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[TST] Refactoring CircleCI setup #1098

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merged 1 commit into from
May 3, 2018
Merged

[TST] Refactoring CircleCI setup #1098

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120 changes: 69 additions & 51 deletions .circleci/config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -108,10 +108,10 @@ jobs:
- run:
name: Get test data from ds000210
command: |
if [[ ! -d /tmp/data/ds000210 ]]; then
if [[ ! -d /tmp/data/ds210 ]]; then
wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-O ds000210_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5a6e952c6396f90010bb7a26"
tar xvzf ds000210_downsampled.tar.gz -C /tmp/data/
-O ds210_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5ae9e37b9a64d7000ce66c21"
tar xvzf ds210_downsampled.tar.gz -C /tmp/data/
else
echo "Dataset ds000210 was cached"
fi
Expand All @@ -135,12 +135,12 @@ jobs:
- run:
name: Create Nipype config files
command: |
mkdir -p /tmp/ds005 /tmp/ds054 /tmp/ds000210
mkdir -p /tmp/ds005 /tmp/ds054 /tmp/ds210
printf "[execution]\nstop_on_first_crash = true\nremove_unnecessary_outputs = false\n" > /tmp/ds005/nipype.cfg
echo "poll_sleep_duration = 0.2" >> /tmp/ds005/nipype.cfg
echo "hash_method = content" >> /tmp/ds005/nipype.cfg
cp /tmp/ds005/nipype.cfg /tmp/ds054/nipype.cfg
cp /tmp/ds005/nipype.cfg /tmp/ds000210/nipype.cfg
cp /tmp/ds005/nipype.cfg /tmp/ds210/nipype.cfg
- persist_to_workspace:
root: /tmp
paths:
Expand All @@ -149,7 +149,7 @@ jobs:
- ds005/nipype.cfg
- ds005/derivatives
- ds054/nipype.cfg
- ds000210/nipype.cfg
- ds210/nipype.cfg
- save_cache:
key: data-v5-{{ epoch }}
paths:
Expand Down Expand Up @@ -296,10 +296,10 @@ jobs:
at: /tmp
- restore_cache:
keys:
- ds005-anat-v5-{{ .Branch }}-{{ epoch }}
- ds005-anat-v5-{{ .Branch }}
- ds005-anat-v5-master
- ds005-anat-v5-
- ds005-anat-v6-{{ .Branch }}-{{ epoch }}
- ds005-anat-v6-{{ .Branch }}
- ds005-anat-v6-master
- ds005-anat-v6-
- run:
name: Setting up test
command: |
Expand Down Expand Up @@ -332,7 +332,7 @@ jobs:
--debug --write-graph --mem_mb 4096 \
--nthreads 2 --anat-only -vv
- save_cache:
key: ds005-anat-v5-{{ .Branch }}-{{ epoch }}
key: ds005-anat-v6-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds005/work
- /tmp/ds005/derivatives/fmriprep
Expand All @@ -341,11 +341,14 @@ jobs:
name: Run full fMRIPrep on ds005
no_output_timeout: 2h
command: |
sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/derivatives && \
sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/derivatives
sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
fmriprep-docker -i poldracklab/fmriprep:latest \
--config $PWD/nipype.cfg -w /tmp/ds005/work \
/tmp/data/ds005 /tmp/ds005/derivatives participant \
--debug --write-graph --use-syn-sdc --use-aroma \
--ignore-aroma-denoising-errors --mem_mb 4096 \
--debug --write-graph --use-syn-sdc --mem_mb 4096 \
--output-space T1w template fsaverage5 \
--template-resampling-grid native \
--nthreads 2 --cifti-output -vv
Expand All @@ -359,7 +362,7 @@ jobs:
name: Checking outputs of full fMRIPrep run
command: |
mkdir -p /tmp/ds005/test
find /tmp/ds005/derivatives | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
find /tmp/ds005/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
diff /tmp/src/fmriprep/.circleci/ds005_outputs.txt /tmp/ds005/test/outputs.out
exit $?
- run:
Expand All @@ -370,8 +373,7 @@ jobs:
fmriprep-docker -i poldracklab/fmriprep:latest \
--config $PWD/nipype.cfg -w /tmp/ds005/work \
/tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
--debug --write-graph --use-syn-sdc --use-aroma \
--ignore-aroma-denoising-errors --mem_mb 4096 \
--debug --write-graph --use-syn-sdc --mem_mb 4096 \
--output-space T1w template fsaverage5 \
--template-resampling-grid native \
--nthreads 2 --cifti-output -vv
Expand All @@ -380,16 +382,19 @@ jobs:
command: |
mkdir -p /tmp/ds005/test
sudo rm -rf /tmp/ds005/derivatives_partial/freesurfer
find /tmp/ds005/derivatives_partial | sed s+/tmp/ds005/derivatives_partial/++ | sort > /tmp/ds005/test/outputs.out
find /tmp/ds005/derivatives_partial -path */figures -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives_partial/++ | sort > /tmp/ds005/test/outputs.out
diff /tmp/src/fmriprep/.circleci/ds005_partial_outputs.txt /tmp/ds005/test/outputs.out
exit $?
- run:
name: Clean working directory
when: always
command: |
sudo find /tmp/ds005/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
sudo chown $(id -un):$(id -gn) -R /tmp/ds005
find /tmp/ds005/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
-not -name "*.mat" -not -name "*.lta" -type f -delete
sudo find /tmp/ds005/work_partial -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
find /tmp/ds005/work_partial -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
-not -name "*.mat" -not -name "*.lta" -type f -delete
# tar cf - work_partial/ | pigz -2 -p 2 > ds005_workdir.tar.gz && sudo rm -fr work work_partial

