From a643677632bc688bc5e7599d957778a3c24a30cd Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 16:59:44 -0500
Subject: [PATCH 01/16] Create bootstrap-xcp-qc-testing.sh

Copy-pasted from aslprep script, will work on editing for xcp
---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 241 ++++++++++++++++++++++
 1 file changed, 241 insertions(+)
 create mode 100644 scripts/cubic/bootstrap-xcp-qc-testing.sh

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
new file mode 100644
index 0000000..8597bac
--- /dev/null
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -0,0 +1,241 @@
+## NOTE ##
+# THIS SCRIPT IS STILL BEING TESTED AND NOT READY FOR USE
+# This workflow is derived from the Datalad Handbook
+## Ensure the environment is ready to bootstrap the analysis workspace
+# Check that we have conda installed
+
+DATALAD_VERSION=$(datalad --version)
+
+if [ $? -gt 0 ]; then
+    echo "No datalad available in your conda environment."
+    echo "Try pip install datalad"
+    # exit 1
+fi
+
+echo USING DATALAD VERSION ${DATALAD_VERSION}
+
+set -e -u
+
+
+## Set up the directory that will contain the necessary directories
+PROJECTROOT=${PWD}/ASLPREP_QC
+if [[ -d ${PROJECTROOT} ]]
+then
+    echo ${PROJECTROOT} already exists
+    # exit 1
+fi
+
+if [[ ! -w $(dirname ${PROJECTROOT}) ]]
+then
+    echo Unable to write to ${PROJECTROOT}\'s parent. Change permissions and retry
+    # exit 1
+fi
+
+mkdir -p $PROJECTROOT
+
+## DERIVATIVE_BOOTSTRAP_DIR will be the path to the bootstrap directory containing your derivatives
+DERIVATIVE_BOOTSTRAP_DIR=$1
+DERIVATIVE_INPUT=ria+file://${DERIVATIVE_BOOTSTRAP_DIR}"/output_ria#~data"
+if [[ -z ${DERIVATIVE_BOOTSTRAP_DIR} ]]
+then
+    echo "Required argument is the path to the aslprep bootstrap directory."
+    echo "This directory should contain analysis/, input_ria/ and output_ria/."
+    # exit 1
+fi
+
+# Jobs are set up to not require a shared filesystem (except for the lockfile)
+# ------------------------------------------------------------------------------
+# RIA-URL to a different RIA store from which the dataset will be cloned from.
+# Both RIA stores will be created
+input_store="ria+file://${PROJECTROOT}/input_ria"
+output_store="ria+file://${PROJECTROOT}/output_ria"
+
+# Create a source dataset with all analysis components as an analysis access
+# point.
+cd $PROJECTROOT
+datalad create -c yoda analysis
+cd analysis
+
+# create dedicated input and output locations. Results will be pushed into the
+# output sibling and the analysis will start with a clone from the input sibling.
+datalad create-sibling-ria -s output "${output_store}"
+pushremote=$(git remote get-url --push output)
+datalad create-sibling-ria -s input --storage-sibling off "${input_store}"
+
+datalad install -d . -r --source ${DERIVATIVE_INPUT} inputs/data
+
+# amend the previous commit with a nicer commit message
+git commit --amend -m 'Register input data dataset as a subdataset'
+
+ZIPS=$(find inputs/data -name 'sub-*aslprep*' | cut -d '/' -f 3 | sort)
+if [ -z "${ZIPS}" ]
+then
+    echo "No subjects found in input data"
+    # exit 1
+fi
+
+## the actual compute job specification
+cat > code/participant_job.sh << "EOT"
+#!/bin/bash
+#$ -S /bin/bash
+#$ -l h_vmem=25G
+#$ -l tmpfree=200G
+#$ -R y
+#$ -l h_rt=24:00:00
+# Set up the correct conda environment
+source ${CONDA_PREFIX}/bin/activate base
+echo I\'m in $PWD using `which python`
+# fail whenever something is fishy, use -x to get verbose logfiles
+set -e -u -x
+# Set up the remotes and get the subject id from the call
+dssource="$1"
+pushgitremote="$2"
+subid="$3"
+# change into the cluster-assigned temp directory. Not done by default in SGE
+cd ${CBICA_TMPDIR}
+# OR Run it on a shared network drive
+# cd /cbica/comp_space/$(basename $HOME)
+# Used for the branch names and the temp dir
+BRANCH="job-${JOB_ID}-${subid}"
+mkdir ${BRANCH}
+cd ${BRANCH}
+# get the analysis dataset, which includes the inputs as well
+# importantly, we do not clone from the lcoation that we want to push the
+# results to, in order to avoid too many jobs blocking access to
+# the same location and creating a throughput bottleneck
+datalad clone "${dssource}" ds
+# all following actions are performed in the context of the superdataset
+cd ds
+git remote add outputstore "$pushgitremote"
+git checkout -b "${BRANCH}"
+# ------------------------------------------------------------------------------
+# Do the run!
+datalad run \
+    -i code/get_files.sh \
+    -i inputs/data/${subid}_aslprep*.zip \
+    --explicit \
+    -o ${subid}*quality*.csv \
+    -m "unzipped ${subid}" \
+    "bash code/get_files.sh inputs/data/${subid}_aslprep*.zip"
+# file content first -- does not need a lock, no interaction with Git
+datalad push --to output-storage
+# and the output branch
+flock $DSLOCKFILE git push outputstore
+echo TMPDIR TO DELETE
+echo ${BRANCH}
+datalad drop -r . --nocheck
+datalad uninstall -r inputs/data
+git annex dead here
+cd ../..
+rm -rf $BRANCH
+echo SUCCESS
+# job handler should clean up workspace
+EOT
+
+chmod +x code/participant_job.sh
+
+## the actual compute job specification
+echo writing script to file...
+cat > code/get_files.sh << "EOT"
+#!/bin/bash
+set -e -u -x
+ZIP_FILE=$1
+subid=$(basename $ZIP_FILE | cut -d '_' -f 1)
+# unzip outputs
+unzip -n $ZIP_FILE 'aslprep/*' -d .
+cp aslprep/${subid}/*/perf/*quality*.csv .
+# remove unzip dir
+rm -rf aslprep
+EOT
+
+chmod +x code/get_files.sh
+
+##### concat_outputs.sh START ####
+
+cat > code/concat_outputs.sh << "EOT"
+#!/bin/bash
+set -e -u -x
+EOT
+
+echo "PROJECT_ROOT=${PROJECTROOT}" >> code/concat_outputs.sh
+echo "cd ${PROJECTROOT}" >> code/concat_outputs.sh
+
+cat >> code/concat_outputs.sh << "EOT"
+# set up concat_ds and run concatenator on it
+cd ${CBICA_TMPDIR}
+datalad clone ria+file://${PROJECT_ROOT}/output_ria#~data concat_ds
+cd concat_ds/code
+wget https://raw.githubusercontent.com/PennLINC/RBC/master/PennLINC/Generic/concatenator.py
+cd ..
+datalad save -m "added concatenator script"
+datalad run -i 'sub-*quality*.csv' -o '${PROJECT_ROOT}/ASLPREP_QC.csv' --expand inputs --explicit "python code/concatenator.py $PWD ${PROJECT_ROOT}/ASLPREP_QC.csv"
+datalad save -m "generated report"
+# push changes
+datalad push
+# remove concat_ds
+git annex dead here
+cd ..
+chmod +w -R concat_ds
+rm -rf concat_ds
+echo SUCCESS
+EOT
+
+#### concat_output.sh END ####
+
+mkdir logs
+echo .SGE_datalad_lock >> .gitignore
+echo logs >> .gitignore
+
+datalad save -m "Participant compute job implementation"
+
+# Add a script for merging outputs
+MERGE_POSTSCRIPT=https://raw.githubusercontent.com/PennLINC/TheWay/main/scripts/cubic/merge_outputs_postscript.sh
+cat > code/merge_outputs.sh << "EOT"
+#!/bin/bash
+set -e -u -x
+EOT
+echo "outputsource=${output_store}#$(datalad -f '{infos[dataset][id]}' wtf -S dataset)" \
+    >> code/merge_outputs.sh
+echo "cd ${PROJECTROOT}" >> code/merge_outputs.sh
+wget -qO- ${MERGE_POSTSCRIPT} >> code/merge_outputs.sh
+
+################################################################################
+# SGE SETUP START - remove or adjust to your needs
+################################################################################
+env_flags="-v DSLOCKFILE=${PWD}/.SGE_datalad_lock"
+
+echo '#!/bin/bash' > code/qsub_calls.sh
+dssource="${input_store}#$(datalad -f '{infos[dataset][id]}' wtf -S dataset)"
+pushgitremote=$(git remote get-url --push output)
+eo_args="-e ${PWD}/logs -o ${PWD}/logs"
+
+for zip in ${ZIPS}; do
+    subject=`echo ${zip} | cut -d '_' -f 1` 
+    echo "qsub -cwd ${env_flags} -N UNZIP${subject} ${eo_args} \
+    ${PWD}/code/participant_job.sh \
+    ${dssource} ${pushgitremote} ${subject}" >> code/qsub_calls.sh
+done
+datalad save -m "SGE submission setup" code/ .gitignore
+
+################################################################################
+# SGE SETUP END
+################################################################################
+
+# cleanup - we have generated the job definitions, we do not need to keep a
+# massive input dataset around. Having it around wastes resources and makes many
+# git operations needlessly slow
+datalad uninstall -r --nocheck inputs/data
+
+
+# make sure the fully configured output dataset is available from the designated
+# store for initial cloning and pushing the results.
+datalad push --to input
+datalad push --to output
+
+# Add an alias to the data in the RIA store
+RIA_DIR=$(find $PROJECTROOT/output_ria/???/ -maxdepth 1 -type d | sort | tail -n 1)
+mkdir -p ${PROJECTROOT}/output_ria/alias
+ln -s ${RIA_DIR} ${PROJECTROOT}/output_ria/alias/data
+
+# if we get here, we are happy
+echo SUCCESS

