Use JsonUtil.getJsonObject in AbstractApiBean, MakeDataCountApi

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

@@ -47,9 +47,9 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 import edu.harvard.iq.dataverse.util.json.JsonParser;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
 import edu.harvard.iq.dataverse.validation.PasswordValidatorServiceBean;
-import java.io.StringReader;
 import java.net.URI;
 import java.util.Arrays;
 import java.util.Collections;
@@ -62,9 +62,9 @@
 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.JsonValue;
 import jakarta.json.JsonValue.ValueType;
 import jakarta.persistence.EntityManager;
@@ -132,23 +132,21 @@ public Response refineResponse( String message ) {
          * In the common case of the wrapped response being of type JSON,
          * return the message field it has (if any).
          * @return the content of a message field, or {@code null}.
+         * @throws JsonException when JSON parsing fails.
          */
         String getWrappedMessageWhenJson() {
             if ( response.getMediaType().equals(MediaType.APPLICATION_JSON_TYPE) ) {
                 Object entity = response.getEntity();
                 if ( entity == null ) return null;
 
-                String json = entity.toString();
-                try ( StringReader rdr = new StringReader(json) ){
-                    JsonReader jrdr = Json.createReader(rdr);
-                    JsonObject obj = jrdr.readObject();
-                    if ( obj.containsKey("message") ) {
-                        JsonValue message = obj.get("message");
-                        return message.getValueType() == ValueType.STRING ? obj.getString("message") : message.toString();
-                    } else {
-                        return null;
-                    }
+                JsonObject obj = JsonUtil.getJsonObject(entity.toString());
+                if ( obj.containsKey("message") ) {
+                    JsonValue message = obj.get("message");
+                    return message.getValueType() == ValueType.STRING ? obj.getString("message") : message.toString();
+                } else {
+                    return null;
                 }
+
             } else {
                 return null;
             }

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

@@ -8,11 +8,10 @@
 import edu.harvard.iq.dataverse.makedatacount.DatasetMetricsServiceBean;
 import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.util.SystemConfig;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 
-import java.io.FileReader;
 import java.io.IOException;
 import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Iterator;
 import java.util.List;
@@ -83,26 +82,21 @@ public Response sendDataToHub() {
     @Path("{id}/addUsageMetricsFromSushiReport")
     public Response addUsageMetricsFromSushiReport(@PathParam("id") String id, @QueryParam("reportOnDisk") String reportOnDisk) {
 
-        JsonObject report;
-
-        try (FileReader reader = new FileReader(reportOnDisk)) {
-            report = Json.createReader(reader).readObject();
-            Dataset dataset;
-            try {
-                dataset = findDatasetOrDie(id);
-                List<DatasetMetrics> datasetMetrics = datasetMetricsService.parseSushiReport(report, dataset);
-                if (!datasetMetrics.isEmpty()) {
-                    for (DatasetMetrics dm : datasetMetrics) {
-                        datasetMetricsService.save(dm);
-                    }
+        try {
+            JsonObject report = JsonUtil.getJsonObjectFromFile(reportOnDisk);
+            Dataset dataset = findDatasetOrDie(id);
+            List<DatasetMetrics> datasetMetrics = datasetMetricsService.parseSushiReport(report, dataset);
+            if (!datasetMetrics.isEmpty()) {
+                for (DatasetMetrics dm : datasetMetrics) {
+                    datasetMetricsService.save(dm);
                 }
-            } catch (WrappedResponse ex) {
-                Logger.getLogger(MakeDataCountApi.class.getName()).log(Level.SEVERE, null, ex);
-                return error(Status.BAD_REQUEST, "Wrapped response: " + ex.getLocalizedMessage());
             }
+        } catch (WrappedResponse ex) {
+            logger.log(Level.SEVERE, null, ex);
+            return error(Status.BAD_REQUEST, "Wrapped response: " + ex.getLocalizedMessage());
 
