X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=bef1db0ef957658d2a40864aa683c3b46178bbf5;hb=9e5d1bced16aa9975692115a964c661cd7897a7c;hp=9dea886a2726461dfbb7c5d1628dbeb173667f1a;hpb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index 9dea886..bef1db0 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; @@ -29,6 +31,7 @@ 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; @@ -39,9 +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 @@ -50,6 +51,12 @@ 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 @@ -66,17 +73,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @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 = "7.0"; - private static final String LATEST_ENSEMBL_REST_VERSION = "6.1"; + private static final String LATEST_ENSEMBL_REST_VERSION = "7.0"; 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 final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr @@ -156,22 +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 @@ -180,7 +190,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @see http://rest.ensembl.org/documentation/info/ping * @return */ - boolean checkEnsembl() + @SuppressWarnings("unchecked") +boolean checkEnsembl() { BufferedReader br = null; String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON; @@ -188,20 +199,17 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { // 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); + 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) @@ -224,45 +232,45 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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); - } + + 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 + * 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 @@ -271,15 +279,20 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * in milliseconds * @return * @throws IOException - * if response code was not 200, or other I/O error */ - protected BufferedReader getHttpResponse(URL url, List ids, + private BufferedReader getHttpResponse(URL url, List ids, int readTimeout) throws IOException { + 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) { connection = tryConnection(url, ids, readTimeout); @@ -300,18 +313,21 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * 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(); + + if (Platform.isJS()) { + return JSON.getJSONReader(response); + } // 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; + return new BufferedReader(new InputStreamReader(response, "UTF-8")); } /** @@ -326,6 +342,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher int readTimeout) throws IOException, ProtocolException { // System.out.println(System.currentTimeMillis() + " " + url); + HttpURLConnection connection = (HttpURLConnection) url.openConnection(); /* @@ -335,14 +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); @@ -441,8 +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(","); @@ -463,26 +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() { 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); + 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; @@ -536,40 +614,21 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * * @return */ + @SuppressWarnings("unchecked") 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 - } - } - } + 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()