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[VIVO-1320] Convert some org.json usages to Jackson

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This commit is contained in:
Graham Triggs 2017-09-15 21:04:46 +01:00
parent 916640ef43
commit bf450aca21
6 changed files with 195 additions and 178 deletions
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73
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/grefine/GrefineMqlreadServlet.java
View file

@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.grefine;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap; import java.util.HashMap;
import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
@ -14,11 +15,13 @@ import javax.servlet.annotation.WebServlet;
import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpServletResponse;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.JsonNodeFactory;
import com.fasterxml.jackson.databind.node.ObjectNode;
import edu.cornell.mannlib.vitro.webapp.utils.json.JacksonUtils;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties; import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet; import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
@ -57,7 +60,7 @@ public class GrefineMqlreadServlet extends VitroHttpServlet {
try { try {
if (vreq.getParameter("query") != null) { if (vreq.getParameter("query") != null) {
JSONObject qJson = getResult(vreq, req, resp); ObjectNode qJson = getResult(vreq, req, resp);
log.debug("result: " + qJson.toString()); log.debug("result: " + qJson.toString());
String responseStr = (vreq.getParameter("callback") == null) ? qJson String responseStr = (vreq.getParameter("callback") == null) ? qJson
.toString() : vreq.getParameter("callback") + "(" .toString() : vreq.getParameter("callback") + "("
@ -72,55 +75,50 @@ public class GrefineMqlreadServlet extends VitroHttpServlet {
} }
} }
private JSONObject getResult(VitroRequest vreq, HttpServletRequest req, private ObjectNode getResult(VitroRequest vreq, HttpServletRequest req,
HttpServletResponse resp) throws ServletException { HttpServletResponse resp) throws ServletException {
JSONObject resultAllJson = new JSONObject(); ObjectNode resultAllJson = JsonNodeFactory.instance.objectNode();
try {
// parse query // parse query
ArrayList<String> subjectUriList = new ArrayList<String>(); ArrayList<String> subjectUriList = new ArrayList<String>();
Map<String, JSONArray> propertyUriMap = new HashMap<String, JSONArray>(); Map<String, ArrayNode> propertyUriMap = new HashMap<String, ArrayNode>();
String query = vreq.getParameter("query"); String query = vreq.getParameter("query");
parseQuery(query, subjectUriList, propertyUriMap); parseQuery(query, subjectUriList, propertyUriMap);
// run SPARQL query to get the results // run SPARQL query to get the results
JSONArray resultAllJsonArr = new JSONArray(); ArrayNode resultAllJsonArr = JsonNodeFactory.instance.arrayNode();
DataPropertyStatementDao dpsDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyStatementDao(); DataPropertyStatementDao dpsDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyStatementDao();
for (String subjectUri: subjectUriList) { for (String subjectUri: subjectUriList) {
JSONObject subjectPropertyResultJson = new JSONObject(); ObjectNode subjectPropertyResultJson = JsonNodeFactory.instance.objectNode();
subjectPropertyResultJson.put("id", subjectUri); subjectPropertyResultJson.put("id", subjectUri);
for (Map.Entry<String, JSONArray> entry : propertyUriMap.entrySet()) { for (Map.Entry<String, ArrayNode> entry : propertyUriMap.entrySet()) {
int limit = 200; // default int limit = 200; // default
String propertyUri = entry.getKey(); String propertyUri = entry.getKey();
JSONArray propertyUriOptions = entry.getValue(); ArrayNode propertyUriOptions = entry.getValue();
for (int i=0; i<propertyUriOptions.length(); i++) { for (int i=0; i<propertyUriOptions.size(); i++) {
JSONObject propertyUriOption = (JSONObject)propertyUriOptions.get(i); ObjectNode propertyUriOption = (ObjectNode) propertyUriOptions.get(i);
