Empty fields in CSV

CHANGELOG.md

@@ -13,6 +13,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Functional testing framework with concrete tests for `methods.set_env()`
 - Functional test for `bam_parser.parse_bam_header()`.
 - Dump parameters with `json_extractor.store_params_json()`
+- Option to allow empty fields in a CSV to be parsed without error
 - Function to save process logs, even after failure
 
 ### Fixed

config/csv/csv_parser.config

@@ -24,11 +24,14 @@ csv_parser {
     *   Split each line and parse contents into Map.
     *   @throws IllegalArgumentException when a field is missing from a single line.
     */
-    parse_line = { String line, Map field_indices ->
+    parse_line = { String line, Map field_indices, Boolean allow_empty ->
         def line_parts = line.split(',') as List
         def line_fields = [:]
         field_indices.each { field, index ->
             line_fields[field] = line_parts[index]
+            if (allow_empty) {
+                return
+            }
             if (!line_fields[field]) {
                 throw new IllegalArgumentException("Field: ${field} not found for line: ${line}")
             }
@@ -40,15 +43,15 @@ csv_parser {
     /**
     *   Main parsing function for calling. Returns parsed data as a list of Maps.
     */
-    parse_csv = { String csv_file, List fields ->
+    parse_csv = { String csv_file, List fields, Boolean allow_empty=false ->
         def reader = new BufferedReader(new FileReader(csv_file))
         def header = reader.readLine()
         def field_indices = csv_parser.get_field_indices(header, fields)
 
         def parsed_lines = []
         def line = ''
         while ( (line = reader.readLine()) != null ) {
-            parsed_lines.add(csv_parser.parse_line(line, field_indices))
+            parsed_lines.add(csv_parser.parse_line(line, field_indices, allow_empty))
         }
 
         return parsed_lines