X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=e65e7ba108b5c74aad94adc09b5c02a444be988e;hb=refs%2Fheads%2Ffeature%2FJAL-3730ensemblPingRetries;hp=da9d2e5cfa45ab5dd52dd9a4e46d94d1c9ecb77e;hpb=b3a1578f1b29594527e347534f39ffc4e5b37298;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index da9d2e5..e65e7ba 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,18 +20,9 @@ */ package jalview.ext.ensembl; -import jalview.bin.Cache; -import jalview.javascript.json.JSON; -import jalview.util.JSONUtils; -import jalview.util.Platform; -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.io.Reader; import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.ProtocolException; @@ -44,6 +35,10 @@ import javax.ws.rs.HttpMethod; import org.json.simple.parser.ParseException; +import jalview.bin.Cache; +import jalview.util.Platform; +import jalview.util.StringUtils; + /** * Base class for Ensembl REST service clients * @@ -51,38 +46,44 @@ import org.json.simple.parser.ParseException; */ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { - - static { - Cache.addJ2SDirectDatabaseCall("http://rest.ensembl"); - Cache.addJ2SDirectDatabaseCall("https://rest.ensembl"); + private static final int HTTP_OK = 200; + + private static final int HTTP_OVERLOAD = 429; + + static + { + Platform.addJ2SDirectDatabaseCall("http://rest.ensembl"); + Platform.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 + /* + * constants for http retries and timeout; + * not final so they can be changed by a Groovy script + */ + private static int PING_TIMEOUT_MS = 2 * 1000; - private static final int MAX_RETRIES = 3; + private static long PING_RETEST_INTERVAL = 10 * 1000L; // 10 seconds - private static final int HTTP_OK = 200; + private static int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes - private static final int HTTP_OVERLOAD = 429; + private static int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds + + private static int MAX_RETRIES = 3; /* * update these constants when Jalview has been checked / updated for - * changes to Ensembl REST API (ref JAL-2105) + * changes to Ensembl REST API, and updated JAL-3018 * @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 = "7.0"; + private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "12.0"; - private static final String LATEST_ENSEMBL_REST_VERSION = "7.0"; + private static final String LATEST_ENSEMBL_REST_VERSION = "12.0"; 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"; @@ -90,10 +91,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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; @@ -190,83 +192,95 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @see http://rest.ensembl.org/documentation/info/ping * @return */ - @SuppressWarnings("unchecked") -boolean checkEnsembl() + boolean checkEnsembl() { - BufferedReader br = null; String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON; + for (int i = 0 ; i < MAX_RETRIES ; i++) + { + if (pingEnsembl(pingUrl)) + { + if (i > 0) + { + Cache.log.info("Ensembl ping responded on attempt " + (i+1)); + } + return true; + } + } + Cache.log.error("Ensembl ping failed after " + MAX_RETRIES + " retries"); + return false; + } + + /** + * Connects to Ensembl REST service's 'ping' URL and answers true if + * successful, false if no reply, or no reply within the 2 second timeout + * + * @param pingUrl + * @return + */ + @SuppressWarnings("unchecked") + protected boolean pingEnsembl(String pingUrl) + { try { // 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 val = (Map) getJSON(new URL(pingUrl), null, 2 * 1000, MODE_MAP, null); + Map val = (Map) getJSON( + new URL(pingUrl), null, PING_TIMEOUT_MS, MODE_MAP, null); if (val == null) - return false; + { + return false; + } String pingString = val.get("ping").toString(); return pingString != null; } catch (Throwable t) { - System.err.println( + Cache.log.error( "Error connecting to " + pingUrl + ": " + t.getMessage()); - } finally - { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } + return false; } - 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 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 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 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 ids) + // throws IOException + // { + // return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT); + // } /** * Sends