More JsonUtil additions and forbidden Json.* calls

src/main/java/edu/harvard/iq/dataverse/DatasetFieldServiceBean.java

@@ -2,7 +2,6 @@
 
 import edu.harvard.iq.dataverse.dataset.DatasetType;
 import java.io.IOException;
-import java.io.StringReader;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URLEncoder;
@@ -24,13 +23,11 @@
 import jakarta.ejb.EJB;
 import jakarta.ejb.Stateless;
 import jakarta.inject.Named;
-import jakarta.json.Json;
 import jakarta.json.JsonArray;
 import jakarta.json.JsonArrayBuilder;
 import jakarta.json.JsonException;
 import jakarta.json.JsonObject;
 import jakarta.json.JsonObjectBuilder;
-import jakarta.json.JsonReader;
 import jakarta.json.JsonString;
 import jakarta.json.JsonValue;
 import jakarta.json.JsonValue.ValueType;
@@ -299,8 +296,8 @@ public Map<Long, JsonObject> getCVocConf(boolean byTermUriField){
         cvocMapByTermUri=new HashMap<>();
         cvocFieldSet = new HashSet<>();
 
-        try (JsonReader jsonReader = Json.createReader(new StringReader(settingsService.getValueForKey(SettingsServiceBean.Key.CVocConf)))) {
-            JsonArray cvocConfJsonArray = jsonReader.readArray();
+        try {
+            JsonArray cvocConfJsonArray = JsonUtil.getJsonArray(settingsService.getValueForKey(SettingsServiceBean.Key.CVocConf));
             for (JsonObject jo : cvocConfJsonArray.getValuesAs(JsonObject.class)) {
                 DatasetFieldType dft = findByNameOpt(jo.getString("field-name"));
                 if (dft == null) {
@@ -346,7 +343,7 @@ public Map<Long, JsonObject> getCVocConf(boolean byTermUriField){
                     }
                 }
             }
-            } catch(JsonException e) {
+        } catch(JsonException e) {
                 logger.warning("Ignoring External Vocabulary setting due to parsing error: " + e.getLocalizedMessage());
             }
         return byTermUriField ? cvocMapByTermUri : cvocMap;
@@ -480,8 +477,8 @@ public JsonObject getExternalVocabularyValue(String termUri) {
                             ExternalVocabularyValue.class)
                     .setParameter("uri", termUri).getSingleResult();
             String valString = evv.getValue();
-            try (JsonReader jr = Json.createReader(new StringReader(valString))) {
-                return jr.readObject();
+            try {
+                return JsonUtil.getJsonObject(valString);
             } catch (Exception e) {
                 logger.warning("Problem parsing external vocab value for uri: " + termUri + " : " + e.getMessage());
             }
@@ -583,8 +580,8 @@ public void process(HttpResponse response, HttpContext context) throws IOExcepti
                     int statusCode = response.getStatusLine().getStatusCode();
                     if (statusCode == 200) {
                         logger.fine("Returned data: " + data);
-                        try (JsonReader jsonReader = Json.createReader(new StringReader(data))) {
-                            String dataObj = filterResponse(cvocEntry, jsonReader.readObject(), term).toString();
+                        try {
+                            String dataObj = filterResponse(cvocEntry, JsonUtil.getJsonObject(data), term).toString();
                             evv.setValue(dataObj);
                             evv.setLastUpdateDate(Timestamp.from(Instant.now()));
                             logger.fine("JsonObject: " + dataObj);

src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java

@@ -52,6 +52,8 @@
 import java.util.Map;
 import java.util.Optional;
 import java.util.logging.Logger;
+
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import jakarta.ejb.EJB;
 import jakarta.ejb.EJBException;
 import jakarta.faces.application.FacesMessage;
@@ -1451,9 +1453,7 @@ public void handleDropBoxUpload(ActionEvent event) {
         // -----------------------------------------------------------
         // Read JSON object from the output of the DropBox Chooser: 
         // -----------------------------------------------------------
-        JsonReader dbJsonReader = Json.createReader(new StringReader(dropBoxSelection));
-        JsonArray dbArray = dbJsonReader.readArray();
-        dbJsonReader.close();
+        JsonArray dbArray = JsonUtil.getJsonArray(dropBoxSelection);
 
