+/*
+ * 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.DataSourceType;
import jalview.io.FileParse;
+import jalview.util.StringUtils;
import java.io.BufferedReader;
import java.io.DataOutputStream;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
+import java.net.ProtocolException;
import java.net.URL;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import javax.ws.rs.HttpMethod;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
+import com.stevesoft.pat.Regex;
+
/**
* Base class for Ensembl REST service clients
*
*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
- protected final static String ENSEMBL_REST = "http://rest.ensembl.org";
+ private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
- protected static final String SEQUENCE_ID_URL = ENSEMBL_REST
- + "/sequence/id";
+ private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
+
+ /*
+ * update these constants when Jalview has been checked / updated for
+ * changes to Ensembl REST API (ref JAL-2105)
+ * @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 = "5.0";
+
+ private static final String LATEST_ENSEMBL_REST_VERSION = "5.0";
+
+ private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
+
+ private static Map<String, EnsemblInfo> domainData;
// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
- private final static long RETEST_INTERVAL = 10000L; // 10 seconds
+ private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
+
+ private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
- private static boolean ensemblRestAvailable = false;
+ private static final Regex PROTEIN_REGEX = new Regex(
+ "(ENS)([A-Z]{3}|)P[0-9]{11}$");
- private static long lastCheck = -1;
+ private static final Regex TRANSCRIPT_REGEX = new Regex(
+ "(ENS)([A-Z]{3}|)T[0-9]{11}$");
+
+ private static final Regex GENE_REGEX = new Regex(
+ "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+
+ static
+ {
+ domainData = new HashMap<String, EnsemblInfo>();
+ domainData.put(ENSEMBL_REST,
+ new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
+ domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
+ ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
+ }
protected volatile boolean inProgress = false;
+ /**
+ * Default constructor to use rest.ensembl.org
+ */
+ public EnsemblRestClient()
+ {
+ this(ENSEMBL_REST);
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblRestClient(String d)
+ {
+ setDomain(d);
+ }
+
+ /**
+ * Answers true if the query matches the regular expression pattern for an
+ * Ensembl transcript stable identifier
+ *
+ * @param query
+ * @return
+ */
+ public boolean isTranscriptIdentifier(String query)
+ {
+ return query == null ? false : TRANSCRIPT_REGEX.search(query);
+ }
+
+ /**
+ * Answers true if the query matches the regular expression pattern for an
+ * Ensembl protein stable identifier
+ *
+ * @param query
+ * @return
+ */
+ public boolean isProteinIdentifier(String query)
+ {
+ return query == null ? false : PROTEIN_REGEX.search(query);
+ }
+
+ /**
+ * Answers true if the query matches the regular expression pattern for an
+ * Ensembl gene stable identifier
+ *
+ * @param query
+ * @return
+ */
+ public boolean isGeneIdentifier(String query)
+ {
+ return query == null ? false : GENE_REGEX.search(query);
+ }
+
@Override
public boolean queryInProgress()
{
/**
* Return the desired value for the Content-Type request header
*
+ * @param multipleIds
+ *
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
- protected abstract String getRequestMimeType();
+ protected abstract String getRequestMimeType(boolean multipleIds);
/**
* Return the desired value for the Accept request header
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()
{
+ BufferedReader br = null;
try
{
- URL ping = new URL(PING_URL);
- HttpURLConnection conn = (HttpURLConnection) ping.openConnection();
- int rc = conn.getResponseCode();
- conn.disconnect();
- if (rc >= 200 && rc < 300)
- {
- return true;
- }
+ // 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");
+
+ /*
+ * expect {"ping":1} if ok
+ * if ping takes more than 2 seconds to respond, treat as if unavailable
+ */
+ br = getHttpResponse(ping, null, 2 * 1000);
+ 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());
+ System.err.println(
+ "Error connecting to " + PING_URL + ": " + t.getMessage());
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
return false;
}
* @return
* @throws IOException
*/
- protected FileParse getSequenceReader(List<String> ids)
- throws IOException
+ protected FileParse getSequenceReader(List<String> ids) 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(),
+ DataSourceType.URL);
+ return fp;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * Writes the HTTP request and gets the response as a reader.
