From 8219948382ea3a287f7fb780023854e5a981d103 Mon Sep 17 00:00:00 2001
From: Travis Beckwith <113939491+TravisBeckwith@users.noreply.github.com>
Date: Fri, 17 Jul 2026 15:40:06 -0400
Subject: [PATCH] Add files via upload

---
 bids_convert.sh            | 30 +++++++++++++++++++-----------
 tests/test_bids_convert.sh | 27 +++++++++++++++++----------
 2 files changed, 36 insertions(+), 21 deletions(-)

diff --git a/bids_convert.sh b/bids_convert.sh
index 2dc6d05..bc1e185 100644
--- a/bids_convert.sh
+++ b/bids_convert.sh
@@ -515,7 +515,7 @@ convert_folder() {
                     log_dbg "  Renamed: $(basename "$old_file") → $(basename "$new_file")"
                 fi
             done
-            ((run_num++))
+            ((run_num++)) || true
         done
     fi
 
@@ -800,7 +800,7 @@ detect_structure() {
             local imaging_child=false
             for gc in "$child"/*/; do
                 [ ! -d "$gc" ] && continue
-                ((grandchild_count++))
+                ((grandchild_count++)) || true
                 local gc_name
                 gc_name="$(basename "$gc")"
                 if match_folder "$gc_name" 2>/dev/null; then
@@ -833,13 +833,19 @@ normalize_subject_id() {
     local raw="$1"
     local id="$raw"
 
-    # Strip known prefixes (most specific first)
+    # Strip known prefixes — longest/most-specific first. Order matters:
+    # each ${id#pattern} only strips once, against whatever id currently is,
+    # so a short prefix tried before a longer one that contains it (e.g.
+    # "SUB" before "SUBJECT_") will consume part of the longer prefix and
+    # leave the rest stuck to the id (SUBJECT_001 -> SUB stripped -> JECT_001).
+    id="${id#SUBJECT_}"
+    id="${id#SUBJECT}"
+    id="${id#subject_}"
+    id="${id#subject}"
     id="${id#sub-}"
-    id="${id#sub}"
     id="${id#SUB-}"
+    id="${id#sub}"
     id="${id#SUB}"
-    id="${id#SUBJECT_}"
-    id="${id#SUBJECT}"
 
     # Remove leading underscores/hyphens
     id="${id#_}"
@@ -860,12 +866,14 @@ normalize_session_id() {
     local raw="$1"
     local id="$raw"
 
+    id="${id#SESSION_}"
+    id="${id#SESSION}"
+    id="${id#session_}"
+    id="${id#session}"
     id="${id#ses-}"
-    id="${id#ses}"
     id="${id#SES-}"
+    id="${id#ses}"
     id="${id#SES}"
-    id="${id#SESSION_}"
-    id="${id#SESSION}"
     id="${id#VISIT}"
     id="${id#TIMEPOINT}"
     id="${id#TP}"
@@ -1050,7 +1058,7 @@ fixup_run_numbers() {
                     fi
                 done
             fi
-            ((run_num++))
+            ((run_num++)) || true
         done
     done
 }
@@ -1295,7 +1303,7 @@ main() {
             process_subject "$sub_dir" "$sub_label" "$structure"
         fi
 
-        ((sub_count++))
+        ((sub_count++)) || true
         echo ""
     done
     shopt -u nullglob
diff --git a/tests/test_bids_convert.sh b/tests/test_bids_convert.sh
index 329cdde..3a3e3d2 100644
--- a/tests/test_bids_convert.sh
+++ b/tests/test_bids_convert.sh
@@ -29,12 +29,12 @@ assert_eq() {
     local label="$1" expected="$2" actual="$3"
     if [ "$expected" = "$actual" ]; then
         echo "  ✅ PASS: $label"
-        ((PASS++))
+        ((PASS++)) || true
     else
         echo "  ❌ FAIL: $label"
         echo "       expected: '$expected'"
         echo "       actual:   '$actual'"
-        ((FAIL++))
+        ((FAIL++)) || true
     fi
 }
 
@@ -42,10 +42,10 @@ assert_file_exists() {
     local label="$1" filepath="$2"
     if [ -f "$filepath" ]; then
         echo "  ✅ PASS: $label"
-        ((PASS++))
+        ((PASS++)) || true
     else
         echo "  ❌ FAIL: $label — file not found: $filepath"
-        ((FAIL++))
+        ((FAIL++)) || true
     fi
 }
 
@@ -53,10 +53,10 @@ assert_contains() {
     local label="$1" filepath="$2" pattern="$3"
     if grep -q "$pattern" "$filepath" 2>/dev/null; then
         echo "  ✅ PASS: $label"
-        ((PASS++))
+        ((PASS++)) || true
     else
         echo "  ❌ FAIL: $label — pattern '$pattern' not found in $filepath"
-        ((FAIL++))
+        ((FAIL++)) || true
     fi
 }
 
@@ -88,9 +88,16 @@ test_dry_run_creates_no_files() {
     touch "${input_dir}/SUBJECT_001/SAG_T1/dummy.dcm"
 
     # Dry-run should NOT create actual NIfTI files (dcm2niix won't run)
-    bash "$SCRIPT" -i "$input_dir" -o "$output_dir" -n 2>&1 | grep -q "DRY-RUN" && \
-        echo "  ✅ PASS: dry-run mode activated" && ((PASS++)) || \
-        { echo "  ❌ FAIL: dry-run mode not detected"; ((FAIL++)); }
+    # Capture output first rather than piping straight into `grep -q`: with
+    # pipefail (set above) and DRY-RUN appearing early in the output, grep -q
+    # exits as soon as it finds a match while bids_convert.sh is still
+    # writing later lines, which kills it with SIGPIPE (exit 141) — pipefail
+    # then reports the pipeline as failed even though grep did match.
+    local out
+    out="$(bash "$SCRIPT" -i "$input_dir" -o "$output_dir" -n 2>&1)" || true
+    echo "$out" | grep -q "DRY-RUN" && \
+        echo "  ✅ PASS: dry-run mode activated" && { ((PASS++)) || true; } || \
+        { echo "  ❌ FAIL: dry-run mode not detected"; ((FAIL++)) || true; }
 
     teardown_tmp
 }
@@ -111,7 +118,7 @@ test_bids_scaffold_creation() {
     # In dry-run the scaffold won't be created, so we test the help works
     # and the script doesn't crash
     echo "  ✅ PASS: script completed without error in dry-run"
-    ((PASS++))
+    ((PASS++)) || true
 
     teardown_tmp
 }