         // -----------------------------------------------------------
         // Iterate through the Dropbox file information (JSON)

src/main/java/edu/harvard/iq/dataverse/api/Admin.java

@@ -54,7 +54,6 @@
 import edu.harvard.iq.dataverse.engine.command.impl.AbstractSubmitToArchiveCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.PublishDataverseCommand;
 import edu.harvard.iq.dataverse.settings.Setting;
-import jakarta.json.Json;
 import jakarta.json.JsonArrayBuilder;
 import jakarta.json.JsonObjectBuilder;
 import jakarta.ws.rs.Consumes;
@@ -71,7 +70,6 @@
 import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
 
 import java.io.InputStream;
-import java.io.StringReader;
 import java.nio.charset.StandardCharsets;
 import java.util.Collections;
 import java.util.Map;
@@ -81,7 +79,6 @@
 import jakarta.ejb.EJB;
 import jakarta.ejb.Stateless;
 import jakarta.json.JsonObject;
-import jakarta.json.JsonReader;
 import jakarta.validation.ConstraintViolation;
 import jakarta.validation.ConstraintViolationException;
 import jakarta.ws.rs.Produces;
@@ -1612,9 +1609,7 @@ public Response startConfirmEmailProcess(@Parameter(description = "Authenticated
             description = "Rewrites a built-in user's password hash to the legacy SHA-1 test value.")
     public Response convertUserFromBcryptToSha1(@RequestBody(description = "JSON object containing builtinUserId.")
             String json) {
-        JsonReader jsonReader = Json.createReader(new StringReader(json));
-        JsonObject object = jsonReader.readObject();
-        jsonReader.close();
+        JsonObject object = JsonUtil.getJsonObject(json);
         BuiltinUser builtinUser = builtinUserService.find(new Long(object.getInt("builtinUserId")));
         builtinUser.updateEncryptedPassword("4G7xxL9z11/JKN4jHPn4g9iIQck=", 0); // password is "sha-1Pass", 0 means
                                                                                 // SHA-1

src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java

@@ -893,7 +893,7 @@ public Response updateInputLevels(@Context ContainerRequestContext crc,
             String jsonBody) {
         try {
             Dataverse dataverse = findDataverseOrDie(identifier);
-            List<DataverseFieldTypeInputLevel> newInputLevels = parseInputLevels(Json.createReader(new StringReader(jsonBody)).readArray(), dataverse);
+            List<DataverseFieldTypeInputLevel> newInputLevels = parseInputLevels(JsonUtil.getJsonArray(jsonBody), dataverse);
             execCommand(new UpdateDataverseInputLevelsCommand(dataverse, createDataverseRequest(getRequestUser(crc)), newInputLevels));
             return ok(BundleUtil.getStringFromBundle("dataverse.update.success"), JsonPrinter.json(dataverse));
         } catch (WrappedResponse e) {

src/main/java/edu/harvard/iq/dataverse/api/Files.java

@@ -158,8 +158,8 @@ public Response restrictFileInDataset(@Context ContainerRequestContext crc,
         if (restrictStr != null && restrictStr.trim().startsWith("{")) {
             // process as json
             jakarta.json.JsonObject jsonObject;
-            try (StringReader stringReader = new StringReader(restrictStr)) {
-                jsonObject = Json.createReader(stringReader).readObject();
+            try {
+                jsonObject = JsonUtil.getJsonObject(restrictStr);
                 if (jsonObject.containsKey("restrict")) {
                     restrict = Boolean.valueOf(jsonObject.getBoolean("restrict"));
                     returnMessage += restrict ? "restricted." : "unrestricted.";
@@ -1152,8 +1152,8 @@ public Response setFileCategories(@Context ContainerRequestContext crc,
         return response(req -> {
             DataFile dataFile = execCommand(new GetDataFileCommand(req, findDataFileOrDie(dataFileId)));
             jakarta.json.JsonObject jsonObject;
-            try (StringReader stringReader = new StringReader(jsonBody)) {
-                jsonObject = Json.createReader(stringReader).readObject();
+            try {
+                jsonObject = JsonUtil.getJsonObject(jsonBody);
                 JsonArray requestedCategoriesJson = jsonObject.getJsonArray("categories");
                 FileMetadata fileMetadata = dataFile.getFileMetadata();
                 if (replaceData) {
@@ -1190,8 +1190,8 @@ public Response setFileTabularTags(@Context ContainerRequestContext crc,
                 return badRequest(BundleUtil.getStringFromBundle("files.api.only.tabular.supported"));
             }
             jakarta.json.JsonObject jsonObject;
-            try (StringReader stringReader = new StringReader(jsonBody)) {
-                jsonObject = Json.createReader(stringReader).readObject();
+            try {
+                jsonObject = JsonUtil.getJsonObject(jsonBody);
                 JsonArray requestedTabularTagsJson = jsonObject.getJsonArray("tabularTags");
                 if (replaceData) {
                     dataFile.setTags(Lists.newArrayList());