         } catch (IOException ex) {
-            System.out.print(ex.getMessage());
+            logger.log(Level.WARNING, ex.getMessage());
             return error(Status.BAD_REQUEST, "IOException: " + ex.getLocalizedMessage());
         }
         String msg = "Dummy Data has been added to dataset " + id;
@@ -113,10 +107,8 @@ public Response addUsageMetricsFromSushiReport(@PathParam("id") String id, @Quer
     @Path("/addUsageMetricsFromSushiReport")
     public Response addUsageMetricsFromSushiReportAll(@PathParam("id") String id, @QueryParam("reportOnDisk") String reportOnDisk) {
 
-        JsonObject report;
-
-        try (FileReader reader = new FileReader(reportOnDisk)) {
-            report = Json.createReader(reader).readObject();
+        try {
+            JsonObject report = JsonUtil.getJsonObjectFromFile(reportOnDisk);
 
             List<DatasetMetrics> datasetMetrics = datasetMetricsService.parseSushiReport(report, null);
             if (!datasetMetrics.isEmpty()) {
@@ -126,7 +118,7 @@ public Response addUsageMetricsFromSushiReportAll(@PathParam("id") String id, @Q
             }
 
         } catch (IOException ex) {
-            System.out.print(ex.getMessage());
+            logger.log(Level.WARNING, ex.getMessage());
             return error(Status.BAD_REQUEST, "IOException: " + ex.getLocalizedMessage());
         }
         String msg = "Usage Metrics Data has been added to all datasets from file  " + reportOnDisk;
@@ -135,7 +127,7 @@ public Response addUsageMetricsFromSushiReportAll(@PathParam("id") String id, @Q
 
     @POST
     @Path("{id}/updateCitationsForDataset")
-    public Response updateCitationsForDataset(@PathParam("id") String id) throws MalformedURLException, IOException {
+    public Response updateCitationsForDataset(@PathParam("id") String id) throws IOException {
         try {
             Dataset dataset = findDatasetOrDie(id);
             String persistentId = dataset.getGlobalId().toString();
@@ -158,7 +150,7 @@ public Response updateCitationsForDataset(@PathParam("id") String id) throws Mal
                     logger.warning("Failed to get citations from " + url.toString());
                     return error(Status.fromStatusCode(status), "Failed to get citations from " + url.toString());
                 }
-                JsonObject report = Json.createReader(connection.getInputStream()).readObject();
+                JsonObject report = JsonUtil.getJsonObject(connection.getInputStream());
                 JsonObject links = report.getJsonObject("links");
                 JsonArray data = report.getJsonArray("data");
                 Iterator<JsonValue> iter = data.iterator();

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetProvJsonCommand.java

@@ -9,12 +9,12 @@
 import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
 import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
+
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.logging.Logger;
-import jakarta.json.Json;
 import jakarta.json.JsonObject;
-import jakarta.json.JsonReader;
 
 @RequiredPermissions(Permission.EditDataset)
 public class GetProvJsonCommand extends AbstractCommand<JsonObject> {
@@ -37,9 +37,8 @@ public JsonObject execute(CommandContext ctxt) throws CommandException {
             StorageIO<DataFile> dataAccess = dataFile.getStorageIO();
             InputStream inputStream = dataAccess.getAuxFileAsInputStream(provJsonExtension);
             JsonObject jsonObject = null;
-            if(null != inputStream) {
-                JsonReader jsonReader = Json.createReader(inputStream);
-                jsonObject = jsonReader.readObject();
+            if (null != inputStream) {
+                jsonObject = JsonUtil.getJsonObject(inputStream);
             }
             return jsonObject;
         } catch (IOException ex) {

src/main/java/edu/harvard/iq/dataverse/util/json/JsonUtil.java

@@ -1,16 +1,17 @@
 package edu.harvard.iq.dataverse.util.json;
 
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
-import com.google.gson.JsonObject;
-
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.logging.Logger;
 import jakarta.json.Json;
 import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
 import jakarta.json.JsonReader;
 import jakarta.json.JsonWriter;
 import jakarta.json.JsonWriterFactory;
@@ -20,17 +21,19 @@ public class JsonUtil {
 
     private static final Logger logger = Logger.getLogger(JsonUtil.class.getCanonicalName());
 
