fix: quote NegBio pipeline paths for ShellCheck SC2086

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: Chessing234

mimic-iv-cxr/txt/negbio/run_negbio.sh

@@ -38,25 +38,25 @@ do
   fn=$(basename "$fn_path")
   echo "Looping through files with mimic_cxr_###.csv pattern."
   # validate it's a mimic_cxr sections file
-  if [[ $fn =~ ^mimic_cxr_[0-9]+.csv$ ]];
+  if [[ "$fn" =~ ^mimic_cxr_[0-9]+\.csv$ ]];
   then
-    export INPUT_FILE=$fn_path
+    export INPUT_FILE="$fn_path"
     # remove extension from filename
     # sets the folder location to stem of original filename
     # all intermediate files will be saved in this folder
-    export OUTPUT_DIR=${INPUT_FILE::-4}
+    export OUTPUT_DIR="${INPUT_FILE%.csv}"
 
     echo "$OUTPUT_DIR - running NegBio.."
     python "$NEGBIO_PATH/negbio/negbio_csv2bioc.py" --output "$OUTPUT_DIR/report" "$INPUT_FILE"
-    python $NEGBIO_PATH/negbio/negbio_pipeline.py section_split --pattern $NEGBIO_PATH/patterns/section_titles_cxr8.txt --output $OUTPUT_DIR/sections $OUTPUT_DIR/report/* --workers=6
-    python $NEGBIO_PATH/negbio/negbio_pipeline.py ssplit --output $OUTPUT_DIR/ssplit $OUTPUT_DIR/sections/* --workers=6
-    python $NEGBIO_PATH/negbio/negbio_pipeline.py parse --output $OUTPUT_DIR/parse $OUTPUT_DIR/ssplit/* --workers=6
-    python $NEGBIO_PATH/negbio/negbio_pipeline.py ptb2ud --output $OUTPUT_DIR/ud $OUTPUT_DIR/parse/* --workers=6
-    python $NEGBIO_PATH/negbio/negbio_pipeline.py dner_regex --phrases_file $NEGBIO_PATH/patterns/chexpert_phrases.yml --output $OUTPUT_DIR/dner $OUTPUT_DIR/ud/* --suffix=.chexpert-regex.xml --workers=6 --overwrite
-    python $NEGBIO_PATH/negbio/negbio_pipeline.py neg2 --output $OUTPUT_DIR/neg --pre-negation-uncertainty-patterns $NEGBIO_PATH/patterns/chexpert_pre_negation_uncertainty.yml --neg-patterns $NEGBIO_PATH/patterns/neg_patterns2.yml --post-negation-uncertainty-patterns $NEGBIO_PATH/patterns/post_negation_uncertainty.yml --neg-regex-patterns $NEGBIO_PATH/patterns/neg_regex_patterns.yml --uncertainty-regex-patterns $NEGBIO_PATH/patterns/uncertainty_regex_patterns.yml $OUTPUT_DIR/dner/* --workers=6
+    python "$NEGBIO_PATH/negbio/negbio_pipeline.py" section_split --pattern "$NEGBIO_PATH/patterns/section_titles_cxr8.txt" --output "$OUTPUT_DIR/sections" "$OUTPUT_DIR"/report/* --workers=6
+    python "$NEGBIO_PATH/negbio/negbio_pipeline.py" ssplit --output "$OUTPUT_DIR/ssplit" "$OUTPUT_DIR"/sections/* --workers=6
+    python "$NEGBIO_PATH/negbio/negbio_pipeline.py" parse --output "$OUTPUT_DIR/parse" "$OUTPUT_DIR"/ssplit/* --workers=6
+    python "$NEGBIO_PATH/negbio/negbio_pipeline.py" ptb2ud --output "$OUTPUT_DIR/ud" "$OUTPUT_DIR"/parse/* --workers=6
+    python "$NEGBIO_PATH/negbio/negbio_pipeline.py" dner_regex --phrases_file "$NEGBIO_PATH/patterns/chexpert_phrases.yml" --output "$OUTPUT_DIR/dner" "$OUTPUT_DIR"/ud/* --suffix=.chexpert-regex.xml --workers=6 --overwrite
+    python "$NEGBIO_PATH/negbio/negbio_pipeline.py" neg2 --output "$OUTPUT_DIR/neg" --pre-negation-uncertainty-patterns "$NEGBIO_PATH/patterns/chexpert_pre_negation_uncertainty.yml" --neg-patterns "$NEGBIO_PATH/patterns/neg_patterns2.yml" --post-negation-uncertainty-patterns "$NEGBIO_PATH/patterns/post_negation_uncertainty.yml" --neg-regex-patterns "$NEGBIO_PATH/patterns/neg_regex_patterns.yml" --uncertainty-regex-patterns "$NEGBIO_PATH/patterns/uncertainty_regex_patterns.yml" "$OUTPUT_DIR"/dner/* --workers=6
 
     # ultimate filename we save the labels to
-    export OUTPUT_LABELS=$OUTPUT_DIR/${fn::-4}_labels.csv
+    export OUTPUT_LABELS="$OUTPUT_DIR/${fn%.csv}_labels.csv"
     python "$NEGBIO_PATH/negbio/ext/chexpert_collect_labels.py" --phrases_file "$NEGBIO_PATH/patterns/chexpert_phrases.yml" --output "$OUTPUT_LABELS" "$OUTPUT_DIR"/neg/*
   fi
 done