limit = ((Integer)propertyUriOption.get("limit")).intValue(); limit = propertyUriOption.get("limit").asInt();
} }
List<Literal> literals = dpsDao.getDataPropertyValuesForIndividualByProperty(subjectUri, propertyUri); List<Literal> literals = dpsDao.getDataPropertyValuesForIndividualByProperty(subjectUri, propertyUri);
// Make sure the subject has a value for this property // Make sure the subject has a value for this property
if (literals.size() > 0) { if (literals.size() > 0) {
int counter = 0; int counter = 0;
JSONArray valueJsonArr = new JSONArray(); ArrayNode valueJsonArr = JsonNodeFactory.instance.arrayNode();
for (Literal literal: literals) { for (Literal literal: literals) {
if (counter <= limit) { if (counter <= limit) {
String value = literal.getLexicalForm(); String value = literal.getLexicalForm();
valueJsonArr.put(value); valueJsonArr.add(value);
} }
counter++; counter++;
} }
subjectPropertyResultJson.put(propertyUri, valueJsonArr); subjectPropertyResultJson.put(propertyUri, valueJsonArr);
} }
} }
resultAllJsonArr.put(subjectPropertyResultJson); resultAllJsonArr.add(subjectPropertyResultJson);
} }
resultAllJson.put("result", resultAllJsonArr); resultAllJson.put("result", resultAllJsonArr);
} catch (JSONException e) {
log.error("GrefineMqlreadServlet getResult JSONException: " + e);
}
// System.out.println(resultAllJson); // System.out.println(resultAllJson);
return resultAllJson; return resultAllJson;
} }
@ -131,31 +129,32 @@ public class GrefineMqlreadServlet extends VitroHttpServlet {
* @param subjectUriList Subject URIs * @param subjectUriList Subject URIs
* @param propertyUriMap Property maps * @param propertyUriMap Property maps
*/ */
private void parseQuery(String query, ArrayList<String> subjectUriList, Map<String, JSONArray> propertyUriMap) { private void parseQuery(String query, ArrayList<String> subjectUriList, Map<String, ArrayNode> propertyUriMap) {
try { try {
JSONObject rawJson = new JSONObject(query); ObjectMapper mapper = new ObjectMapper();
JSONArray qJsonArr = rawJson.getJSONArray("query"); ObjectNode rawJson = (ObjectNode)mapper.readTree(query);
for (int i=0; i<qJsonArr.length(); i++) { ArrayNode qJsonArr = (ArrayNode)rawJson.get("query");
for (int i=0; i<qJsonArr.size(); i++) {
Object obj = qJsonArr.get(i); Object obj = qJsonArr.get(i);
if (obj instanceof JSONObject) { if (obj instanceof ObjectNode) {
JSONObject jsonObj = (JSONObject)obj; ObjectNode jsonObj = (ObjectNode) obj;
JSONArray jsonObjNames = jsonObj.names(); Iterator<String> jsonObjNames = jsonObj.fieldNames();
for (int j=0; j<jsonObjNames.length(); j++) { while (jsonObjNames.hasNext()) {
String objName = (String)jsonObjNames.get(j); String objName = (String)jsonObjNames.next();
if (objName.contains("http://")) { // most likely this is a propertyUri if (objName.contains("http://")) { // most likely this is a propertyUri
// e.g. http://weill.cornell.edu/vivo/ontology/wcmc#cwid // e.g. http://weill.cornell.edu/vivo/ontology/wcmc#cwid
Object propertyUriObj = jsonObj.get(objName); Object propertyUriObj = jsonObj.get(objName);
if (propertyUriObj instanceof JSONArray) { if (propertyUriObj instanceof ArrayNode) {
propertyUriMap.put(objName, (JSONArray)propertyUriObj); propertyUriMap.put(objName, (ArrayNode) propertyUriObj);
} }
} else if ("id".equals(objName)) { // id } else if ("id".equals(objName)) { // id
Object idObj = jsonObj.get(objName); // TODO: This is a String object but not sure what it is for Object idObj = jsonObj.get(objName); // TODO: This is a String object but not sure what it is for
} else if ("id|=".equals(objName)) { // list of subject uri } else if ("id|=".equals(objName)) { // list of subject uri
Object subjectUriObj = jsonObj.get(objName); Object subjectUriObj = jsonObj.get(objName);
if (subjectUriObj instanceof JSONArray) { if (subjectUriObj instanceof ArrayNode) {
JSONArray subjectUriUriArr = (JSONArray)subjectUriObj; ArrayNode subjectUriUriArr = (ArrayNode) subjectUriObj;
for (int k=0; k<subjectUriUriArr.length(); k++) { for (int k=0; k<subjectUriUriArr.size(); k++) {