the HTTP request and gets the response as a reader. Returns null if @@ -279,20 +293,22 @@ boolean checkEnsembl() * in milliseconds * @return * @throws IOException + * @throws ParseException */ - private BufferedReader getHttpResponse(URL url, List ids, - int readTimeout) throws IOException + private Object getJSON(URL url, List ids, int readTimeout) + throws IOException, ParseException { - 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); - } - + + Platform.setAjaxJSON(url); + while (retriesLeft > 0) { connection = tryConnection(url, ids, readTimeout); @@ -313,21 +329,18 @@ boolean checkEnsembl() * 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); + Cache.log.error("Response code " + responseCode);// + " for " + url); return null; } - InputStream response = connection.getInputStream(); - - if (Platform.isJS()) { - return JSON.getJSONReader(response); - } - // System.out.println(getClass().getName() + " took " - // + (System.currentTimeMillis() - now) + "ms to fetch"); + // Platform.timeCheck(null, Platform.TIME_MARK); + Object ret = Platform.parseJSON(response); + // Platform.timeCheck("EnsemblRestClient.getJSON " + url, + // Platform.TIME_MARK); - return new BufferedReader(new InputStreamReader(response, "UTF-8")); + return ret; } /** @@ -342,7 +355,7 @@ boolean checkEnsembl() int readTimeout) throws IOException, ProtocolException { // System.out.println(System.currentTimeMillis() + " " + url); - + HttpURLConnection connection = (HttpURLConnection) url.openConnection(); /* @@ -390,8 +403,8 @@ boolean checkEnsembl() 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); } @@ -420,7 +433,7 @@ boolean checkEnsembl() * recheck if Ensembl is up if it was down, or the recheck period has elapsed */ boolean retestAvailability = (now - - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL; + - info.lastAvailableCheckTime) > PING_RETEST_INTERVAL; if (!info.restAvailable || retestAvailability) { info.restAvailable = checkEnsembl(); @@ -480,71 +493,56 @@ boolean checkEnsembl() 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 ids, int msDelay, int mode, String mapKey) throws IOException, ParseException { - - if (url == null) - url = getUrl(ids); - -// Platform.timeCheck("EnsembleRestClient.getJSON0 " + url, Platform.TIME_MARK); - - Reader br = null; - try { - br = (url == null ? null : getHttpResponse(url, ids, msDelay)); - -// Platform.timeCheck("EnsembleRestClient.getJSON1 parsing... ", Platform.TIME_MARK); - - Object ret = (br == null ? null : JSONUtils.parse(br)); - -// Platform.timeCheck("EnsembleRestClient.getJSON2 ...done ", Platform.TIME_MARK); - - if (ret != null && mapKey != null) - ret = ((Map) ret).get(mapKey); - if (ret == null) - { - return null; - } - switch (mode) { - case MODE_ARRAY: - case MODE_MAP: - break; - case MODE_ITERATOR: - ret = ((List) ret).iterator(); - break; - } - return ret; - - } finally + protected Object getJSON(URL url, List ids, int msDelay, int mode, + String mapKey) throws IOException, ParseException + { + if (url == null) { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } + url = getUrl(ids); } - } + Object json = (url == null ? null : getJSON(url, ids, msDelay)); + if (json != null && mapKey != null) + { + json = ((Map) json).get(mapKey); + } + if (json == null) + { + return null; + } + switch (mode) + { + case MODE_ARRAY: + case MODE_MAP: + break; + case MODE_ITERATOR: + json = ((List) json).iterator(); + break; + } + return json; + } /** * Fetches and checks Ensembl's REST version number @@ -558,9 +556,13 @@ boolean checkEnsembl() try { - Map val = (Map) getJSON(new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON), null, -1, MODE_MAP, null); + Map val = (Map) 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; @@ -618,17 +620,22 @@ boolean checkEnsembl() private void checkEnsemblDataVersion() { Map val; - try - { - val = (Map) getJSON( - new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON), null, -1, MODE_MAP, null); - if (val == null) - return; - List versions = (List) 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) getJSON( + new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON), null, + -1, MODE_MAP, null); + if (val == null) + { + return; + } + List versions = (List) 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()