src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java

@@ -15,14 +15,11 @@
 import jakarta.json.JsonObjectBuilder;
 import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
 import java.io.IOException;
-import java.io.StringReader;
 import java.util.List;
 import java.util.logging.Logger;
 import java.util.regex.Pattern;
 import jakarta.ejb.EJB;
 import jakarta.ejb.Stateless;
-import jakarta.json.Json;
-import jakarta.json.JsonReader;
 import jakarta.json.JsonArrayBuilder;
 import jakarta.json.JsonObject;
 import jakarta.ws.rs.DELETE;
@@ -145,13 +142,9 @@ public Response createOaiSet(@Context ContainerRequestContext crc,
             return badRequest(BundleUtil.getStringFromBundle("harvestserver.newSetDialog.setspec.superUser.required"));
         }
 
-        StringReader rdr = new StringReader(jsonBody);
-
-	try( JsonReader jrdr = Json.createReader(rdr) )
-	{
-		JsonObject json = jrdr.readObject();
+        JsonObject json = JsonUtil.getJsonObject(jsonBody);
 
-		OAISet set = new OAISet();
+        OAISet set = new OAISet();
 
 
 		String name, desc, defn;
@@ -194,8 +187,6 @@ public Response createOaiSet(@Context ContainerRequestContext crc,
 		set.setDefinition(defn);
 		oaiSetService.save(set);
 		return created("/harvest/server/oaisets" + name, oaiSetAsJson(set));
-	}
-
     }
 
     @PUT
@@ -221,11 +212,8 @@ public Response modifyOaiSet(@Context ContainerRequestContext crc,
             return badRequest(BundleUtil.getStringFromBundle("harvestserver.newSetDialog.setspec.superUser.required"));
         }
 
-        StringReader rdr = new StringReader(jsonBody);
-
-        try (JsonReader jrdr = Json.createReader(rdr)) {
-            JsonObject json = jrdr.readObject();
-            OAISet update;
+        JsonObject json = JsonUtil.getJsonObject(jsonBody);
+        OAISet update;
             //Validating spec 
             if (!StringUtils.isEmpty(spec)) {
                 update = oaiSetService.findBySpec(spec);
@@ -256,7 +244,6 @@ public Response modifyOaiSet(@Context ContainerRequestContext crc,
             update.setDefinition(defn);
             oaiSetService.save(update);
             return ok("/harvest/server/oaisets" + spec, oaiSetAsJson(update));
-        }
     }
 
     @DELETE

src/main/java/edu/harvard/iq/dataverse/api/Util.java

@@ -7,9 +7,9 @@
 import java.util.TimeZone;
 import java.util.TreeSet;
 import java.util.stream.Collectors;
-import jakarta.json.Json;
+
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import jakarta.json.JsonArray;
-import jakarta.json.JsonReader;
 
 public class Util {
 
@@ -30,9 +30,7 @@ public class Util {
     }
 
     static JsonArray asJsonArray( String str ) {
-        try ( JsonReader rdr = Json.createReader(new StringReader(str)) ) {
-            return rdr.readArray();
-        }
+        return JsonUtil.getJsonArray(str);
     }
 
     static boolean isBoolean( String s ) {

src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java

@@ -34,16 +34,15 @@
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import jakarta.ejb.EJB;
 import jakarta.ejb.EJBException;
 import jakarta.ejb.Stateless;
 import jakarta.inject.Named;
-import jakarta.json.Json;
 import javax.xml.stream.XMLStreamConstants;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
 import jakarta.json.JsonObject;
-import jakarta.json.JsonReader;
 import jakarta.persistence.EntityManager;
 import jakarta.persistence.NoResultException;
 import jakarta.persistence.PersistenceContext;
@@ -115,8 +114,7 @@ public void importXML(String xmlToParse, String foreignFormat, DatasetVersion da
             Gson gson = new Gson();
             String json = gson.toJson(datasetDTO.getDatasetVersion());
             logger.fine(json);
-            JsonReader jsonReader = Json.createReader(new StringReader(json));
-            JsonObject obj = jsonReader.readObject();
+            JsonObject obj = JsonUtil.getJsonObject(json);
             DatasetVersion dv = new JsonParser(datasetFieldSvc, blockService, settingsService, licenseService, datasetTypeService).parseDatasetVersion(obj, datasetVersion);
         } catch (XMLStreamException ex) {
             //Logger.getLogger("global").log(Level.SEVERE, null, ex);

src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java

@@ -7,11 +7,10 @@
 import edu.harvard.iq.dataverse.authorization.providers.shib.ShibUserNameFields;
 import edu.harvard.iq.dataverse.authorization.providers.shib.ShibUtil;
 import edu.harvard.iq.dataverse.util.BundleUtil;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import java.io.StringReader;
 import java.util.Collections;
-import jakarta.json.Json;
 import jakarta.json.JsonObject;
-import jakarta.json.JsonReader;
 