// e.g. http://vivo.med.cornell.edu/individual/cwid-jsd2002 // e.g. http://vivo.med.cornell.edu/individual/cwid-jsd2002
Object subjectUriUriObj = subjectUriUriArr.get(k); Object subjectUriUriObj = subjectUriUriArr.get(k);
if (subjectUriUriObj instanceof String) { if (subjectUriUriObj instanceof String) {
@ -167,7 +166,7 @@ public class GrefineMqlreadServlet extends VitroHttpServlet {
} }
} }
} }
} catch (JSONException e) { } catch (IOException e) {
log.error("GrefineMqlreadServlet parseQuery JSONException: " + e); log.error("GrefineMqlreadServlet parseQuery JSONException: " + e);
} }
} }

40
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/grefine/GrefinePropertyListServlet.java
View file

@ -18,12 +18,12 @@ import javax.servlet.annotation.WebServlet;
import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpServletResponse;
import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.JsonNodeFactory;
import com.fasterxml.jackson.databind.node.ObjectNode;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.json.JSONArray;
import org.json.JSONObject;
import org.apache.jena.vocabulary.OWL; import org.apache.jena.vocabulary.OWL;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty; import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
@ -81,8 +81,8 @@ public class GrefinePropertyListServlet extends VitroHttpServlet {
// Construct json String // Construct json String
JSONObject completeJson = new JSONObject(); ObjectNode completeJson = JsonNodeFactory.instance.objectNode();
JSONArray propertiesJsonArr = new JSONArray(); ArrayNode propertiesJsonArr = JsonNodeFactory.instance.arrayNode();
if (classPropertiesMap.size() > 0) { if (classPropertiesMap.size() > 0) {
for (Iterator<VClass> iter = classPropertiesMap.keySet().iterator(); iter.hasNext();) { // add results to schema for (Iterator<VClass> iter = classPropertiesMap.keySet().iterator(); iter.hasNext();) { // add results to schema
VClass vc = (VClass) iter.next(); VClass vc = (VClass) iter.next();
@ -95,24 +95,24 @@ public class GrefinePropertyListServlet extends VitroHttpServlet {
//System.out.println("--- uri: " + prop.getURI()); //System.out.println("--- uri: " + prop.getURI());
//System.out.println("--- name: " + nameStr); //System.out.println("--- name: " + nameStr);
// top level // top level
JSONObject propertiesItemJson = new JSONObject(); ObjectNode propertiesItemJson = JsonNodeFactory.instance.objectNode();
JSONObject rootSchemaJson = new JSONObject(); ObjectNode rootSchemaJson = JsonNodeFactory.instance.objectNode();
rootSchemaJson.put("id", vc.getURI()); rootSchemaJson.put("id", vc.getURI());
rootSchemaJson.put("name", vc.getName()); rootSchemaJson.put("name", vc.getName());
rootSchemaJson.put("alias", new JSONArray()); rootSchemaJson.put("alias", JsonNodeFactory.instance.arrayNode());
propertiesItemJson.put("schema", rootSchemaJson); propertiesItemJson.put("schema", rootSchemaJson);
// second level // second level
propertiesItemJson.put("id", prop.getURI()); propertiesItemJson.put("id", prop.getURI());
propertiesItemJson.put("name", nameStr); propertiesItemJson.put("name", nameStr);
propertiesItemJson.put("alias", new JSONArray()); propertiesItemJson.put("alias", JsonNodeFactory.instance.arrayNode());
JSONObject expectsJson = new JSONObject(); ObjectNode expectsJson = JsonNodeFactory.instance.objectNode();
expectsJson.put("id", prop.getURI()); expectsJson.put("id", prop.getURI());
expectsJson.put("name", nameStr); expectsJson.put("name", nameStr);
expectsJson.put("alias", new JSONArray()); expectsJson.put("alias", JsonNodeFactory.instance.arrayNode());
propertiesItemJson.put("expects", expectsJson); propertiesItemJson.put("expects", expectsJson);
propertiesJsonArr.put(propertiesItemJson); propertiesJsonArr.add(propertiesItemJson);
} }
} }
} }
@ -154,30 +154,30 @@ public class GrefinePropertyListServlet extends VitroHttpServlet {
for (DataProperty prop: vcProps) { for (DataProperty prop: vcProps) {
