All working, able to be built to .jar

src/main/java/PlateFileReader.java

@@ -0,0 +1,61 @@
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVParser;
+import org.apache.commons.csv.CSVRecord;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.sql.Array;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
+public class PlateFileReader {
+
+    private List<List<Integer[]>> wells = new ArrayList<>();
+
+    public PlateFileReader(String filename){
+
+        if(!filename.matches(".*\\.csv")){
+            filename = filename + ".csv";
+        }
+
+        CSVFormat plateFileFormat = CSVFormat.Builder.create()
+                .setCommentMarker('#')
+                .build();
+
+        try(//don't need to close reader bc of try-with-resources auto-closing
+            BufferedReader reader = Files.newBufferedReader(Path.of(filename));
+            CSVParser parser = new CSVParser(reader, plateFileFormat);
+        ){
+            for(CSVRecord record: parser.getRecords()) {
+                List<Integer[]> well = new ArrayList<>();
+                for(String s: record) {
+                    if(!"".equals(s)) {
+                        String[] intString = s.replaceAll("\\[", "")
+                                .replaceAll("]", "")
+                                .replaceAll(" ", "")
+                                .split(",");
+                        //System.out.println(intString);
+                        Integer[] arr = new Integer[intString.length];
+                        for (int i = 0; i < intString.length; i++) {
+                            arr[i] = Integer.valueOf(intString[i]);
+                        }
+                        well.add(arr);
+                    }
+                }
+                wells.add(well);
+            }
+        } catch(IOException ex){
+            System.out.println("plate file " + filename + " not found.");
+            System.err.println(ex);
+        }
+
+    }
+
+    public List<List<Integer[]>> getWells() {
+        return wells;
+    }
+
+}