package jalview.ext.ensembl;
import jalview.bin.Cache;
-import jalview.javascript.json.JSON;
-import jalview.util.JSONUtils;
import jalview.util.Platform;
import jalview.util.StringUtils;
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.ProtocolException;
* in milliseconds
* @return
* @throws IOException
+ * @throws ParseException
*/
- private BufferedReader getHttpResponse(URL url, List<String> ids,
- int readTimeout) throws IOException
+ private Object getJSON(URL url, List<String> ids, int readTimeout)
+ throws IOException, ParseException
{
+
if (readTimeout < 0)
{
readTimeout = DEFAULT_READ_TIMEOUT;
HttpURLConnection connection = null;
int responseCode = 0;
- if (Platform.isJS())
- {
- JSON.setAjax(url);
- }
+ Platform.setAjaxJSON(url);
while (retriesLeft > 0)
{
InputStream response = connection.getInputStream();
- if (Platform.isJS())
- {
- return JSON.getJSONReader(response);
- }
-
- // System.out.println(getClass().getName() + " took "
- // + (System.currentTimeMillis() - now) + "ms to fetch");
+ Platform.timeCheck(null, Platform.TIME_MARK);
+ Object ret = Platform.parseJSON(response);
+ Platform.timeCheck("EnsemblRestClient.getJSON " + url,
+ Platform.TIME_MARK);
- return new BufferedReader(new InputStreamReader(response, "UTF-8"));
+ return ret;
}
/**
url = getUrl(ids);
}
- Reader br = null;
- try
- {
- Platform.timeCheck(null, Platform.TIME_MARK);
-
- br = (url == null ? null : getHttpResponse(url, ids, msDelay));
-
- Object ret = (br == null ? null : JSONUtils.parse(br));
-
- Platform.timeCheck("EnsemblRestClient.getJSON " + url,
- Platform.TIME_MARK);
+ Object json = (url == null ? null : getJSON(url, ids, msDelay));
- if (ret != null && mapKey != null)
- {
- ret = ((Map<String, Object>) ret).get(mapKey);
- }
- if (ret == null)
- {
- return null;
- }
- switch (mode)
- {
- case MODE_ARRAY:
- case MODE_MAP:
- break;
- case MODE_ITERATOR:
- ret = ((List<Object>) ret).iterator();
- break;
- }
- return ret;
-
- } finally
+ if (json != null && mapKey != null)
{
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
+ json = ((Map<String, Object>) json).get(mapKey);
+ }
+ if (json == null)
+ {
+ return null;
+ }
+ switch (mode)
+ {
+ case MODE_ARRAY:
+ case MODE_MAP:
+ break;
+ case MODE_ITERATOR:
+ json = ((List<Object>) json).iterator();
+ break;
}
+ return json;
}
/**
URI uri = webResource.getURI();
+ System.out.println(uri);
+
// Execute the REST request
ClientResponse clientResponse = webResource
.accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
- // Get the JSON string from the response object
- String responseString = clientResponse.getEntity(String.class);
+ int status = clientResponse.getStatus();
+
+ // Get the JSON string from the response object or directly from the
+ // client (JavaScript)
+ Map<String, Object> jsonObj = (status == 200
+ ? clientResponse.getEntity(Map.class)
+ : null);
+ String responseString = (jsonObj == null
+ ? clientResponse.getEntity(String.class)
+ : null);
+
// System.out.println("query >>>>>>> " + pdbRestRequest.toString());
// Check the response status and report exception if one occurs
- if (clientResponse.getStatus() != 200)
+ switch (status)
{
- String errorMessage = "";
- if (clientResponse.getStatus() == 400)
- {
- errorMessage = parseJsonExceptionString(responseString);
- throw new Exception(errorMessage);
- }
- else
- {
- errorMessage = getMessageByHTTPStatusCode(
- clientResponse.getStatus(), "PDB");
- throw new Exception(errorMessage);
- }
+ case 200:
+ break;
+ case 400:
+ throw new Exception(parseJsonExceptionString(responseString));
+ default:
+ throw new Exception(getMessageByHTTPStatusCode(status, "PDB"));
}
// Make redundant objects eligible for garbage collection to conserve
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();
* 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
{
- Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
+ 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();
import java.io.BufferedReader;
import java.io.InputStream;
-import java.io.Reader;
import java.net.URL;
/**
return /** @j2sNative swingjs.JSUtil.getJSONReader$O(is) || */null;
}
- @SuppressWarnings("resource")
- public static Object parse(String json) {
- return /** @j2sNative swingjs.JSUtil.parseJSONRaw$S(json) || */
+ /**
+ *
+ * @param obj
+ * as String, Reader, InputStream, or JavaScript Object or Array
+ * @return Map or List
+ */
+ public static Object parse(Object obj)
+ {
+ return /** @j2sNative swingjs.JSUtil.parseJSON$O(obj) || */
null;
- }
-
- public static Object parse(Reader br) {
- return /** @j2sNative swingjs.JSUtil.parseJSON$O(br) || */null;
- }
+ }
public static String stringify(Object obj) {
- // not actually implemented.
