+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
import jalview.io.FileParse;
* update these constants when Jalview has been checked / updated for
* changes to Ensembl REST API
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
+ * @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.4";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.6";
- private static final String LATEST_ENSEMBL_REST_VERSION = "4.5";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "4.7";
+
+ private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
private static Map<String, EnsemblInfo> domainData;
private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
private static final Regex TRANSCRIPT_REGEX = new Regex(
- "(ENS)([A-Z]{3}|)T[0-9]{11}$");
+ "(ENS)([A-Z]{3}|)T[0-9]{11}$");
private static final Regex GENE_REGEX = new Regex(
- "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+ "(ENS)([A-Z]{3}|)G[0-9]{11}$");
static
{
protected abstract String getResponseMimeType();
/**
- * Tries to connect to Ensembl's REST 'ping' endpoint, and returns true if
- * successful, else false
+ * Checks Ensembl's REST 'ping' endpoint, and returns true if response
+ * indicates available, else false
*
+ * @see http://rest.ensembl.org/documentation/info/ping
* @return
*/
private boolean checkEnsembl()
{
+ HttpURLConnection conn = null;
try
{
// note this format works for both ensembl and ensemblgenomes
// info/ping.json works for ensembl only (March 2016)
URL ping = new URL(getDomain()
+ "/info/ping?content-type=application/json");
- HttpURLConnection conn = (HttpURLConnection) ping.openConnection();
- int rc = conn.getResponseCode();
- conn.disconnect();
- if (rc >= 200 && rc < 300)
- {
- return true;
- }
+
+ /*
+ * expect {"ping":1} if ok
+ */
+ BufferedReader br = getHttpResponse(ping, null);
+ JSONParser jp = new JSONParser();
+ JSONObject val = (JSONObject) jp.parse(br);
+ String pingString = val.get("ping").toString();
+ return pingString != null;
} catch (Throwable t)
{
System.err.println("Error connecting to " + PING_URL + ": "
+ t.getMessage());
+ } finally
+ {
+ if (conn != null)
+ {
+ conn.disconnect();
+ }
}
return false;
}
throws IOException
{
URL url = getUrl(ids);
-
+
BufferedReader reader = getHttpResponse(url, ids);
+ if (reader == null)
+ {
+ // request failed
+ return null;
+ }
FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
return fp;
}
{
// long now = System.currentTimeMillis();
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
-
+
/*
* POST method allows multiple queries in one request; it is supported for
* sequence queries, but not for overlap
{
writePostBody(connection, ids);
}
-
- InputStream response = connection.getInputStream();
+
int responseCode = connection.getResponseCode();
-
+
if (responseCode != 200)
{
/*
* 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
*/
- throw new IOException(
- "Response code was not 200. Detected response was "
- + responseCode);
+ System.err.println("Response code " + responseCode + " for " + url);
+ return null;
}
+ // get content
+ InputStream response = connection.getInputStream();
+
// System.out.println(getClass().getName() + " took "
// + (System.currentTimeMillis() - now) + "ms to fetch");
checkRateLimits(connection);
-
+
BufferedReader reader = null;
reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
return reader;
// remaining, limit, reset));
}
}
-
+
/**
* Rechecks if Ensembl is responding, unless the last check was successful and
* the retest interval has not yet elapsed. Returns true if Ensembl is up,
if (laterVersion)
{
System.err.println(String.format(
- "Expected %s REST version %s but found %s", getDbSource(),
- expected,
- version));
+ "Expected %s REST version %s but found %s, see %s",
+ getDbSource(), expected, version, REST_CHANGE_LOG));
}
info.restVersion = version;
} catch (Throwable t)
git://source.jalview.org / jalview.git / blobdiff