package jalview.ext.ensembl;
import jalview.bin.Cache;
-import jalview.bin.Jalview;
+import jalview.javascript.json.JSON;
+import jalview.util.JSONUtils;
+import jalview.util.Platform;
import jalview.util.StringUtils;
import java.io.BufferedReader;
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;
import javax.ws.rs.HttpMethod;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
/**
* Base class for Ensembl REST service clients
* @see http://rest.ensembl.org/documentation/info/ping
* @return
*/
- boolean checkEnsembl()
+ @SuppressWarnings("unchecked")
+boolean checkEnsembl()
{
BufferedReader br = null;
String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
{
// note this format works for both ensembl and ensemblgenomes
// info/ping.json works for ensembl only (March 2016)
- URL ping = new URL(pingUrl);
-
+
+
+
+
/*
* expect {"ping":1} if ok
* if ping takes more than 2 seconds to respond, treat as if unavailable
*/
- br = getHttpResponse(ping, null, 2 * 1000);
- if (br == null)
- {
- // error reponse status
- return false;
- }
- JSONParser jp = new JSONParser();
- JSONObject val = (JSONObject) jp.parse(br);
+ Map<String, Object> val = (Map<String, Object>) getJSON(new URL(pingUrl), null, 2 * 1000, MODE_MAP, null);
+ if (val == null)
+ return false;
String pingString = val.get("ping").toString();
return pingString != null;
} catch (Throwable t)
return false;
}
- /**
- * Returns a reader to a (Json) response from the Ensembl sequence endpoint.
- * If the request failed the return value may be null.
- *
- * @param ids
- * @return
- * @throws IOException
- */
- protected BufferedReader getSequenceReader(List<String> ids)
- throws IOException
- {
- URL url = getUrl(ids);
-
- BufferedReader reader = getHttpResponse(url, ids);
- return reader;
- }
-
- /**
- * Gets a reader to the HTTP response, using the default read timeout of 5
- * minutes
- *
- * @param url
- * @param ids
- * @return
- * @throws IOException
- */
- protected BufferedReader getHttpResponse(URL url, List<String> ids)
- throws IOException
- {
- return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
- }
+
+ protected final static int MODE_ARRAY = 0;
+ protected final static int MODE_MAP = 1;
+ protected final static int MODE_ITERATOR = 2;
+
+// /**
+// * Returns a reader to a (Json) response from the Ensembl sequence endpoint.
+// * If the request failed the return value may be null.
+// *
+// * @param ids
+// * @return
+// * @throws IOException
+// * @throws ParseException
+// */
+// protected Object getSequenceJSON(List<String> ids, int mode)
+// throws IOException, ParseException
+// {
+// URL url = getUrl(ids);
+// return getJSON(url, ids, -1, mode);
+// }
+//
+// /**
+// * Gets a reader to the HTTP response, using the default read timeout of 5
+// * minutes
+// *
+// * @param url
+// * @param ids
+// * @return
+// * @throws IOException
+// */
+// protected BufferedReader getHttpResponse(URL url, List<String> ids)
+// throws IOException
+// {
+// return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
+// }
/**
* Sends the HTTP request and gets the response as a reader. Returns null if
* @return
* @throws IOException
*/
- protected BufferedReader getHttpResponse(URL url, List<String> ids,
+ private BufferedReader getHttpResponse(URL url, List<String> ids,
int readTimeout) throws IOException
{
+ if (readTimeout < 0)
+ readTimeout = DEFAULT_READ_TIMEOUT;
int retriesLeft = MAX_RETRIES;
HttpURLConnection connection = null;
int responseCode = 0;
-
+
+ if (Platform.isJS()) {
+ JSON.setAjax(url);
+ }
+
while (retriesLeft > 0)
{
connection = tryConnection(url, ids, readTimeout);
* note: a GET request for an invalid id returns an error code e.g. 415
* but POST request returns 200 and an empty Fasta response
*/
- System.err.println("Response code " + responseCode + " for " + url);
+ System.err.println("Response code " + responseCode);// + " for " + url);
return null;
}
+
InputStream response = connection.getInputStream();
+
+ if (Platform.isJS()) {
+ return JSON.getJSONReader(response);
+ }
// System.out.println(getClass().getName() + " took "
// + (System.currentTimeMillis() - now) + "ms to fetch");
- BufferedReader reader = null;
- reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
- return reader;
+ return new BufferedReader(new InputStreamReader(response, "UTF-8"));
}
/**
int readTimeout) throws IOException, ProtocolException
{
// System.out.println(System.currentTimeMillis() + " " + url);
+
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
/*
wr.close();
}
+ /**
+ * Primary access point to parsed JSON data, including the call to retrieve and
+ * parsing.
