JAL-2253 safer simpler resolution of identifiers using lookup endpoint;

[jalview.git] / src / jalview / ext / ensembl / EnsemblRestClient.java

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index ad6c70c..7752e9c 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -42,8 +42,6 @@ import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 
-import com.stevesoft.pat.Regex;
-
 /**
  * Base class for Ensembl REST service clients
  * 
@@ -76,15 +74,6 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
 
-  private static final Regex PROTEIN_REGEX = new Regex(
-          "(ENS)([A-Z]{3}|)P[0-9]{11}$");
-
-  private static final Regex TRANSCRIPT_REGEX = new Regex(
-          "(ENS)([A-Z]{3}|)T[0-9]{11}$");
-
-  private static final Regex GENE_REGEX = new Regex(
-          "(ENS)([A-Z]{3}|)G[0-9]{11}$");
-
   static
   {
     domainData = new HashMap<String, EnsemblInfo>();
@@ -114,42 +103,6 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     setDomain(d);
   }
 
-  /**
-   * Answers true if the query matches the regular expression pattern for an
-   * Ensembl transcript stable identifier
-   * 
-   * @param query
-   * @return
-   */
-  public boolean isTranscriptIdentifier(String query)
-  {
-    return query == null ? false : TRANSCRIPT_REGEX.search(query);
-  }
-
-  /**
-   * Answers true if the query matches the regular expression pattern for an
-   * Ensembl protein stable identifier
-   * 
-   * @param query
-   * @return
-   */
-  public boolean isProteinIdentifier(String query)
-  {
-    return query == null ? false : PROTEIN_REGEX.search(query);
-  }
-
-  /**
-   * Answers true if the query matches the regular expression pattern for an
-   * Ensembl gene stable identifier
-   * 
-   * @param query
-   * @return
-   */
-  public boolean isGeneIdentifier(String query)
-  {
-    return query == null ? false : GENE_REGEX.search(query);
-  }
-
   @Override
   public boolean queryInProgress()
   {
@@ -219,6 +172,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
        * if ping takes more than 2 seconds to respond, treat as if unavailable
        */
       br = getHttpResponse(ping, null, 2 * 1000);
+      if (br == null)
+      {
+        // error reponse status
+        return false;
+      }
       JSONParser jp = new JSONParser();
       JSONObject val = (JSONObject) jp.parse(br);
       String pingString = val.get("ping").toString();
@@ -355,13 +313,13 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   void checkRateLimits(HttpURLConnection connection)
   {
     // number of requests allowed per time interval:
-    String limit = connection.getHeaderField("X-RateLimit-Limit");
+    // 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");
+    // String reset = connection.getHeaderField("X-RateLimit-Reset");
     // number of requests remaining from quota for current period:
-    String remaining = connection.getHeaderField("X-RateLimit-Remaining");
+    // String remaining = connection.getHeaderField("X-RateLimit-Remaining");
     // number of seconds to wait before retrying (if remaining == 0)
     String retryDelay = connection.getHeaderField("Retry-After");
 
@@ -500,6 +458,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       url = new URL(
               getDomain() + "/info/rest?content-type=application/json");
       BufferedReader br = getHttpResponse(url, null);
+      if (br == null)
+      {
+        return;
+      }
       JSONObject val = (JSONObject) jp.parse(br);
       String version = val.get("release").toString();
       String majorVersion = version.substring(0, version.indexOf("."));
@@ -563,9 +525,13 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       url = new URL(
               getDomain() + "/info/data?content-type=application/json");
       BufferedReader br = getHttpResponse(url, null);
-      JSONObject val = (JSONObject) jp.parse(br);
-      JSONArray versions = (JSONArray) val.get("releases");
-      domainData.get(getDomain()).dataVersion = versions.get(0).toString();
+      if (br != null)
+      {
+        JSONObject val = (JSONObject) jp.parse(br);
+        JSONArray versions = (JSONArray) val.get("releases");
+        domainData.get(getDomain()).dataVersion = versions.get(0)
+                .toString();
+      }
     } catch (Throwable t)
     {
       System.err.println(