return /** @j2sNative swingjs.JSUtil.stringifyJSON$O(obj) || */null;
}
package jalview.javascript.web;
-import java.net.URI;
+import jalview.javascript.json.JSON;
+import jalview.util.Platform;
+
+import java.net.URL;
/**
* minimal implementation of com.sun.jersey.api.client.ClientResponse
*/
public class ClientResponse
{
-
+
private String response;
- private String[] encoding;
- public ClientResponse(String response, String... encoding)
+ private boolean isJSON;
+
+ private Object jsonData;
+
+ int responseCode = -1;
+
+ public ClientResponse(URL url, String[] encoding)
{
- this.response = response;
- this.encoding = encoding;
+ // OK, so it turns out that ajax "json" format - or for that matter, any
+ // format for json is still just text. There is no point in getting this
+ // using special jQuery "json" formats. Duh. BH wasted a whole day try to
+ // "do it right".
+ response = Platform.getFileAsString(url.toString());
+ responseCode = (response == null || response == "" ? 404 : 200);
+ isJSON = encoding[0].equals("application/json");
+ if (isJSON)
+ {
+ try
+ {
+ jsonData = JSON.parse(response);
+ } catch (Exception e)
+ {
+ jsonData = null;
+ }
+ if (jsonData == null)
+ {
+ responseCode = 400;
+ }
+ }
}
- public String getEntity(Class<?> c)
- {
-
- // c will be String.class
-
+ public Object getEntity(Class<?> c)
+ {
+
+ if (c == java.util.Map.class)
+ {
+ return jsonData;
+ }
return response;
}
public int getStatus()
{
- // note, we could get the actual response. I am just assuming it is 200 or 400
- return (response != null && (response.startsWith("{") == encoding[0].equals("application/json"))
- ? 200 : 400);
+ return responseCode;
+ }
+
+ public Object getJSONData()
+ {
+ return jsonData;
}
}
import jalview.util.Platform;
+import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
+import java.net.URL;
/*
* A JavaScript-only proxy for com.sun.jersey.api.client.WebResource
*/
public ClientResponse get(Class<?> c)
{
- return new ClientResponse(Platform.getFileAsString(uri.toString()),
- encoding);
+ try
+ {
+ return new ClientResponse(new URL(uri.toString()), encoding);
+ } catch (MalformedURLException e)
+ {
+ return null;
+ }
}
}
public IdentifiersUrlProvider(String cachedUrlList)
{
urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
- selectedUrls = new ArrayList<String>();
+ selectedUrls = new ArrayList<>();
checkSelectionMatchesUrls(cachedUrlList);
}
private HashMap<String, UrlLink> readIdentifiers(String idFileName)
{
// identifiers.org data
- HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
+ HashMap<String, UrlLink> idData = new HashMap<>();
String errorMessage = null;
try
// Typical report here is "NetworkError" because the file does not exist.
// "https://." is coming from System.getProperty("user.home"), but this could
// be set by the page developer to anything, of course.
