X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=34f8816f9708dff2f15f23eeda9fa23f5f56fd43;hb=b9df385dd6b61f92577c68b9f39ca0f9fc4d3993;hp=2fd7fa3211aa81f3072c0f53919e950db0b7ec6a;hpb=a9f0472fe6fd4737b47d7955d198e76923e6aabc;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 2fd7fa3..34f8816 100644
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -14,6 +14,8 @@ import java.util.List;
 
 import javax.ws.rs.HttpMethod;
 
+import com.stevesoft.pat.Regex;
+
 /**
  * Base class for Ensembl REST service clients
  * 
@@ -21,22 +23,72 @@ import javax.ws.rs.HttpMethod;
  */
 abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 {
-  protected final static String ENSEMBL_REST = "http://rest.ensembl.org";
+  private final static String ENSEMBL_REST = "http://rest.ensembl.org";
 
-  protected static final String SEQUENCE_ID_URL = ENSEMBL_REST
-          + "/sequence/id";
+  protected final static String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
 
   // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
   private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
 
   private final static long RETEST_INTERVAL = 10000L; // 10 seconds
 
+  private static final Regex TRANSCRIPT_REGEX = new Regex(
+            "(ENS)([A-Z]{3}|)T[0-9]{11}$");
+
+  private static final Regex GENE_REGEX = new Regex(
+            "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+
+  private String domain = ENSEMBL_REST;
+
   private static boolean ensemblRestAvailable = false;
 
   private static long lastCheck = -1;
 
+  /*
+   * absolute time to wait till if we overloaded the REST service
+   */
+  private static long retryAfter;
+
   protected volatile boolean inProgress = false;
 
+  /**
+   * Default constructor to use rest.ensembl.org
+   */
+  public EnsemblRestClient()
+  {
+    this(ENSEMBL_REST);
+  }
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblRestClient(String d)
+  {
+    domain = d;
+  }
+
+  String getDomain()
+  {
+    return domain;
+  }
+
+  void setDomain(String d)
+  {
+    domain = d;
+  }
+
+  public boolean isTranscriptIdentifier(String query)
+  {
+    return query == null ? false : TRANSCRIPT_REGEX.search(query);
+  }
+
+  public boolean isGeneIdentifier(String query)
+  {
+    return query == null ? false : GENE_REGEX.search(query);
+  }
+
   @Override
   public boolean queryInProgress()
   {
@@ -94,7 +146,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   {
     try
     {
-      URL ping = new URL(PING_URL);
+      // note this format works for both ensembl and ensemblgenomes
+      // info/ping.json works for ensembl only (March 2016)
+      URL ping = new URL(getDomain()
+              + "/info/ping?content-type=application/json");
       HttpURLConnection conn = (HttpURLConnection) ping.openConnection();
       int rc = conn.getResponseCode();
       conn.disconnect();
@@ -140,6 +195,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected BufferedReader getHttpResponse(URL url, List<String> ids)
           throws IOException
   {
+    // long now = System.currentTimeMillis();
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
   
     /*
@@ -175,6 +231,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
               "Response code was not 200. Detected response was "
                       + responseCode);
     }
+    // System.out.println(getClass().getName() + " took "
+    // + (System.currentTimeMillis() - now) + "ms to fetch");
+
+    checkRateLimits(connection);
   
     BufferedReader reader = null;
     reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
@@ -182,6 +242,52 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   }
 
   /**
+   * Inspect response headers for any sign of server overload and respect any
+   * 'retry-after' directive
+   * 
+   * @see https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits
+   * @param connection
+   */
+  void checkRateLimits(HttpURLConnection connection)
+  {
+    // number of requests allowed per time interval:
+    String limit = connection.getHeaderField("X-RateLimit-Limit");
+    // length of quota time interval in seconds:
+    // String period = connection.getHeaderField("X-RateLimit-Period");
+    // seconds remaining until usage quota is reset:
+    String reset = connection.getHeaderField("X-RateLimit-Reset");
+    // number of requests remaining from quota for current period:
+    String remaining = connection.getHeaderField("X-RateLimit-Remaining");
+    // number of seconds to wait before retrying (if remaining == 0)
+    String retryDelay = connection.getHeaderField("Retry-After");
+
+    // to test:
+    // retryDelay = "5";
+
+    if (retryDelay != null)
+    {
+      System.err.println("Ensembl REST service rate limit exceeded, wait "
+              + retryDelay + " seconds before retrying");
+      try
+      {
+        retryAfter = System.currentTimeMillis()
+                + (1000 * Integer.valueOf(retryDelay));
+      } catch (NumberFormatException e)
+      {
+        System.err.println("Unexpected value for Retry-After: "
+                + retryDelay);
+      }
+    }
+    else
+    {
+      retryAfter = 0;
+      // debug:
+      // System.out.println(String.format(
+      // "%s Ensembl requests remaining of %s (reset in %ss)",
+      // remaining, limit, reset));
+    }
+  }
+  /**
    * Rechecks if Ensembl is responding, unless the last check was successful and
    * the retest interval has not yet elapsed. Returns true if Ensembl is up,
    * else false.
@@ -191,6 +297,21 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected boolean isEnsemblAvailable()
   {
     long now = System.currentTimeMillis();
+
+    /*
+     * check if we are waiting for 'Retry-After' to expire
+     */
+    if (retryAfter > now)
+    {
+      System.err.println("Still " + (1 + (retryAfter - now) / 1000)
+              + " secs to wait before retrying Ensembl");
+      return false;
+    }
+    else
+    {
+      retryAfter = 0;
+    }
+
     boolean retest = now - lastCheck > RETEST_INTERVAL;
     if (ensemblRestAvailable && !retest)
     {