String nameStr = prop.getPublicName()==null ? prop.getName()==null ? null : prop.getName() : prop.getPublicName(); String nameStr = prop.getPublicName()==null ? prop.getName()==null ? null : prop.getName() : prop.getPublicName();
// top level // top level
JSONObject propertiesItemJson = new JSONObject(); ObjectNode propertiesItemJson = JsonNodeFactory.instance.objectNode();
JSONObject rootSchemaJson = new JSONObject(); ObjectNode rootSchemaJson = JsonNodeFactory.instance.objectNode();
rootSchemaJson.put("id", topClass.getURI()); rootSchemaJson.put("id", topClass.getURI());
rootSchemaJson.put("name", topClass.getName()); rootSchemaJson.put("name", topClass.getName());
rootSchemaJson.put("alias", new JSONArray()); rootSchemaJson.put("alias", JsonNodeFactory.instance.arrayNode());
propertiesItemJson.put("schema", rootSchemaJson); propertiesItemJson.put("schema", rootSchemaJson);
// second level // second level
propertiesItemJson.put("id", vc.getURI()); propertiesItemJson.put("id", vc.getURI());
propertiesItemJson.put("name", vc.getName()); propertiesItemJson.put("name", vc.getName());
propertiesItemJson.put("alias", new JSONArray()); propertiesItemJson.put("alias", JsonNodeFactory.instance.arrayNode());
propertiesItemJson.put("id2", prop.getURI()); propertiesItemJson.put("id2", prop.getURI());
propertiesItemJson.put("name2", nameStr); propertiesItemJson.put("name2", nameStr);
propertiesItemJson.put("alias2", new JSONArray()); propertiesItemJson.put("alias2", JsonNodeFactory.instance.arrayNode());
JSONObject expectsJson = new JSONObject(); ObjectNode expectsJson = JsonNodeFactory.instance.objectNode();
expectsJson.put("id", prop.getURI()); expectsJson.put("id", prop.getURI());
expectsJson.put("name", nameStr); expectsJson.put("name", nameStr);
expectsJson.put("alias", new JSONArray()); expectsJson.put("alias", JsonNodeFactory.instance.arrayNode());
propertiesItemJson.put("expects", expectsJson); propertiesItemJson.put("expects", expectsJson);
propertiesJsonArr.put(propertiesItemJson); propertiesJsonArr.add(propertiesItemJson);
} }
} }

121
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/grefine/JSONReconcileServlet.java
View file

@ -16,12 +16,15 @@ import javax.servlet.annotation.WebServlet;
import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpServletResponse;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.JsonNodeFactory;
import com.fasterxml.jackson.databind.node.ObjectNode;
import edu.cornell.mannlib.vitro.webapp.utils.json.JacksonUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils; import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties; import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
@ -45,6 +48,8 @@ import edu.cornell.mannlib.vitro.webapp.search.VitroSearchTermNames;
@WebServlet(name = "JSON Reconcile Service", urlPatterns = {"/reconcile"} ) @WebServlet(name = "JSON Reconcile Service", urlPatterns = {"/reconcile"} )
public class JSONReconcileServlet extends VitroHttpServlet { public class JSONReconcileServlet extends VitroHttpServlet {
private static final String INTERNAL_QUERY_NAME = "A0B1C2";
private static final String PARAM_QUERY = "term"; private static final String PARAM_QUERY = "term";
private static final long serialVersionUID = 1L; private static final long serialVersionUID = 1L;
private static String QUERY_PARAMETER_NAME = "term"; private static String QUERY_PARAMETER_NAME = "term";
@ -70,7 +75,7 @@ public class JSONReconcileServlet extends VitroHttpServlet {
try { try {
if (vreq.getParameter("query") != null if (vreq.getParameter("query") != null
|| vreq.getParameter("queries") != null) { || vreq.getParameter("queries") != null) {
JSONObject qJson = getResult(vreq, req, resp); ObjectNode qJson = getResult(vreq, req, resp);
log.debug("result: " + qJson.toString()); log.debug("result: " + qJson.toString());
String responseStr = (vreq.getParameter("callback") == null) ? qJson String responseStr = (vreq.getParameter("callback") == null) ? qJson
.toString() : vreq.getParameter("callback") + "(" .toString() : vreq.getParameter("callback") + "("
@ -89,7 +94,7 @@ public class JSONReconcileServlet extends VitroHttpServlet {
} }
defaultTypeList = ConfigurationProperties.getBean(req).getProperty("Vitro.reconcile.defaultTypeList"); defaultTypeList = ConfigurationProperties.getBean(req).getProperty("Vitro.reconcile.defaultTypeList");
serverName = req.getServerName(); serverName = req.getServerName();
JSONObject metaJson = getMetadata(req, resp, defaultNamespace, defaultTypeList, serverName, serverPort); ObjectNode metaJson = getMetadata(req, resp, defaultNamespace, defaultTypeList, serverName, serverPort);
String callbackStr = (vreq.getParameter("callback") == null) ? "" String callbackStr = (vreq.getParameter("callback") == null) ? ""
: vreq.getParameter("callback"); : vreq.getParameter("callback");
ServletOutputStream out = resp.getOutputStream(); ServletOutputStream out = resp.getOutputStream();
@ -100,16 +105,21 @@ public class JSONReconcileServlet extends VitroHttpServlet {
} }
} }
private JSONObject getResult(VitroRequest vreq, HttpServletRequest req, private ObjectNode getResult(VitroRequest vreq, HttpServletRequest req,
HttpServletResponse resp) throws ServletException { HttpServletResponse resp) throws ServletException {
HashMap<String, JSONObject> searchWithTypeMap = new HashMap<String, JSONObject>(); HashMap<String, JsonNode> searchWithTypeMap = new HashMap<String, JsonNode>();
HashMap<String, JSONObject> searchNoTypeMap = new HashMap<String, JSONObject>(); HashMap<String, JsonNode> searchNoTypeMap = new HashMap<String, JsonNode>();
ArrayList<String> queries = new ArrayList<String>(); ArrayList<String> queries = new ArrayList<String>();
Object qObj = vreq.getParameter("queries"); Object qObj = vreq.getParameter("queries");
if (qObj == null) { if (qObj == null) {
qObj = vreq.getParameter("query"); qObj = vreq.getParameter("query");
if (qObj instanceof String) {
if (!((String)qObj).contains("{")) {
qObj = "{ \"query\" : \"" + qObj + "\" }";
}
}
} }
if (qObj != null && qObj instanceof String) { if (qObj != null && qObj instanceof String) {
@ -126,21 +136,21 @@ public class JSONReconcileServlet extends VitroHttpServlet {
try { try {
for (int i = 0; i < queries.size(); i++) { for (int i = 0; i < queries.size(); i++) {
String queryStr = queries.get(i); String queryStr = queries.get(i);
JSONObject json = new JSONObject(queryStr); ObjectMapper mapper = new ObjectMapper();
JsonNode json = mapper.readTree(queryStr);
if (json.has("query")) { // single query if (json.has("query")) { // single query
if (json.has("type")) { if (json.has("type")) {
searchWithTypeMap.put("query", json); searchWithTypeMap.put(INTERNAL_QUERY_NAME, json);
} else { } else {
// user did not specify a type // user did not specify a type
searchNoTypeMap.put("query", json); searchNoTypeMap.put(INTERNAL_QUERY_NAME, json);
} }
} else { // multiple queries } else { // multiple queries
for (Iterator<String> iter = json.keys(); iter.hasNext();) { for (Iterator<String> iter = json.fieldNames(); iter.hasNext();) {
ArrayList<JSONObject> jsonList = new ArrayList<JSONObject>(); ArrayList<JsonNode> jsonList = new ArrayList<JsonNode>();
String key = iter.next(); String key = iter.next();
Object obj = json.get(key); JsonNode jsonLvl2 = json.get(key);
JSONObject jsonLvl2 = (JSONObject) obj;
if (jsonLvl2.has("query")) { if (jsonLvl2.has("query")) {
if (jsonLvl2.has("type")) { if (jsonLvl2.has("type")) {
searchWithTypeMap.put(key, jsonLvl2); searchWithTypeMap.put(key, jsonLvl2);
@ -152,14 +162,14 @@ public class JSONReconcileServlet extends VitroHttpServlet {
} }
} }
} }
} catch (JSONException ex) { } catch (IOException ex) {
log.error("JSONException: " + ex); log.error("JSONException: " + ex);
throw new ServletException("JSONReconcileServlet JSONException: " throw new ServletException("JSONReconcileServlet JSONException: "
+ ex); + ex);
} }
// Run index search // Run index search
JSONObject qJson = null; ObjectNode qJson = null;
if (searchWithTypeMap.size() > 0) { if (searchWithTypeMap.size() > 0) {
qJson = runSearch(searchWithTypeMap); qJson = runSearch(searchWithTypeMap);
