Merge branch 'rest-so' into 'develop'

Rest stackoverflow

This fixes a stackoverflow which was occurring when displaying json for Collections which also had connected PeerCollections. 

It also folds in updates for jackson and jersey.

See merge request !4

ace-am/pom.xml

@@ -117,9 +117,9 @@
 
         <!-- for json -->
         <dependency>
-            <groupId>org.codehaus.jackson</groupId>
-            <artifactId>jackson-mapper-asl</artifactId>
-            <version>1.8.1</version>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+            <version>2.8.1</version>
         </dependency>
 
         <dependency>
@@ -243,7 +243,7 @@
             </exclusions>
         </dependency> -->
         
-        <!-- web services -->
+        <!-- web services
         <dependency>
             <groupId>com.sun.jersey</groupId>
             <artifactId>jersey-server</artifactId>
@@ -254,6 +254,17 @@
             <artifactId>jersey-json</artifactId>
             <version>1.6</version>
         </dependency>
+        -->
+        <dependency>
+            <groupId>org.glassfish.jersey.containers</groupId>
+            <artifactId>jersey-container-servlet</artifactId>
+            <version>2.24</version>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.media</groupId>
+            <artifactId>jersey-media-json-jackson</artifactId>
+            <version>2.24</version>
+        </dependency>
         <dependency>
             <groupId>edu.umiacs.ace</groupId>
             <artifactId>ace-ims-ws</artifactId>

ace-am/src/main/java/edu/umiacs/ace/monitor/core/Collection.java

@@ -31,6 +31,7 @@
 
 package edu.umiacs.ace.monitor.core;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import edu.umiacs.ace.monitor.peers.PeerCollection;
 import edu.umiacs.util.Argument;
 
@@ -50,7 +51,6 @@ import javax.persistence.OneToMany;
 import javax.persistence.Table;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
-import javax.xml.bind.annotation.XmlRootElement;
 import java.io.Serializable;
 import java.util.Date;
 import java.util.List;
@@ -79,11 +79,11 @@ import java.util.Map;
     @NamedQuery(name = "Collection.getCollectionsInGroup", query =
     "SELECT c FROM Collection c WHERE c.group = :group")
 })
-@XmlRootElement
 public class Collection implements Serializable {
 
     @OneToMany(mappedBy = "parent", cascade = CascadeType.ALL)
     private List<PeerCollection> peerCollections;
+
     private static final long serialVersionUID = 1L;
 
     @Id
@@ -134,6 +134,7 @@ public class Collection implements Serializable {
         this.peerCollections = peerCollections;
     }
 
+    @JsonIgnore
     public List<PeerCollection> getPeerCollections() {
         return peerCollections;
     }

ace-am/src/main/java/edu/umiacs/ace/monitor/reporting/ReportJob.java

@@ -31,15 +31,9 @@
 
 package edu.umiacs.ace.monitor.reporting;
 
-import com.sun.jersey.api.MessageException;
 import edu.umiacs.ace.monitor.log.LogEnum;
 import edu.umiacs.ace.monitor.log.LogEventManager;
 import edu.umiacs.ace.util.PersistUtil;
-import java.text.ParseException;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.GregorianCalendar;
-import javax.persistence.EntityManager;
 import org.apache.log4j.Logger;
 import org.apache.log4j.NDC;
 import org.quartz.CronExpression;
@@ -48,6 +42,13 @@ import org.quartz.Job;
 import org.quartz.JobExecutionContext;
 import org.quartz.JobExecutionException;
 
+import javax.mail.MessagingException;
+import javax.persistence.EntityManager;
+import java.text.ParseException;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
+
 /**
  * Report Generation job for quartz
  * @author toaster
@@ -90,9 +91,9 @@ public class ReportJob implements Job {
         } catch ( ParseException ex ) {
             LOG.error("Unknown parse exception", ex);
             throw new JobExecutionException(ex);
-        } catch ( MessageException ex) {
+        } catch (MessagingException ex) {
             EntityManager em = PersistUtil.getEntityManager();
-            logManager.persistCollectionEvent(LogEnum.SMTP_ERROR, 
+            logManager.persistCollectionEvent(LogEnum.SMTP_ERROR,
                                               ex.getMessage(), em);
             em.close();
             LOG.error("Could not send report summary", ex);

ace-am/src/main/java/edu/umiacs/ace/remote/AceItem.java

@@ -31,10 +31,11 @@
 
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import edu.umiacs.util.Argument;
+
 import java.util.Date;
-import org.codehaus.jackson.annotate.JsonIgnoreProperties;
-import org.codehaus.jackson.map.annotate.JsonDeserialize;
 @JsonIgnoreProperties(ignoreUnknown=true)
 public class AceItem {
 

ace-am/src/main/java/edu/umiacs/ace/remote/CustomBooleanDeserializer.java

@@ -31,12 +31,13 @@
 
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
 import edu.umiacs.util.Strings;
+
 import java.io.IOException;
-import org.codehaus.jackson.JsonParser;
-import org.codehaus.jackson.JsonProcessingException;
-import org.codehaus.jackson.map.DeserializationContext;
-import org.codehaus.jackson.map.JsonDeserializer;
 
