Migrate labkey-client-api to use a modern JSON library: JSON-java (#38)

Co-authored-by: labkey-tchad <tchad@labkey.com>

Author: labkey-adam

labkey-client-api/CHANGELOG.md

@@ -1,7 +1,12 @@
 # The LabKey Remote API Library for Java - Change Log
 
-## version TBD
+## version 4.0.0
 *Released*: TBD
+* Replace the internal JSON library with [JSON-java](https://github.com/stleary/JSON-java). The previous library,
+  [json-simple](https://github.com/fangyidong/json-simple) is no longer maintained (last released in early 2012) and
+  lacks support for basic features like generics. This is an incompatible API change for developers who *write* their own
+  Command classes; they will need to update their Command classes if/when they upgrade to v4.0.0. Developers who simply
+  *use* Command classes should be able to upgrade without changes.
 * Issue 46321: Remove `lib` directory from `fatJar` in favor of pulling dependencies via the published pom files when needed
 * Remove artifactory plugin since we use the maven `publish` command now
 

labkey-client-api/build.gradle

@@ -1,5 +1,4 @@
 import org.labkey.gradle.plugin.LabKey
-import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.GroupNames
 import org.labkey.gradle.util.PomFileHelper
 
@@ -49,14 +48,10 @@ repositories {
 
 group "org.labkey.api"
 
-version "3.2.0-SNAPSHOT"
+version "4.0.0-SNAPSHOT"
 
 dependencies {
-    api ("com.googlecode.json-simple:json-simple:${jsonSimpleVersion}")
-            {
-                // exclude this because it gets in the way of our own JSON object implementations from server/api
-                exclude group: "org.json", module:"json"
-            }
+    api "org.json:json:${jsonObjectVersion}"
     api "org.apache.httpcomponents.client5:httpclient5:${httpclient5Version}"
     api "org.apache.httpcomponents.core5:httpcore5:${httpcore5Version}"
     implementation "net.sf.opencsv:opencsv:${opencsvVersion}"

labkey-client-api/gradle.properties

@@ -18,6 +18,7 @@ httpclient5Version=5.1.3
 httpcore5Version=5.1.4
 
 jsonSimpleVersion=1.1.1
+jsonObjectVersion=20220924
 
 junitVersion=4.13.2
 

labkey-client-api/src/org/labkey/remoteapi/ApiVersionException.java

@@ -15,7 +15,7 @@
  */
 package org.labkey.remoteapi;
 
-import java.util.Map;
+import org.json.JSONObject;
 
 /**
  * User: adam
@@ -24,8 +24,8 @@
  */
 public class ApiVersionException extends CommandException
 {
-    ApiVersionException(String message, int statusCode, Map<String, Object> properties, String responseText, String contentType)
+    ApiVersionException(String message, int statusCode, JSONObject jsonProperties, String responseText, String contentType)
     {
-        super(message, statusCode, properties, responseText, contentType);
+        super(message, statusCode, jsonProperties, responseText, contentType);
     }
 }

labkey-client-api/src/org/labkey/remoteapi/Command.java

@@ -22,17 +22,10 @@
 import org.apache.hc.client5.http.impl.classic.CloseableHttpResponse;
 import org.apache.hc.core5.http.Header;
 import org.apache.hc.core5.net.URIBuilder;
-import org.json.simple.JSONObject;
-import org.json.simple.JSONValue;
-
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.Closeable;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
+import org.json.JSONObject;
+import org.json.JSONTokener;
+
+import java.io.*;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.nio.charset.StandardCharsets;
@@ -218,7 +211,10 @@ public ResponseType execute(Connection connection, String folderPath) throws IOE
                 if (null != contentType && contentType.contains(Command.CONTENT_TYPE_JSON))
                 {
                     // Read entire response body and parse into JSON object
-                    json = (JSONObject) JSONValue.parse(response.getReader());
+                    try (Reader reader = response.getReader())
+                    {
+                        json = new JSONObject(new JSONTokener(reader));
+                    }
                 }
                 else
                 {
@@ -387,12 +383,12 @@ private void throwError(Response r, boolean throwByDefault) throws IOException,
             // Parse JSON
             if (responseText != null && responseText.length() > 0)
             {
-                json = (JSONObject) JSONValue.parse(responseText);
-                if (json != null && json.containsKey("exception"))
+                json = new JSONObject(responseText);
+                if (json.has("exception"))
                 {
                     message = (String)json.get("exception");
 
