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psychoinformatics-de / datalad-hirni

DataLad extension for (semi-)automated, reproducible processing of (medical/neuro)imaging data
http://datalad.org
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Seemingly superfluous addition of a submodule on `import-dcm` #9

Closed mih closed 6 years ago

mih commented 6 years ago

The subdatset get's a container added as a submodule, but I do not see why this needs to be done. Possibly, this should go into the primary study dataset.

Moreover, there seems to be something going wrong while setting this up:

<snip>
[INFO   ] Cloning http://psydata.ovgu.de/cbbs-imaging/conv-container/.git to '/home/data/psyinf/scratch/multires3t/raw/datalad_hirni_import/dicoms/.datalad/environments/import-container' 
[INFO   ] access to dataset sibling "psydata-store" not auto-enabled, enable with:           
|               datalad siblings -d "/home/data/psyinf/scratch/multires3t/raw/datalad_hirni_import/dicoms/.datalad/environments/import-container" enable -s psydata-store 
[INFO   ] Aggregate metadata for dataset /home/data/psyinf/scratch/multires3t/raw/REDACTED/dicoms 
[WARNING] Running find resulted in stderr output: git-annex: ds not found
git-annex: find: 1 failed
<snip>
bpoldrack commented 6 years ago

The actual idea was to reference a container with the version of the import routine that was used to create that very subdataset. The currently referenced one is wrong of course, but I'm not sure whether this should really go into the studydataset, since those containers could differ across imported acquisitions/sessions/whatever-term-we-eventually-agree-on. To me feels intuitive to bind it to the very thing it's supposed to be associated with.

Re failure: Yes, need to figure out, what that strange ds is about.

mih commented 6 years ago

That would be fine with me, but at present it adds noise, and it should only do it, if it is actually done in a container -- which is also not the case, right?

bpoldrack commented 6 years ago

Agree. Will disable that "experimental" default ...

bpoldrack commented 6 years ago

FTR: The repeatedly observed 

[WARNING] Running find resulted in stderr output: git-annex: ds not found
git-annex: find: 1 failed

is unrelated and fixed in datalad-core PR https://github.com/datalad/datalad/pull/2595

mih commented 6 years ago

Import done with #17