X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblInfo.java;h=37dff519ced50f13fe935840d308e8584fa1ada6;hb=ff425ad8a4419c01b52734dc4054a509961c15c0;hp=88b5ac4998f2b0ee9fdb0d20ed45eae6d1cffae5;hpb=a96386b344a49391588762301ad71f1d39c11ca7;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index 88b5ac4..37dff51 100644
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -1,71 +1,185 @@
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(), ensemblDomain);
- /*
- * absolute time to wait till if we overloaded the REST service
+ BufferedReader br = null;
+ try
+ {
+ URL url = getDivisionsUrl(ensemblGenomesDomain);
+ if (url != null)
+ {
+ br = getHttpResponse(url, null);
+ }
+ parseResponse(br, ensemblGenomesDomain);
+ } 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();
+ }
}