From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 1 May 2015 11:02:17 +0000 (+0100)
Subject: JAL-1726 Added external integration test for PDB Rest API
X-Git-Tag: Jalview_2_9~29^2~1^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dc53250eeeb8c854c876b0fc896c541bd8cd8710;hp=9e8c6798b524aa8743c271a3115f6cb307eb83ea;p=jalview.git

JAL-1726 Added external integration test for PDB Rest API
---

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index c5642a9..02523da 100644
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -31,7 +31,7 @@ import com.sun.jersey.api.json.JSONConfiguration;
  */
 public class PDBRestClient
 {
-  private static String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
+  public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
 
   private static int DEFAULT_RESPONSE_SIZE = 200;
 
@@ -240,6 +240,7 @@ public class PDBRestClient
     return pdbFeildIndexCounter;
   }
 
+
   /**
    * This enum represents the fields available in the PDB JSON response
    *
diff --git a/test/jalview/ws/dbsources/PDBRestClientTest.java b/test/jalview/ws/dbsources/PDBRestClientTest.java
index 181fcf1..86cb3a3 100644
--- a/test/jalview/ws/dbsources/PDBRestClientTest.java
+++ b/test/jalview/ws/dbsources/PDBRestClientTest.java
@@ -2,6 +2,7 @@ package jalview.ws.dbsources;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
 import jalview.ws.uimodel.PDBRestRequest;
 import jalview.ws.uimodel.PDBRestResponse;
@@ -10,12 +11,25 @@ import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
+import javax.ws.rs.core.MediaType;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
+import com.sun.jersey.api.client.Client;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.api.client.config.ClientConfig;
+import com.sun.jersey.api.client.config.DefaultClientConfig;
+
 public class PDBRestClientTest
 {
 
@@ -162,6 +176,75 @@ public class PDBRestClientTest
     assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false));
   }
 
+  @Test
+  public void externalServiceIntegrationTest()
+  {
+    ClientConfig clientConfig = new DefaultClientConfig();
+    Client client = Client.create(clientConfig);
+
+    // Build request parameters for the REST Request
+    WebResource webResource = client
+            .resource(PDBRestClient.PDB_SEARCH_ENDPOINT)
+            .queryParam("wt", "json").queryParam("rows", String.valueOf(1))
+            .queryParam("q", "text:abc AND molecule_sequence:['' TO *]");
+
+    // Execute the REST request
+    ClientResponse clientResponse = webResource.accept(
+            MediaType.APPLICATION_JSON).get(ClientResponse.class);
+
+    // Get the JSON string from the response object
+    String pdbJsonResponseString = clientResponse.getEntity(String.class);
+
+    // Check the response status and report exception if one occurs
+    if (clientResponse.getStatus() != 200)
+    {
+      fail("Webservice call failed!!!");
+    }
+    else
+    {
+      try
+      {
+        JSONParser jsonParser = new JSONParser();
+        JSONObject jsonObj = (JSONObject) jsonParser
+                .parse(pdbJsonResponseString);
+        JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
+        String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
+                .get("QTime").toString();
+        String numFound = pdbResponse.get("numFound").toString();
+        JSONArray docs = (JSONArray) pdbResponse.get("docs");
+        Iterator<JSONObject> docIter = docs.iterator();
+
+        assertTrue("Couldn't Retrieve 'response' object",
+                pdbResponse != null);
+        assertTrue("Couldn't Retrieve 'QTime' value", queryTime != null);
+        assertTrue("Couldn't Retrieve 'numFound' value", numFound != null);
+        assertTrue("Couldn't Retrieve 'docs' object", docs != null
+                || !docIter.hasNext());
+
+        JSONObject pdbJsonDoc = docIter.next();
+
+        for (PDBDocField field : PDBDocField.values())
+        {
+          if (field == PDBDocField.ALL)
+          {
+            continue;
+          }
+          if (pdbJsonDoc.get(field.getCode()) == null)
+          {
+            // System.out.println(">>>\t" + field.getCode());
+            assertTrue(field.getClass()
+                    + " has been removed from PDB doc Entity",
+                    !pdbJsonResponseString.contains(field.getCode()));
+          }
+        }
+      } catch (ParseException e)
+      {
+        fail(">>>  Test failed due to exception while parsing pdb response json !!!");
+        e.printStackTrace();
+      }
+    }
+  }
+
   public String readJsonStringFromFile(String filePath) throws IOException
   {
     String fileContent;
@@ -185,5 +268,4 @@ public class PDBRestClientTest
     return fileContent;
   }
 
-
 }