Initialize Gson with custom Instance serializer

Since Instant is immutable in Java 17, we need to implement serialize and de-serialize methods to convert Instant object into gson.

src/main/java/org/mskcc/oncokb/curation/service/EnsemblService.java

@@ -9,6 +9,7 @@
 import org.json.JSONException;
 import org.json.JSONObject;
 import org.mskcc.oncokb.curation.domain.enumeration.ReferenceGenome;
+import org.mskcc.oncokb.curation.util.GsonUtils;
 import org.mskcc.oncokb.curation.vm.ensembl.EnsemblArchiveId;
 import org.mskcc.oncokb.curation.vm.ensembl.EnsemblSequence;
 import org.mskcc.oncokb.curation.vm.ensembl.EnsemblTranscript;
@@ -162,7 +163,7 @@ public List<org.mskcc.oncokb.curation.vm.ensembl.EnsemblArchiveId> getArchiveIds
 
         RestTemplate restTemplate = new RestTemplate();
         String response = restTemplate.postForObject(getArchiveIdPOSTUrl(referenceGenome), entity, String.class);
-        Gson gson = new Gson();
+        Gson gson = GsonUtils.create();
         Type type = new TypeToken<Map<String, EnsemblArchiveId>>() {}.getType();
         Map<String, org.mskcc.oncokb.curation.vm.ensembl.EnsemblArchiveId> archiveMap = gson.fromJson(response, type);
         return archiveMap.values().stream().filter(val -> val != null).collect(Collectors.toList());
@@ -207,9 +208,8 @@ public List<org.mskcc.oncokb.curation.vm.ensembl.EnsemblTranscript> getIds(
         try {
             RestTemplate restTemplate = new RestTemplate();
             String response = restTemplate.postForObject(getLookupPOSTUrl(referenceGenome, includeUtr, expand), entity, String.class);
-            Gson gson = new Gson();
             Type type = new TypeToken<Map<String, EnsemblTranscript>>() {}.getType();
-            Map<String, org.mskcc.oncokb.curation.vm.ensembl.EnsemblTranscript> transcriptMap = gson.fromJson(response, type);
+            Map<String, org.mskcc.oncokb.curation.vm.ensembl.EnsemblTranscript> transcriptMap = GsonUtils.create().fromJson(response, type);
             return transcriptMap.values().stream().filter(val -> val != null).collect(Collectors.toList());
         } catch (Exception e) {
             log.error(e.getMessage());

src/main/java/org/mskcc/oncokb/curation/service/dto/pubmed/PubMedDTO.java

@@ -1,7 +1,6 @@
 package org.mskcc.oncokb.curation.service.dto.pubmed;
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.google.gson.Gson;
 import java.io.Serializable;
 import java.time.Instant;
 import java.util.HashSet;
@@ -10,6 +9,7 @@
 import org.mskcc.oncokb.curation.domain.Flag;
 import org.mskcc.oncokb.curation.domain.Synonym;
 import org.mskcc.oncokb.curation.domain.enumeration.ArticleType;
+import org.mskcc.oncokb.curation.util.GsonUtils;
 
 public class PubMedDTO implements Serializable {
 
@@ -136,7 +136,7 @@ public PubMedDTO(Article article) {
         this.link = article.getLink();
         this.authors = article.getAuthors();
         this.date = article.getDate();
-        this.additionalInfo = new Gson().fromJson(article.getAdditionalInfo(), AdditionalInfoDTO.class);
+        this.additionalInfo = GsonUtils.create().fromJson(article.getAdditionalInfo(), AdditionalInfoDTO.class);
         this.flags = article.getFlags();
         this.synonyms = article.getSynonyms();
     }

src/main/java/org/mskcc/oncokb/curation/service/mapper/PubMedMapper.java

@@ -1,11 +1,11 @@
 package org.mskcc.oncokb.curation.service.mapper;
 
-import com.google.gson.Gson;
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;
 import org.mskcc.oncokb.curation.domain.Article;
 import org.mskcc.oncokb.curation.service.dto.pubmed.PubMedDTO;
+import org.mskcc.oncokb.curation.util.GsonUtils;
 import org.springframework.stereotype.Service;
 
 /**
@@ -42,7 +42,7 @@ public Article pubMedDTOToArticle(PubMedDTO pubMedDTO) {
             article.setLink(pubMedDTO.getLink());
             article.setDate(pubMedDTO.getDate());
             article.setAuthors(pubMedDTO.getAuthors());
-            article.setAdditionalInfo(new Gson().toJson(pubMedDTO.getAdditionalInfo()));
+            article.setAdditionalInfo(GsonUtils.create().toJson(pubMedDTO.getAdditionalInfo()));
             article.setFlags(pubMedDTO.getFlags());
             article.setSynonyms(pubMedDTO.getSynonyms());
             return article;

src/main/java/org/mskcc/oncokb/curation/util/GsonUtils.java

@@ -0,0 +1,14 @@
+package org.mskcc.oncokb.curation.util;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import java.time.Instant;
+import org.mskcc.oncokb.curation.config.InstantTypeAdapter;
+
+public class GsonUtils {
+
+    public static Gson create() {
+        // https://medium.com/@pratiktikarye/instant-to-gson-conversion-in-java-17-2673bb59fbea
+        return new GsonBuilder().registerTypeAdapter(Instant.class, new InstantTypeAdapter()).create();
+    }
+}