Merge branch 'develop' into imp/JAL-2775

[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 c06d13e..b1bc8e5 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -43,8 +43,6 @@ 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
  * 
@@ -68,9 +66,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
    * @see http://rest.ensembl.org/info/rest?content-type=application/json
    */
-  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "5.0";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "6.0";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "5.0";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "6.1";
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
@@ -83,18 +81,11 @@ 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}$");
+  protected static final String CONTENT_TYPE_JSON = "?content-type=application/json";
 
   static
   {
-    domainData = new HashMap<String, EnsemblInfo>();
+    domainData = new HashMap<>();
     domainData.put(ENSEMBL_REST,
             new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
     domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
@@ -121,42 +112,6 @@ 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()
   {
@@ -218,8 +173,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     {
       // 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");
+      URL ping = new URL(getDomain() + "/info/ping" + CONTENT_TYPE_JSON);
 
       /*
        * expect {"ping":1} if ok
@@ -228,6 +182,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       br = getHttpResponse(ping, null, 2 * 1000);
       if (br == null)
       {
+        // error reponse status
         return false;
       }
       JSONParser jp = new JSONParser();
@@ -506,9 +461,12 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     URL url = null;
     try
     {
-      url = new URL(
-              getDomain() + "/info/rest?content-type=application/json");
+      url = new URL(getDomain() + "/info/rest" + CONTENT_TYPE_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("."));
@@ -571,8 +529,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
     try
     {
-      url = new URL(
-              getDomain() + "/info/data?content-type=application/json");
+      url = new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON);
       br = getHttpResponse(url, null);
       if (br != null)
       {