From 21be5363b2f7b61aade8a4b4caf54da28d8cd82a Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 13 Oct 2016 16:43:52 +0100 Subject: [PATCH] JAL-2253 2 second timeout on ping URL, default 5 minutes on others --- src/jalview/ext/ensembl/EnsemblRestClient.java | 43 ++++++++++++++++++++---- 1 file changed, 37 insertions(+), 6 deletions(-) diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index b7b1985..5903f69 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -50,6 +50,10 @@ import com.stevesoft.pat.Regex; */ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { + private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes + + private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds + /* * update these constants when Jalview has been checked / updated for * changes to Ensembl REST API @@ -186,7 +190,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher */ private boolean checkEnsembl() { - HttpURLConnection conn = null; + BufferedReader br = null; try { // note this format works for both ensembl and ensemblgenomes @@ -196,8 +200,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher /* * expect {"ping":1} if ok + * if ping takes more than 2 seconds to respond, treat as if unavailable */ - BufferedReader br = getHttpResponse(ping, null); + br = getHttpResponse(ping, null, 2 * 1000); JSONParser jp = new JSONParser(); JSONObject val = (JSONObject) jp.parse(br); String pingString = val.get("ping").toString(); @@ -208,9 +213,15 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher + t.getMessage()); } finally { - if (conn != null) + if (br != null) { - conn.disconnect(); + try + { + br.close(); + } catch (IOException e) + { + // ignore + } } } return false; @@ -239,17 +250,34 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher } /** + * 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); + } + + /** * 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 */ - protected BufferedReader getHttpResponse(URL url, List ids) - throws IOException + protected BufferedReader getHttpResponse(URL url, List ids, + int readTimeout) throws IOException { // long now = System.currentTimeMillis(); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); @@ -269,6 +297,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher connection.setDoInput(true); connection.setDoOutput(multipleIds); + connection.setConnectTimeout(CONNECT_TIMEOUT_MS); + connection.setReadTimeout(readTimeout); + if (multipleIds) { writePostBody(connection, ids); -- 1.7.10.2