-                    if ("org.labkey.api.action.ApiVersionException".equals(json.get("exceptionClass")))
+                    if ("org.labkey.api.action.ApiVersionException".equals(json.opt("exceptionClass")))
                         throw new ApiVersionException(message, r.getStatusCode(), json, responseText, contentType);
 
                     throw new CommandException(message, r.getStatusCode(), json, responseText, contentType);

labkey-client-api/src/org/labkey/remoteapi/CommandException.java

@@ -16,6 +16,7 @@
 package org.labkey.remoteapi;
 
 import org.apache.hc.core5.http.impl.EnglishReasonPhraseCatalog;
+import org.json.JSONObject;
 
 import java.util.Locale;
 import java.util.Map;
@@ -38,7 +39,7 @@ public class CommandException extends Exception
 {
     private final String _contentType;
     private final int _statusCode;
-    private final Map<String, Object> _properties;
+    private final JSONObject _jsonProperties;
     private final String _responseText;
 
     /**
@@ -56,15 +57,15 @@ public CommandException(String message)
      * exception property map, responseText, and contentType.
      * @param message The message text (should not be null).
      * @param statusCode The HTTP status code.
-     * @param properties The exception property map (may be null)
+     * @param jsonProperties The exception property JSONObject (may be null)
      * @param responseText The full response text (may be null)
      * @param contentType The response content type (may be null)
      */
-    public CommandException(String message, int statusCode, Map<String, Object> properties, String responseText, String contentType)
+    public CommandException(String message, int statusCode, JSONObject jsonProperties, String responseText, String contentType)
     {
         super(buildMessage(message, statusCode));
         _statusCode = statusCode;
-        _properties = properties;
+        _jsonProperties = jsonProperties;
         _responseText = responseText;
         _contentType = contentType;
     }
@@ -119,6 +120,6 @@ public String getResponseText()
      */
     public Map<String, Object> getProperties()
     {
-        return _properties;
+        return null == _jsonProperties ? null : _jsonProperties.toMap();
     }
 }

labkey-client-api/src/org/labkey/remoteapi/CommandResponse.java

@@ -15,8 +15,7 @@
  */
 package org.labkey.remoteapi;
 
-import org.json.simple.JSONObject;
-import org.json.simple.JSONValue;
+import org.json.JSONObject;
 
 import java.util.List;
 import java.util.Map;
@@ -43,11 +42,12 @@
  */
 public class CommandResponse
 {
-    private String _text;
-    private int _statusCode;
-    private String _contentType;
-    private JSONObject _data = null;
-    private Command _sourceCommand;
+    private final String _text;
+    private final int _statusCode;
+    private final String _contentType;
+    private final Command _sourceCommand;
+
+    private Map<String, Object> _data;
 
     /**
      * Constructs a new CommandResponse, initialized with the provided
@@ -63,7 +63,7 @@ public CommandResponse(String text, int statusCode, String contentType, JSONObje
         _text = text;
         _statusCode = statusCode;
         _contentType = contentType;
-        _data = json;
+        _data = null != json ? json.toMap() : null;
         _sourceCommand = sourceCommand;
     }
 
@@ -134,9 +134,9 @@ public Command getSourceCommand()
     @SuppressWarnings("unchecked")
     public Map<String, Object> getParsedData()
     {
-        if(null == _data && null != getText()
+        if (null == _data && null != getText()
                 && null != _contentType && _contentType.contains(Command.CONTENT_TYPE_JSON))
-            _data = (JSONObject)JSONValue.parse(getText());
+            _data = new JSONObject(getText()).toMap();
         return _data;
     }
 
@@ -158,9 +158,9 @@ public <T> T getProperty(String path)
     {
         assert null != path;
         String[] pathParts = path.split("\\.");
-        if(null == pathParts || pathParts.length == 0)
+        if (pathParts.length == 0)
             return null;
-        return (T)getProperty(pathParts, 0, getParsedData());
+        return getProperty(pathParts, 0, getParsedData());
     }
 
