From: gmungoc Date: Mon, 15 Apr 2019 08:47:50 +0000 (+0100) Subject: Merge branch 'develop' into Jalview-JS/develop X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~162 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b3d9eaf8829a3aeb2bbc522315207a7940b0844e;hp=-c;p=jalview.git Merge branch 'develop' into Jalview-JS/develop --- b3d9eaf8829a3aeb2bbc522315207a7940b0844e diff --combined src/jalview/ext/ensembl/EnsemblRestClient.java index b605232,617ab21..bf151bf --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@@ -20,13 -20,13 +20,13 @@@ */ package jalview.ext.ensembl; +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.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.ProtocolException; @@@ -37,7 -37,9 +37,7 @@@ 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 @@@ -46,13 -48,6 +46,13 @@@ */ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { + + 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 @@@ -69,9 -64,9 +69,9 @@@ * @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 = "9.0"; + private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "10.0"; - private static final String LATEST_ENSEMBL_REST_VERSION = "9.0"; + 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"; @@@ -86,11 -81,10 +86,11 @@@ 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; @@@ -187,7 -181,6 +187,7 @@@ * @see http://rest.ensembl.org/documentation/info/ping * @return */ + @SuppressWarnings("unchecked") boolean checkEnsembl() { BufferedReader br = null; @@@ -196,17 -189,20 +196,17 @@@ { // 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) + Map val = (Map) getJSON( + new URL(pingUrl), null, 2 * 1000, MODE_MAP, null); + if (val == 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) @@@ -229,42 -225,37 +229,42 @@@ return false; } - /** - * 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 - */ - protected BufferedReader getSequenceReader(List ids) - throws IOException - { - URL url = getUrl(ids); - - BufferedReader reader = getHttpResponse(url, ids); - return reader; - } - - /** - * 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); - } + 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); + // } /** * Sends the HTTP request and gets the response as a reader. Returns null if @@@ -277,22 -268,14 +277,22 @@@ * in milliseconds * @return * @throws IOException + * @throws ParseException */ - protected 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; + } int retriesLeft = MAX_RETRIES; HttpURLConnection connection = null; int responseCode = 0; + Platform.setAjaxJSON(url); + while (retriesLeft > 0) { connection = tryConnection(url, ids, readTimeout); @@@ -313,18 -296,18 +313,18 @@@ * 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); + 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"); + Platform.timeCheck(null, Platform.TIME_MARK); + Object ret = Platform.parseJSON(response); + Platform.timeCheck("EnsemblRestClient.getJSON " + url, + Platform.TIME_MARK); - BufferedReader reader = null; - reader = new BufferedReader(new InputStreamReader(response, "UTF-8")); - return reader; + return ret; } /** @@@ -339,7 -322,6 +339,7 @@@ int readTimeout) throws IOException, ProtocolException { // System.out.println(System.currentTimeMillis() + " " + url); + HttpURLConnection connection = (HttpURLConnection) url.openConnection(); /* @@@ -352,10 -334,10 +352,10 @@@ connection.setRequestProperty("Content-Type", getRequestMimeType()); connection.setRequestProperty("Accept", getResponseMimeType()); connection.setDoInput(true); connection.setDoOutput(multipleIds); + connection.setUseCaches(false); connection.setConnectTimeout(CONNECT_TIMEOUT_MS); connection.setReadTimeout(readTimeout); @@@ -387,8 -369,8 +387,8 @@@ 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); } @@@ -454,9 -436,8 +454,9 @@@ 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(","); @@@ -478,75 -459,25 +478,75 @@@ } /** + * 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); + } + + 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 * * @return */ + @SuppressWarnings("unchecked") 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) + Map val = (Map) getJSON( + new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON), null, + -1, MODE_MAP, null); + if (val == 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; @@@ -600,25 -531,39 +600,25 @@@ * * @return */ + @SuppressWarnings("unchecked") private void checkEnsemblDataVersion() { - JSONParser jp = new JSONParser(); - URL url = null; - BufferedReader br = null; - + Map val; try { - url = new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON); - br = getHttpResponse(url, null); - if (br != null) + val = (Map) getJSON( + new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON), null, + -1, MODE_MAP, null); + if (val == null) { - JSONObject val = (JSONObject) jp.parse(br); - JSONArray versions = (JSONArray) val.get("releases"); - domainData.get(getDomain()).dataVersion = versions.get(0) - .toString(); + return; } - } catch (Throwable t) - { + 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: " + t.getMessage()); - } finally - { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } + "Error checking Ensembl data version: " + e.getMessage()); } }