Minor cleaning and streamlining

src/main/java/nl/fairbydesign/backend/ncbi/NCBI_Matrices.java

@@ -16,81 +16,9 @@ import java.time.format.DateTimeFormatter;
 import java.util.*;
 
 public class NCBI_Matrices {
-    static String newline = System.getProperty("line.separator");
     static String startTime = LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd_HH-mm-ss"));
     static String targetDir = "./json/all";
 
-    @Test
-    public void sampleAttributeValueCount() throws IOException {
-        File root = new File(targetDir+"/fetch");
-        Map<String, Map<String, Integer>> SAMap = new HashMap<>();
-        int fileCounter = 0;
-
-        for (File dir : Objects.requireNonNull(root.listFiles())) {
-            for (File bpFile : Objects.requireNonNull(dir.listFiles())) {
-                fileCounter++;
-
-                JsonFactory jsonFactory = new MappingJsonFactory();
-                JsonParser jsonParser = jsonFactory.createParser(bpFile);
-                JsonToken current = jsonParser.nextToken();
-
-                if (current != JsonToken.START_OBJECT) {
-                    System.out.println("ERROR: root should be object: quiting.");
-                    return;
-                }
-
-                while (jsonParser.nextToken() != null) {
-                    String fieldName = jsonParser.getCurrentName();
-                    current = jsonParser.nextToken();
-                    if (Objects.equals(fieldName, "SAMPLE_ATTRIBUTE")) {
-                        if (current == JsonToken.START_ARRAY) {
-                            while (jsonParser.nextToken() != JsonToken.END_ARRAY) {
-                                SAVCAppendMap(SAMap, jsonParser.readValueAsTree());
-                            }
-                        } else if (current == JsonToken.START_OBJECT) {
-                            SAVCAppendMap(SAMap, jsonParser.readValueAsTree());
-                        } else if (current != JsonToken.END_ARRAY && current != JsonToken.END_OBJECT) {
-                            System.out.println("Error: " + current.name() + " in " + jsonParser.getCurrentName() + ": skipping to next in file: " + bpFile.getAbsolutePath());
-                            jsonParser.skipChildren();
-                        }
-//                    } else {
-//                        System.out.println("Unprocessed property: " + fieldName);
-                    }
-                }
-            }
-        }
-        String dir = targetDir+"/parsings";
-        boolean isDirCreated = new File(dir).exists() || new File(dir).mkdirs();
-        PrintWriter writer = new PrintWriter(new FileWriter(dir+"/sampleAttributeValueCount"+startTime+".txt"));
-        System.out.println("Processed " + fileCounter + " files.");
-        for (Map.Entry<String, Map<String, Integer>> tag : SAMap.entrySet()) {
-            System.out.println(tag.getKey() + " => ");
-            writer.println(tag.getKey() + " => ");
-            for (Map.Entry<String, Integer> entry : tag.getValue().entrySet()) {
-                System.out.println("\t" + entry.getKey() + " => " + entry.getValue());
-                writer.println("\t" + entry.getKey() + " => " + entry.getValue());
-            }
-        }
-        writer.close();
-    }
-
-    private void SAVCAppendMap(Map<String, Map<String, Integer>> SAMap, JsonNode jsonNode) {
-        String tag = jsonNode.get("TAG").asText();
-        String value = jsonNode.get("VALUE").asText();
-
-        Map<String, Integer> values = SAMap.get(tag);
-        if (values == null) {
-            values = new HashMap<>();
-            values.put(value, 1);
-            SAMap.put(tag, values);
-        } else if (SAMap.get(tag).get(value) == null) {
-            SAMap.get(tag).put(value, 1);
-        } else {
-            Integer count = SAMap.get(tag).get(value);
-            SAMap.get(tag).put(value, ++count);
-        }
-    }
-
     @Test
     public void attributeAbundanceMatrix() throws IOException {
         File root = new File(targetDir+"/fetch");

src/main/java/nl/fairbydesign/backend/ncbi/NCBI_NLP.java

@@ -8,8 +8,6 @@ import org.apache.commons.io.FileUtils;
 import org.junit.Test;
 
 import java.io.*;
-import java.time.LocalDateTime;
-import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Scanner;
 import java.util.regex.Matcher;
@@ -18,7 +16,7 @@ import java.util.regex.Pattern;
 public class NCBI_NLP {
 
     @Test
-    public void cleanInput() throws IOException {
+    public void cleanInput() {
         File file = new File("./nlp/Input/AllAttributes_Raw.txt");
         ArrayList<String> list = new ArrayList<>();
         Pattern pattern = Pattern.compile("[^a-zA-Z\\d\\s]|\\s\\S\\s|\\s\\S$|^\\S\\s|\\s+");
@@ -39,7 +37,14 @@ public class NCBI_NLP {
         }
 
         File outputFile = new File("./nlp/Output/AllAttributes_Processed.txt");
-        FileUtils.writeLines(outputFile, list, false);
+        try {
+            FileUtils.writeLines(outputFile, list, false);
+        } catch (IOException e) {
+            System.out.println(e +"\nFailed to save results to file, see error message above.\nResults are instead provided below:\n");
+            for (String line : list) {
+                System.out.println(line);
+            }
+        }
     }
 
     @Test