From fc07a043c80a393765160ce7e672e9fdb4719599 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 31 Aug 2020 10:33:14 +0100 Subject: [PATCH] JAL-3730 retry ping before failing; sysout logging changed to Cache.log --- src/jalview/ext/ensembl/EnsemblMap.java | 19 ++++--- src/jalview/ext/ensembl/EnsemblRestClient.java | 70 +++++++++++++++--------- src/jalview/ext/ensembl/EnsemblSeqProxy.java | 8 +-- 3 files changed, 57 insertions(+), 40 deletions(-) diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java index cfc679c..16d16d2 100644 --- a/src/jalview/ext/ensembl/EnsemblMap.java +++ b/src/jalview/ext/ensembl/EnsemblMap.java @@ -20,13 +20,6 @@ */ package jalview.ext.ensembl; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefSource; -import jalview.datamodel.GeneLociI; -import jalview.datamodel.GeneLocus; -import jalview.datamodel.Mapping; -import jalview.util.MapList; - import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; @@ -38,6 +31,14 @@ import java.util.Map; import org.json.simple.parser.ParseException; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.GeneLociI; +import jalview.datamodel.GeneLocus; +import jalview.datamodel.Mapping; +import jalview.util.MapList; + /** * A client for the Ensembl REST service /map endpoint, to convert from * coordinates of one genome assembly to another. @@ -157,7 +158,7 @@ public class EnsemblMap extends EnsemblRestClient return (parseAssemblyMappingResponse(url)); } catch (Throwable t) { - System.out.println("Error calling " + url + ": " + t.getMessage()); + Cache.log.error("Error calling " + url + ": " + t.getMessage()); return null; } } @@ -264,7 +265,7 @@ public class EnsemblMap extends EnsemblRestClient return null; } catch (Throwable t) { - System.out.println("Error calling " + url + ": " + t.getMessage()); + Cache.log.error("Error calling " + url + ": " + t.getMessage()); return null; } } diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index f75b4b9..e65e7ba 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,7 +20,6 @@ */ package jalview.ext.ensembl; -import java.io.BufferedReader; import java.io.DataOutputStream; import java.io.IOException; import java.io.InputStream; @@ -36,6 +35,7 @@ import javax.ws.rs.HttpMethod; import org.json.simple.parser.ParseException; +import jalview.bin.Cache; import jalview.util.Platform; import jalview.util.StringUtils; @@ -46,6 +46,9 @@ import jalview.util.StringUtils; */ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { + private static final int HTTP_OK = 200; + + private static final int HTTP_OVERLOAD = 429; static { @@ -53,15 +56,19 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher Platform.addJ2SDirectDatabaseCall("https://rest.ensembl"); } - private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes + /* + * constants for http retries and timeout; + * not final so they can be changed by a Groovy script + */ + private static int PING_TIMEOUT_MS = 2 * 1000; - private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds + private static long PING_RETEST_INTERVAL = 10 * 1000L; // 10 seconds - private static final int MAX_RETRIES = 3; + private static int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes - private static final int HTTP_OK = 200; + private static int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds - private static final int HTTP_OVERLOAD = 429; + private static int MAX_RETRIES = 3; /* * update these constants when Jalview has been checked / updated for @@ -77,8 +84,6 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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 protected static final String CONTENT_TYPE_JSON = "?content-type=application/json"; @@ -187,11 +192,34 @@ 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; + for (int i = 0 ; i < MAX_RETRIES ; i++) + { + if (pingEnsembl(pingUrl)) + { + if (i > 0) + { + Cache.log.info("Ensembl ping responded on attempt " + (i+1)); + } + return true; + } + } + Cache.log.error("Ensembl ping failed after " + MAX_RETRIES + " retries"); + return false; + } + + /** + * Connects to Ensembl REST service's 'ping' URL and answers true if + * successful, false if no reply, or no reply within the 2 second timeout + * + * @param pingUrl + * @return + */ + @SuppressWarnings("unchecked") + protected boolean pingEnsembl(String pingUrl) + { try { // note this format works for both ensembl and ensemblgenomes @@ -202,7 +230,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * if ping takes more than 2 seconds to respond, treat as if unavailable */ Map val = (Map) getJSON( - new URL(pingUrl), null, 2 * 1000, MODE_MAP, null); + new URL(pingUrl), null, PING_TIMEOUT_MS, MODE_MAP, null); if (val == null) { return false; @@ -211,22 +239,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher return pingString != null; } catch (Throwable t) { - System.err.println( + Cache.log.error( "Error connecting to " + pingUrl + ": " + t.getMessage()); - } finally - { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } + return false; } - return false; } protected final static int MODE_ARRAY = 0; @@ -313,7 +329,7 @@ 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); + Cache.log.error("Response code " + responseCode);// + " for " + url); return null; } @@ -417,7 +433,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * recheck if Ensembl is up if it was down, or the recheck period has elapsed */ boolean retestAvailability = (now - - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL; + - info.lastAvailableCheckTime) > PING_RETEST_INTERVAL; if (!info.restAvailable || retestAvailability) { info.restAvailable = checkEnsembl(); diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index fd8800f..fe61a87 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -265,12 +265,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient String accId = querySeq.getName(); try { - System.out.println("Adding protein product for " + accId); + Cache.log.info("Adding protein product for " + accId); AlignmentI protein = new EnsemblProtein(getDomain()) .getSequenceRecords(accId); if (protein == null || protein.getHeight() == 0) { - System.out.println("No protein product found for " + accId); + Cache.log.info("No protein product found for " + accId); return; } SequenceI proteinSeq = protein.getSequenceAt(0); @@ -429,7 +429,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (seqs.size() != ids.size()) { - System.out.println(String.format( + Cache.log.warn(String.format( "Only retrieved %d sequences for %d query strings", seqs.size(), ids.size())); } @@ -657,7 +657,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (regions.isEmpty()) { - System.out.println("Failed to identify target sequence for " + accId + Cache.log.warn("Failed to identify target sequence for " + accId + " from genomic features"); return null; } -- 1.7.10.2