X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=f75b4b9395598cd6fbab64cffb3a881bc8558322;hb=e3ea9b3630ecd79ad7bb7245dc2d6b252f99176f;hp=ad6c70cb28e99269c963fc78d34c1a257b8d3eb2;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index ad6c70c..f75b4b9 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,17 +20,13 @@ */ 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; import java.net.URL; import java.util.HashMap; import java.util.List; @@ -38,11 +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 com.stevesoft.pat.Regex; +import jalview.util.Platform; +import jalview.util.StringUtils; /** * Base class for Ensembl REST service clients @@ -51,47 +46,51 @@ import com.stevesoft.pat.Regex; */ 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 + 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 = "5.0"; + private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "12.0"; - private static final String LATEST_ENSEMBL_REST_VERSION = "5.0"; + private static final String LATEST_ENSEMBL_REST_VERSION = "12.0"; 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 - private static final Regex PROTEIN_REGEX = new Regex( - "(ENS)([A-Z]{3}|)P[0-9]{11}$"); - - private static final Regex TRANSCRIPT_REGEX = new Regex( - "(ENS)([A-Z]{3}|)T[0-9]{11}$"); - - private static final Regex GENE_REGEX = new Regex( - "(ENS)([A-Z]{3}|)G[0-9]{11}$"); + 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; @@ -101,7 +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)); + } } /** @@ -114,42 +127,6 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher setDomain(d); } - /** - * Answers true if the query matches the regular expression pattern for an - * Ensembl transcript stable identifier - * - * @param query - * @return - */ - public boolean isTranscriptIdentifier(String query) - { - return query == null ? false : TRANSCRIPT_REGEX.search(query); - } - - /** - * Answers true if the query matches the regular expression pattern for an - * Ensembl protein stable identifier - * - * @param query - * @return - */ - public boolean isProteinIdentifier(String query) - { - return query == null ? false : PROTEIN_REGEX.search(query); - } - - /** - * Answers true if the query matches the regular expression pattern for an - * Ensembl gene stable identifier - * - * @param query - * @return - */ - public boolean isGeneIdentifier(String query) - { - return query == null ? false : GENE_REGEX.search(query); - } - @Override public boolean queryInProgress() { @@ -180,22 +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 @@ -204,29 +187,32 @@ 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); - 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) @@ -243,59 +229,117 @@ 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 + * @throws ParseException */ - protected FileParse getSequenceReader(List ids) throws IOException + private Object getJSON(URL url, List ids, int readTimeout) + throws IOException, ParseException { - URL url = getUrl(ids); - BufferedReader reader = getHttpResponse(url, ids); - if (reader == null) + if (readTimeout < 0) { - // request failed + 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); + 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(); + + // Platform.timeCheck(null, Platform.TIME_MARK); + Object ret = Platform.parseJSON(response); + // Platform.timeCheck("EnsemblRestClient.getJSON " + url, + // Platform.TIME_MARK); + + return ret; } /** - * 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(); /* @@ -305,14 +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); @@ -320,77 +363,40 @@ 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)); - } } /** @@ -403,25 +409,11 @@ 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 @@ -462,8 +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(","); @@ -485,22 +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() { - 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); - 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; @@ -554,22 +600,25 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * * @return */ + @SuppressWarnings("unchecked") private void checkEnsemblDataVersion() { - JSONParser jp = new JSONParser(); - URL url = null; + Map val; try { - url = new URL( - getDomain() + "/info/data?content-type=application/json"); - BufferedReader br = getHttpResponse(url, null); - JSONObject val = (JSONObject) jp.parse(br); - JSONArray versions = (JSONArray) val.get("releases"); + 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 t) - { + } catch (Throwable e) + {// could be IOException | ParseException e) { System.err.println( - "Error checking Ensembl data version: " + t.getMessage()); + "Error checking Ensembl data version: " + e.getMessage()); } }