â-lâ, ââshow-originâ] with status 0
[DEBUG ] Run [âgitâ, âconfigâ, â-zâ, â-lâ, ââshow-originâ, ââfileâ, â/data/proj_bitter-reward/firstlevel/.datalad/configâ] (protocol_class=StdOutErrCapture) (cwd=/data/proj_bitter-reward/firstlevel)
[DEBUG ] Finished [âgitâ, âconfigâ, â-zâ, â-lâ, ââshow-originâ, ââfileâ, â/data/proj_bitter-reward/firstlevel/.datalad/configâ] with status 0
[DEBUG ] Discovered 1 datasets to drop (from)
[DEBUG ] Starting to drop filecontent at Dataset(/data/proj_bitter-reward/firstlevel)
[DEBUG ] Start dropping for Dataset(/data/proj_bitter-reward/firstlevel)
[DEBUG ] Determined class of decorated function: <class âdatalad.core.local.status.Statusâ>
[DEBUG ] Resolved dataset to report status: /data/proj_bitter-reward/firstlevel
[DEBUG ] Querying AnnexRepo(/data/proj_bitter-reward/firstlevel).diffstatus() for paths: None
[DEBUG ] Run [âgitâ, â-câ, âdiff.ignoreSubmodules=noneâ, ârev-parseâ, ââquietâ, ââverifyâ, âHEAD^{commit}â] (protocol_class=GeneratorStdOutErrCapture) (cwd=/data/proj_bitter-reward/firstlevel)
[DEBUG ] AnnexRepo(/data/proj_bitter-reward/firstlevel).get_content_info(âŚ)
[DEBUG ] Query repo: [âls-filesâ, ââstageâ, â-zâ, ââexclude-standardâ, â-oâ, ââdirectoryâ, ââno-empty-directoryâ]
[DEBUG ] Run [âgitâ, â-câ, âdiff.ignoreSubmodules=noneâ, âls-filesâ, ââstageâ, â-zâ, ââexclude-standardâ, â-oâ, ââdirectoryâ, ââno-empty-directoryâ] (protocol_class=GeneratorStdOutErrCapture) (cwd=/data/proj_bitter-reward/firstlevel)
[DEBUG ] Done query repo: [âls-filesâ, ââstageâ, â-zâ, ââexclude-standardâ, â-oâ, ââdirectoryâ, ââno-empty-directoryâ]
[DEBUG ] Done AnnexRepo(/data/proj_bitter-reward/firstlevel).get_content_info(âŚ)
[DEBUG ] Run [âgitâ, â-câ, âdiff.ignoreSubmodules=noneâ, âls-filesâ, â-zâ, â-mâ, â-dâ] (protocol_class=GeneratorStdOutErrCapture) (cwd=/data/proj_bitter-reward/firstlevel)
[DEBUG ] AnnexRepo(/data/proj_bitter-reward/firstlevel).get_content_info(âŚ)
[DEBUG ] Query repo: [âls-treeâ, âHEADâ, â-zâ, â-râ, ââfull-treeâ, â-lâ]
[DEBUG ] Run [âgitâ, â-câ, âdiff.ignoreSubmodules=noneâ, âls-treeâ, âHEADâ, â-zâ, â-râ, ââfull-treeâ, â-lâ] (protocol_class=GeneratorStdOutErrCapture) (cwd=/data/proj_bitter-reward/firstlevel)
[DEBUG ] Done query repo: [âls-treeâ, âHEADâ, â-zâ, â-râ, ââfull-treeâ, â-lâ]
[DEBUG ] Done AnnexRepo(/data/proj_bitter-reward/firstlevel).get_content_info(âŚ)
[DEBUG ] Run [âgitâ, âannexâ, âversionâ, âârawâ] (protocol_class=StdOutErrCapture) (cwd=None)
[DEBUG ] Finished [âgitâ, âannexâ, âversionâ, âârawâ] with status 0
[DEBUG ] Run [âgitâ, â-câ, âdiff.ignoreSubmodules=noneâ, âannexâ, âdropâ, ââforceâ, ââjsonâ, ââjson-error-messagesâ, â-câ, âannex.dotfiles=trueâ, âââ, â.â] (protocol_class=GeneratorAnnexJsonNoStderrProtocol) (cwd=/data/proj_bitter-reward/firstlevel)
[DEBUG ] nothing to drop from /data/proj_bitter-reward/firstlevel [drop(/data/proj_bitter-reward/firstlevel)]
[DEBUG ] Finished dropping filecontent at Dataset(/data/proj_bitter-reward/firstlevel)
Finally, here is some relevant output from datalad wtf
in the superdataset, lmk if you need more
datalad
dataset
- branches:
- git-annex@cc502fe
- master@f0a881d
- id: 9a242ace-8b4d-4405-8d8d-0b195590b30c
- metadata: <SENSITIVE, report disabled by configuration>
- path: /data/proj_bitter-reward
- repo: AnnexRepo
dependencies
- annexremote: 1.5.0
- boto: 2.49.0
- cmd:7z: 16.02
- cmd:annex: 10.20220822-1~ndall+1
- cmd:bundled-git: 2.30.2
- cmd:git: 2.30.2
- cmd:ssh: 8.2p1
- cmd:system-git: 2.39.0
- cmd:system-ssh: 8.2p1
- exifread: 2.3.2
- humanize: 3.11.0
- iso8601: 0.1.16
- keyring: 23.2.1
- keyrings.alt: 4.1.0
- msgpack: 1.0.0
- mutagen: 1.45.1
- platformdirs: 2.4.0
- requests: 2.26.0
Thanks a lot in advance!
Best wishes,
Lukas