- errorMessage = (/** @j2sNative String.fromCharCode.apply(null, reader.$in.is.buf.slice(0,12)) || */e.toString());
+ errorMessage = e.toString();
idData.clear();
}
// BH 2018 -- added more valuable report
if (errorMessage != null)
+ {
System.err.println("IdentifiersUrlProvider: cannot read " + idFileName + ": " + errorMessage);
+ }
return idData;
}
@Override
public List<String> getLinksForMenu()
{
- List<String> links = new ArrayList<String>();
+ List<String> links = new ArrayList<>();
for (String key : selectedUrls)
{
links.add(urls.get(key).toStringWithTarget());
@Override
public void setUrlData(List<UrlLinkDisplay> links)
{
- selectedUrls = new ArrayList<String>();
+ selectedUrls = new ArrayList<>();
Iterator<UrlLinkDisplay> it = links.iterator();
while (it.hasNext())
package jalview.util;
-import jalview.javascript.json.JSON;
-import jalview.json.binding.biojson.v1.AlignmentPojo;
-
-import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import java.util.List;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
public class JSONUtils
*/
public static String arrayToStringList(List<Object> jsonArray)
{
- int n;
-
+ int n;
+
if (jsonArray == null || (n = jsonArray.size()) == 0)
{
return null;
/**
* @j2sNative
*
- * return jsonArray.elementData.slice(0, n).join(",");
+ * return jsonArray.elementData.slice(0, n).join(",");
*/
{
- StringBuilder sb = new StringBuilder();
- for (int i = 0; i < n; i++)
- {
- if (i > 0)
- {
- sb.append(",");
- }
- sb.append(jsonArray.get(i).toString());
- }
- return sb.toString();
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < n; i++)
+ {
+ if (i > 0)
+ {
+ sb.append(",");
+ }
+ sb.append(jsonArray.get(i).toString());
+ }
+ return sb.toString();
}
}
/**
- * The method all JSON parsing must go through for JavaScript.
- * @param r a BufferedReader or a javascript.json.JSON.JSONReader
+ * The method all JSON parsing must go through for JavaScript.
+ *
+ * @param r
+ * a BufferedReader or a javascript.json.JSON.JSONReader
* @return
* @throws IOException
* @throws ParseException
*/
- public static Object parse(Reader r) throws IOException, ParseException
+ public static Object parse(Reader r) throws IOException, ParseException
{
- // Using a file reader is not currently supported in SwingJS JavaScript
-
- if (r == null)
- return null;
-//
-// Platform.timeCheck("JSONUtils.parse0 ", Platform.TIME_MARK);
-
- Object ret;
- if (Platform.isJS())
- {
- if (r instanceof FileReader)
- {
- throw new IOException("StringJS does not support FileReader parsing for JSON -- but it could...");
- }
- return JSON.parse(r);
- } else {
- ret = new JSONParser().parse(r);
- }
-// Platform.timeCheck("JSONUtils.parse1 ", Platform.TIME_MARK);
- return ret;
+ return Platform.parseJSON(r);
}
- public static Object parse(String json) throws ParseException
+ public static Object parse(String json) throws ParseException
{
- return (Platform.isJS() ? JSON.parse(json) : new JSONParser().parse(json));
+ return Platform.parseJSON(json);
}
-public static String stringify(Object obj) {
- return new org.json.JSONObject(obj).toString();
-}
+ public static String stringify(Object obj)
+ {
+ return new org.json.JSONObject(obj).toString();
+ }
}
*/
package jalview.util;
+import jalview.javascript.json.JSON;
+
import java.awt.Toolkit;
import java.awt.event.MouseEvent;
+import java.io.BufferedReader;
import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.URL;
import java.util.Properties;
import javax.swing.SwingUtilities;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
/**
* System platform information used by Applet and Application
*
*/
}
+ public static void setAjaxJSON(URL url)
+ {
+ if (isJS())
+ {
+ JSON.setAjax(url);
+ }
+ }
+
+ public static Object parseJSON(InputStream response)
+ throws IOException, ParseException
+ {
+ if (isJS())
+ {
+ return JSON.getJSONReader(response);
+ }
+
+ BufferedReader br = null;
+ try
+ {
+ br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
+ return parseJSON(br);
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ public static Object parseJSON(String json) throws ParseException
+ {
+ return (isJS() ? JSON.parse(json)
+ : new JSONParser().parse(json));
+ }
+
+ public static Object parseJSON(Reader r)
+ throws IOException, ParseException
+ {
+ if (r == null)
+ {
+ return null;
+ }
+
+ if (!isJS())
+ {
+ return new JSONParser().parse(r);
+ }
+ // Using a file reader is not currently supported in SwingJS JavaScript
+
+ if (r instanceof FileReader)
+ {
+ throw new IOException(
+ "StringJS does not support FileReader parsing for JSON -- but it could...");
+ }
+ return JSON.parse(r);
+
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff