fix(add-intended-for):ses-xyz/ in IntendedFor path

Also fixed tests and added some for sess

Author: WillForan

add-intended-for

@@ -46,7 +46,7 @@ FIND_EXCLUDE=" -not -name *echo-*"
 # does this session have func and/or dwi directories?
 func_andor_dwi(){
    [[ -d func ]] && echo func/
-   [[ -d dir/dwi ]] && echo dwi/
+   [[ -d dwi ]] && echo dwi/
    return 0
 }
 
@@ -76,6 +76,8 @@ csv_niifiles(){
     funcdwi=($(func_andor_dwi));
     [ ${#funcdwi[@]} -le 0 ] && echo "ERROR: no '$sesdir' has no func/ nor dwi/" >&2 && return 1
     find "${funcdwi[@]}" \( $find_names \) $FIND_EXCLUDE ) |
+    # if ses-xyz, we need that in the file path
+    sed "s:^:$(echo $sesdir/|grep -m1 -Po 'ses-[^/_-]+/'):" |
     sed 's/^\|$/"/g'|
     paste -sd,
 }
@@ -131,6 +133,7 @@ _intendedFor() {
      mapfile -t sefiles < <(find_se_file "$sesdir" "$sepatt")
      for sefile in "${sefiles[@]}"; do
         forfilescsv=$(csv_niifiles "$sesdir" "${boldpatt[@]}")
+	#echo "XX: $forfilescsv" >&2
         [ -z "$forfilescsv" ] &&
            warn "no matching files in $sesdir/{func,dwi}/ matching ${boldpatt[*]}" && return 1
 	check_shims "$sesdir" "$sefile" ${forfilescsv//,/ }

t/add-intended-for.bats

@@ -1,17 +1,33 @@
+touchjson(){ echo -e '{\n"ShimSetting":[0,0]\n}' > "$1"; }
+touchnii(){
+  3dUndump -dimen 2 2 2 -ijk  -prefix "${1:?output nifti}" -overwrite <(echo 0 0 0 1) 2>/dev/null;
+  touchjson ${1/.nii.gz/}.json;
+}
 setup(){
   SUBJ1=$BATS_TEST_TMPDIR/sub-1
   mkdir -p $SUBJ1/{fmap,func,dwi}/
 
-  echo -e '{\n}' > $SUBJ1/fmap/sub-1_epi.json
-  echo -e '{\n}' > $SUBJ1/fmap/sub-1_decoy__epi.json
+  touchnii $SUBJ1/fmap/sub-1_epi.nii.gz
+  touchnii $SUBJ1/func/sub-1_task-rest_bold.nii.gz
+  touchnii $SUBJ1/dwi/sub-1_dwi.nii.gz
+  touchnii $SUBJ1/func/sub-1_task-me-echo-1_bold.nii.gz
+
+
+  # various ways to have issues: intentional bad files
+  mkdir -p  $SUBJ1/sub-1/fmap
+  touchnii $SUBJ1/sub-1/fmap/sub-1_epi.nii.gz
+  touchnii $SUBJ1/fmap/sub-1_decoy__epi.nii.gz
+  touchnii $SUBJ1/func/sub-1_task-decoy_bold.nii.gz
+  touchnii $SUBJ1/dwi/sub-1_acq-decoy_dwi.nii.gz
 
-  touch $SUBJ1/func/sub-1_task-rest_bold.nii.gz
-  touch $SUBJ1/dwi/sub-1_dwi.nii.gz
 
-  touch $SUBJ1/func/sub-1_task-me-echo-1_bold.nii.gz
+  # 20260724 - need ses-xyz in IntendedFor path
+  SES1=$BATS_TEST_TMPDIR/bids2/sub-1/ses-1
+  mkdir -p $SES1/{fmap,func,dwi}/
+  touchnii $SES1/fmap/sub-1_ses-1_epi.nii.gz
+  touchnii $SES1/func/sub-1_ses-1_task-rest_bold.nii.gz
+  touchnii $SES1/dwi/sub-1_ses-1_dwi.nii.gz
 
-  touch $SUBJ1/func/sub-1_task-decoy_bold.nii.gz
-  touch $SUBJ1/dwi/sub-1_acq-decoy_dwi.nii.gz
 
   source add-intended-for
 }
@@ -36,6 +52,15 @@ AIF_find_se_file() { #@test
    ! [[ "$output"  =~ decoy ]]
 }
 
+csv_with_ses-rest() { #@test
+  run csv_niifiles $SES1/ "*_task-rest*nii.gz"
+  [[ $output  =~ '"ses-1/func/sub-1_ses-1_task-rest_bold.nii.gz"' ]]
+}
+csv_with_ses-many() { #@test
+  run csv_niifiles $SES1/ "*_task-rest*nii.gz" "*1_dwi.nii.gz"
+  [[ $output  =~ '"ses-1/func/sub-1_ses-1_task-rest_bold.nii.gz","ses-1/dwi/sub-1_ses-1_dwi.nii.gz"' ]]
+}
+
 add-intended-for-full() { #@test
    run ./add-intended-for \
       -fmap '*1_epi.json' \