+ *
+ * @param url
+ * @param ids
+ * written as Json POST body if more than one
+ * @param readTimeout
+ * in milliseconds
+ * @return
+ * @throws IOException
+ * if response code was not 200, or other I/O error
+ */
+ protected BufferedReader getHttpResponse(URL url, List<String> ids,
+ int readTimeout) throws IOException
+ {
+ // long now = System.currentTimeMillis();
+ int maxRetries = 3;
+ int retriesLeft = maxRetries;
+ HttpURLConnection connection = null;
+ while (retriesLeft > 0)
+ {
+ connection = tryConnection(url, ids, readTimeout);
+ }
+
+ 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
+ */
+ 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;
+ }
+
+ /**
+ * @param url
+ * @param ids
+ * @param readTimeout
+ * @return
+ * @throws IOException
+ * @throws ProtocolException
+ */
+ protected HttpURLConnection tryConnection(URL url, List<String> ids,
+ int readTimeout) throws IOException, ProtocolException
+ {
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
-
+
/*
* POST method allows multiple queries in one request; it is supported for
* sequence queries, but not for overlap
*/
- connection.setRequestMethod(useGetRequest() ? HttpMethod.GET
- : HttpMethod.POST);
- connection.setRequestProperty("Content-Type", getRequestMimeType());
+ boolean multipleIds = ids != null && ids.size() > 1;
+ connection.setRequestMethod(
+ multipleIds ? HttpMethod.POST : HttpMethod.GET);
+ connection.setRequestProperty("Content-Type",
+ getRequestMimeType(multipleIds));
connection.setRequestProperty("Accept", getResponseMimeType());
connection.setUseCaches(false);
connection.setDoInput(true);
- connection.setDoOutput(true);
+ connection.setDoOutput(multipleIds);
+
+ connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
+ connection.setReadTimeout(readTimeout);
- if (!useGetRequest())
+ if (multipleIds)
{
writePostBody(connection, ids);
}
-
- InputStream response = connection.getInputStream();
- int responseCode = connection.getResponseCode();
-
- if (responseCode != 200)
+ return connection;
+ }
+
+ /**
+ * Inspect response headers for any sign of server overload and respect any
+ * 'retry-after' directive
+ *
+ * @see https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits
+ * @param connection
+ */
+ void checkRateLimits(HttpURLConnection connection)
+ {
+ // number of requests allowed per time interval:
+ String limit = connection.getHeaderField("X-RateLimit-Limit");
+ // length of quota time interval in seconds:
+ // String period = connection.getHeaderField("X-RateLimit-Period");
+ // seconds remaining until usage quota is reset:
+ String reset = connection.getHeaderField("X-RateLimit-Reset");
+ // number of requests remaining from quota for current period:
+ String remaining = connection.getHeaderField("X-RateLimit-Remaining");
+ // number of seconds to wait before retrying (if remaining == 0)
+ String retryDelay = connection.getHeaderField("Retry-After");
+
+ // to test:
+ // retryDelay = "5";
+
+ EnsemblInfo info = domainData.get(getDomain());
+ if (retryDelay != null)
{
- throw new RuntimeException(
- "Response code was not 200. Detected response was "
- + responseCode);
+ System.err.println("Ensembl REST service rate limit exceeded, wait "
+ + retryDelay + " seconds before retrying");
+ try
+ {
+ info.retryAfter = System.currentTimeMillis()
+ + (1000 * Integer.valueOf(retryDelay));
+ } catch (NumberFormatException e)
+ {
+ System.err
+ .println("Unexpected value for Retry-After: " + retryDelay);
+ }
+ }
+ else
+ {
+ info.retryAfter = 0;
+ // debug:
+ // System.out.println(String.format(
+ // "%s Ensembl requests remaining of %s (reset in %ss)",
+ // remaining, limit, reset));
}
-
- BufferedReader reader = null;
- reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
- FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
- return fp;
}
/**
* 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,
- * else false.
+ * else false. Also retrieves and saves the current version of Ensembl data
+ * and REST services at intervals.