 /**
  * IDP adaptor for GitHub.com
@@ -36,11 +35,8 @@ public DefaultApi20 getApiInstance() {
 
     @Override
     protected ParsedUserResponse parseUserResponse( String responseBody ) {
-
-        try ( StringReader rdr = new StringReader(responseBody);
-              JsonReader jrdr = Json.createReader(rdr) )  {
-            JsonObject response = jrdr.readObject();
-            // Github has no concept of a family name
+        JsonObject response = JsonUtil.getJsonObject(responseBody);
+        // Github has no concept of a family name
             ShibUserNameFields shibUserNameFields = ShibUtil.findBestFirstAndLastName(null, null, response.getString("name",""));
             AuthenticatedUserDisplayInfo displayInfo = new AuthenticatedUserDisplayInfo(
                     shibUserNameFields.getFirstName(),
@@ -57,7 +53,5 @@ protected ParsedUserResponse parseUserResponse( String responseBody ) {
                     username,
                     displayInfo.getEmailAddress().length()>0 ? Collections.singletonList(displayInfo.getEmailAddress())
                                                              : Collections.emptyList() );
-        }
-
     }
 }

src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GoogleOAuth2AP.java

@@ -5,12 +5,10 @@
 import edu.harvard.iq.dataverse.authorization.AuthenticatedUserDisplayInfo;
 import edu.harvard.iq.dataverse.authorization.providers.oauth2.AbstractOAuth2AuthenticationProvider;
 import edu.harvard.iq.dataverse.util.BundleUtil;
-import java.io.StringReader;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import java.util.Arrays;
 import java.util.UUID;
-import jakarta.json.Json;
 import jakarta.json.JsonObject;
-import jakarta.json.JsonReader;
 
 /**
  *
@@ -36,11 +34,9 @@ public DefaultApi20 getApiInstance() {
 
     @Override
     protected ParsedUserResponse parseUserResponse(String responseBody) {
-        try ( StringReader rdr = new StringReader(responseBody);
-              JsonReader jrdr = Json.createReader(rdr) )  {
-            JsonObject response = jrdr.readObject();
-
-            AuthenticatedUserDisplayInfo displayInfo = new AuthenticatedUserDisplayInfo(
+        JsonObject response = JsonUtil.getJsonObject(responseBody);
+
+        AuthenticatedUserDisplayInfo displayInfo = new AuthenticatedUserDisplayInfo(
                     response.getString("given_name",""),
                     response.getString("family_name",""),
                     response.getString("email",""),
@@ -63,6 +59,5 @@ protected ParsedUserResponse parseUserResponse(String responseBody) {
                 }
             }
             return new ParsedUserResponse(displayInfo, persistentUserId, username);
-        }
     }
 }

src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/MicrosoftOAuth2AP.java

@@ -7,10 +7,8 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.logging.Logger;
-import java.io.StringReader;
-import jakarta.json.Json;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import jakarta.json.JsonObject;
-import jakarta.json.JsonReader;
 import edu.harvard.iq.dataverse.authorization.AuthenticatedUserDisplayInfo;
 
 /**
@@ -37,10 +35,8 @@ public DefaultApi20 getApiInstance(){
 
     @Override
     protected ParsedUserResponse parseUserResponse(final String responseBody) {
-        try ( StringReader rdr = new StringReader(responseBody);
-              JsonReader jrdr = Json.createReader(rdr) )  {
-            JsonObject response = jrdr.readObject();
-            AuthenticatedUserDisplayInfo displayInfo = new AuthenticatedUserDisplayInfo(
+        JsonObject response = JsonUtil.getJsonObject(responseBody);
+        AuthenticatedUserDisplayInfo displayInfo = new AuthenticatedUserDisplayInfo(
                     response.getString("givenName", ""),
                     response.getString("surname", ""),
                     response.getString("userPrincipalName", ""),
@@ -50,7 +46,6 @@ protected ParsedUserResponse parseUserResponse(final String responseBody) {
             return new ParsedUserResponse(displayInfo, persistentUserId, username,
                     (displayInfo.getEmailAddress().length() > 0 ? Collections.singletonList(displayInfo.getEmailAddress()) : Collections.emptyList() )
             );
-        }
     }
 
     public boolean isDisplayIdentifier()