Japanese translation (#76)

* Adding pilot Japanese translation

* Adding pilot Japanese translation

* new HPO contains portuguese, fixed code so it does not output error. In Japanese it said the instructions were given in German, probably a copy paste error, fixed

* got rid of leftover German translations using DeepL

---------

Co-authored-by: Leonardo macOS <[email protected]>

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>org.monarchinitiative</groupId>
     <artifactId>phenopacket2prompt</artifactId>
-    <version>0.4.6</version>
+    <version>0.4.7</version>
 
     <name>phenopacket2prompt</name>
     <url>https://github.com/monarch-initiative/phenopacket2prompt</url>

src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/BatchMineCommand.java

@@ -15,7 +15,6 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
-import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.List;
@@ -49,7 +48,7 @@ public class BatchMineCommand implements Callable<Integer> {
 
 
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
         File inDirectory = new File(input);
         if (!inDirectory.isDirectory()) {
             throw new PhenolRuntimeException("Could not find directory at " + input);

src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/GbtTranslateBatchCommand.java

@@ -42,7 +42,7 @@ public class GbtTranslateBatchCommand implements Callable<Integer> {
 
 
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
         File hpJsonFile = new File(hpoJsonPath);
         boolean useExactMatching = true;
         if (! hpJsonFile.isFile()) {
@@ -107,6 +107,13 @@ public Integer call() throws Exception {
         Utility.writeMissingTranslations(chinese.getMissingTranslations(),
                 missingTranslationsPath, "chinese.txt");
 
+        // Japanese
+        // Note official two-letter language code for Japanese is JP, but our files have JA
+        PromptGenerator japanese = utility.japanese();
+        Utility.outputPromptsInternational(ppktFiles,"ja", japanese);
+        Utility.writeMissingTranslations(japanese.getMissingTranslations(),
+                missingTranslationsPath, "japanese.txt");
+
         // output original phenopackets
         PpktCopy pcopy = new PpktCopy(new File(outdirname));
         for (var file : ppktFiles) {

src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/GptTranslateCommand.java

@@ -45,7 +45,7 @@ public class GptTranslateCommand implements Callable<Integer> {
 
 
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
         File hpJsonFile = new File(hpoJsonPath);
         if (! hpJsonFile.isFile()) {
             throw new PhenolRuntimeException("Could not find hp.json at " + hpJsonFile.getAbsolutePath());
@@ -84,6 +84,11 @@ public Integer call() throws Exception {
                 PromptGenerator italian = PromptGenerator.italian(internationalMap.get("it"));
                 prompt = italian.createPrompt(individual);
             }
+            case "jp" -> {
+                // Note the official code for Japanese is jp, but our files have ja
+                PromptGenerator japanese = PromptGenerator.japanese(internationalMap.get("ja"));
+                prompt = japanese.createPrompt(individual);
+            }
             case "tr" -> {
                 PromptGenerator turkish = PromptGenerator.turkish(internationalMap.get("tr"));
                 prompt = turkish.createPrompt(individual);

src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/TestDriveCommand.java

@@ -346,15 +346,21 @@ public Integer call() {
         sb.append("German\n");
         sb.append(HEADER_LINE);
         sb.append(deText);
+        // ITALIAN
         String itText = createPrompts(individualList, utility.italian());
         sb.append("Italian\n");
         sb.append(HEADER_LINE);
         sb.append(itText);
-        // ITALIAN
+        // Turkish
         String trText = createPrompts(individualList, utility.turkish());
         sb.append("Turkish\n");
         sb.append(HEADER_LINE);
         sb.append(trText);
+        // Japanese
+        String jpText = createPrompts(individualList, utility.japanese());
+        sb.append("Japanese");
+        sb.append(HEADER_LINE);
+        sb.append(jpText);
         System.out.println(sb);
         System.out.println("Wrote to " + outfileName);
         try {

src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/TextMineCommand.java

@@ -34,7 +34,7 @@ public class TextMineCommand implements Callable<Integer> {
 
 
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
         LOGGER.info("TextMine command, input = {}", input);
         File hpoJsonFile = new File(datadir + File.separator + "hp.json");
         if (! hpoJsonFile.isFile()) {

src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/Utility.java

@@ -66,6 +66,10 @@ public PromptGenerator chinese() {
         return PromptGenerator.chinese(internationalMap.get("zh"));
     }
 
+    public PromptGenerator japanese() {
+        return PromptGenerator.japanese(internationalMap.get("ja"));
+    }
+
     public PromptGenerator czech() {
         return PromptGenerator.czech(internationalMap.get("cs"));
     }

src/main/java/org/monarchinitiative/phenopacket2prompt/international/HpInternationalOboParser.java

@@ -42,7 +42,7 @@ public static Optional<String> getLanguage(String annots) {
     public HpInternationalOboParser(File file) {
         languageToInternationalMap = new HashMap<>();
         String pattern = "id: (HP:\\d{7,7})";
-        Set<String> acronyms = Set.of("cs", "en", "de", "dtp", "it", "es", "fr", "ja", "nl", "nna", "tr", "tw", "zh");
+        Set<String> acronyms = Set.of("cs", "en", "de", "dtp", "es", "fr", "it", "ja", "nl", "nna", "pt", "tr", "tw", "zh");
         for (String acronym : acronyms) {
             languageToInternationalMap.put(acronym, new HpInternational(acronym));
         }

src/main/java/org/monarchinitiative/phenopacket2prompt/output/PromptGenerator.java