From 374869f8fb9971fd9dd6b06fb2e8f1c0cb81070a Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 17:11:44 -0500
Subject: [PATCH 02/16] Update bootstrap-xcp-qc-testing.sh

changed all ASL to XCP
---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 8597bac..247ae8d 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -1,5 +1,4 @@
 ## NOTE ##
-# THIS SCRIPT IS STILL BEING TESTED AND NOT READY FOR USE
 # This workflow is derived from the Datalad Handbook
 ## Ensure the environment is ready to bootstrap the analysis workspace
 # Check that we have conda installed
@@ -18,7 +17,7 @@ set -e -u
 
 
 ## Set up the directory that will contain the necessary directories
-PROJECTROOT=${PWD}/ASLPREP_QC
+PROJECTROOT=${PWD}/XCP _QC
 if [[ -d ${PROJECTROOT} ]]
 then
     echo ${PROJECTROOT} already exists
@@ -38,7 +37,7 @@ DERIVATIVE_BOOTSTRAP_DIR=$1
 DERIVATIVE_INPUT=ria+file://${DERIVATIVE_BOOTSTRAP_DIR}"/output_ria#~data"
 if [[ -z ${DERIVATIVE_BOOTSTRAP_DIR} ]]
 then
-    echo "Required argument is the path to the aslprep bootstrap directory."
+    echo "Required argument is the path to the xcp bootstrap directory."
     echo "This directory should contain analysis/, input_ria/ and output_ria/."
     # exit 1
 fi
@@ -67,7 +66,7 @@ datalad install -d . -r --source ${DERIVATIVE_INPUT} inputs/data
 # amend the previous commit with a nicer commit message
 git commit --amend -m 'Register input data dataset as a subdataset'
 
-ZIPS=$(find inputs/data -name 'sub-*aslprep*' | cut -d '/' -f 3 | sort)
+ZIPS=$(find inputs/data -name 'sub-*xcp*' | cut -d '/' -f 3 | sort)
 if [ -z "${ZIPS}" ]
 then
     echo "No subjects found in input data"
@@ -112,11 +111,11 @@ git checkout -b "${BRANCH}"
 # Do the run!
 datalad run \
     -i code/get_files.sh \
-    -i inputs/data/${subid}_aslprep*.zip \
+    -i inputs/data/${subid}_xcp.zip \
     --explicit \
     -o ${subid}*quality*.csv \
     -m "unzipped ${subid}" \
-    "bash code/get_files.sh inputs/data/${subid}_aslprep*.zip"
+    "bash code/get_files.sh inputs/data/${subid}_xcp*.zip"
 # file content first -- does not need a lock, no interaction with Git
 datalad push --to output-storage
 # and the output branch
@@ -142,10 +141,10 @@ set -e -u -x
 ZIP_FILE=$1
 subid=$(basename $ZIP_FILE | cut -d '_' -f 1)
 # unzip outputs
-unzip -n $ZIP_FILE 'aslprep/*' -d .
-cp aslprep/${subid}/*/perf/*quality*.csv .
+unzip -n $ZIP_FILE 'xcp/*' -d .
+cp xcp/${subid}/*/perf/*quality*.csv .
 # remove unzip dir
-rm -rf aslprep
+rm -rf xcp
 EOT
 
 chmod +x code/get_files.sh
@@ -168,7 +167,7 @@ cd concat_ds/code
 wget https://raw.githubusercontent.com/PennLINC/RBC/master/PennLINC/Generic/concatenator.py
 cd ..
 datalad save -m "added concatenator script"
-datalad run -i 'sub-*quality*.csv' -o '${PROJECT_ROOT}/ASLPREP_QC.csv' --expand inputs --explicit "python code/concatenator.py $PWD ${PROJECT_ROOT}/ASLPREP_QC.csv"
+datalad run -i 'sub-*quality*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator.py $PWD ${PROJECT_ROOT}/XCP_QC.csv"
 datalad save -m "generated report"
 # push changes
 datalad push

From 9f13f1f5d4bd921249e189fe3474b75dc2b2a685 Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 17:14:48 -0500
Subject: [PATCH 03/16] Update bootstrap-xcp-qc-testing.sh

Updated concatenator to be used
---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 247ae8d..3607f1d 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -164,10 +164,10 @@ cat >> code/concat_outputs.sh << "EOT"
 cd ${CBICA_TMPDIR}
 datalad clone ria+file://${PROJECT_ROOT}/output_ria#~data concat_ds
 cd concat_ds/code
-wget https://raw.githubusercontent.com/PennLINC/RBC/master/PennLINC/Generic/concatenator.py
+wget https://raw.githubusercontent.com/PennLINC/RBC/kahinimehta-patch-1/PennLINC/Generic/concatenator_task.py
 cd ..
 datalad save -m "added concatenator script"
-datalad run -i 'sub-*quality*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator.py $PWD ${PROJECT_ROOT}/XCP_QC.csv"
+datalad run -i 'sub-*quality*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT}/XCP_QC.csv"
 datalad save -m "generated report"
 # push changes
 datalad push

