X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=540fc980d290f4114e124c7b51b4cd6f9818da13;hb=3b74463d9ba726384240d7707b6ea416a24c6b59;hp=56d63bb968a38d3621722ea3a25cb2068b8b6c3e;hpb=c389306ad8eca96fe2476197d7ae63f94c4ee483;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index 56d63bb..540fc98 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,18 +20,10 @@ */ package jalview.ext.ensembl; -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; 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; @@ -44,6 +36,9 @@ import javax.ws.rs.HttpMethod; import org.json.simple.parser.ParseException; +import jalview.util.Platform; +import jalview.util.StringUtils; + /** * Base class for Ensembl REST service clients * @@ -54,8 +49,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher static { - Cache.addJ2SDirectDatabaseCall("http://rest.ensembl"); - Cache.addJ2SDirectDatabaseCall("https://rest.ensembl"); + Platform.addJ2SDirectDatabaseCall("http://rest.ensembl"); + Platform.addJ2SDirectDatabaseCall("https://rest.ensembl"); } private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes @@ -74,9 +69,9 @@ 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 = "9.0"; + private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "15.2"; - private static final String LATEST_ENSEMBL_REST_VERSION = "9.0"; + 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"; @@ -216,7 +211,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher return pingString != null; } catch (Throwable t) { - System.err.println( + jalview.bin.Console.errPrintln( "Error connecting to " + pingUrl + ": " + t.getMessage()); } finally { @@ -282,10 +277,12 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * in milliseconds * @return * @throws IOException + * @throws ParseException */ - private 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; @@ -294,10 +291,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher HttpURLConnection connection = null; int responseCode = 0; - if (Platform.isJS()) - { - JSON.setAjax(url); - } + Platform.setAjaxJSON(url); while (retriesLeft > 0) { @@ -319,21 +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); + jalview.bin.Console.errPrintln("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"); + // Platform.timeCheck(null, Platform.TIME_MARK); + Object ret = Platform.parseJSON(response); + // Platform.timeCheck("EnsemblRestClient.getJSON " + url, + // Platform.TIME_MARK); - return new BufferedReader(new InputStreamReader(response, "UTF-8")); + return ret; } /** @@ -347,7 +338,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher protected HttpURLConnection tryConnection(URL url, List ids, int readTimeout) throws IOException, ProtocolException { - // System.out.println(System.currentTimeMillis() + " " + url); + // jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); @@ -396,14 +387,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher int retrySecs = Integer.valueOf(retryDelay); if (retrySecs > 0 && retrySecs < 10) { - System.err.println( + jalview.bin.Console.errPrintln( "Ensembl REST service rate limit exceeded, waiting " + retryDelay + " seconds before retrying"); Thread.sleep(1000 * retrySecs); } } catch (NumberFormatException | InterruptedException e) { - System.err.println("Error handling Retry-After: " + e.getMessage()); + jalview.bin.Console.errPrintln("Error handling Retry-After: " + e.getMessage()); } } } @@ -515,50 +506,26 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher url = getUrl(ids); } - Reader br = null; - try - { - Platform.timeCheck(null, Platform.TIME_MARK); - - br = (url == null ? null : getHttpResponse(url, ids, msDelay)); + Object json = (url == null ? null : getJSON(url, ids, msDelay)); - Object ret = (br == null ? null : JSONUtils.parse(br)); - - Platform.timeCheck("EnsemblRestClient.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 (json != null && mapKey != null) { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } + 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; } /** @@ -599,7 +566,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher } } catch (NumberFormatException e) { - System.err.println("Error in REST version: " + e.toString()); + jalview.bin.Console.errPrintln("Error in REST version: " + e.toString()); } /* @@ -611,14 +578,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher expected) == 1; if (laterVersion) { - System.err.println(String.format( + jalview.bin.Console.errPrintln(String.format( "EnsemblRestClient expected %s REST version %s but found %s, see %s", getDbSource(), expected, version, REST_CHANGE_LOG)); } info.restVersion = version; } catch (Throwable t) { - System.err.println( + jalview.bin.Console.errPrintln( "Error checking Ensembl REST version: " + t.getMessage()); } } @@ -650,7 +617,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher domainData.get(getDomain()).dataVersion = versions.get(0).toString(); } catch (Throwable e) {// could be IOException | ParseException e) { - System.err.println( + jalview.bin.Console.errPrintln( "Error checking Ensembl data version: " + e.getMessage()); } }