} else { } else {
@ -176,19 +186,18 @@ public class JSONReconcileServlet extends VitroHttpServlet {
* *
* @param req Servlet Request * @param req Servlet Request
* @param resp Servlet Response * @param resp Servlet Response
* @throws ServletException
*/ */
protected JSONObject getMetadata(HttpServletRequest req, HttpServletResponse resp, String defaultNamespace, protected ObjectNode getMetadata(HttpServletRequest req, HttpServletResponse resp, String defaultNamespace,
String defaultTypeList, String serverName, int serverPort) throws ServletException { String defaultTypeList, String serverName, int serverPort) throws ServletException {
JSONObject json = new JSONObject(); ObjectNode json = JsonNodeFactory.instance.objectNode();
try {
json.put("name", "VIVO Reconciliation Service"); json.put("name", "VIVO Reconciliation Service");
if (defaultNamespace != null) { if (defaultNamespace != null) {
json.put("identifierSpace", defaultNamespace); json.put("identifierSpace", defaultNamespace);
json.put("schemaSpace", defaultNamespace); json.put("schemaSpace", defaultNamespace);
} }
JSONObject viewJson = new JSONObject(); ObjectNode viewJson = JsonNodeFactory.instance.objectNode();
StringBuffer urlBuf = new StringBuffer(); StringBuffer urlBuf = new StringBuffer();
urlBuf.append("http://" + serverName); urlBuf.append("http://" + serverName);
if (serverPort == 8080) { if (serverPort == 8080) {
@ -208,33 +217,29 @@ public class JSONReconcileServlet extends VitroHttpServlet {
idNameArray[i] = splitList[i].split(","); idNameArray[i] = splitList[i].split(",");
} }
// process and add to json defaultTypes // process and add to json defaultTypes
JSONArray defaultTypesJsonArr = new JSONArray(); ArrayNode defaultTypesJsonArr = JsonNodeFactory.instance.arrayNode();
for (int i = 0; i<idNameArray.length; i++) { for (int i = 0; i<idNameArray.length; i++) {
JSONObject defaultTypesJson = new JSONObject(); ObjectNode defaultTypesJson = JsonNodeFactory.instance.objectNode();
defaultTypesJson.put("id", idNameArray[i][0].trim()); defaultTypesJson.put("id", idNameArray[i][0].trim());
defaultTypesJson.put("name", idNameArray[i][1].trim()); defaultTypesJson.put("name", idNameArray[i][1].trim());
defaultTypesJsonArr.put(defaultTypesJson); defaultTypesJsonArr.add(defaultTypesJson);
} }
json.put("defaultTypes", defaultTypesJsonArr); json.put("defaultTypes", defaultTypesJsonArr);
} }
} catch (JSONException ex) {
throw new ServletException(
"JSONReconcileServlet: Could not create metadata: " + ex);
}
return json; return json;
} }
private JSONObject runSearch(HashMap<String, JSONObject> currMap) throws ServletException { private ObjectNode runSearch(HashMap<String, JsonNode> currMap) throws ServletException {
JSONObject qJson = new JSONObject(); ObjectNode qJson = JsonNodeFactory.instance.objectNode();
try { try {
for (Map.Entry<String, JSONObject> entry : currMap.entrySet()) { for (Map.Entry<String, JsonNode> entry : currMap.entrySet()) {
JSONObject resultAllJson = new JSONObject(); ObjectNode resultAllJson = JsonNodeFactory.instance.objectNode();
String key = entry.getKey(); String key = entry.getKey();
JSONObject json = entry.getValue(); JsonNode json = entry.getValue();
String queryVal = json.getString("query"); String queryVal = json.get("query").asText();
// System.out.println("query: " + json.toString()); // System.out.println("query: " + json.toString());
@ -245,22 +250,24 @@ public class JSONReconcileServlet extends VitroHttpServlet {
ArrayList<String[]> propertiesList = new ArrayList<String[]>(); ArrayList<String[]> propertiesList = new ArrayList<String[]>();
if (json.has("type")) { if (json.has("type")) {
searchType = json.getString("type"); searchType = json.get("type").asText();
} }
if (json.has("limit")) { if (json.has("limit")) {
limit = json.getInt("limit"); limit = json.get("limit").asInt();
} }
if (json.has("type_strict")) { // Not sure what this variable if (json.has("type_strict")) { // Not sure what this variable
// represents. Skip for now. // represents. Skip for now.