From 44d34af9e262d28841c1317caa69a65fa5c1b3d8 Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 17:30:20 -0500
Subject: [PATCH 04/16] Update bootstrap-xcp-qc-testing.sh

updated file
---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 3607f1d..7c6cb6d 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -113,7 +113,7 @@ datalad run \
     -i code/get_files.sh \
     -i inputs/data/${subid}_xcp.zip \
     --explicit \
-    -o ${subid}*quality*.csv \
+    -o ${subid}*qc*.csv \
     -m "unzipped ${subid}" \
     "bash code/get_files.sh inputs/data/${subid}_xcp*.zip"
 # file content first -- does not need a lock, no interaction with Git
@@ -142,7 +142,7 @@ ZIP_FILE=$1
 subid=$(basename $ZIP_FILE | cut -d '_' -f 1)
 # unzip outputs
 unzip -n $ZIP_FILE 'xcp/*' -d .
-cp xcp/${subid}/*/perf/*quality*.csv .
+cp xcp/${subid}/*/func/*qc*.csv .
 # remove unzip dir
 rm -rf xcp
 EOT
@@ -167,7 +167,7 @@ cd concat_ds/code
 wget https://raw.githubusercontent.com/PennLINC/RBC/kahinimehta-patch-1/PennLINC/Generic/concatenator_task.py
 cd ..
 datalad save -m "added concatenator script"
-datalad run -i 'sub-*quality*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT}/XCP_QC.csv"
+datalad run -i 'sub-*qc*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT}/XCP_QC.csv"
 datalad save -m "generated report"
 # push changes
 datalad push

From 5acf7bf4bb27f52624eac1bb1e86c0c9435275fa Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 17:31:38 -0500
Subject: [PATCH 05/16] Update bootstrap-xcp-qc-testing.sh

---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 7c6cb6d..4c20ce4 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -17,7 +17,7 @@ set -e -u
 
 
 ## Set up the directory that will contain the necessary directories
-PROJECTROOT=${PWD}/XCP _QC
+PROJECTROOT=${PWD}/XCP_QC
 if [[ -d ${PROJECTROOT} ]]
 then
     echo ${PROJECTROOT} already exists

From d5d575f0249d1922ee5e6f0a54e20429867f390e Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 18:18:21 -0500
Subject: [PATCH 06/16] Update bootstrap-xcp-qc-testing.sh

---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 4c20ce4..ec58502 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -111,7 +111,7 @@ git checkout -b "${BRANCH}"
 # Do the run!
 datalad run \
     -i code/get_files.sh \
-    -i inputs/data/${subid}_xcp.zip \
+    -i inputs/data/${subid}_xcp*.zip \
     --explicit \
     -o ${subid}*qc*.csv \
     -m "unzipped ${subid}" \

From e384ebfa75630b41783739c7d74a2b5c8e47f6e4 Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 19:19:37 -0500
Subject: [PATCH 07/16] Update bootstrap-xcp-qc-testing.sh

---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index ec58502..6dc0c6e 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -82,7 +82,7 @@ cat > code/participant_job.sh << "EOT"
 #$ -R y
 #$ -l h_rt=24:00:00
 # Set up the correct conda environment
-source ${CONDA_PREFIX}/bin/activate base
+source ${CONDA_PREFIX}/bin/activate flywheel
 echo I\'m in $PWD using `which python`
 # fail whenever something is fishy, use -x to get verbose logfiles
 set -e -u -x
@@ -91,9 +91,9 @@ dssource="$1"
 pushgitremote="$2"
 subid="$3"
 # change into the cluster-assigned temp directory. Not done by default in SGE
-cd ${CBICA_TMPDIR}
+#cd ${CBICA_TMPDIR}
 # OR Run it on a shared network drive
-# cd /cbica/comp_space/$(basename $HOME)
+ cd /cbica/comp_space/$(basename $HOME)
 # Used for the branch names and the temp dir
 BRANCH="job-${JOB_ID}-${subid}"
 mkdir ${BRANCH}
@@ -141,10 +141,10 @@ set -e -u -x
 ZIP_FILE=$1
 subid=$(basename $ZIP_FILE | cut -d '_' -f 1)
 # unzip outputs
-unzip -n $ZIP_FILE 'xcp/*' -d .
-cp xcp/${subid}/*/func/*qc*.csv .
+unzip -n $ZIP_FILE 'xcp*/*' -d .
+cp xcp*/${subid}/*/func/*qc*.csv .
 # remove unzip dir
-rm -rf xcp
+rm -rf xcp*
 EOT
 