     /**
@@ -176,7 +176,7 @@ public <T> T getProperty(String path)
     @SuppressWarnings("unchecked")
     protected <T> T getProperty(String[] path, int pathIndex, Map<String, Object> parent)
     {
-        if(null == parent)
+        if (null == parent)
             return null;
 
         String key = path[pathIndex];
@@ -192,20 +192,20 @@ protected <T> T getProperty(String[] path, int pathIndex, Map<String, Object> pa
         Object prop = parent.get(key);
         if (arrayIndex != null)
         {
-            if (prop != null && prop instanceof List && ((List)prop).size() > arrayIndex)
+            if (prop instanceof List && ((List) prop).size() > arrayIndex)
                 prop = ((List)prop).get(arrayIndex);
             else
                 return null;
         }
 
         //if this was the last path part, return the prop
         //will return null if final path part not found
-        if(pathIndex == (path.length -1))
+        if (pathIndex == (path.length -1))
             return (T)prop;
         else
         {
             //recurse if prop is non-null and instance of map
-            return (null != prop && prop instanceof Map)
+            return (prop instanceof Map)
                 ? (T)getProperty(path, pathIndex + 1, (Map<String, Object>)prop)
                 : null;
         }

labkey-client-api/src/org/labkey/remoteapi/PostCommand.java

@@ -19,7 +19,7 @@
 import org.apache.hc.client5.http.classic.methods.HttpUriRequest;
 import org.apache.hc.core5.http.ContentType;
 import org.apache.hc.core5.http.io.entity.StringEntity;
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 
 import java.net.URI;
 
@@ -108,7 +108,7 @@ protected HttpUriRequest createRequest(URI uri)
 
         if (null != json)
         {
-            if (!json.containsKey(CommonParameters.apiVersion.name()) && getRequiredVersion() > 0)
+            if (!json.has(CommonParameters.apiVersion.name()) && getRequiredVersion() > 0)
                 json.put(CommonParameters.apiVersion.name(), getRequiredVersion());
 
             request.setEntity(new StringEntity(json.toString(), ContentType.APPLICATION_JSON));

labkey-client-api/src/org/labkey/remoteapi/assay/AssayListCommand.java

@@ -15,7 +15,7 @@
  */
 package org.labkey.remoteapi.assay;
 
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 import org.labkey.remoteapi.PostCommand;
 
 import java.util.HashMap;

labkey-client-api/src/org/labkey/remoteapi/assay/AssayListResponse.java

@@ -15,7 +15,7 @@
  */
 package org.labkey.remoteapi.assay;
 
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 import org.labkey.remoteapi.CommandResponse;
 
 import java.util.List;

labkey-client-api/src/org/labkey/remoteapi/assay/Batch.java

@@ -15,8 +15,8 @@
  */
 package org.labkey.remoteapi.assay;
 
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
+import org.json.JSONArray;
+import org.json.JSONObject;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -37,9 +37,9 @@ public Batch()
     public Batch(JSONObject json)
     {
         super(json);
-        if (json.containsKey("runs"))
+        if (json.has("runs"))
         {
-            JSONArray array = (JSONArray)json.get("runs");
+            JSONArray array = json.getJSONArray("runs");
             for (Object o : array)
             {
                 JSONObject run = (JSONObject) o;
@@ -65,7 +65,7 @@ public JSONObject toJSONObject()
         JSONArray runs = new JSONArray();
         for (Run run : _runs)
         {
-            runs.add(run.toJSONObject());
+            runs.put(run.toJSONObject());
         }
         result.put("runs", runs);
         return result;

labkey-client-api/src/org/labkey/remoteapi/assay/Data.java

@@ -15,7 +15,7 @@
  */
 package org.labkey.remoteapi.assay;
 
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 
 /**
 * Represents a data file that may be used in a run. In order to successfully look up a data file when saving a run,
@@ -38,9 +38,9 @@ public Data()
     public Data(JSONObject json)
     {
         super(json);
-        _dataFileURL = (String)json.get("dataFileURL");
-        _absolutePath = (String)json.get("absolutePath");
-        _pipelinePath = (String)json.get("pipelinePath");
+        _dataFileURL = json.optString("dataFileURL", null);
+        _absolutePath = json.optString("absolutePath", null);
+        _pipelinePath = json.optString("pipelinePath", null);
     }
 
     @Override