+    private JsonUtil() {}
+
     /**
      * Make an attempt at pretty printing a String but will return the original
      * string if it isn't JSON or if there is any exception.
      */
     public static String prettyPrint(String jsonString) {
         try {
-            com.google.gson.JsonParser jsonParser = new com.google.gson.JsonParser();
-            JsonObject jsonObject = jsonParser.parse(jsonString).getAsJsonObject();
-            Gson gson = new GsonBuilder().setPrettyPrinting().create();
-            String prettyJson = gson.toJson(jsonObject);
-            return prettyJson;
+            if (jsonString.trim().startsWith("{")) {
+                return prettyPrint(getJsonObject(jsonString));
+            } else {
+                return prettyPrint(getJsonArray(jsonString));
+            }
         } catch (Exception ex) {
             logger.info("Returning original string due to exception: " + ex);
             return jsonString;
@@ -48,7 +51,7 @@ public static String prettyPrint(JsonArray jsonArray) {
         return stringWriter.toString();
     }
 
-    public static String prettyPrint(jakarta.json.JsonObject jsonObject) {
+    public static String prettyPrint(JsonObject jsonObject) {
         Map<String, Boolean> config = new HashMap<>();
         config.put(JsonGenerator.PRETTY_PRINTING, true);
         JsonWriterFactory jsonWriterFactory = Json.createWriterFactory(config);
@@ -59,15 +62,40 @@ public static String prettyPrint(jakarta.json.JsonObject jsonObject) {
         return stringWriter.toString();
     }
 
-    public static jakarta.json.JsonObject getJsonObject(String serializedJson) {
+    public static JsonObject getJsonObject(String serializedJson) {
         try (StringReader rdr = new StringReader(serializedJson)) {
             try (JsonReader jsonReader = Json.createReader(rdr)) {
                 return jsonReader.readObject();
             }
         }
     }
 
-    public static jakarta.json.JsonArray getJsonArray(String serializedJson) {
+    /**
+     * Return the contents of the {@link InputStream} as a JSON object.
+     * @param stream the input stream to read from
+     * @throws JsonException when parsing fails.
+     */
+    public static JsonObject getJsonObject(InputStream stream) {
+        try (JsonReader jsonReader = Json.createReader(stream)) {
+            return jsonReader.readObject();
+        }
+    }
+
+    /**
+     * Return the contents of the file as a JSON object.
+     * @param fileName the name of the file to read from
+     * @throws FileNotFoundException when the file cannot be opened for reading
+     * @throws JsonException when parsing fails.
+     */
+    public static JsonObject getJsonObjectFromFile(String fileName) throws IOException {
+        try (FileReader rdr = new FileReader(fileName)) {
+            try (JsonReader jsonReader = Json.createReader(rdr)) {
+                return jsonReader.readObject();
+            }
+        }
+    }
+
+    public static JsonArray getJsonArray(String serializedJson) {
         try (StringReader rdr = new StringReader(serializedJson)) {
             try (JsonReader jsonReader = Json.createReader(rdr)) {
                 return jsonReader.readArray();

src/test/java/edu/harvard/iq/dataverse/util/json/JsonUtilTest.java

@@ -3,17 +3,17 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import org.junit.jupiter.api.Test;
 
-public class JsonUtilTest {
+class JsonUtilTest {
 
     @Test
-    public void testPrettyPrint() {
-        JsonUtil jsonUtil = new JsonUtil();
+    void testPrettyPrint() {
         String nullString = null;
         assertEquals(null, JsonUtil.prettyPrint(nullString));
         assertEquals("", JsonUtil.prettyPrint(""));
         assertEquals("junk", JsonUtil.prettyPrint("junk"));
-        assertEquals("{}", JsonUtil.prettyPrint("{}"));
-        assertEquals("{\n" + "  \"foo\": \"bar\"\n" + "}", JsonUtil.prettyPrint("{\"foo\": \"bar\"}"));
+        assertEquals("{\n}", JsonUtil.prettyPrint("{}"));
+        assertEquals("[\n    \"junk\"\n]", JsonUtil.prettyPrint("[\"junk\"]"));
+        assertEquals("{\n" + "    \"foo\": \"bar\"\n" + "}", JsonUtil.prettyPrint("{\"foo\": \"bar\"}"));
     }
 
 }