 chmod +x code/get_files.sh

From 9570b6b9026c0b0e96bfa62dbe7cfbb2fbe7614b Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 21:20:02 -0500
Subject: [PATCH 08/16] Update bootstrap-xcp-qc-testing.sh

---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 6dc0c6e..5234692 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -166,8 +166,9 @@ datalad clone ria+file://${PROJECT_ROOT}/output_ria#~data concat_ds
 cd concat_ds/code
 wget https://raw.githubusercontent.com/PennLINC/RBC/kahinimehta-patch-1/PennLINC/Generic/concatenator_task.py
 cd ..
+ARGS=$1
 datalad save -m "added concatenator script"
-datalad run -i 'sub-*qc*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT}/XCP_QC.csv"
+datalad run -i 'sub-*qc*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT} $ARGS"
 datalad save -m "generated report"
 # push changes
 datalad push
@@ -177,6 +178,7 @@ cd ..
 chmod +w -R concat_ds
 rm -rf concat_ds
 echo SUCCESS
+
 EOT
 
 #### concat_output.sh END ####

From 62e9b67a60dae9cddc052a3010e64545bc685fbe Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 21:29:36 -0500
Subject: [PATCH 09/16] Update bootstrap-xcp-qc-testing.sh

---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 5234692..09de705 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -82,7 +82,7 @@ cat > code/participant_job.sh << "EOT"
 #$ -R y
 #$ -l h_rt=24:00:00
 # Set up the correct conda environment
-source ${CONDA_PREFIX}/bin/activate flywheel
+source ${CONDA_PREFIX}/bin/activate base
 echo I\'m in $PWD using `which python`
 # fail whenever something is fishy, use -x to get verbose logfiles
 set -e -u -x

From 69fa70c1ca017e277fc5191b8b2e1e4b3b33230d Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 21:43:35 -0500
Subject: [PATCH 10/16] Update bootstrap-xcp-qc-testing.sh

---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 09de705..04073c9 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -166,7 +166,7 @@ datalad clone ria+file://${PROJECT_ROOT}/output_ria#~data concat_ds
 cd concat_ds/code
 wget https://raw.githubusercontent.com/PennLINC/RBC/kahinimehta-patch-1/PennLINC/Generic/concatenator_task.py
 cd ..
-ARGS=$1
+ARGS=$@
 datalad save -m "added concatenator script"
 datalad run -i 'sub-*qc*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT} $ARGS"
 datalad save -m "generated report"

From 4c36e5ef28a8518deba6e80524cb657fe8180522 Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 22:10:10 -0500
Subject: [PATCH 11/16] Update bootstrap-xcp-qc-testing.sh

---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index 04073c9..e6ca2c3 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -160,6 +160,7 @@ echo "PROJECT_ROOT=${PROJECTROOT}" >> code/concat_outputs.sh
 echo "cd ${PROJECTROOT}" >> code/concat_outputs.sh
 
 cat >> code/concat_outputs.sh << "EOT"
+# takes argument in format of individual QC file names without subject and session, eg: task-fracback_acq-singleband_space-fsLR_desc-qc_bold.csv
 # set up concat_ds and run concatenator on it
 cd ${CBICA_TMPDIR}
 datalad clone ria+file://${PROJECT_ROOT}/output_ria#~data concat_ds

From 2f630e585a10bbcb5d93f389998beff3e3799632 Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 24 Feb 2022 22:11:10 -0500
Subject: [PATCH 12/16] Update bootstrap-xcp-qc-testing.sh

