fix: glob + quote paths in chexpert runner too

Author: Chessing234

mimic-iv-cxr/txt/chexpert/run_chexpert_on_files.sh

@@ -22,11 +22,20 @@ fi
 sleep 2
 
 # loop through each .csv file in the section folder
-for fn in `ls $REPORT_PATH`; do
-    echo `date`: $fn
-    fn_stem=`echo $fn | cut -d. -f 1`
+for fn_path in "$REPORT_PATH"/*.csv; do
+    [ -f "$fn_path" ] || continue
+    fn=$(basename "$fn_path")
+    echo "$(date): $fn"
+    fn_stem=${fn%.csv}
     # run chexpert - must be run from chexpert folder
-    python $CHEXPERT_PATH/label.py  --verbose --reports_path $REPORT_PATH/$fn --output_path ${fn_stem}_labeled.csv --mention_phrases_dir $CHEXPERT_PATH/phrases/mention --unmention_phrases_dir $CHEXPERT_PATH/phrases/unmention --pre_negation_uncertainty_path $CHEXPERT_PATH/patterns/pre_negation_uncertainty.txt --negation_path $CHEXPERT_PATH/patterns/negation.txt --post_negation_uncertainty_path $CHEXPERT_PATH/patterns/post_negation_uncertainty.txt
-    echo `date`: done!
+    python "$CHEXPERT_PATH/label.py" --verbose \
+      --reports_path "$fn_path" \
+      --output_path "${fn_stem}_labeled.csv" \
+      --mention_phrases_dir "$CHEXPERT_PATH/phrases/mention" \
+      --unmention_phrases_dir "$CHEXPERT_PATH/phrases/unmention" \
+      --pre_negation_uncertainty_path "$CHEXPERT_PATH/patterns/pre_negation_uncertainty.txt" \
+      --negation_path "$CHEXPERT_PATH/patterns/negation.txt" \
+      --post_negation_uncertainty_path "$CHEXPERT_PATH/patterns/post_negation_uncertainty.txt"
+    echo "$(date): done!"
     echo ''
-done
+done

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

@@ -46,7 +46,7 @@ do
     # all intermediate files will be saved in this folder
     export OUTPUT_DIR=${INPUT_FILE::-4}
 
-    echo $OUTPUT_DIR - running NegBio..
+    echo "$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
@@ -57,7 +57,7 @@ do
 
     # ultimate filename we save the labels to
     export OUTPUT_LABELS=$OUTPUT_DIR/${fn::-4}_labels.csv
-    python $NEGBIO_PATH/negbio/ext/chexpert_collect_labels.py --phrases_file $NEGBIO_PATH/patterns/chexpert_phrases.yml --output $OUTPUT_LABELS $OUTPUT_DIR/neg/*
+    python "$NEGBIO_PATH/negbio/ext/chexpert_collect_labels.py" --phrases_file "$NEGBIO_PATH/patterns/chexpert_phrases.yml" --output "$OUTPUT_LABELS" "$OUTPUT_DIR"/neg/*
   fi
 done
 echo "Done looping through files."