- store_artifacts:
path: /tmp/ds005
Expand All @@ -415,10 +420,10 @@ jobs:
at: /tmp
- restore_cache:
keys:
- ds054-anat-v3-{{ .Branch }}-{{ epoch }}
- ds054-anat-v3-{{ .Branch }}
- ds054-anat-v3-master
- ds054-anat-v3-
- ds054-anat-v4-{{ .Branch }}-{{ epoch }}
- ds054-anat-v4-{{ .Branch }}
- ds054-anat-v4-master
- ds054-anat-v4-
- run:
name: Setting up test
command: |
Expand Down Expand Up @@ -451,7 +456,7 @@ jobs:
--fs-no-reconall --debug --write-graph \
--mem_mb 4096 --nthreads 2 --anat-only -vv
- save_cache:
key: ds054-anat-v3-{{ .Branch }}-{{ epoch }}
key: ds054-anat-v4-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds054/work
- /tmp/ds054/derivatives
Expand All @@ -460,18 +465,23 @@ jobs:
name: Run full fMRIPrep on ds054
no_output_timeout: 2h
command: |
sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds054/derivatives && \
sudo setfacl -m group:$(id -gn):rwx /tmp/ds054/derivatives
sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds054/work && \
sudo setfacl -m group:$(id -gn):rwx /tmp/ds054/work
fmriprep-docker -i poldracklab/fmriprep:latest \
--config $PWD/nipype.cfg -w /tmp/ds054/work \
/tmp/data/ds054 /tmp/ds054/derivatives participant \
--fs-no-reconall --debug --force-syn \
--fs-no-reconall --debug \
--ignore-aroma-denoising-errors --use-aroma \
--output-space T1w template \
--template-resampling-grid 2mm \
--mem_mb 4096 --nthreads 2 -vv
- run:
name: Checking outputs of fMRIPrep
command: |
mkdir -p /tmp/ds054/test
find /tmp/ds054/derivatives | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
diff /tmp/src/fmriprep/.circleci/ds054_outputs.txt /tmp/ds054/test/outputs.out
exit $?
- run:
Expand All @@ -487,24 +497,29 @@ jobs:
fmriprep-docker -i poldracklab/fmriprep:latest \
--config $PWD/nipype.cfg -w /tmp/ds054/work \
/tmp/data/ds054 /tmp/ds054/derivatives participant \
--fs-no-reconall --debug --write-graph --force-syn \
--fs-no-reconall --debug --write-graph \
--ignore-aroma-denoising-errors --use-aroma \
--output-space T1w template \
--template-resampling-grid 2mm \
--reports-only --run-uuid $UUID
RET=$?
set -e
[[ "$RET" -eq "1" ]]
- run:
name: Clean-up work work directory
name: Clean-up work directory
when: always
command: |
sudo find /tmp/ds054/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
sudo chown $(id -un):$(id -gn) -R /tmp/ds054
find /tmp/ds054/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
-not -name "*.mat" -not -name "*.lta" -type f -delete
# tar cf - work/ | pigz -2 -p 2 > ds054_workdir.tar.gz && sudo rm -fr work
- store_artifacts:
path: /tmp/ds054

