X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=1d04351f06a9f057a9b6d1e5e58dab20ae245998;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=c7f6bb884c8b9feb12060e20981d05427efe5b9c;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index c7f6bb8..1d04351 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,227 +1,295 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-package jalview.ws.ebi;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.InputStreamReader;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.StringTokenizer;
-
-/**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
- */
-public class EBIFetchClient
-{
-  String format = "default";
-
-  String style = "raw";
-
-  /**
-   * Creates a new EBIFetchClient object.
-   */
-  public EBIFetchClient()
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedDBs()
-  {
-    // TODO - implement rest call for dbfetch getSupportedDBs
-    throw new Error("Not yet implemented");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedFormats()
-  {
-    // TODO - implement rest call for dbfetch getSupportedFormats
-    throw new Error("Not yet implemented");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedStyles()
-  {
-    // TODO - implement rest call for dbfetch getSupportedStyles
-    throw new Error("Not yet implemented");
-  }
-
-  public File fetchDataAsFile(String ids, String f, String s)
-          throws OutOfMemoryError
-  {
-    File outFile = null;
-    try
-    {
-      outFile = File.createTempFile("jalview", ".xml");
-      outFile.deleteOnExit();
-      fetchData(ids, f, s, outFile);
-      if (outFile.length() == 0)
-      {
-        outFile.delete();
-        return null;
-      }
-    } catch (Exception ex)
-    {
-    }
-    return outFile;
-  }
-
-  /**
-   * Single DB multiple record retrieval
-   * 
-   * @param ids
-   *          db:query1;query2;query3
-   * @param f
-   *          raw/xml
-   * @param s
-   *          ?
-   * 
-   * @return Raw string array result of query set
-   */
-  public String[] fetchData(String ids, String f, String s)
-          throws OutOfMemoryError
-  {
-    return fetchData(ids, f, s, null);
-  }
-
-  public String[] fetchData(String ids, String f, String s, File outFile)
-          throws OutOfMemoryError
-  {
-    // Need to split
-    // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
-    String[] rslts = new String[0];
-    StringTokenizer queries = new StringTokenizer(ids, ";");
-    String db = null;
-    StringBuffer querystring = null;
-    int nq = 0;
-    while (queries.hasMoreTokens())
-    {
-      String query = queries.nextToken();
-      int p;
-      if ((p = query.indexOf(':')) > -1)
-      {
-        db = query.substring(0, p);
-        query = query.substring(p + 1);
-      }
-      if (querystring == null)
-      {
-        querystring = new StringBuffer(query);
-        nq++;
-      }
-      else
-      {
-        querystring.append("," + query);
-        nq++;
-      }
-    }
-    if (db == null)
-    {
-      System.err.println("Invalid Query string : '" + ids
-              + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
-      return null;
-    }
-    String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);
-    if (rslt != null)
-    {
-      String[] nrslts = new String[rslt.length + rslts.length];
-      System.arraycopy(rslts, 0, nrslts, 0, rslts.length);
-      System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);
-      rslts = nrslts;
-    }
-
-    return (rslts.length == 0 ? null : rslts);
-  }
-
-  public String[] fetchBatch(String ids, String db, String f, String s,
-          File outFile) throws OutOfMemoryError
-  {
-    long time = System.currentTimeMillis();
-    // max 200 ids can be added at one time
-    try
-    {
-      URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
-              + db.toLowerCase() + "/" + ids.toLowerCase()
-              + (f != null ? "/" + f : ""));
-
-      BufferedInputStream is = new BufferedInputStream(rcall.openStream());
-      if (outFile != null)
-      {
-        FileOutputStream fio = new FileOutputStream(outFile);
-        byte[] bb = new byte[32 * 1024];
-        int l;
-        while ((l = is.read(bb)) > 0)
-        {
-          fio.write(bb, 0, l);
-        }
-        fio.close();
-        is.close();
-      }
-      else
-      {
-        BufferedReader br = new BufferedReader(new InputStreamReader(is));
-        String rtn;
-        ArrayList<String> arl = new ArrayList<String>();
-        while ((rtn = br.readLine()) != null)
-        {
-          arl.add(rtn);
-        }
-        return arl.toArray(new String[arl.size()]);
-      }
-    } catch (OutOfMemoryError er)
-    {
-
-      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
-              + ":\n" + ids);
-      throw er;
-    } catch (Exception ex)
-    {
-      if (ex.getMessage().startsWith(
-              "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
-      {
-        return null;
-      }
-      System.err.println("Unexpected exception when retrieving from " + db
-              + "\nQuery was : '" + ids + "'");
-      ex.printStackTrace(System.err);
-      return null;
-    } finally
-    {
-      //System.err.println("Took " + (System.currentTimeMillis() - time)
-      //        / 1000 + " secs for one call.");
-    }
-    return null;
-  }
-}
+package jalview.ws.ebi;
 
+import java.util.Locale;
+
+import jalview.datamodel.DBRefSource;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
+
+  /**
+   * Creates a new EBIFetchClient object.
+   */
+  public EBIFetchClient()
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedDBs()
+  {
+    // TODO - implement rest call for dbfetch getSupportedDBs
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedFormats()
+  {
+    // TODO - implement rest call for dbfetch getSupportedFormats
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedStyles()
+  {
+    // TODO - implement rest call for dbfetch getSupportedStyles
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
+  }
+
+  /**
+   * Send an HTTP fetch request to EBI and save the reply in a temporary file.
