*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
-
- static {
- Cache.addJ2SDirectDatabaseCall("http://rest.ensembl");
- Cache.addJ2SDirectDatabaseCall("https://rest.ensembl");
+
+ static
+ {
+ Cache.addJ2SDirectDatabaseCall("http://rest.ensembl");
+ Cache.addJ2SDirectDatabaseCall("https://rest.ensembl");
}
-
+
private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
static
{
domainData = new HashMap<>();
- domainData.put(DEFAULT_ENSEMBL_BASEURL,
- new EnsemblData(DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
- domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL, new EnsemblData(
- DEFAULT_ENSEMBL_GENOMES_BASEURL, LATEST_ENSEMBLGENOMES_REST_VERSION));
+ domainData.put(DEFAULT_ENSEMBL_BASEURL, new EnsemblData(
+ DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
+ domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL,
+ new EnsemblData(DEFAULT_ENSEMBL_GENOMES_BASEURL,
+ LATEST_ENSEMBLGENOMES_REST_VERSION));
}
protected volatile boolean inProgress = false;
* @return
*/
@SuppressWarnings("unchecked")
-boolean checkEnsembl()
+ 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)
-
-
-
-
+
/*
* expect {"ping":1} if ok
* if ping takes more than 2 seconds to respond, treat as if unavailable
*/
- Map<String, Object> val = (Map<String, Object>) getJSON(new URL(pingUrl), null, 2 * 1000, MODE_MAP, null);
+ Map<String, Object> val = (Map<String, Object>) getJSON(
+ new URL(pingUrl), null, 2 * 1000, MODE_MAP, null);
if (val == null)
- return false;
+ {
+ return false;
+ }
String pingString = val.get("ping").toString();
return pingString != null;
} catch (Throwable t)
return false;
}
-
- protected final static int MODE_ARRAY = 0;
- protected final static int MODE_MAP = 1;
+ 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);
-// }
+
+ // /**
+ // * 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
private BufferedReader getHttpResponse(URL url, List<String> ids,
int readTimeout) throws IOException
{
- if (readTimeout < 0)
- readTimeout = DEFAULT_READ_TIMEOUT;
+ if (readTimeout < 0)
+ {
+ readTimeout = DEFAULT_READ_TIMEOUT;
+ }
int retriesLeft = MAX_RETRIES;
HttpURLConnection connection = null;
int responseCode = 0;
-
- if (Platform.isJS()) {
- JSON.setAjax(url);
+
+ if (Platform.isJS())
+ {
+ JSON.setAjax(url);
}
-
+
while (retriesLeft > 0)
{
connection = tryConnection(url, ids, readTimeout);
return null;
}
-
InputStream response = connection.getInputStream();
-
- if (Platform.isJS()) {
- return JSON.getJSONReader(response);
+
+ if (Platform.isJS())
+ {
+ return JSON.getJSONReader(response);
}
// System.out.println(getClass().getName() + " took "
int readTimeout) throws IOException, ProtocolException
{
// System.out.println(System.currentTimeMillis() + " " + url);
-
+
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
/*
int retrySecs = Integer.valueOf(retryDelay);
if (retrySecs > 0 && retrySecs < 10)
{
- System.err
- .println("Ensembl REST service rate limit exceeded, waiting "
+ System.err.println(
+ "Ensembl REST service rate limit exceeded, waiting "
+ retryDelay + " seconds before retrying");
Thread.sleep(1000 * retrySecs);
}
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
- */
+ /**
+ * 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 {
+ protected Object getJSON(URL url, List<String> ids, int msDelay, int mode,
+ String mapKey) throws IOException, ParseException
+ {
+ if (url == null)
+ {
+ url = getUrl(ids);
+ }
- if (url == null)
- url = getUrl(ids);
-
- Reader br = null;
- try {
+ Reader br = null;
+ try
+ {
+ Platform.timeCheck(null, Platform.TIME_MARK);
- Platform.timeCheck(null, Platform.TIME_MARK);
-
br = (url == null ? null : getHttpResponse(url, ids, msDelay));
Object ret = (br == null ? null : JSONUtils.parse(br));
- Platform.timeCheck("EnsembleRestClient.getJSON " + url, Platform.TIME_MARK);
-
+ Platform.timeCheck("EnsemblRestClient.getJSON " + url,
+ Platform.TIME_MARK);
if (ret != null && mapKey != null)
- ret = ((Map<String, Object>) ret).get(mapKey);
- if (ret == null)
{
- return null;
+ ret = ((Map<String, Object>) ret).get(mapKey);
}
- switch (mode) {
+ if (ret == null)
+ {
+ return null;
+ }
+ switch (mode)
+ {
case MODE_ARRAY:
case MODE_MAP:
- break;
+ break;
case MODE_ITERATOR:
- ret = ((List<Object>) ret).iterator();
- break;
+ ret = ((List<Object>) ret).iterator();
+ break;
}
return ret;
-
+
} finally
{
if (br != null)
br.close();
} catch (IOException e)
{
- // ignore
+ // ignore
}
- }
+ }
}
}
-
-
/**
* Fetches and checks Ensembl's REST version number
*
try
{
- Map<String, Object> val = (Map<String, Object>) getJSON(new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON), null, -1, MODE_MAP, null);
+ 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;
+ {
+ return;
+ }
String version = val.get("release").toString();
String majorVersion = version.substring(0, version.indexOf("."));
String expected = info.expectedRestVersion;
private void checkEnsemblDataVersion()
{
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());
- }
+ 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 / commitdiff