X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=01b26d051366b8157b3db2323e2b684e0b78d701;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=17f99864f058727f184185a2f6d6d6ba4502220b;hpb=6ce6753f747f2b8872993e8355c2fa163b8c24b1;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index 17f9986..01b26d0 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,8 +20,10 @@ */ package jalview.ext.ensembl; -import jalview.io.DataSourceType; -import jalview.io.FileParse; +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; @@ -29,8 +31,10 @@ 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; import java.net.URL; import java.util.HashMap; import java.util.List; @@ -38,9 +42,7 @@ 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 org.json.simple.parser.ParseException; /** * Base class for Ensembl REST service clients @@ -49,38 +51,49 @@ import org.json.simple.parser.JSONParser; */ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { + + static { + Cache.addJ2SDirectDatabaseCall("http://rest.ensembl"); + Cache.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 + 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) + * 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 = "6.0"; + private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "9.0"; - private static final String LATEST_ENSEMBL_REST_VERSION = "6.1"; + private static final String LATEST_ENSEMBL_REST_VERSION = "9.0"; private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log"; - private static Map 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 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(ENSEMBL_REST, - new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION)); - domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo( - ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION)); + 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; @@ -90,7 +103,21 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher */ public EnsemblRestClient() { - this(ENSEMBL_REST); + 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)); + } } /** @@ -133,22 +160,28 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher protected abstract boolean useGetRequest(); /** - * Return the desired value for the Content-Type request header - * - * @param multipleIds + * Returns the desired value for the Content-Type request header. Default is + * application/json, override if required to vary this. * * @return * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers */ - protected abstract String getRequestMimeType(boolean multipleIds); + protected String getRequestMimeType() + { + return "application/json"; + } /** - * Return the desired value for the Accept request header + * Return the desired value for the Accept request header. Default is + * application/json, override if required to vary this. * * @return * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers */ - protected abstract String getResponseMimeType(); + protected String getResponseMimeType() + { + return "application/json"; + } /** * Checks Ensembl's REST 'ping' endpoint, and returns true if response @@ -157,34 +190,32 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @see http://rest.ensembl.org/documentation/info/ping * @return */ - private boolean checkEnsembl() + @SuppressWarnings("unchecked") +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( - 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); - if (br == null) - { - // error reponse status - return false; - } - JSONParser jp = new JSONParser(); - JSONObject val = (JSONObject) jp.parse(br); + Map val = (Map) getJSON(new URL(pingUrl), null, 2 * 1000, MODE_MAP, null); + if (val == null) + return false; String pingString = val.get("ping").toString(); return pingString != null; } catch (Throwable t) { System.err.println( - "Error connecting to " + PING_URL + ": " + t.getMessage()); + "Error connecting to " + pingUrl + ": " + t.getMessage()); } finally { if (br != null) @@ -201,59 +232,117 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher return false; } + + 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 Fasta response from the Ensembl sequence endpoint + * Sends the HTTP request and gets the response as a reader. Returns null if + * the HTTP response code was not 200. * + * @param url * @param ids + * written as Json POST body if more than one + * @param readTimeout + * in milliseconds * @return * @throws IOException */ - protected FileParse getSequenceReader(List ids) throws IOException + private BufferedReader getHttpResponse(URL url, List ids, + int readTimeout) throws IOException { - URL url = getUrl(ids); - - BufferedReader reader = getHttpResponse(url, ids); - if (reader == null) + if (readTimeout < 0) + readTimeout = DEFAULT_READ_TIMEOUT; + int retriesLeft = MAX_RETRIES; + HttpURLConnection connection = null; + int responseCode = 0; + + if (Platform.isJS()) { + JSON.setAjax(url); + } + + while (retriesLeft > 0) { - // request failed + 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; } - 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); + + InputStream response = connection.getInputStream(); + + if (Platform.isJS()) { + return JSON.getJSONReader(response); + } + + // System.out.println(getClass().getName() + " took " + // + (System.currentTimeMillis() - now) + "ms to fetch"); + + return new BufferedReader(new InputStreamReader(response, "UTF-8")); } /** - * 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 + * @throws ProtocolException */ - protected BufferedReader getHttpResponse(URL url, List ids, - int readTimeout) throws IOException + protected HttpURLConnection tryConnection(URL url, List ids, + int readTimeout) throws IOException, ProtocolException { - // long now = System.currentTimeMillis(); + // System.out.println(System.currentTimeMillis() + " " + url); + HttpURLConnection connection = (HttpURLConnection) url.openConnection(); /* @@ -263,14 +352,13 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher boolean multipleIds = ids != null && ids.size() > 1; connection.setRequestMethod( multipleIds ? HttpMethod.POST : HttpMethod.GET); - connection.setRequestProperty("Content-Type", - getRequestMimeType(multipleIds)); + connection.setRequestProperty("Content-Type", getRequestMimeType()); connection.setRequestProperty("Accept", getResponseMimeType()); - connection.setUseCaches(false); connection.setDoInput(true); connection.setDoOutput(multipleIds); + connection.setUseCaches(false); connection.setConnectTimeout(CONNECT_TIMEOUT_MS); connection.setReadTimeout(readTimeout); @@ -278,77 +366,40 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { writePostBody(connection, ids); } - - 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; + return connection; } /** - * Inspect response headers for any sign of server overload and respect any - * 'retry-after' directive + * 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 checkRateLimits(HttpURLConnection connection) + void checkRetryAfter(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) { - 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) + 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("Unexpected value for Retry-After: " + retryDelay); + System.err.println("Error handling Retry-After: " + e.getMessage()); } } - else - { - info.retryAfter = 0; - // debug: - // System.out.println(String.format( - // "%s Ensembl requests remaining of %s (reset in %ss)", - // remaining, limit, reset)); - } } /** @@ -361,25 +412,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher */ protected boolean isEnsemblAvailable() { - EnsemblInfo info = domainData.get(getDomain()); + EnsemblData info = domainData.get(getDomain()); long now = System.currentTimeMillis(); /* - * 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 @@ -420,8 +457,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher StringBuilder postBody = new StringBuilder(64); postBody.append("{\"ids\":["); first = true; - for (String id : ids) + for (int i = 0, n = ids.size(); i < n; i++) { + String id = ids.get(i); if (!first) { postBody.append(","); @@ -442,27 +480,87 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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 + */ + @SuppressWarnings("unchecked") + protected Object getJSON(URL url, List ids, int msDelay, int mode, String mapKey) throws IOException, ParseException { + + if (url == null) + url = getUrl(ids); + + Reader br = null; + try { + + Platform.timeCheck(null, Platform.TIME_MARK); + + br = (url == null ? null : getHttpResponse(url, ids, msDelay)); + + Object ret = (br == null ? null : JSONUtils.parse(br)); + + Platform.timeCheck("EnsembleRestClient.getJSON " + url, 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 + { + if (br != null) + { + try + { + br.close(); + } catch (IOException e) + { + // ignore + } + } + } + } + + + /** * Fetches and checks Ensembl's REST version number * * @return */ + @SuppressWarnings("unchecked") private void checkEnsemblRestVersion() { - EnsemblInfo info = domainData.get(getDomain()); + EnsemblData 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); - if (br == null) - { - return; - } - JSONObject val = (JSONObject) jp.parse(br); + Map val = (Map) getJSON(new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON), null, -1, MODE_MAP, null); + if (val == null) + return; String version = val.get("release").toString(); String majorVersion = version.substring(0, version.indexOf(".")); String expected = info.expectedRestVersion; @@ -516,27 +614,21 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * * @return */ + @SuppressWarnings("unchecked") 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); - 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()); - } + 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()); + } } public String getEnsemblDataVersion()