ds210:
machine:
image: circleci/classic:201711-01
working_directory: /tmp/ds000210
working_directory: /tmp/ds210
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
steps:
Expand All @@ -522,12 +537,12 @@ jobs:
at: /tmp
- restore_cache:
keys:
- ds000210-anat-v2-{{ epoch }}
- ds000210-anat-v2-
- ds210-anat-v1-{{ epoch }}
- ds210-anat-v1-
- run:
name: Setting up test
command: |
mkdir -p /tmp/ds000210/derivatives && sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds000210/derivatives && sudo setfacl -m group:$(id -gn):rwx /tmp/ds000210/derivatives
mkdir -p /tmp/ds210/derivatives && sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds210/derivatives && sudo setfacl -m group:$(id -gn):rwx /tmp/ds210/derivatives
pip install future numpy
pip install --upgrade /tmp/src/fmriprep/wrapper/
- run:
Expand All @@ -545,46 +560,49 @@ jobs:
name: Run anatomical workflow on ds000210
no_output_timeout: 2h
command: |
mkdir -p /tmp/ds000210/work /tmp/ds000210/derivatives
sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds000210/derivatives && \
sudo setfacl -m group:$(id -gn):rwx /tmp/ds000210/derivatives
sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds000210/work && \
sudo setfacl -m group:$(id -gn):rwx /tmp/ds000210/work
mkdir -p /tmp/ds210/work /tmp/ds210/derivatives
sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds210/derivatives && \
sudo setfacl -m group:$(id -gn):rwx /tmp/ds210/derivatives
sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds210/work && \
sudo setfacl -m group:$(id -gn):rwx /tmp/ds210/work
fmriprep-docker -i poldracklab/fmriprep:latest \
--config $PWD/nipype.cfg -w /tmp/ds000210/work \
/tmp/data/ds000210 /tmp/ds000210/derivatives participant \
--config $PWD/nipype.cfg -w /tmp/ds210/work \
/tmp/data/ds210 /tmp/ds210/derivatives participant \
--fs-no-reconall --debug --write-graph \
--mem_mb 4096 --nthreads 2 --anat-only -vv
- save_cache:
key: ds000210-anat-v2-{{ epoch }}
key: ds210-anat-v1-{{ epoch }}
paths:
- /tmp/ds000210/work
- /tmp/ds000210/derivatives
- /tmp/ds210/work
- /tmp/ds210/derivatives

- run:
name: Run full fMRIPrep on ds000210
no_output_timeout: 2h
command: |
fmriprep-docker -i poldracklab/fmriprep:latest \
--config $PWD/nipype.cfg -w /tmp/ds000210/work \
/tmp/data/ds000210 /tmp/ds000210/derivatives participant \
--config $PWD/nipype.cfg -w /tmp/ds210/work \
/tmp/data/ds210 /tmp/ds210/derivatives participant \
--fs-no-reconall --t2s-coreg --use-syn-sdc \
--template-resampling-grid native \
--debug --write-graph --mem_mb 4096 --nthreads 2 -vv
- run:
name: Checking outputs of fMRIPrep
command: |
mkdir -p /tmp/ds000210/test
find /tmp/ds000210/derivatives | sed s+/tmp/ds000210/derivatives/++ | sort > /tmp/ds000210/test/outputs.out
diff /tmp/src/fmriprep/.circleci/ds000210_outputs.txt /tmp/ds000210/test/outputs.out
mkdir -p /tmp/ds210/test
find /tmp/ds210/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds210/derivatives/++ | sort > /tmp/ds210/test/outputs.out
diff /tmp/src/fmriprep/.circleci/ds210_outputs.txt /tmp/ds210/test/outputs.out
exit $?
- run:
name: Clean-up work work directory
name: Clean-up work directory
when: always
command: |
sudo find /tmp/ds000210/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
sudo chown $(id -un):$(id -gn) -R /tmp/ds210
find /tmp/ds210/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
-not -name "*.mat" -not -name "*.lta" -type f -delete
# tar cf - work/ | pigz -2 -p 2 > ds054_workdir.tar.gz && sudo rm -fr work
- store_artifacts:
path: /tmp/ds000210
path: /tmp/ds210

deploy:
machine:
Expand Down
18 changes: 0 additions & 18 deletions .circleci/ds005_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,43 +28,25 @@ fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
fmriprep/sub-01/anat/sub-01_T1w_space-orig_target-T1w_affine.txt
fmriprep/sub-01/anat/sub-01_T1w_target-fsnative_affine.txt
fmriprep/sub-01/anat/sub-01_T1w_target-MNI152NLin2009cAsym_warp.h5
fmriprep/sub-01/figures
fmriprep/sub-01/figures/sub-01_T1w_reconall.svg
fmriprep/sub-01/figures/sub-01_T1w_seg_brainmask.svg
fmriprep/sub-01/figures/sub-01_T1w_t1_2_mni.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_bbr.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_ica_aroma.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_rois.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_sdc_syn.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_bbr.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_ica_aroma.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_rois.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_sdc_syn.svg
fmriprep/sub-01/func
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.R.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-fsaverage5.R.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_label-aseg_roi.nii.gz
Expand Down
15 changes: 0 additions & 15 deletions .circleci/ds005_partial_outputs.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -28,29 +28,14 @@ fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
fmriprep/sub-01/anat/sub-01_T1w_space-orig_target-T1w_affine.txt
fmriprep/sub-01/anat/sub-01_T1w_target-fsnative_affine.txt
fmriprep/sub-01/anat/sub-01_T1w_target-MNI152NLin2009cAsym_warp.h5
fmriprep/sub-01/figures
fmriprep/sub-01/figures/sub-01_T1w_reconall.svg
fmriprep/sub-01/figures/sub-01_T1w_seg_brainmask.svg
fmriprep/sub-01/figures/sub-01_T1w_t1_2_mni.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_bbr.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_ica_aroma.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_rois.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_sdc_syn.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_bbr.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_ica_aroma.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_rois.svg
fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_sdc_syn.svg
fmriprep/sub-01/func
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.R.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aseg_roi.nii.gz
Expand Down
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