+   * 
+   * @param ids
+   *          the query formatted as db:query1;query2;query3
+   * @param format
+   *          the format wanted
+   * @param ext
+   *          for the temporary file to hold response (without separator)
+   * @return the file holding the response
+   * @throws OutOfMemoryError
+   */
+
+  public File fetchDataAsFile(String ids, String format, String ext)
+          throws OutOfMemoryError
+  {
+    File outFile = null;
+    try
+    {
+      outFile = File.createTempFile("jalview", "." + ext);
+      outFile.deleteOnExit();
+      fetchData(ids, format, outFile);
+      if (outFile.length() == 0)
+      {
+        outFile.delete();
+        return null;
+      }
+    } catch (Exception ex)
+    {
+    }
+    return outFile;
+  }
+
+  /**
+   * Fetches queries and either saves the response to a file or returns as
+   * string data
+   * 
+   * @param ids
+   * @param format
+   * @param outFile
+   * @return
+   * @throws OutOfMemoryError
+   */
+  String[] fetchData(String ids, String format, File outFile)
+          throws OutOfMemoryError
+  {
+    StringBuilder querystring = new StringBuilder(ids.length());
+    String database = parseIds(ids, querystring);
+    if (database == null)
+    {
+      System.err.println("Invalid Query string : '" + ids + "'");
+      System.err.println("Should be of form 'dbname:q1;q2;q3;q4'");
+      return null;
+    }
+
+    // note: outFile is currently always specified, so return value is null
+    String[] rslt = fetchBatch(querystring.toString(), database, format,
+            outFile);
+
+    return (rslt != null && rslt.length > 0 ? rslt : null);
+  }
+
+  /**
+   * Parses ids formatted as dbname:q1;q2;q3, returns the dbname and adds
+   * queries as comma-separated items to the querystring. dbname must be
+   * specified for at least one queryId. Returns null if a mixture of different
+   * dbnames is found (ignoring case).
+   * 
+   * @param ids
+   * @param queryString
+   * @return
+   */
+  static String parseIds(String ids, StringBuilder queryString)
+  {
+    String database = null;
+    StringTokenizer queries = new StringTokenizer(ids, ";");
+    boolean appending = queryString.length() > 0;
+    while (queries.hasMoreTokens())
+    {
+      String query = queries.nextToken();
+      int p = query.indexOf(':');
+      if (p > -1)
+      {
+        String db = query.substring(0, p);
+        if (database != null && !db.equalsIgnoreCase(database))
+        {
+          /*
+           * different databases mixed in together - invalid
+           */
+          return null;
+        }
+        database = db;
+        query = query.substring(p + 1);
+      }
+      queryString.append(appending ? "," : "");
+      queryString.append(query);
+      appending = true;
+    }
+    return database;
+  }
+
+  /**
+   * Fetches queries and either saves the response to a file or (if no file
+   * specified) returns as string data
+   * 
+   * @param ids
+   * @param database
+   * @param format
+   * @param outFile
+   * @return array of lines from EBI only if outFile is null (which it will not
+   *         be)
+   * @throws OutOfMemoryError
+   */
+  String[] fetchBatch(String ids, String database, String format,
+          File outFile) throws OutOfMemoryError
+  {
+    String url = buildUrl(ids, database, format);
+    InputStream is = null;
+    BufferedReader br = null;
+    try
+    {
+      URL rcall = new URL(url);
+      HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
+      int responseCode = conn.getResponseCode();
+      if (responseCode == 200)
+      {
+        is = conn.getInputStream();
+        if (outFile != null)
+        {
+          Platform.streamToFile(is, outFile);
+          return null;
+        }
+        br = new BufferedReader(new InputStreamReader(is));
+        String rtn;
+        List<String> arl = new ArrayList<>();
+        while ((rtn = br.readLine()) != null)
+        {
+          arl.add(rtn);
+        }
+        return (String[]) arl.toArray();
+      }
+      System.err.println(
+              "Warning: response code " + responseCode + " for " + url);
+    } catch (OutOfMemoryError er)
+    {
+      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
+              + ":\n" + ids);
+      throw er;
+    } catch (Exception ex)
+    {
+      if (!ex.getMessage().startsWith(
+              "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
+      {
+        System.err.println("Unexpected exception when retrieving from "
+                + database + "\nQuery was : '" + ids + "'");
+        ex.printStackTrace(System.err);
+      }
+    } finally
+    {
+      if (is != null)
+      {
+        try
+        {
+          is.close();
+        } catch (IOException e)
+        {
+        }
+      }
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+        }
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Constructs the URL to fetch from
+   * 
+   * @param ids
+   * @param database
+   * @param format
+   * @return
+   */
+  static String buildUrl(String ids, String database, String format)
+  {
+    String url;
+    if (database.equalsIgnoreCase(DBRefSource.EMBL)
+            || database.equalsIgnoreCase(DBRefSource.EMBLCDS))
+    {
+      url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
+              + ids.toLowerCase(Locale.ROOT) + "?download=true&gzip=true";
+    }
+    else
+    {
+      url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+              + database.toLowerCase(Locale.ROOT) + "/" + ids.toLowerCase(Locale.ROOT)
+              + (format != null ? "/" + format : "");
+    }
+    return url;
+  }
+}