typeStrict = json.getString("type_strict"); typeStrict = json.get("type_strict").asText();
} }
if (json.has("properties")) { if (json.has("properties")) {
JSONArray properties = json.getJSONArray("properties"); JsonNode propertiesNode = json.get("properties");
for (int i = 0; i < properties.length(); i++) { if (propertiesNode instanceof ArrayNode) {
ArrayNode properties = (ArrayNode)propertiesNode;
for (int i = 0; i < properties.size(); i++) {
String[] pvPair = new String[2]; String[] pvPair = new String[2];
JSONObject jsonProperty = properties.getJSONObject(i); JsonNode jsonProperty = properties.get(i);
String pid = jsonProperty.getString("pid"); String pid = JacksonUtils.getString(jsonProperty, "pid");
String v = jsonProperty.getString("v"); String v = JacksonUtils.getString(jsonProperty, "v");
if (pid != null && v != null) { if (pid != null && v != null) {
pvPair[0] = pid; pvPair[0] = pid;
pvPair[1] = v; pvPair[1] = v;
@ -268,9 +275,10 @@ public class JSONReconcileServlet extends VitroHttpServlet {
} }
} }
} }
}
// begin search // begin search
JSONArray resultJsonArr = new JSONArray(); ArrayNode resultJsonArr = JsonNodeFactory.instance.arrayNode();
SearchQuery query = getQuery(queryVal, searchType, limit, propertiesList); SearchQuery query = getQuery(queryVal, searchType, limit, propertiesList);
SearchResponse queryResponse = null; SearchResponse queryResponse = null;
@ -299,14 +307,19 @@ public class JSONReconcileServlet extends VitroHttpServlet {
SearchResult result = new SearchResult(name, uri); SearchResult result = new SearchResult(name, uri);
// populate result for Google Refine // populate result for Google Refine
JSONObject resultJson = new JSONObject(); ObjectNode resultJson = JsonNodeFactory.instance.objectNode();
resultJson.put("score", doc.getFirstValue("score")); Object score = doc.getFirstValue("score");
if (score instanceof Double) {
resultJson.put("score", (Double)score);
} else if (score instanceof Float) {
resultJson.put("score", (Float)score);
}
String modUri = result.getUri().replace("#", "%23"); String modUri = result.getUri().replace("#", "%23");
resultJson.put("id", modUri); resultJson.put("id", modUri);
resultJson.put("name", result.getLabel()); resultJson.put("name", result.getLabel());
Collection<Object> rdfTypes = doc.getFieldValues(VitroSearchTermNames.RDFTYPE); Collection<Object> rdfTypes = doc.getFieldValues(VitroSearchTermNames.RDFTYPE);
JSONArray typesJsonArr = new JSONArray(); ArrayNode typesJsonArr = JsonNodeFactory.instance.arrayNode();
if (rdfTypes != null) { if (rdfTypes != null) {
for (Object rdfType : rdfTypes) { for (Object rdfType : rdfTypes) {
@ -317,17 +330,17 @@ public class JSONReconcileServlet extends VitroHttpServlet {
int lastIndex2 = type.lastIndexOf('/') + 1; int lastIndex2 = type.lastIndexOf('/') + 1;
String typeName = type.substring(lastIndex2); String typeName = type.substring(lastIndex2);
typeName = typeName.replace("#", ":"); typeName = typeName.replace("#", ":");
JSONObject typesJson = new JSONObject(); ObjectNode typesJson = JsonNodeFactory.instance.objectNode();
typesJson.put("id", type); typesJson.put("id", type);
typesJson.put("name", typeName); typesJson.put("name", typeName);
typesJsonArr.put(typesJson); typesJsonArr.add(typesJson);
} }
} }
resultJson.put("type", typesJsonArr); resultJson.put("type", typesJsonArr);
resultJson.put("match", "false"); resultJson.put("match", "false");
resultJsonArr.put(resultJson); resultJsonArr.add(resultJson);
} catch (Exception e) { } catch (Exception e) {
log.error("problem getting usable individuals from search " log.error("problem getting usable individuals from search "
@ -342,16 +355,16 @@ public class JSONReconcileServlet extends VitroHttpServlet {