---
 scripts/cubic/bootstrap-xcp-qc-testing.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc-testing.sh
index e6ca2c3..e02c4a2 100644
--- a/scripts/cubic/bootstrap-xcp-qc-testing.sh
+++ b/scripts/cubic/bootstrap-xcp-qc-testing.sh
@@ -160,7 +160,8 @@ echo "PROJECT_ROOT=${PROJECTROOT}" >> code/concat_outputs.sh
 echo "cd ${PROJECTROOT}" >> code/concat_outputs.sh
 
 cat >> code/concat_outputs.sh << "EOT"
-# takes argument in format of individual QC file names without subject and session, eg: task-fracback_acq-singleband_space-fsLR_desc-qc_bold.csv
+# takes argument in format of individual QC file names without subject and session separated by space, eg. below: 
+# task-fracback_acq-singleband_space-fsLR_desc-qc_bold.csv task-rest_acq-singleband_space-MNI152NLin6Asym_desc-qc_res-2_bold.csv
 # set up concat_ds and run concatenator on it
 cd ${CBICA_TMPDIR}
 datalad clone ria+file://${PROJECT_ROOT}/output_ria#~data concat_ds

From 56505a164ac6efd12f25828ecab722c760318404 Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Fri, 25 Feb 2022 07:28:26 -0500
Subject: [PATCH 13/16] Rename bootstrap-xcp-qc-testing.sh to
 bootstrap-xcp-qc.sh

---
 .../cubic/{bootstrap-xcp-qc-testing.sh => bootstrap-xcp-qc.sh}    | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename scripts/cubic/{bootstrap-xcp-qc-testing.sh => bootstrap-xcp-qc.sh} (100%)

diff --git a/scripts/cubic/bootstrap-xcp-qc-testing.sh b/scripts/cubic/bootstrap-xcp-qc.sh
similarity index 100%
rename from scripts/cubic/bootstrap-xcp-qc-testing.sh
rename to scripts/cubic/bootstrap-xcp-qc.sh

From 5495e4c77707ed67965322e0c23239021876775e Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Fri, 25 Feb 2022 16:01:36 -0500
Subject: [PATCH 14/16] Update bootstrap-xcp-qc.sh

---
 scripts/cubic/bootstrap-xcp-qc.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc.sh b/scripts/cubic/bootstrap-xcp-qc.sh
index e02c4a2..eb8adde 100644
--- a/scripts/cubic/bootstrap-xcp-qc.sh
+++ b/scripts/cubic/bootstrap-xcp-qc.sh
@@ -160,13 +160,13 @@ echo "PROJECT_ROOT=${PROJECTROOT}" >> code/concat_outputs.sh
 echo "cd ${PROJECTROOT}" >> code/concat_outputs.sh
 
 cat >> code/concat_outputs.sh << "EOT"
-# takes argument in format of individual QC file names without subject and session separated by space, eg. below: 
-# task-fracback_acq-singleband_space-fsLR_desc-qc_bold.csv task-rest_acq-singleband_space-MNI152NLin6Asym_desc-qc_res-2_bold.csv
+# takes argument in format of individual QC file names without subject and session separated by space and * after band, eg. below: 
+# task-fracback_acq-singleband*_space-fsLR_desc-qc_bold.csv task-rest_acq-singleband*_space-MNI152NLin6Asym_desc-qc_res-2_bold.csv
 # set up concat_ds and run concatenator on it
 cd ${CBICA_TMPDIR}
 datalad clone ria+file://${PROJECT_ROOT}/output_ria#~data concat_ds
 cd concat_ds/code
-wget https://raw.githubusercontent.com/PennLINC/RBC/kahinimehta-patch-1/PennLINC/Generic/concatenator_task.py
+wget https://raw.githubusercontent.com/PennLINC/RBC/kahinimehta-patch-1/PennLINC/Generic/concatenator_task.py # will need to be edited
 cd ..
 ARGS=$@
 datalad save -m "added concatenator script"

