/*
* 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 .
* 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.IOException;
import java.io.InputStream;
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;
/**
* Base class for Ensembl REST service clients
*
* @author gmcarstairs
*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
private static final int MAX_RETRIES = 3;
private static final int HTTP_OK = 200;
private static final int HTTP_OVERLOAD = 429;
/*
* 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 = "6.3";
private static final String LATEST_ENSEMBL_REST_VERSION = "6.3";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
private static Map domainData;
private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
protected static final String CONTENT_TYPE_JSON = "?content-type=application/json";
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));
}
protected volatile boolean inProgress = false;
/**
* Default constructor to use rest.ensembl.org
*/
public EnsemblRestClient()
{
super();
/*
* initialise domain info lazily
*/
if (!domainData.containsKey(ensemblDomain))
{
domainData.put(ensemblDomain,
new EnsemblData(ensemblDomain, LATEST_ENSEMBL_REST_VERSION));
}
if (!domainData.containsKey(ensemblGenomesDomain))
{
domainData.put(ensemblGenomesDomain, new EnsemblData(
ensemblGenomesDomain, LATEST_ENSEMBLGENOMES_REST_VERSION));
}
}
/**
* Constructor given the target domain to fetch data from
*
* @param d
*/
public EnsemblRestClient(String d)
{
setDomain(d);
}
@Override
public boolean queryInProgress()
{
return inProgress;
}
@Override
public StringBuffer getRawRecords()
{
return null;
}
/**
* Returns the URL for the client http request
*
* @param ids
* @return
* @throws MalformedURLException
*/
protected abstract URL getUrl(List ids)
throws MalformedURLException;
/**
* Returns true if client uses GET method, false if it uses POST
*
* @return
*/
protected abstract boolean useGetRequest();
/**
* 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(boolean multipleIds);
/**
* Return the desired value for the Accept request header
*
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
protected abstract String getResponseMimeType();
/**
* Checks Ensembl's REST 'ping' endpoint, and returns true if response
* indicates available, else false
*
* @see http://rest.ensembl.org/documentation/info/ping
* @return
*/
boolean checkEnsembl()
{
BufferedReader br = null;
String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
try
{
// 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);
String pingString = val.get("ping").toString();
return pingString != null;
} catch (Throwable t)
{
System.err.println(
"Error connecting to " + pingUrl + ": " + t.getMessage());
} finally
{
if (br != null)
{
try
{
br.close();
} catch (IOException e)
{
// ignore
}
}
}
return false;
}
/**
* returns a reader to a Fasta response from the Ensembl sequence endpoint
*
* @param ids
* @return
* @throws IOException
*/
protected FileParse getSequenceReader(List 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 ids)
throws IOException
{
return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
}
/**
* Sends 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 ids,
int readTimeout) throws IOException
{
int retriesLeft = MAX_RETRIES;
HttpURLConnection connection = null;
int responseCode = 0;
while (retriesLeft > 0)
{
connection = tryConnection(url, ids, readTimeout);
responseCode = connection.getResponseCode();
if (responseCode == HTTP_OVERLOAD) // 429
{
retriesLeft--;
checkRetryAfter(connection);
}
else
{
retriesLeft = 0;
}
}
if (responseCode != HTTP_OK) // 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;
}
InputStream response = connection.getInputStream();
// 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;
}
/**
* @param url
* @param ids
* @param readTimeout
* @return
* @throws IOException
* @throws ProtocolException
*/
protected HttpURLConnection tryConnection(URL url, List ids,
int readTimeout) throws IOException, ProtocolException
{
// System.out.println(System.currentTimeMillis() + " " + url);
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
/*
* POST method allows multiple queries in one request; it is supported for
* sequence queries, but not for overlap
*/
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(multipleIds);
connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
connection.setReadTimeout(readTimeout);
if (multipleIds)
{
writePostBody(connection, ids);
}
return connection;
}
/**
* Inspects response headers for a 'retry-after' directive, and waits for the
* directed period (if less than 10 seconds)
*
* @see https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits
* @param connection
*/
void checkRetryAfter(HttpURLConnection connection)
{
String retryDelay = connection.getHeaderField("Retry-After");
// to test:
// retryDelay = "5";
if (retryDelay != null)
{
try
{
int retrySecs = Integer.valueOf(retryDelay);
if (retrySecs > 0 && retrySecs < 10)
{
System.err
.println("Ensembl REST service rate limit exceeded, waiting "
+ retryDelay + " seconds before retrying");
Thread.sleep(1000 * retrySecs);
}
} catch (NumberFormatException | InterruptedException e)
{
System.err.println("Error handling Retry-After: " + e.getMessage());
}
}
}
/**
* 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. Also retrieves and saves the current version of Ensembl data
* and REST services at intervals.
*
* @return
*/
protected boolean isEnsemblAvailable()
{
EnsemblData info = domainData.get(getDomain());
long now = System.currentTimeMillis();
/*
* 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)
{
checkEnsemblRestVersion();
checkEnsemblDataVersion();
info.lastVersionCheckTime = now;
}
return info.restAvailable;
}
/**
* Constructs, writes and flushes the POST body of the request, containing the
* query ids in JSON format
*
* @param connection
* @param ids
* @throws IOException
*/
protected void writePostBody(HttpURLConnection connection,
List ids) throws IOException
{
boolean first;
StringBuilder postBody = new StringBuilder(64);
postBody.append("{\"ids\":[");
first = true;
for (String id : ids)
{
if (!first)
{
postBody.append(",");
}
first = false;
postBody.append("\"");
postBody.append(id.trim());
postBody.append("\"");
}
postBody.append("]}");
byte[] thepostbody = postBody.toString().getBytes();
connection.setRequestProperty("Content-Length",
Integer.toString(thepostbody.length));
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()
{
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);
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;
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
}
}
}
}
public String getEnsemblDataVersion()
{
return domainData.get(getDomain()).dataVersion;
}
@Override
public String getDbVersion()
{
return getEnsemblDataVersion();
}
}