+ *
+ * @param url request url; if null, getUrl(ids) will be used
+ * @param ids optional; may be null
+ * @param msDelay -1 for default delay
+ * @param mode map, array, or array iterator
+ * @param mapKey an optional key for an outer map
+ * @return a Map, List, Iterator, or null
+ * @throws IOException
+ * @throws ParseException
+ *
+ * @author Bob Hanson 2019
+ */
+ @SuppressWarnings("unchecked")
+ protected Object getJSON(URL url, List<String> ids, int msDelay, int mode, String mapKey) throws IOException, ParseException {
+
+ if (url == null)
+ url = getUrl(ids);
+
+ Platform.timeCheck("EnsembleRestClient.getJSON0 " + url, Platform.TIME_MARK);
+
+ Reader br = null;
+ try {
+ br = (url == null ? null : getHttpResponse(url, ids, msDelay));
+
+ Platform.timeCheck("EnsembleRestClient.getJSON1 parsing... ", Platform.TIME_MARK);
+
+ Object ret = (br == null ? null : JSONUtils.parse(br));
+
+ Platform.timeCheck("EnsembleRestClient.getJSON2 ...done ", Platform.TIME_MARK);
+
+ 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 (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+
+
/**
* Fetches and checks Ensembl's REST version number
*
* @return
*/
+ @SuppressWarnings("unchecked")
private void checkEnsemblRestVersion()
{
EnsemblData info = domainData.get(getDomain());
- JSONParser jp = new JSONParser();
- URL url = null;
try
{
- url = new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON);
- BufferedReader br = getHttpResponse(url, null);
- if (br == null)
- {
- return;
- }
- JSONObject val = (JSONObject) jp.parse(br);
+ Map<String, Object> val = (Map<String, Object>) getJSON(new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON), null, -1, MODE_MAP, null);
+ if (val == null)
+ return;
String version = val.get("release").toString();
String majorVersion = version.substring(0, version.indexOf("."));
String expected = info.expectedRestVersion;
*
* @return
*/
+ @SuppressWarnings("unchecked")
private void checkEnsemblDataVersion()
{
- JSONParser jp = new JSONParser();
- URL url = null;
- BufferedReader br = null;
-
- try
- {
- url = new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON);
- br = getHttpResponse(url, null);
- if (br != null)
- {
- JSONObject val = (JSONObject) jp.parse(br);
- JSONArray versions = (JSONArray) val.get("releases");
- domainData.get(getDomain()).dataVersion = versions.get(0)
- .toString();
- }
- } catch (Throwable t)
- {
- System.err.println(
- "Error checking Ensembl data version: " + t.getMessage());
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
+ Map<String, Object> val;
+ try
+ {
+ val = (Map<String, Object>) getJSON(
+ new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON), null, -1, MODE_MAP, null);
+ if (val == null)
+ return;
+ List<Object> versions = (List<Object>) val.get("releases");
+ domainData.get(getDomain()).dataVersion = versions.get(0).toString();
+ } catch (Throwable e) {//could be IOException | ParseException e) {
+ System.err.println("Error checking Ensembl data version: " + e.getMessage());
+ }
}
public String getEnsemblDataVersion()
git://source.jalview.org / jalview.git / blobdiff