Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

[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 d457668..e64c51a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -20,8 +20,6 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
 import jalview.util.StringUtils;
 
 import java.io.BufferedReader;
@@ -62,17 +60,17 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   /*
    * update these constants when Jalview has been checked / updated for
-   * changes to Ensembl REST API (ref JAL-2105)
+   * changes to Ensembl REST API, and updated JAL-3018
    * @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 = "6.0";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "9.0";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "6.1";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "9.0";
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
-  private static Map<String, EnsemblInfo> domainData = new HashMap<>();
+  private static Map<String, EnsemblData> domainData;
 
   private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
 
@@ -82,10 +80,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   static
   {
-    domainData.put(DEFAULT_ENSEMBL_DOMAIN,
-            new EnsemblInfo(DEFAULT_ENSEMBL_DOMAIN, LATEST_ENSEMBL_REST_VERSION));
-    domainData.put(DEFAULT_ENSEMBL_GENOMES_DOMAIN, new EnsemblInfo(
-            DEFAULT_ENSEMBL_GENOMES_DOMAIN, LATEST_ENSEMBLGENOMES_REST_VERSION));
+    domainData = new HashMap<>();
+    domainData.put(DEFAULT_ENSEMBL_BASEURL,
+            new EnsemblData(DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
+    domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL, new EnsemblData(
+            DEFAULT_ENSEMBL_GENOMES_BASEURL, LATEST_ENSEMBLGENOMES_REST_VERSION));
   }
 
   protected volatile boolean inProgress = false;
@@ -103,11 +102,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     if (!domainData.containsKey(ensemblDomain))
     {
       domainData.put(ensemblDomain,
-              new EnsemblInfo(ensemblDomain, LATEST_ENSEMBL_REST_VERSION));
+              new EnsemblData(ensemblDomain, LATEST_ENSEMBL_REST_VERSION));
     }
     if (!domainData.containsKey(ensemblGenomesDomain))
     {
-      domainData.put(ensemblGenomesDomain, new EnsemblInfo(
+      domainData.put(ensemblGenomesDomain, new EnsemblData(
               ensemblGenomesDomain, LATEST_ENSEMBLGENOMES_REST_VERSION));
     }
   }
@@ -152,22 +151,28 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected abstract boolean useGetRequest();
 
   /**
-   * Return the desired value for the Content-Type request header
-   * 
-   * @param multipleIds
+   * Returns the desired value for the Content-Type request header. Default is
+   * application/json, override if required to vary this.
    * 
    * @return
    * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
    */
-  protected abstract String getRequestMimeType(boolean multipleIds);
+  protected String getRequestMimeType()
+  {
+    return "application/json";
+  }
 
   /**
-   * Return the desired value for the Accept request header
+   * Return the desired value for the Accept request header. Default is
+   * application/json, override if required to vary this.
    * 
    * @return
    * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
    */
-  protected abstract String getResponseMimeType();
+  protected String getResponseMimeType()
+  {
+    return "application/json";
+  }
 
   /**
    * Checks Ensembl's REST 'ping' endpoint, and returns true if response
@@ -221,25 +226,20 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   }
 
   /**
-   * returns a reader to a Fasta response from the Ensembl sequence endpoint
+   * Returns a reader to a (Json) response from the Ensembl sequence endpoint.
+   * If the request failed the return value may be null.
    * 
    * @param ids
    * @return
    * @throws IOException
    */
-  protected FileParse getSequenceReader(List<String> ids) throws IOException
+  protected BufferedReader getSequenceReader(List<String> ids)
+          throws IOException
   {
     URL url = getUrl(ids);
 
     BufferedReader reader = getHttpResponse(url, ids);
-    if (reader == null)
-    {
-      // request failed
-      return null;
-    }
-    FileParse fp = new FileParse(reader, url.toString(),
-            DataSourceType.URL);
-    return fp;
+    return reader;
   }
 
   /**
@@ -258,7 +258,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   }
 
   /**
-   * Sends the HTTP request and gets the response as a reader
+   * Sends the HTTP request and gets the response as a reader. Returns null if
+   * the HTTP response code was not 200.
    * 
    * @param url
    * @param ids
@@ -267,7 +268,6 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    *          in milliseconds
    * @return
    * @throws IOException
-   *           if response code was not 200, or other I/O error
    */
   protected BufferedReader getHttpResponse(URL url, List<String> ids,
           int readTimeout) throws IOException
@@ -331,8 +331,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     boolean multipleIds = ids != null && ids.size() > 1;
     connection.setRequestMethod(
             multipleIds ? HttpMethod.POST : HttpMethod.GET);
-    connection.setRequestProperty("Content-Type",
-            getRequestMimeType(multipleIds));
+    connection.setRequestProperty("Content-Type", getRequestMimeType());
     connection.setRequestProperty("Accept", getResponseMimeType());
 
     connection.setUseCaches(false);
@@ -392,7 +391,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    */
   protected boolean isEnsemblAvailable()
   {
-    EnsemblInfo info = domainData.get(getDomain());
+    EnsemblData info = domainData.get(getDomain());
 
     long now = System.currentTimeMillis();
 
@@ -466,7 +465,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    */
   private void checkEnsemblRestVersion()
   {
-    EnsemblInfo info = domainData.get(getDomain());
+    EnsemblData info = domainData.get(getDomain());
 
     JSONParser jp = new JSONParser();
     URL url = null;