 /**
  * 
@@ -45,7 +46,7 @@ import org.codehaus.jackson.map.JsonDeserializer;
 public class CustomBooleanDeserializer extends JsonDeserializer<Boolean> {
 
     @Override
-    public Boolean deserialize( JsonParser arg0, DeserializationContext arg1 )
+    public Boolean deserialize(JsonParser arg0, DeserializationContext arg1 )
             throws IOException,
             JsonProcessingException {
 

ace-am/src/main/java/edu/umiacs/ace/remote/CustomCharDeserializer.java

@@ -31,12 +31,13 @@
 
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
 import edu.umiacs.util.Strings;
+
 import java.io.IOException;
-import org.codehaus.jackson.JsonParser;
-import org.codehaus.jackson.JsonProcessingException;
-import org.codehaus.jackson.map.DeserializationContext;
-import org.codehaus.jackson.map.JsonDeserializer;
 
 /**
  * 
@@ -45,7 +46,7 @@ import org.codehaus.jackson.map.JsonDeserializer;
 public class CustomCharDeserializer extends JsonDeserializer<Character> {
 
     @Override
-    public Character deserialize( JsonParser arg0, DeserializationContext arg1 )
+    public Character deserialize(JsonParser arg0, DeserializationContext arg1 )
             throws IOException,
             JsonProcessingException {
 

ace-am/src/main/java/edu/umiacs/ace/remote/CustomDateDeserializer.java

@@ -31,12 +31,13 @@
 
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
+
 import java.io.IOException;
 import java.util.Date;
-import org.codehaus.jackson.JsonParser;
-import org.codehaus.jackson.JsonProcessingException;
-import org.codehaus.jackson.map.DeserializationContext;
-import org.codehaus.jackson.map.JsonDeserializer;
 
 /**
  * 
@@ -45,7 +46,7 @@ import org.codehaus.jackson.map.JsonDeserializer;
 public class CustomDateDeserializer extends JsonDeserializer<Date> {
 
     @Override
-    public Date deserialize( JsonParser arg0, DeserializationContext arg1 ) throws IOException,
+    public Date deserialize(JsonParser arg0, DeserializationContext arg1 ) throws IOException,
             JsonProcessingException {
         try {
             return arg1.parseDate(arg0.getText());

ace-am/src/main/java/edu/umiacs/ace/remote/CustomLongDeserializer.java

@@ -31,12 +31,13 @@
 
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
 import edu.umiacs.util.Strings;
+
 import java.io.IOException;
-import org.codehaus.jackson.JsonParser;
-import org.codehaus.jackson.JsonProcessingException;
-import org.codehaus.jackson.map.DeserializationContext;
-import org.codehaus.jackson.map.JsonDeserializer;
 
 /**
  * 
@@ -45,7 +46,7 @@ import org.codehaus.jackson.map.JsonDeserializer;
 public class CustomLongDeserializer extends JsonDeserializer<Long> {
 
     @Override
-    public Long deserialize( JsonParser arg0, DeserializationContext arg1 ) throws IOException,
+    public Long deserialize(JsonParser arg0, DeserializationContext arg1 ) throws IOException,
             JsonProcessingException {
         try {
             if ( Strings.isEmpty(arg1) ) {

ace-am/src/main/java/edu/umiacs/ace/remote/JsonGateway.java

@@ -31,6 +31,8 @@
 
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.databind.DeserializationConfig;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import edu.umiacs.ace.monitor.peers.PartnerSite;
 import edu.umiacs.util.Strings;
 import org.apache.http.HttpResponse;
@@ -42,8 +44,6 @@ import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.BasicCredentialsProvider;
 import org.apache.http.impl.client.HttpClients;
 import org.apache.log4j.Logger;
-import org.codehaus.jackson.map.DeserializationConfig;
-import org.codehaus.jackson.map.ObjectMapper;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -78,7 +78,7 @@ public class JsonGateway {
         mapper = new ObjectMapper();
 
