X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=4a5544e299670a6b1d38ef23ed34c9289f3ff284;hb=ca74027f55fb1f8af9fef0d77348449a07a1b5d5;hp=e3d121516208fe0ea3c7a8b3ede166ea6271a3d4;hpb=8d3aefef72e993e55c0f6b5c26e3979ae7269e0f;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index e3d1215..4a5544e 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,15 +20,10 @@ */ package jalview.ext.ensembl; -import jalview.io.DataSourceType; -import jalview.io.FileParse; -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; @@ -39,9 +34,10 @@ 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; + +import jalview.util.Platform; +import jalview.util.StringUtils; /** * Base class for Ensembl REST service clients @@ -50,6 +46,13 @@ import org.json.simple.parser.JSONParser; */ 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 @@ -62,21 +65,18 @@ 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 = "6.0"; + private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "15.2"; - private static final String LATEST_ENSEMBL_REST_VERSION = "6.1"; + private static final String LATEST_ENSEMBL_REST_VERSION = "15.2"; 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 @@ -86,10 +86,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher static { domainData = new HashMap<>(); - domainData.put(ENSEMBL_REST, - new EnsemblData(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION)); - domainData.put(ENSEMBL_GENOMES_REST, new EnsemblData( - ENSEMBL_GENOMES_REST, 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; @@ -99,7 +100,21 @@ 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)); + } } /** @@ -142,22 +157,28 @@ 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 @@ -166,33 +187,32 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @see http://rest.ensembl.org/documentation/info/ping * @return */ + @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_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) + 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) { System.err.println( - "Error connecting to " + PING_URL + ": " + t.getMessage()); + "Error connecting to " + pingUrl + ": " + t.getMessage()); } finally { if (br != null) @@ -209,45 +229,46 @@ 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; - } + 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); + // } /** - * 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 @@ -256,15 +277,22 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * in milliseconds * @return * @throws IOException - * if response code was not 200, or other I/O error + * @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); @@ -285,18 +313,18 @@ 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(); - // 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; } /** @@ -311,6 +339,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher int readTimeout) throws IOException, ProtocolException { // System.out.println(System.currentTimeMillis() + " " + url); + HttpURLConnection connection = (HttpURLConnection) url.openConnection(); /* @@ -320,14 +349,13 @@ 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); @@ -359,8 +387,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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); } @@ -426,8 +454,9 @@ 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(","); @@ -449,25 +478,75 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher } /** + * 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; @@ -521,39 +600,25 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * * @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()); } }