From 2e174677b7a2a17e009e0c4ba7ed2235af9c3932 Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 10 Mar 2022 15:02:10 -0500
Subject: [PATCH 15/16] Update bootstrap-xcp-qc.sh

---
 scripts/cubic/bootstrap-xcp-qc.sh | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc.sh b/scripts/cubic/bootstrap-xcp-qc.sh
index eb8adde..9d2dd58 100644
--- a/scripts/cubic/bootstrap-xcp-qc.sh
+++ b/scripts/cubic/bootstrap-xcp-qc.sh
@@ -160,17 +160,19 @@ echo "PROJECT_ROOT=${PROJECTROOT}" >> code/concat_outputs.sh
 echo "cd ${PROJECTROOT}" >> code/concat_outputs.sh
 
 cat >> code/concat_outputs.sh << "EOT"
-# takes argument in format of individual QC file names without subject and session separated by space and * after band, eg. below: 
-# task-fracback_acq-singleband*_space-fsLR_desc-qc_bold.csv task-rest_acq-singleband*_space-MNI152NLin6Asym_desc-qc_res-2_bold.csv
 # set up concat_ds and run concatenator on it
 cd ${CBICA_TMPDIR}
 datalad clone ria+file://${PROJECT_ROOT}/output_ria#~data concat_ds
 cd concat_ds/code
-wget https://raw.githubusercontent.com/PennLINC/RBC/kahinimehta-patch-1/PennLINC/Generic/concatenator_task.py # will need to be edited
+rm -rf concatenator_task.py*
+wget https://raw.githubusercontent.com/PennLINC/RBC/kahinimehta-patch-1/PennLINC/Generic/concatenator_task.py #might need to change this if pull request is resolved 
 cd ..
-ARGS=$@
+tasks=$1
+spaces=$2
+bands=$3
+echo USAGE = bash code/concat_outputs.sh rest fsLR multi OR comma-separated for multiple arguments, eg: bash code/concat_outputs.sh rest,fracback,face MNI152NLin6Asym,fsLR multi,single
 datalad save -m "added concatenator script"
-datalad run -i 'sub-*qc*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT} $ARGS"
+datalad run -i 'sub-*qc*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT} $tasks $spaces $bands"
 datalad save -m "generated report"
 # push changes
 datalad push

From 83ba269d127cfbda2ded67ed08cc0fabb8d54f46 Mon Sep 17 00:00:00 2001
From: kahinimehta <68132139+kahinimehta@users.noreply.github.com>
Date: Thu, 10 Mar 2022 17:02:49 -0500
Subject: [PATCH 16/16] Update bootstrap-xcp-qc.sh

---
 scripts/cubic/bootstrap-xcp-qc.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/cubic/bootstrap-xcp-qc.sh b/scripts/cubic/bootstrap-xcp-qc.sh
index 9d2dd58..8316a1b 100644
--- a/scripts/cubic/bootstrap-xcp-qc.sh
+++ b/scripts/cubic/bootstrap-xcp-qc.sh
@@ -170,9 +170,9 @@ cd ..
 tasks=$1
 spaces=$2
 bands=$3
-echo USAGE = bash code/concat_outputs.sh rest fsLR multi OR comma-separated for multiple arguments, eg: bash code/concat_outputs.sh rest,fracback,face MNI152NLin6Asym,fsLR multi,single
+res=$4
 datalad save -m "added concatenator script"
-datalad run -i 'sub-*qc*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT} $tasks $spaces $bands"
+datalad run -i 'sub-*qc*.csv' -o '${PROJECT_ROOT}/XCP_QC.csv' --expand inputs --explicit "python code/concatenator_task.py $PWD ${PROJECT_ROOT} $tasks $spaces $bands $res"
 datalad save -m "generated report"
 # push changes
 datalad push