import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import jalview.util.JSONUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import java.net.URI;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.Objects;
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 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;
/**
* A rest client for querying the Search endpoint of the PDB API
*
* @author tcnofoegbu
- *
*/
public class PDBFTSRestClient extends FTSRestClient
{
* @return the pdbResponse object for the given request
* @throws Exception
*/
+ @SuppressWarnings({ "unused", "unchecked" })
@Override
public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
throws Exception
{
try
{
- ClientConfig clientConfig = new DefaultClientConfig();
- Client client = Client.create(clientConfig);
-
String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
pdbRestRequest.getWantedFields());
int responseSize = (pdbRestRequest.getResponseSize() == 0)
: " AND status:REL");
// Build request parameters for the REST Request
- WebResource webResource = null;
+
+ // BH 2018 the trick here is to coerce the classes in Javascript to be
+ // different from the ones in Java yet still allow this to be correct for Java
+ Client client;
+ Class<ClientResponse> clientResponseClass;
+ if (Platform.isJS())
+ {
+ // JavaScript only -- coerce types to Java types for Java
+ client = (Client) (Object) new jalview.javascript.web.Client();
+ clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ client = Client.create(new DefaultClientConfig());
+ clientResponseClass = ClientResponse.class;
+ }
+
+ WebResource webResource;
if (pdbRestRequest.isFacet())
{
webResource = client.resource(PDB_SEARCH_ENDPOINT)
.queryParam("start", String.valueOf(offSet))
.queryParam("q", query).queryParam("sort", sortParam);
}
+
+ URI uri = webResource.getURI();
+
+ System.out.println(uri);
+
// Execute the REST request
ClientResponse clientResponse = webResource
- .accept(MediaType.APPLICATION_JSON).get(ClientResponse.class);
+ .accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
+
+ // Get the JSON string from the response object or directly from the
+ // client (JavaScript)
+ Map<String, Object> jsonObj = null;
+ String responseString = null;
- // Get the JSON string from the response object
- String responseString = clientResponse.getEntity(String.class);
// System.out.println("query >>>>>>> " + pdbRestRequest.toString());
// Check the response status and report exception if one occurs
int responseStatus = clientResponse.getStatus();
- if (responseStatus != 200)
+ switch (responseStatus)
{
- String errorMessage = "";
- if (responseStatus == 400)
+ case 200:
+ if (Platform.isJS())
{
- errorMessage = parseJsonExceptionString(responseString);
- throw new Exception(errorMessage);
+ jsonObj = clientResponse.getEntity(Map.class);
}
else
{
- errorMessage = getMessageByHTTPStatusCode(
- responseStatus, "PDB");
- throw new Exception(errorMessage);
+ responseString = clientResponse.getEntity(String.class);
}
+ break;
+ case 400:
+ throw new Exception(parseJsonExceptionString(responseString));
+ default:
+ throw new Exception(
+ getMessageByHTTPStatusCode(responseStatus, "PDB"));
}
- // Make redundant objects eligible for garbage collection to conserve
- // memory
- clientResponse = null;
- client = null;
-
// Process the response and return the result to the caller.
- return parsePDBJsonResponse(responseString, pdbRestRequest);
+ return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
} catch (Exception e)
{
String exceptionMsg = e.getMessage();
* the JSON string containing error message from the server
* @return the processed error message from the JSON string
*/
- public static String parseJsonExceptionString(String jsonErrorResponse)
+ @SuppressWarnings("unchecked")
+public static String parseJsonExceptionString(String jsonErrorResponse)
{
StringBuilder errorMessage = new StringBuilder(
"\n============= PDB Rest Client RunTime error =============\n");
+
+// {
+// "responseHeader":{
+// "status":0,
+// "QTime":0,
+// "params":{
+// "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
+// "fl":"pdb_id,title,experimental_method,resolution",
+// "start":"0",
+// "sort":"overall_quality desc",
+// "rows":"500",
+// "wt":"json"}},
+// "response":{"numFound":1,"start":0,"docs":[
+// {
+// "experimental_method":["X-ray diffraction"],
+// "pdb_id":"4zhp",
+// "resolution":2.46,
+// "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}]
+// }}
+//
try
{
- JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
- JSONObject errorResponse = (JSONObject) jsonObj.get("error");
+ Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(jsonErrorResponse);
+ Map<String, Object> errorResponse = (Map<String, Object>) jsonObj.get("error");
- JSONObject responseHeader = (JSONObject) jsonObj
+ Map<String, Object> responseHeader = (Map<String, Object>) jsonObj
.get("responseHeader");
- JSONObject paramsObj = (JSONObject) responseHeader.get("params");
+ Map<String, Object> paramsObj = (Map<String, Object>) responseHeader.get("params");
String status = responseHeader.get("status").toString();
String message = errorResponse.get("msg").toString();
String query = paramsObj.get("q").toString();
* JSON string
* @return
*/
- @SuppressWarnings("unchecked")
public static FTSRestResponse parsePDBJsonResponse(
String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
{
+ return parsePDBJsonResponse(pdbJsonResponseString,
+ (Map<String, Object>) null, pdbRestRequest);
+ }
+
+ @SuppressWarnings("unchecked")
+ public static FTSRestResponse parsePDBJsonResponse(
+ String pdbJsonResponseString, Map<String, Object> jsonObj,
+ FTSRestRequest pdbRestRequest)
+ {
FTSRestResponse searchResult = new FTSRestResponse();
List<FTSData> result = null;
try
{
- JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser
- .parse(pdbJsonResponseString);
-
- JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
- String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
+ if (jsonObj == null)
+ {
+ jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
+ }
+ Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj.get("response");
+ String queryTime = ((Map<String, Object>) jsonObj.get("responseHeader"))
.get("QTime").toString();
int numFound = Integer
.valueOf(pdbResponse.get("numFound").toString());
if (numFound > 0)
{
- result = new ArrayList<FTSData>();
- JSONArray docs = (JSONArray) pdbResponse.get("docs");
- for (Iterator<JSONObject> docIter = docs.iterator(); docIter
+ result = new ArrayList<>();
+ List<Object> docs = (List<Object>) pdbResponse.get("docs");
+ for (Iterator<Object> docIter = docs.iterator(); docIter
.hasNext();)
{
- JSONObject doc = docIter.next();
+ Map<String, Object> doc = (Map<String, Object>) docIter.next();
result.add(getFTSData(doc, pdbRestRequest));
}
searchResult.setNumberOfItemsFound(numFound);
return searchResult;
}
- public static FTSData getFTSData(JSONObject pdbJsonDoc,
+ public static FTSData getFTSData(Map<String, Object> pdbJsonDoc,
FTSRestRequest request)
{
if (allDefaultDisplayedStructureDataColumns == null
|| allDefaultDisplayedStructureDataColumns.isEmpty())
{
- allDefaultDisplayedStructureDataColumns = new ArrayList<FTSDataColumnI>();
+ allDefaultDisplayedStructureDataColumns = new ArrayList<>();
allDefaultDisplayedStructureDataColumns
.addAll(super.getAllDefaultDisplayedFTSDataColumns());
}
return allDefaultDisplayedStructureDataColumns;
}
+
+
}
git://source.jalview.org / jalview.git / blobdiff