-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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
*
- * @author gmcarstairs
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-class EnsemblInfo
+package jalview.ext.ensembl;
+
+import java.util.Locale;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.util.JSONUtils;
+
+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.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
+ * <pre>
+ * {
+ * { "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" }
+ * }
+ * </pre>
+ * 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<String, String> 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
- */
- boolean restAvailable;
+ @Override
+ protected URL getUrl(List<String> ids) throws MalformedURLException
+ {
+ return null;
+ }
- /*
- * absolute time when availability was last checked
- */
- long lastAvailableCheckTime;
+ @Override
+ protected boolean useGetRequest()
+ {
+ return true;
+ }
- /*
- * absolute time when version numbers were last checked
+ /**
+ * 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 lastVersionCheckTime;
-
- // flag set to true if REST major version is not the one expected
- boolean restMajorVersionMismatch;
+ public String getDomain(String division)
+ {
+ if (divisions == null)
+ {
+ fetchDivisions();
+ }
+ return divisions.get(division.toUpperCase(Locale.ROOT));
+ }
- /*
- * absolute time to wait till if we overloaded the REST service
+ /**
+ * On first request only, populate the lookup map by fetching the list of
+ * divisions known to EnsemblGenomes.
*/
- long retryAfter;
+ void fetchDivisions()
+ {
+ divisions = new HashMap<>();
+
+ /*
+ * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
+ */
+ divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT), ensemblDomain);
+ try
+ {
+ @SuppressWarnings("unchecked")
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(getDivisionsUrl(ensemblGenomesDomain), null, -1, MODE_ITERATOR, null);
+ if (rvals == null)
+ return;
+ while (rvals.hasNext())
+ {
+ String division = rvals.next().toString();
+ divisions.put(division.toUpperCase(Locale.ROOT), ensemblGenomesDomain);
+ }
+ } 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<String> getDivisions() {
+ if (divisions == null)
+ {
+ fetchDivisions();
+ }
+
+ return divisions.keySet();
+ }
}