develop merge

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

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
new file mode 100644 (file)
index 0000000..f19b4d4
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -0,0 +1,188 @@
+package jalview.ext.ensembl;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.util.DBRefUtils;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+/**
+ * A class to fetch cross-references from Ensembl by calling the /xrefs REST
+ * service
+ * 
+ * @author gmcarstairs
+ * @see http://rest.ensembl.org/documentation/info/xref_id
+ */
+class EnsemblXref extends EnsemblRestClient
+{
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblXref(String d)
+  {
+    super(d);
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "ENSEMBL (xref)";
+  }
+
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    return null;
+  }
+
+  @Override
+  protected URL getUrl(List<String> ids) throws MalformedURLException
+  {
+    return getUrl(ids.get(0));
+  }
+
+  @Override
+  protected boolean useGetRequest()
+  {
+    return true;
+  }
+
+  @Override
+  protected String getRequestMimeType(boolean multipleIds)
+  {
+    return "application/json";
+  }
+
+  @Override
+  protected String getResponseMimeType()
+  {
+    return "application/json";
+  }
+
+  /**
+   * Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
+   * ("primary_id") for the given identifier (Ensembl accession id) and database
+   * names. The "dbname" returned by Ensembl is canonicalised to Jalview's
+   * standard version, and a DBRefEntry constructed. If no databases are
+   * specified, all available cross-references are retrieved.
+   * 
+   * @param identifier
+   * @param databases
+   * @return
+   */
+  public List<DBRefEntry> getCrossReferences(String identifier,
+          List<String> databases)
+  {
+    List<DBRefEntry> result = new ArrayList<DBRefEntry>();
+    List<String> ids = new ArrayList<String>();
+    ids.add(identifier);
+
+    BufferedReader br = null;
+    try
+    {
+      URL url = getUrl(identifier);
+        if (url != null)
+        {
+          br = getHttpResponse(url, ids);
+        }
+      return (parseResponse(br, databases));
+    } catch (IOException e)
+    {
+      // ignore
+    } finally
+    {
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
+    }
+
+    return result;
+  }
+
+  /**
+   * Parses "primary_id" and "dbname" values from the JSON response and
+   * constructs a DBRefEntry if the dbname is in the list supplied. Returns a
+   * list of DBRefEntry created.
+   * 
+   * @param br
+   * @param databases
+   * @return
+   * @throws IOException
+   */
+  protected List<DBRefEntry> parseResponse(BufferedReader br,
+          List<String> databases)
+          throws IOException
+  {
+    JSONParser jp = new JSONParser();
+    List<DBRefEntry> result = new ArrayList<DBRefEntry>();
+    try
+    {
+      JSONArray responses = (JSONArray) jp.parse(br);
+      Iterator rvals = responses.iterator();
+      while (rvals.hasNext())
+      {
+        JSONObject val = (JSONObject) rvals.next();
+        String dbName = val.get("dbname").toString();
+        if (databases != null && !databases.isEmpty()
+                && !databases.contains(dbName))
+        {
+          continue;
+        }
+        String id = val.get("primary_id").toString();
+        if (dbName != null && id != null)
+        {
+          dbName = DBRefUtils.getCanonicalName(dbName);
+          DBRefEntry dbref = new DBRefEntry(dbName, "0", id);
+          result.add(dbref);
+        }
+      }
+    } catch (ParseException e)
+    {
+      // ignore
+    }
+    return result;
+  }
+
+  /**
+   * Returns the URL for the REST endpoint to fetch all cross-references for an
+   * identifier. Note this may return protein cross-references for nucleotide.
+   * Filter the returned list as required.
+   * 
+   * @param identifier
+   * @return
+   */
+  protected URL getUrl(String identifier)
+  {
+    String url = getDomain() + "/xrefs/id/" + identifier
+            + "?content-type=application/json&all_levels=1";
+    try
+    {
+      return new URL(url);
+    } catch (MalformedURLException e)
+    {
+      return null;
+    }
+  }
+
+}