Logging upgraded and bug fixed

container_run.sh

@@ -5,15 +5,27 @@ mkdir /common
 mkdir /common/processed_ttl
 
 for archive in "${archives[@]}"; do
-    mkdir /home/output_ttl_files/$archive
+    archive_dir=/home/output_ttl_files/$archive
+    if [ ! -d "$archive_dir" ]; then
+        mkdir $archive_dir
+    fi
     for dir in "/input_pdf_files/$archive"/*; do
         if [ -d "$dir" ]; then
-            mkdir /home/output_ttl_files/$archive/$(basename "$dir")
+            volume_dir=/home/output_ttl_files/$archive/$(basename "$dir")
+            if [ ! -d "$volume_dir" ]; then
+                mkdir $volume_dir
+            fi
             for file in "$dir"/*; do
                 if [ -f "$file" ]; then
                     cp "$file" /common/$(basename "$file" .pdf).pdf
                     bash ./run.sh /common/$(basename "$file" .pdf).pdf
-                    cp /common/processed_ttl/$(basename "$file" .pdf | tr '[:upper:]' '[:lower:]' | tr -d '_').ttl /home/output_ttl_files/$archive/$(basename "$dir")/$(basename "$file" .pdf).ttl
+                    final_basename=$(basename "$file" .pdf | tr '[:upper:]' '[:lower:]' | tr -d '_')
+                    if [ -e "/common/processed_ttl/$final_basename.ttl" ]; then
+                        cp /common/processed_ttl/$final_basename.ttl /home/output_ttl_files/$archive/$(basename "$dir")/$(basename "$file" .pdf).ttl
+                    else
+                        echo "Grobid failed with scraping file, information from it will be skipped"
+                    fi
+
                 fi
             done
         fi