2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.ensembl;
23 import jalview.io.DataSourceType;
24 import jalview.io.FileParse;
25 import jalview.util.StringUtils;
27 import java.io.BufferedReader;
28 import java.io.DataOutputStream;
29 import java.io.IOException;
30 import java.io.InputStream;
31 import java.io.InputStreamReader;
32 import java.net.HttpURLConnection;
33 import java.net.MalformedURLException;
35 import java.util.HashMap;
36 import java.util.List;
39 import javax.ws.rs.HttpMethod;
41 import org.json.simple.JSONArray;
42 import org.json.simple.JSONObject;
43 import org.json.simple.parser.JSONParser;
46 * Base class for Ensembl REST service clients
50 abstract class EnsemblRestClient extends EnsemblSequenceFetcher
52 private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
54 private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
57 * update these constants when Jalview has been checked / updated for
58 * changes to Ensembl REST API (ref JAL-2105)
59 * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
60 * @see http://rest.ensembl.org/info/rest?content-type=application/json
62 private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "5.0";
64 private static final String LATEST_ENSEMBL_REST_VERSION = "5.0";
66 private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
68 private static Map<String, EnsemblInfo> domainData;
70 // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
71 private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
73 private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
75 private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
79 domainData = new HashMap<String, EnsemblInfo>();
80 domainData.put(ENSEMBL_REST,
81 new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
82 domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
83 ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
86 protected volatile boolean inProgress = false;
89 * Default constructor to use rest.ensembl.org
91 public EnsemblRestClient()
97 * Constructor given the target domain to fetch data from
101 public EnsemblRestClient(String d)
107 public boolean queryInProgress()
113 public StringBuffer getRawRecords()
119 * Returns the URL for the client http request
123 * @throws MalformedURLException
125 protected abstract URL getUrl(List<String> ids)
126 throws MalformedURLException;
129 * Returns true if client uses GET method, false if it uses POST
133 protected abstract boolean useGetRequest();
136 * Return the desired value for the Content-Type request header
141 * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
143 protected abstract String getRequestMimeType(boolean multipleIds);
146 * Return the desired value for the Accept request header
149 * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
151 protected abstract String getResponseMimeType();
154 * Checks Ensembl's REST 'ping' endpoint, and returns true if response
155 * indicates available, else false
157 * @see http://rest.ensembl.org/documentation/info/ping
160 private boolean checkEnsembl()
162 BufferedReader br = null;
165 // note this format works for both ensembl and ensemblgenomes
166 // info/ping.json works for ensembl only (March 2016)
168 getDomain() + "/info/ping?content-type=application/json");
171 * expect {"ping":1} if ok
172 * if ping takes more than 2 seconds to respond, treat as if unavailable
174 br = getHttpResponse(ping, null, 2 * 1000);
177 // error reponse status
180 JSONParser jp = new JSONParser();
181 JSONObject val = (JSONObject) jp.parse(br);
182 String pingString = val.get("ping").toString();
183 return pingString != null;
184 } catch (Throwable t)
187 "Error connecting to " + PING_URL + ": " + t.getMessage());
195 } catch (IOException e)
205 * returns a reader to a Fasta response from the Ensembl sequence endpoint
209 * @throws IOException
211 protected FileParse getSequenceReader(List<String> ids) throws IOException
213 URL url = getUrl(ids);
215 BufferedReader reader = getHttpResponse(url, ids);
221 FileParse fp = new FileParse(reader, url.toString(),
227 * Gets a reader to the HTTP response, using the default read timeout of 5
233 * @throws IOException
235 protected BufferedReader getHttpResponse(URL url, List<String> ids)
238 return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
242 * Writes the HTTP request and gets the response as a reader.
246 * written as Json POST body if more than one
250 * @throws IOException
251 * if response code was not 200, or other I/O error
253 protected BufferedReader getHttpResponse(URL url, List<String> ids,
254 int readTimeout) throws IOException
256 // long now = System.currentTimeMillis();
257 HttpURLConnection connection = (HttpURLConnection) url.openConnection();
260 * POST method allows multiple queries in one request; it is supported for
261 * sequence queries, but not for overlap
263 boolean multipleIds = ids != null && ids.size() > 1;
264 connection.setRequestMethod(
265 multipleIds ? HttpMethod.POST : HttpMethod.GET);
266 connection.setRequestProperty("Content-Type",
267 getRequestMimeType(multipleIds));
268 connection.setRequestProperty("Accept", getResponseMimeType());
270 connection.setUseCaches(false);
271 connection.setDoInput(true);
272 connection.setDoOutput(multipleIds);
274 connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
275 connection.setReadTimeout(readTimeout);
279 writePostBody(connection, ids);
282 int responseCode = connection.getResponseCode();
284 if (responseCode != 200)
287 * note: a GET request for an invalid id returns an error code e.g. 415
288 * but POST request returns 200 and an empty Fasta response
290 System.err.println("Response code " + responseCode + " for " + url);
294 InputStream response = connection.getInputStream();
296 // System.out.println(getClass().getName() + " took "
297 // + (System.currentTimeMillis() - now) + "ms to fetch");
299 checkRateLimits(connection);
301 BufferedReader reader = null;
302 reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
307 * Inspect response headers for any sign of server overload and respect any
308 * 'retry-after' directive
310 * @see https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits
313 void checkRateLimits(HttpURLConnection connection)
315 // number of requests allowed per time interval:
316 // String limit = connection.getHeaderField("X-RateLimit-Limit");
317 // length of quota time interval in seconds:
318 // String period = connection.getHeaderField("X-RateLimit-Period");
319 // seconds remaining until usage quota is reset:
320 // String reset = connection.getHeaderField("X-RateLimit-Reset");
321 // number of requests remaining from quota for current period:
322 // String remaining = connection.getHeaderField("X-RateLimit-Remaining");
323 // number of seconds to wait before retrying (if remaining == 0)
324 String retryDelay = connection.getHeaderField("Retry-After");
329 EnsemblInfo info = domainData.get(getDomain());
330 if (retryDelay != null)
332 System.err.println("Ensembl REST service rate limit exceeded, wait "
333 + retryDelay + " seconds before retrying");
336 info.retryAfter = System.currentTimeMillis()
337 + (1000 * Integer.valueOf(retryDelay));
338 } catch (NumberFormatException e)
341 .println("Unexpected value for Retry-After: " + retryDelay);
348 // System.out.println(String.format(
349 // "%s Ensembl requests remaining of %s (reset in %ss)",
350 // remaining, limit, reset));
355 * Rechecks if Ensembl is responding, unless the last check was successful and
356 * the retest interval has not yet elapsed. Returns true if Ensembl is up,
357 * else false. Also retrieves and saves the current version of Ensembl data
358 * and REST services at intervals.