         DeserializationConfig cfg = mapper.getDeserializationConfig();
-        cfg.setDateFormat(new SimpleDateFormat("EEE MMM dd hh:mm:ss zzz yyyy"));
+        cfg.with(new SimpleDateFormat("EEE MMM dd hh:mm:ss zzz yyyy"));
     }
 
     public static final JsonGateway getGateway() {

ace-am/src/main/java/edu/umiacs/ace/remote/ParentChildBean.java

@@ -31,8 +31,9 @@
 
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+
 import java.util.List;
-import org.codehaus.jackson.annotate.JsonIgnoreProperties;
 
 /**
  *

ace-am/src/main/java/edu/umiacs/ace/remote/ReportBean.java

@@ -31,10 +31,11 @@
 
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+
 import java.io.Serializable;
 import java.util.List;
-import org.codehaus.jackson.annotate.JsonIgnoreProperties;
-import org.codehaus.jackson.map.annotate.JsonDeserialize;
 
 /**
  * representation of ace report json

ace-am/src/main/java/edu/umiacs/ace/remote/StatusBean.java

@@ -30,12 +30,13 @@
 // $Id$
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import edu.umiacs.util.Argument;
+
 import java.io.Serializable;
 import java.util.Date;
 import java.util.List;
-import org.codehaus.jackson.annotate.JsonIgnoreProperties;
-import org.codehaus.jackson.map.annotate.JsonDeserialize;
 
 /**
  *

ace-am/src/main/java/edu/umiacs/ace/remote/SummaryBean.java

@@ -30,15 +30,16 @@
 // $Id$
 package edu.umiacs.ace.remote;
 
+import com.fasterxml.jackson.annotation.JsonAnySetter;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import edu.umiacs.util.Argument;
+
 import java.io.Serializable;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import org.codehaus.jackson.annotate.JsonAnySetter;
-import org.codehaus.jackson.annotate.JsonIgnoreProperties;
-import org.codehaus.jackson.map.annotate.JsonDeserialize;
 
 /**
  *

ace-am/src/main/java/edu/umiacs/ace/rest/CollectionManagement.java

@@ -5,6 +5,8 @@
 
 package edu.umiacs.ace.rest;
 
+import atg.taglib.json.util.JSONException;
+import atg.taglib.json.util.JSONObject;
 import edu.umiacs.ace.driver.StorageDriver;
 import edu.umiacs.ace.driver.StorageDriverFactory;
 import edu.umiacs.ace.monitor.access.CollectionCountContext;
@@ -13,8 +15,6 @@ import edu.umiacs.ace.monitor.core.Collection;
 import edu.umiacs.ace.monitor.core.MonitoredItem;
 import edu.umiacs.ace.util.PersistUtil;
 import org.apache.log4j.Logger;
-import org.codehaus.jettison.json.JSONException;
-import org.codehaus.jettison.json.JSONObject;
 
 import javax.annotation.security.RolesAllowed;
 import javax.persistence.EntityManager;

ace-am/src/main/java/edu/umiacs/ace/rest/ListController.java

@@ -2,7 +2,6 @@ package edu.umiacs.ace.rest;
 
 import edu.umiacs.ace.monitor.core.Collection;
 import edu.umiacs.ace.util.PersistUtil;
-import org.codehaus.jettison.json.JSONArray;
 
 import javax.persistence.EntityManager;
 import javax.persistence.Query;
@@ -28,11 +27,10 @@ public class ListController {
     @GET
     @Produces(MediaType.APPLICATION_JSON)
     @Path("groups")
-    public JSONArray getGroups() {
+    public List<String> getGroups() {
         EntityManager em = PersistUtil.getEntityManager();
         Query q = em.createNamedQuery("Collection.listGroups");
-        List<String> groups = q.getResultList();
-        return new JSONArray(q.getResultList());
+        return q.getResultList();
     }
 
     /**

ace-am/src/main/webapp/WEB-INF/web.xml

@@ -82,9 +82,9 @@
     </listener>
     <servlet>
         <servlet-name>ServletAdaptor</servlet-name>
-        <servlet-class>com.sun.jersey.spi.container.servlet.ServletContainer</servlet-class>
+        <servlet-class>org.glassfish.jersey.servlet.ServletContainer</servlet-class>
         <init-param>
-            <param-name>com.sun.jersey.config.property.packages</param-name>
+            <param-name>jersey.config.server.provider.packages</param-name>
             <param-value>edu.umiacs.ace.rest</param-value>
         </init-param>
         <load-on-startup>1</load-on-startup>