CORR_cat12.8.1/code/participant_job

#!/bin/bash

# the job assumes that it is a good idea to run everything in PWD
# the job manager should make sure that is true

# fail whenever something is fishy, use -x to get verbose logfiles
set -e -u -x

dssource="$1"
pushgitremote="$2"
subd="$3"
subid=$(basename $3)

# get the analysis dataset, which includes the inputs as well
# importantly, we do not clone from the lcoation that we want to push the
# results too, in order to avoid too many jobs blocking access to
# the same location and creating a throughput bottleneck
datalad clone "${dssource}" ds

# all following actions are performed in the context of the superdataset
cd ds

# in order to avoid accumulation temporary git-annex availability information
# and to avoid a syncronization bottleneck by having to consolidate the
# git-annex branch across jobs, we will only push the main tracking branch
# back to the output store (plus the actual file content). Final availability
# information can be establish via an eventual "git-annex fsck -f cat12.8.1_out-storage".
# this remote is never fetched, it accumulates a larger number of branches
# and we want to avoid progressive slowdown. Instead we only ever push
# a unique branch per each job (subject AND process specific name)
git remote add outputstore "$pushgitremote"

# all results of this job will be put into a dedicated branch
git checkout -b "job-${JOBID}"

# we pull down the input subject manually in order to discover relevant
# files. We do this outside the recorded call, because on a potential
# re-run we want to be able to do fine-grained recomputing of individual
# outputs. The recorded calls will have specific paths that will enable
# recomputation outside the scope of the original Condor setup
datalad get -n "inputs/CORR/${subd}"

# the meat of the matter
# look for T1w files in the input data for the given participant
# it is critical for reproducibility that the command given to
# "containers-run" does not rely on any property of the immediate
# computational environment (env vars, services, etc)
find \
  inputs/CORR/${subd} \
  -name "${subid}*T1w.nii.gz" \
  -exec sh -c '
    odir=$(echo {} | cut -d / -f3-5);
    datalad containers-run \
      -m "Compute $odir" \
      -n cat12-8-1\
      --explicit \
      -o $odir \
      -i {} \
      sh -e -u -x -c "
        rm -rf {outputs[0]} ;
        mkdir -p {outputs[0]} \
        && cp {inputs[0]} {outputs[0]} \
        && /singularity -b code/cat_standalone_segment_enigma_subdir_rp_MSA.m {outputs[0]}/*.nii.gz \
        && /singularity -b code/pipeline/batches/cat_standalone_batch-surfext.m {outputs[0]}/surf/lh.central.* \
        && /singularity -b code/pipeline/batches/cat_standalone_batch-thick1.m {outputs[0]}/surf/lh.thickness.* \
        && /singularity -b code/pipeline/batches/cat_standalone_batch-thick2.m {outputs[0]}/surf/lh.thickness.* \
        && rm -f {outputs[0]}/*.nii* \
        && gzip {outputs[0]}/*/*.nii \
        " \
  ' \;

# remove big files from results after hashing before pushing to ria
datalad drop --what filecontent --reckless kill   */sub-*/*/mri/iy* */sub-*/*/mri/y*   */sub-*/*/mri/anon_m* */sub-*/*/*/*.pdf   */sub-*/*/surf/*sphere*

#### Maybe remove simlinks without data and commit ???
# rm -f */sub-*/*/mri/iy* */sub-*/*/mri/y* #   */sub-*/*/mri/anon_m* */sub-*/*/*/*.pdf #   */sub-*/*/surf/*sphere*
# datalad save -m "remove simlinks without data"

# file content first -- does not need a lock, no interaction with Git
datalad push --to cat12.8.1_out-storage
# and the output branch
flock --verbose $DSLOCKFILE git push outputstore

echo SUCCESS
# job handler should clean up workspace