77 lines
2 KiB
Shell
Executable file
77 lines
2 KiB
Shell
Executable file
#!/bin/bash
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# fail whenever something is fishy, use -x to get verbose logfiles
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set -e -x
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# finalize FAIRly Big Workflow dataset
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dssource="$1"
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if [[ ! -z ${dssource} ]]; then
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datalad clone "${dssource}" ds
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cd ds
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else
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datalad update -s mriqc_out
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fi
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# octopus merge job branches and move data to root
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git merge -m "Merge results" $(git branch -al | grep 'job_' | tr -d ' ')
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git mv mriqc/.bidsignore mriqc/* .
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datalad save -m "move data to dataset root"
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# clean git annex branch
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if [[ ! -z ${dssource} ]]; then
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git annex fsck --fast
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else
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git annex fsck -f mriqc_out --fast
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fi
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# declare local data clone as dead
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git annex dead here
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# datalad push merged results
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if [[ ! -z ${dssource} ]]; then
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datalad push --data nothing
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else
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datalad push --data nothing --to mriqc_out
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fi
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export DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__201="/p/scratch/icei-hbp-00000000004/STAGE/OpenNeuro/ds005134.git" DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__102container="ria+file:///p/data1/inm7/containerstores#{id}" REPRONIM_USE_DUCT=1 DUCT_OUTPUT_PREFIX="logs/duct/mriqc-group-stats_{datetime_filesafe}-{pid}_"
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# get mri input for MRIQC group stats
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datalad get -n sourcedata/raw
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datalad get sourcedata/raw/dataset_description.json \
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$(find sourcedata/raw -maxdepth 3 -name anat) \
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$(find sourcedata/raw -maxdepth 3 -name func) \
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$(find sourcedata/raw -maxdepth 3 -name dwi)
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# run mriqc group stats
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datalad containers-run \
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-m "Compute MRIQC group stats" \
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-n bids-mriqc \
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--explicit \
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-o 'group*' \
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-o .bidsignore \
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mriqc sourcedata/raw . group \
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--no-datalad-get \
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--notrack \
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--verbose \
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--work-dir tmp
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datalad drop --what datasets --reckless kill -r -d sourcedata/raw
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# run mriqc quality classifier
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datalad containers-run \
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-m "run MRIQC classifier" \
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-n bids-mriqc-clf \
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-i group_T1w.tsv \
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"mriqc_clf --load-classifier -X group_T1w.tsv; \
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mv mclf_run*data-unseen_pred.csv mclf_data-unseen_pred.csv"
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if [[ ! -z ${dssource} ]]; then
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datalad push --data nothing
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else
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datalad push --data nothing --to mriqc_out
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fi
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echo SUCCESS
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