362 protected boolean isEnsemblAvailable()
364 EnsemblInfo info = domainData.get(getDomain());
366 long now = System.currentTimeMillis();
369 * check if we are waiting for 'Retry-After' to expire
371 if (info.retryAfter > now)
373 System.err.println("Still " + (1 + (info.retryAfter - now) / 1000)
374 + " secs to wait before retrying Ensembl");
383 * recheck if Ensembl is up if it was down, or the recheck period has elapsed
385 boolean retestAvailability = (now
386 - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
387 if (!info.restAvailable || retestAvailability)
389 info.restAvailable = checkEnsembl();
390 info.lastAvailableCheckTime = now;
394 * refetch Ensembl versions if the recheck period has elapsed
396 boolean refetchVersion = (now
397 - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
400 checkEnsemblRestVersion();
401 checkEnsemblDataVersion();
402 info.lastVersionCheckTime = now;
405 return info.restAvailable;
409 * Constructs, writes and flushes the POST body of the request, containing the
410 * query ids in JSON format
414 * @throws IOException
416 protected void writePostBody(HttpURLConnection connection,
417 List<String> ids) throws IOException
420 StringBuilder postBody = new StringBuilder(64);
421 postBody.append("{\"ids\":[");
423 for (String id : ids)
427 postBody.append(",");
430 postBody.append("\"");
431 postBody.append(id.trim());
432 postBody.append("\"");
434 postBody.append("]}");
435 byte[] thepostbody = postBody.toString().getBytes();
436 connection.setRequestProperty("Content-Length",
437 Integer.toString(thepostbody.length));
438 DataOutputStream wr = new DataOutputStream(
439 connection.getOutputStream());
440 wr.write(thepostbody);
446 * Fetches and checks Ensembl's REST version number
450 private void checkEnsemblRestVersion()
452 EnsemblInfo info = domainData.get(getDomain());
454 JSONParser jp = new JSONParser();
459 getDomain() + "/info/rest?content-type=application/json");
460 BufferedReader br = getHttpResponse(url, null);
465 JSONObject val = (JSONObject) jp.parse(br);
466 String version = val.get("release").toString();
467 String majorVersion = version.substring(0, version.indexOf("."));
468 String expected = info.expectedRestVersion;
469 String expectedMajorVersion = expected.substring(0,
470 expected.indexOf("."));
471 info.restMajorVersionMismatch = false;
475 * if actual REST major version is ahead of what we expect,
476 * record this in case we want to warn the user
478 if (Float.valueOf(majorVersion) > Float
479 .valueOf(expectedMajorVersion))
481 info.restMajorVersionMismatch = true;
483 } catch (NumberFormatException e)
485 System.err.println("Error in REST version: " + e.toString());
489 * check if REST version is later than what Jalview has tested against,
490 * if so warn; we don't worry if it is earlier (this indicates Jalview has
491 * been tested in advance against the next pending REST version)
493 boolean laterVersion = StringUtils.compareVersions(version,
497 System.err.println(String.format(
498 "EnsemblRestClient expected %s REST version %s but found %s, see %s",
499 getDbSource(), expected, version, REST_CHANGE_LOG));
501 info.restVersion = version;
502 } catch (Throwable t)
505 "Error checking Ensembl REST version: " + t.getMessage());
509 public boolean isRestMajorVersionMismatch()
511 return domainData.get(getDomain()).restMajorVersionMismatch;
515 * Fetches and checks Ensembl's data version number
519 private void checkEnsemblDataVersion()
521 JSONParser jp = new JSONParser();
526 getDomain() + "/info/data?content-type=application/json");
527 BufferedReader br = getHttpResponse(url, null);
530 JSONObject val = (JSONObject) jp.parse(br);
531 JSONArray versions = (JSONArray) val.get("releases");
532 domainData.get(getDomain()).dataVersion = versions.get(0)
535 } catch (Throwable t)
538 "Error checking Ensembl data version: " + t.getMessage());
542 public String getEnsemblDataVersion()
544 return domainData.get(getDomain()).dataVersion;
548 public String getDbVersion()
550 return getEnsemblDataVersion();