X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=771980c11b600495fbc6aa6443477362bb745f1a;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=bef1db0ef957658d2a40864aa683c3b46178bbf5;hpb=9e5d1bced16aa9975692115a964c661cd7897a7c;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index bef1db0..771980c 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,18 +20,10 @@ */ 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 +36,9 @@ import javax.ws.rs.HttpMethod; import org.json.simple.parser.ParseException; +import jalview.util.Platform; +import jalview.util.StringUtils; + /** * Base class for Ensembl REST service clients * @@ -51,12 +46,13 @@ import org.json.simple.parser.ParseException; */ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { - - static { - Cache.addJ2SDirectDatabaseCall("http://rest.ensembl"); - Cache.addJ2SDirectDatabaseCall("https://rest.ensembl"); + + 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 @@ -69,13 +65,13 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher /* * 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 = "10.0"; - private static final String LATEST_ENSEMBL_REST_VERSION = "7.0"; + private static final String LATEST_ENSEMBL_REST_VERSION = "10.0"; private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log"; @@ -90,10 +86,11 @@ 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; @@ -191,7 +188,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @return */ @SuppressWarnings("unchecked") -boolean checkEnsembl() + boolean checkEnsembl() { BufferedReader br = null; String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON; @@ -199,17 +196,17 @@ boolean checkEnsembl() { // 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, 2 * 1000, MODE_MAP, null); if (val == null) - return false; + { + return false; + } String pingString = val.get("ping").toString(); return pingString != null; } catch (Throwable t) @@ -232,41 +229,42 @@ boolean checkEnsembl() 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 +277,22 @@ 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); @@ -317,17 +317,14 @@ boolean checkEnsembl() 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 +339,7 @@ boolean checkEnsembl() int readTimeout) throws IOException, ProtocolException { // System.out.println(System.currentTimeMillis() + " " + url); - + HttpURLConnection connection = (HttpURLConnection) url.openConnection(); /* @@ -390,8 +387,8 @@ 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); } @@ -480,72 +477,57 @@ 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); - - 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)); + 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.getJSON " + url, Platform.TIME_MARK); - + Object json = (url == null ? null : getJSON(url, ids, msDelay)); - 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 (json != null && mapKey != null) { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } + 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 +540,13 @@ 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 +604,22 @@ 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()