Bring harden-parsing (#28) into master

generate_entity_patterns.sh

@@ -53,5 +53,5 @@ printf '@(%s)\n' "$(jq -r '.objects.extensions[].value' schema.json \
   | paste -sd'|')"
 
 echo
-echo "### datatype regex (for _libBIDSsh_parse_filename) ###"
-printf '(%s)\n' "$(jq -r '.objects.datatypes | keys[]' schema.json | paste -sd'|')"
+echo "### datatype regex (anchored to a whole path component; for _libBIDSsh_parse_filename) ###"
+printf '(^|/)(%s)$\n' "$(jq -r '.objects.datatypes | keys[]' schema.json | paste -sd'|')"

libBIDS.sh

@@ -245,11 +245,28 @@ _libBIDSsh_parse_filename() {
 
   # Store the full path and filename
   arr[path]=$(tr -s / <<<"${path}")
+
   arr[extension]="${filename#*.}"
-  # Extract from schema
+
+  # Datatype is the BIDS datatype directory directly containing the file (the
+  # final component of the file's directory). Anchor to a whole path component
+  # so an unrelated substring (e.g. "func" in "study_func/") cannot match.
   # ./generate_entity_patterns.sh -> datatype regex
-  arr[datatype]=$(grep -o -E "(anat|beh|dwi|eeg|emg|fmap|func|ieeg|meg|micr|motion|mrs|nirs|perf|pet|phenotype)" <<<"$(dirname "${path}")" | head -1 || echo "NA")
-  arr[derivatives]=$(grep -o 'derivatives/.*/' <<<"${path}" | awk -F/ '{print $2}' || echo "NA")
+  local dir
+  dir=$(dirname "${path}")
+  if [[ ${dir} =~ (^|/)(anat|beh|dwi|eeg|emg|fmap|func|ieeg|meg|micr|motion|mrs|nirs|perf|pet|phenotype)$ ]]; then
+    arr[datatype]="${BASH_REMATCH[2]}"
+  else
+    arr[datatype]="NA"
+  fi
+
+  # Derivatives pipeline name is the path component immediately following a
+  # "derivatives/" directory; NA when the file is not under one.
+  if [[ ${path} =~ (^|/)derivatives/([^/]+)/ ]]; then
+    arr[derivatives]="${BASH_REMATCH[2]}"
+  else
+    arr[derivatives]="NA"
+  fi
 
   local name_no_ext="${filename%%.*}"
 

test_libBIDS.sh

@@ -70,6 +70,36 @@ test_parse_filename() {
   return 0
 }
 
+test_parse_filename_datatype_derivatives() {
+  # Datatype must come from the file's parent directory anchored to a whole
+  # path component, not a substring anywhere in the path.
+  declare -A a
+  _libBIDSsh_parse_filename "/data/study_func_proj/sub-01/anat/sub-01_T1w.nii.gz" a
+  assert_equals "anat" "${a[datatype]:-}" "datatype must be anat despite 'func' in path" || return 1
+
+  declare -A b
+  _libBIDSsh_parse_filename "/data/sub-01/emg/sub-01_task-rest_emg.edf" b
+  assert_equals "emg" "${b[datatype]:-}" "emg datatype should be detected" || return 1
+
+  # No datatype directory -> NA
+  declare -A c
+  _libBIDSsh_parse_filename "/data/sub-01/sub-01_scans.tsv" c
+  assert_equals "NA" "${c[datatype]:-}" "missing datatype dir should be NA" || return 1
+
+  # Derivatives pipeline is the component right after 'derivatives/'.
+  declare -A d
+  _libBIDSsh_parse_filename "/data/derivatives/fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz" d
+  assert_equals "fmriprep" "${d[derivatives]:-}" "derivatives pipeline should be fmriprep" || return 1
+  assert_equals "anat" "${d[datatype]:-}" "derivative datatype should be anat" || return 1
+
+  # A directory merely containing the word 'derivatives' must not match.
+  declare -A e
+  _libBIDSsh_parse_filename "/data/myderivatives/sub-01/anat/sub-01_T1w.nii.gz" e
+  assert_equals "NA" "${e[derivatives]:-}" "'myderivatives' must not be treated as derivatives" || return 1
+
+  return 0
+}
+
 test_parse_bids_to_table() {
   local bids_dir="bids-examples/ds001"
   local table
@@ -210,6 +240,7 @@ echo "Starting libBIDS.sh test suite..."
 echo "---"
 
 run_test "Internal: _libBIDSsh_parse_filename" test_parse_filename
+run_test "Internal: _libBIDSsh_parse_filename datatype/derivatives" test_parse_filename_datatype_derivatives
 run_test "Public API: libBIDSsh_parse_bids_to_table" test_parse_bids_to_table
 run_test "Public API: libBIDSsh_table_filter" test_table_filter
 run_test "Public API: libBIDSsh_drop_na_columns" test_drop_na_columns