// System.out.println("results: " + qJson.toString()); // System.out.println("results: " + qJson.toString());
} }
} catch (JSONException ex) {
log.error("JSONException: " + ex);
throw new ServletException("JSONReconcileServlet JSONException: "
+ ex);
} catch (SearchEngineException ex) { } catch (SearchEngineException ex) {
log.error("JSONException: " + ex); log.error("JSONException: " + ex);
throw new ServletException("JSONReconcileServlet SearchEngineException: " throw new ServletException("JSONReconcileServlet SearchEngineException: "
+ ex); + ex);
} }
if (qJson.has(INTERNAL_QUERY_NAME)) {
return (ObjectNode)qJson.get(INTERNAL_QUERY_NAME);
}
return qJson; return qJson;
} }

8
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/json/JacksonUtils.java
View file

@ -59,6 +59,14 @@ public class JacksonUtils {
return strings; return strings;
} }
public static String getString(JsonNode node, String name) {
if (node.has(name)) {
return node.get(name).asText();
}
return null;
}
public static class JacksonUtilsException extends RuntimeException { public static class JacksonUtilsException extends RuntimeException {
public JacksonUtilsException() { public JacksonUtilsException() {

9
api/src/test/java/edu/cornell/mannlib/vitro/webapp/controller/grefine/JSONReconcileServletTest.java
View file

@ -10,8 +10,7 @@ import java.util.regex.PatternSyntaxException;
import javax.servlet.ServletException; import javax.servlet.ServletException;
import org.json.JSONException; import com.fasterxml.jackson.databind.node.ObjectNode;
import org.json.JSONObject;
import org.junit.Assert; import org.junit.Assert;
import org.junit.Before; import org.junit.Before;
import org.junit.Test; import org.junit.Test;
@ -53,14 +52,12 @@ public class JSONReconcileServletTest extends AbstractTestClass {
String defaultTypeList = null; String defaultTypeList = null;
String serverName = null; String serverName = null;
String schemaSpaceOutput = null; String schemaSpaceOutput = null;
JSONObject jsonResult = null; ObjectNode jsonResult = null;
try { try {
jsonResult = reconcile.getMetadata(request, response, defaultNamespace, defaultTypeList, serverName, serverPort); jsonResult = reconcile.getMetadata(request, response, defaultNamespace, defaultTypeList, serverName, serverPort);
schemaSpaceOutput = jsonResult.getString("schemaSpace"); schemaSpaceOutput = jsonResult.get("schemaSpace").asText();
} catch (ServletException e) { } catch (ServletException e) {
System.err.println("JSONReconcileServletTest getMetadata ServletException: " + e); System.err.println("JSONReconcileServletTest getMetadata ServletException: " + e);
} catch (JSONException e) {
System.err.println("JSONReconcileServletTest getMetadata JSONException: " + e);
} }
Assert.assertNotNull("output should not be null", jsonResult); Assert.assertNotNull("output should not be null", jsonResult);
Assert.assertEquals("schemaSpaceOutput", defaultNamespace, schemaSpaceOutput); Assert.assertEquals("schemaSpaceOutput", defaultNamespace, schemaSpaceOutput);

4
dependencies/pom.xml vendored
View file

@ -203,11 +203,11 @@
<artifactId>jackson-core</artifactId> <artifactId>jackson-core</artifactId>
<version>2.7.4</version> <version>2.7.4</version>
</dependency> </dependency>
<dependency> <!-- dependency>
<groupId>com.fasterxml.jackson.datatype</groupId> <groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-json-org</artifactId> <artifactId>jackson-datatype-json-org</artifactId>
<version>2.7.4</version> <version>2.7.4</version>
</dependency> </dependency -->
<!-- dependency> <!-- dependency>
<groupId>com.fasterxml.jackson.datatype</groupId> <groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr353</artifactId> <artifactId>jackson-datatype-jsr353</artifactId>