named arguments, bugs fixed and clone datalad handle

brainageR/run_brainageR.sh

@@ -1,8 +1,34 @@
 #!/usr/bin/env bash
 # v 1.0
 DEBUG=1
-# sub_file=/data/project/brainage_underrepresented/data/ds004107/sub-mind010/ses-01/anat/sub-mind010_ses-01_T1w.nii.gz
-sub_path=$1
+
+# Initialize variables with default values
+sub_path=""
+out_dir=""
+container_path=""
+save="no"
+raw="yes"
+model="vanilla"
+
+# Parse command-line arguments
+while [[ "$#" -gt 0 ]]; do
+    case $1 in
+        -input) sub_path="$2"; shift ;;
+        -output) out_dir="$2"; shift ;;
+        -RAW) raw="$2"; shift ;;
+        -SAVE_FILE) save="$2"; shift ;;
+        -CONTAINER_PATH) container_path="$2"; shift ;;
+        -MODEL_NAME) model="$2"; shift ;;
+        -help)
+            echo "Usage: $0 -input <input_dir> -output <output_dir> -RAW <yes/no> -SAVE_FILE <yes/no> -CONTAINER_PATH <path> -MODEL_NAME <name>"
+            exit 0
+            ;;
+        *) echo "Unknown parameter passed: $1"; exit 1 ;;
+    esac
+    shift
+done
+
+
 # check that this is a file
 if [ -e "$sub_path" ] || [ -L "$sub_path" ]; then
     echo "Input file exists or is a symbolic link."
@@ -10,6 +36,8 @@ else
     echo "Input file does not exist, exiting."
     exit 1
 fi
+
+# sub_path=/data/project/brainage_underrepresented/data/ds004107/sub-mind010/ses-01/anat/sub-mind010_ses-01_T1w.nii.gz
 # dir_sub
 dir_path=$(dirname "${sub_path}")
 # sub_file=sub-mind010_ses-01_T1w.nii.gz (or .nii, or .mgz)
@@ -17,18 +45,7 @@ sub_file=$(basename "${sub_path}")
 # sub_name=sub-mind010_ses-01_T1w
 sub_name="${sub_file%%.*}"
 
-# out_dir=derivatives/brainageR/sub-01490270a/ses-BLT11
-out_dir=$2
-
-# Container path
-container_path=$3
-
-# Save or no the intermidiate files
-save=$4
-
-# Raw file ?
-raw=$5
-
+# Debugging or verbose mode can be added here if needed.
 if [ $DEBUG -eq 1 ]; then
     echo "sub_file = $sub_path"
     echo "dir_path = $dir_path"
@@ -37,6 +54,8 @@ if [ $DEBUG -eq 1 ]; then
     echo "out_dir = $out_dir"
     echo "save = $save"
     echo "raw = $raw"
+    echo "container_path = $container_path"
+    echo "model = $model"
 fi
 
 # create result folder and move the results in there
@@ -49,16 +68,43 @@ fi
 
 cd "${dir_path}"
 
-datalad get "${sub_file}"
+datalad_dir_path=$(git -C ${dir_path} rev-parse --show-toplevel)
+
+if [ -d ${datalad_dir_path} ]; then
+    datalad_work_dir=$(mktemp -d)
+    cd ${datalad_work_dir}
+    datalad clone ${datalad_dir_path} .
+
+    # Trying to get sub-mind010/ses-01/anat/sub-mind010_ses-01_T1w.nii.gz
+    complement="${sub_path#"$datalad_dir_path"}"
+    complement_dir_name=$(dirname "$complement" | sed 's|^/||')
+    cd $complement_dir_name 
+    sub_path=$(pwd)/$sub_file
+    datalad get "${sub_file}"
+    # Check the exit status of the previous command
+    if [ $? -ne 0 ]; then
+        echo "datalad cloning failed, exiting." >&2
+        exit 1
+    fi
+fi
 
 
 # define working dir, create a 'data' folder in it and copy the subject in.
 work_dir=$(mktemp -d)
-mkdir ${work_dir}/data
+mkdir -p ${work_dir}/data/anat
 
+cp "${sub_path}" "${work_dir}/data/anat"
 
-cp "${sub_path}" "${work_dir}/data"
-datalad drop "${sub_path}"
+if [ $? -ne 0 ]; then
+    echo "datalad cloning failed, exiting." >&2
+    exit 1
+fi
+
+if [ -d ${datalad_dir_path} ]; then
+    # datalad drop "${sub_path}"
+    chmod -R a+w $datalad_work_dir
+    rm -fr $datalad_work_dir
+fi
 
 cd ${work_dir}
 
@@ -66,21 +112,21 @@ cd ${work_dir}
 # gunzip only if gz file and then delete .gz file
 if [[ "$sub_file" == *.gz ]]; then
     echo "The file is a .gz file."
-    gunzip data/${sub_file}
-    rm -f data/${sub_file}
+    gunzip data/anat/${sub_file}
+    rm -f data/anat/${sub_file}
     sub_file=${sub_file%".gz"}
 else
     echo "The file is not a .gz file."
 fi
 
 # make sure permissions are ok
-chmod +rwx ${work_dir}/data/$sub_file
+chmod +rwx ${work_dir}/data/anat/$sub_file
 
 # run singularity with brainageR code
 # ----------------------------------------------------------
 echo "Running the container"
 #singularity exec /data/project/BrainAge4AD/tools/brainageR_dockerfile/brainageR2.1.sif brainageR -f ${work_dir}/data/${sub_file} -o ${sub_name}_brain_predicted.age.csv
-singularity exec ${container_path} brainageR -f ${work_dir}/data/${sub_file} -o ${sub_name}_brain_predicted.age.csv
+singularity exec ${container_path}/brainageR2.1.sif brainageR -f ${work_dir}/data/anat/${sub_file} -o ${sub_name}_brain_predicted.age.csv
 
 # Check the exit status of the previous command
 if [ $? -ne 0 ]; then
@@ -91,16 +137,29 @@ fi
 
 # Moving the prediction into the output dir
 mv $work_dir/${sub_name}_brain_predicted.age.csv $out_dir/${sub_name}_brainageR.csv
-echo "Prediction file sub${sub_name} saved in $out_dir"
+
+# Check if the last command was successful
+if [ $? -eq 0 ]; then
+    echo "Prediction file ${sub_name} saved in $out_dir"
+else
+    echo "There was a problem"
+fi
 
 # If user wants to save intermidiate files, moving everything into output dir
 if [ $save == "yes" ]; then
     mkdir -p $out_dir/${sub_name}_brainageR
-    mv -r $work_dir/* $out_dir/${sub_name}_brainageR/
+    mv $work_dir/* $out_dir/${sub_name}_brainageR/
     echo "All files of ${sub_name} saved in $out_dir/${sub_name}_brainageR"
+
+    # Check if the last command was successful
+    if [ $? -eq 0 ]; then
+        echo "All files of ${sub_name} saved in $out_dir/${sub_name}_brainageR"
+    else
+        echo "There was a problem"
+    fi
 fi
 
 echo "Cleaning tmp files"
 rm -rf $work_dir
 
-exit
+exit