*
* @return
*/
protected boolean isEnsemblAvailable()
{
+ EnsemblInfo info = domainData.get(getDomain());
+
long now = System.currentTimeMillis();
- boolean retest = now - lastCheck > RETEST_INTERVAL;
- if (ensemblRestAvailable && !retest)
+
+ /*
+ * check if we are waiting for 'Retry-After' to expire
+ */
+ if (info.retryAfter > now)
+ {
+ System.err.println("Still " + (1 + (info.retryAfter - now) / 1000)
+ + " secs to wait before retrying Ensembl");
+ return false;
+ }
+ else
+ {
+ info.retryAfter = 0;
+ }
+
+ /*
+ * recheck if Ensembl is up if it was down, or the recheck period has elapsed
+ */
+ boolean retestAvailability = (now
+ - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
+ if (!info.restAvailable || retestAvailability)
+ {
+ info.restAvailable = checkEnsembl();
+ info.lastAvailableCheckTime = now;
+ }
+
+ /*
+ * refetch Ensembl versions if the recheck period has elapsed
+ */
+ boolean refetchVersion = (now
+ - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
+ if (refetchVersion)
{
- return true;
+ checkEnsemblRestVersion();
+ checkEnsemblDataVersion();
+ info.lastVersionCheckTime = now;
}
- ensemblRestAvailable = checkEnsembl();
- lastCheck = now;
- return ensemblRestAvailable;
+
+ return info.restAvailable;
}
/**
byte[] thepostbody = postBody.toString().getBytes();
connection.setRequestProperty("Content-Length",
Integer.toString(thepostbody.length));
- DataOutputStream wr = new DataOutputStream(connection.getOutputStream());
+ DataOutputStream wr = new DataOutputStream(
+ connection.getOutputStream());
wr.write(thepostbody);
wr.flush();
wr.close();
}
+ /**
+ * Fetches and checks Ensembl's REST version number
+ *
+ * @return
+ */
+ private void checkEnsemblRestVersion()
+ {
+ EnsemblInfo info = domainData.get(getDomain());
+
+ JSONParser jp = new JSONParser();
+ URL url = null;
+ try
+ {
+ url = new URL(
+ getDomain() + "/info/rest?content-type=application/json");
+ BufferedReader br = getHttpResponse(url, null);
+ JSONObject val = (JSONObject) jp.parse(br);
+ String version = val.get("release").toString();
+ String majorVersion = version.substring(0, version.indexOf("."));
+ String expected = info.expectedRestVersion;
+ String expectedMajorVersion = expected.substring(0,
+ expected.indexOf("."));
+ info.restMajorVersionMismatch = false;
+ try
+ {
+ /*
+ * if actual REST major version is ahead of what we expect,
+ * record this in case we want to warn the user
+ */
+ if (Float.valueOf(majorVersion) > Float
+ .valueOf(expectedMajorVersion))
+ {
+ info.restMajorVersionMismatch = true;
+ }
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Error in REST version: " + e.toString());
+ }
+
+ /*
+ * check if REST version is later than what Jalview has tested against,
+ * if so warn; we don't worry if it is earlier (this indicates Jalview has
+ * been tested in advance against the next pending REST version)
+ */
+ boolean laterVersion = StringUtils.compareVersions(version,
+ expected) == 1;
+ if (laterVersion)
+ {
+ System.err.println(String.format(
+ "EnsemblRestClient expected %s REST version %s but found %s, see %s",
+ getDbSource(), expected, version, REST_CHANGE_LOG));
+ }
+ info.restVersion = version;
+ } catch (Throwable t)
+ {
+ System.err.println(
+ "Error checking Ensembl REST version: " + t.getMessage());
+ }
+ }
+
+ public boolean isRestMajorVersionMismatch()
+ {
+ return domainData.get(getDomain()).restMajorVersionMismatch;
+ }
+
+ /**
+ * Fetches and checks Ensembl's data version number
+ *
+ * @return
+ */
+ private void checkEnsemblDataVersion()
+ {
+ JSONParser jp = new JSONParser();
+ URL url = null;
+ try
+ {
+ url = new URL(
+ getDomain() + "/info/data?content-type=application/json");
+ BufferedReader br = getHttpResponse(url, 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());
+ }
+ }
+
+ public String getEnsemblDataVersion()
+ {
+ return domainData.get(getDomain()).dataVersion;
+ }
+
+ @Override
+ public String getDbVersion()
+ {
+ return getEnsemblDataVersion();
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff