From fab471e8ebef16e3cb7328f46b83c3c9c0b8abac Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 19 Oct 2017 14:56:13 +0100 Subject: [PATCH] JAL-2755 rename EnsemblInfo as EnsemblData, add 'true' EnsemblInfo --- src/jalview/ext/ensembl/EnsemblData.java | 91 ++++++++++ src/jalview/ext/ensembl/EnsemblInfo.java | 228 +++++++++++++++++------- src/jalview/ext/ensembl/EnsemblRestClient.java | 14 +- 3 files changed, 259 insertions(+), 74 deletions(-) create mode 100644 src/jalview/ext/ensembl/EnsemblData.java diff --git a/src/jalview/ext/ensembl/EnsemblData.java b/src/jalview/ext/ensembl/EnsemblData.java new file mode 100644 index 0000000..47fe0fc --- /dev/null +++ b/src/jalview/ext/ensembl/EnsemblData.java @@ -0,0 +1,91 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.ext.ensembl; + +/** + * A data class to model the data and rest version of one Ensembl domain, + * currently for rest.ensembl.org and rest.ensemblgenomes.org + * + * @author gmcarstairs + */ +class EnsemblData +{ + /* + * The http domain this object is holding data values for + */ + String domain; + + /* + * The latest version Jalview has tested for, e.g. "4.5"; a minor version change should be + * ok, a major version change may break stuff + */ + String expectedRestVersion; + + /* + * Major / minor / point version e.g. "4.5.1" + * @see http://rest.ensembl.org/info/rest/?content-type=application/json + */ + String restVersion; + + /* + * data version + * @see http://rest.ensembl.org/info/data/?content-type=application/json + */ + String dataVersion; + + /* + * true when http://rest.ensembl.org/info/ping/?content-type=application/json + * returns response code 200 and not {"error":"Database is unavailable"} + */ + boolean restAvailable; + + /* + * absolute time when availability was last checked + */ + long lastAvailableCheckTime; + + /* + * absolute time when version numbers were last checked + */ + long lastVersionCheckTime; + + // flag set to true if REST major version is not the one expected + boolean restMajorVersionMismatch; + + /* + * absolute time to wait till if we overloaded the REST service + */ + long retryAfter; + + /** + * Constructor given expected REST version number e.g 4.5 or 3.4.3 + * + * @param restExpected + */ + EnsemblData(String theDomain, String restExpected) + { + domain = theDomain; + expectedRestVersion = restExpected; + lastAvailableCheckTime = -1; + lastVersionCheckTime = -1; + } + +} diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java index 3108194..de55a53 100644 --- a/src/jalview/ext/ensembl/EnsemblInfo.java +++ b/src/jalview/ext/ensembl/EnsemblInfo.java @@ -1,91 +1,185 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with Jalview. If not, see . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ package jalview.ext.ensembl; -/** - * A data class to model the data and rest version of one Ensembl domain, - * currently for rest.ensembl.org and rest.ensemblgenomes.org - * - * @author gmcarstairs - */ -class EnsemblInfo +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefSource; + +import java.io.BufferedReader; +import java.io.IOException; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.json.simple.JSONArray; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; + +public class EnsemblInfo extends EnsemblRestClient { - /* - * The http domain this object is holding data values for - */ - String domain; /* - * The latest version Jalview has tested for, e.g. "4.5"; a minor version change should be - * ok, a major version change may break stuff + * cached results of REST /info/divisions service, currently + * 
+   * { 
+   *  { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBL", "http://rest.ensembl.org" }
+   *  }
+   *
+ * The values for EnsemblGenomes are retrieved by a REST call, that for + * Ensembl is added programmatically for convenience of lookup */ - String expectedRestVersion; + private static Map divisions; - /* - * Major / minor / point version e.g. "4.5.1" - * @see http://rest.ensembl.org/info/rest/?content-type=application/json - */ - String restVersion; + @Override + public String getDbName() + { + return "ENSEMBL"; + } - /* - * data version - * @see http://rest.ensembl.org/info/data/?content-type=application/json - */ - String dataVersion; + @Override + public AlignmentI getSequenceRecords(String queries) throws Exception + { + return null; + } - /* - * true when http://rest.ensembl.org/info/ping/?content-type=application/json - * returns response code 200 and not {"error":"Database is unavailable"} - */ - boolean restAvailable; + @Override + protected URL getUrl(List ids) throws MalformedURLException + { + return null; + } - /* - * absolute time when availability was last checked + @Override + protected boolean useGetRequest() + { + return true; + } + + @Override + protected String getRequestMimeType(boolean multipleIds) + { + return "application/json"; + } + + @Override + protected String getResponseMimeType() + { + return "application/json"; + } + + /** + * Answers the domain (http://rest.ensembl.org or + * http://rest.ensemblgenomes.org) for the given division, or null if not + * recognised by Ensembl. + * + * @param division + * @return */ - long lastAvailableCheckTime; + public String getDomain(String division) + { + if (divisions == null) + { + fetchDivisions(); + } + return divisions.get(division.toUpperCase()); + } - /* - * absolute time when version numbers were last checked + /** + * On first request only, populate the lookup map by fetching the list of + * divisions known to EnsemblGenomes. */ - long lastVersionCheckTime; + void fetchDivisions() + { + divisions = new HashMap<>(); - // flag set to true if REST major version is not the one expected - boolean restMajorVersionMismatch; + /* + * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL" + */ + divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ENSEMBL_REST); - /* - * absolute time to wait till if we overloaded the REST service + BufferedReader br = null; + try + { + URL url = getDivisionsUrl(ENSEMBL_GENOMES_REST); + if (url != null) + { + br = getHttpResponse(url, null); + } + parseResponse(br, ENSEMBL_GENOMES_REST); + } catch (IOException e) + { + // ignore + } finally + { + if (br != null) + { + try + { + br.close(); + } catch (IOException e) + { + // ignore + } + } + } + } + + /** + * Parses the JSON response to /info/divisions, and add each to the lookup map + * + * @param br + * @param domain */ - long retryAfter; + void parseResponse(BufferedReader br, String domain) + { + JSONParser jp = new JSONParser(); + + try + { + JSONArray parsed = (JSONArray) jp.parse(br); + + Iterator rvals = parsed.iterator(); + while (rvals.hasNext()) + { + String division = rvals.next().toString(); + divisions.put(division.toUpperCase(), domain); + } + } catch (IOException | ParseException | NumberFormatException e) + { + // ignore + } + } /** - * Constructor given expected REST version number e.g 4.5 or 3.4.3 + * Constructs the URL for the EnsemblGenomes /info/divisions REST service + * @param domain TODO * - * @param restExpected + * @return + * @throws MalformedURLException */ - EnsemblInfo(String theDomain, String restExpected) + URL getDivisionsUrl(String domain) throws MalformedURLException { - domain = theDomain; - expectedRestVersion = restExpected; - lastAvailableCheckTime = -1; - lastVersionCheckTime = -1; + return new URL(domain + + "/info/divisions?content-type=application/json"); } + /** + * Returns the set of 'divisions' recognised by Ensembl or EnsemblGenomes + * + * @return + */ + public Set getDivisions() { + if (divisions == null) + { + fetchDivisions(); + } + + return divisions.keySet(); + } } diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index ad6c70c..7cabfbb 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -67,7 +67,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log"; - private static Map domainData; + 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"; @@ -87,10 +87,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher static { - domainData = new HashMap(); + domainData = new HashMap(); domainData.put(ENSEMBL_REST, - new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION)); - domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo( + new EnsemblData(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION)); + domainData.put(ENSEMBL_GENOMES_REST, new EnsemblData( ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION)); } @@ -368,7 +368,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher // to test: // retryDelay = "5"; - EnsemblInfo info = domainData.get(getDomain()); + EnsemblData info = domainData.get(getDomain()); if (retryDelay != null) { System.err.println("Ensembl REST service rate limit exceeded, wait " @@ -403,7 +403,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher */ protected boolean isEnsemblAvailable() { - EnsemblInfo info = domainData.get(getDomain()); + EnsemblData info = domainData.get(getDomain()); long now = System.currentTimeMillis(); @@ -491,7 +491,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher */ private void checkEnsemblRestVersion() { - EnsemblInfo info = domainData.get(getDomain()); + EnsemblData info = domainData.get(getDomain()); JSONParser jp = new JSONParser(); URL url = null; -- 1.7.10.2