@@ -10,6 +10,8 @@
 import org.monarchinitiative.phenopacket2prompt.output.impl.english.EnglishPromptGenerator;
 import org.monarchinitiative.phenopacket2prompt.output.impl.german.GermanPromptGenerator;
 import org.monarchinitiative.phenopacket2prompt.output.impl.german.PpktPhenotypicfeatureGerman;
+import org.monarchinitiative.phenopacket2prompt.output.impl.japanese.JapanesePromptGenerator;
+import org.monarchinitiative.phenopacket2prompt.output.impl.japanese.PpktPhenotypicfeatureJapanese;
 import org.monarchinitiative.phenopacket2prompt.output.impl.spanish.*;
 import org.monarchinitiative.phenopacket2prompt.output.impl.dutch.*;
 import org.monarchinitiative.phenopacket2prompt.output.impl.italian.*;
@@ -65,6 +67,11 @@ static PromptGenerator italian(HpInternational international) {
         return new ItalianPromptGenerator(pfgen);
     }
 
+    static PromptGenerator japanese(HpInternational international) {
+        PpktPhenotypicFeatureGenerator pfgen = new PpktPhenotypicfeatureJapanese(international);
+        return new JapanesePromptGenerator(pfgen);
+    }
+
     static PromptGenerator turkish(HpInternational international) {
         PpktPhenotypicFeatureGenerator pfgen = new PpktPhenotypicfeatureTurkish(international);
         return new TurkishPromptGenerator(pfgen);

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/chinese/ChineseBuildingBlocks.java

@@ -49,7 +49,7 @@ public String monthDayOld(int m, int d) {
         if (components.isEmpty()) {
             return "自出生起";
         } else if (components.size() == 1) {
-            return components.get(0);
+            return components.getFirst();
         } else {
             return String.format("%s%s大时", components.get(0), components.get(1));
         }
@@ -70,7 +70,7 @@ public String yearsMonthsDaysOld(int y, int m, int d) {
         if (components.isEmpty()) {
             return "自出生起";
         } else if (components.size() == 1) {
-            return components.get(0);
+            return components.getFirst();
         } else if (components.size() == 2) {
             return String.format("%s%s大时", components.get(0), components.get(1));
         } else {

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/chinese/PpktIndividualChinese.java

@@ -112,7 +112,7 @@ private String ymd(Iso8601Age iso8601Age) {
         if (components.isEmpty()) {
             return "刚出生";
         } else if (components.size() == 1) {
-            return components.get(0);
+            return components.getFirst();
         } else if (components.size() == 2) {
             return String.format("%s%s大", components.get(0), components.get(1));
         } else {

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/chinese/PpktPhenotypicfeatureChinese.java

@@ -52,7 +52,7 @@ private String getCommaList(List<String> items) {
         String penultimate = items.stream()
                 .limit(items.size() - 1)
                 .collect(Collectors.joining(","));
-        String ultimate = items.get(items.size() - 1);
+        String ultimate = items.getLast();
         return penultimate + "和" + ultimate;
     }
 

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/dutch/PpktPhenotypicFeatureDutch.java

@@ -52,7 +52,7 @@ private String getCommaList(List<String> items) {
         String penultimate = items.stream()
                 .limit(items.size() - 1)
                 .collect(Collectors.joining(", "));
-        String ultimate = items.get(items.size() - 1);
+        String ultimate = items.getLast();
         return penultimate + " en " + ultimate;
     }
 

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/german/GermanBuildingBlocks.java

@@ -49,7 +49,7 @@ public String monthDayOld(int m, int d) {
         if (components.isEmpty()) {
             return "am ersten Lebenstag";
         } else if (components.size() == 1) {
-            return components.get(0);
+            return components.getFirst();
         } else {
             return String.format("im Alter von %s und %s", components.get(0), components.get(1));
         }
@@ -70,7 +70,7 @@ public String yearsMonthsDaysOld(int y, int m, int d) {
         if (components.isEmpty()) {
             return "am ersten Lebenstag";
         } else if (components.size() == 1) {
-            return components.get(0);
+            return components.getFirst();
         } else if (components.size() == 2) {
             return String.format("im Alter von %s und %s", components.get(0), components.get(1));
         } else {

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/german/PpktIndividualGerman.java

@@ -294,7 +294,7 @@ private String dAlter(Iso8601Age iso8601Age, GrammatikalischesGeschlecht geschle
         if (components.isEmpty()) {
             ymd = "";
         } else if (components.size() == 1) {
-            ymd = components.get(0);
+            ymd = components.getFirst();
         } else if (components.size() == 2) {
             ymd = String.format("%s und %s", components.get(0), components.get(1));
         } else {

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/german/PpktPhenotypicfeatureGerman.java

@@ -52,7 +52,7 @@ private String getCommaList(List<String> items) {
         String penultimate = items.stream()
                 .limit(items.size() - 1)
                 .collect(Collectors.joining(", "));
-        String ultimate = items.get(items.size() - 1);
+        String ultimate = items.getLast();
         return penultimate + " und " + ultimate;
     }
 

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/italian/PpktIndividualItalian.java

@@ -115,7 +115,7 @@ private String ymd(Iso8601Age iso8601Age) {
         if (components.isEmpty()) {
             return "nel primo giorno di vita";
         } else if (components.size() == 1) {
-            return components.get(0);
+            return components.getFirst();
         } else if (components.size() == 2) {
             return String.format("all'età di %s y %s", components.get(0), components.get(1));
         } else {

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/italian/PpktPhenotypicfeatureItalian.java

@@ -65,7 +65,7 @@ private String getCommaList(List<String> items) {
         String penultimate = items.stream()
                 .limit(items.size() - 1)
                 .collect(Collectors.joining(", "));
-        String ultimate = items.get(items.size() - 1);
+        String ultimate = items.getLast();
         return penultimate + getConnector(ultimate) + ultimate;
     }