/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.ebi;
+import jalview.datamodel.DBRefSource;
import jalview.util.MessageManager;
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
+import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.ArrayList;
+import java.util.List;
import java.util.StringTokenizer;
/**
throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
- public File fetchDataAsFile(String ids, String f, String s)
+ /**
+ * 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 s
+ * - unused parameter
+ * @return the file holding the response
+ * @throws OutOfMemoryError
+ */
+ public File fetchDataAsFile(String ids, String format, String s)
throws OutOfMemoryError
{
File outFile = null;
{
outFile = File.createTempFile("jalview", ".xml");
outFile.deleteOnExit();
- fetchData(ids, f, s, outFile);
+ fetchData(ids, format, s, outFile);
if (outFile.length() == 0)
{
outFile.delete();
*
* @param ids
* db:query1;query2;query3
- * @param f
+ * @param format
* raw/xml
* @param s
- * ?
+ * not used - remove?
*
* @return Raw string array result of query set
*/
- public String[] fetchData(String ids, String f, String s)
+ public String[] fetchData(String ids, String format, String s)
throws OutOfMemoryError
{
- return fetchData(ids, f, s, null);
+ return fetchData(ids, format, s, null);
}
- public String[] fetchData(String ids, String f, String s, File outFile)
+ String[] fetchData(String ids, String f, String s, File outFile)
throws OutOfMemoryError
{
// Need to split
return (rslts.length == 0 ? null : rslts);
}
- public String[] fetchBatch(String ids, String db, String f, String s,
+ public String[] fetchBatch(String ids, String dbPath, String format, String s,
File outFile) throws OutOfMemoryError
{
- long time = System.currentTimeMillis();
- // max 200 ids can be added at one time
+ // long time = System.currentTimeMillis();
+ /*
+ * JAL-1855 dbfetch from ena_sequence, ena_coding
+ */
+ if (dbPath.equalsIgnoreCase(DBRefSource.EMBL))
+ {
+ dbPath = "ena_sequence";
+ }
+ else if (dbPath.equalsIgnoreCase(DBRefSource.EMBLCDS))
+ {
+ dbPath = "ena_coding";
+ }
+
try
{
URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
- + db.toLowerCase() + "/" + ids.toLowerCase()
- + (f != null ? "/" + f : ""));
+ + dbPath.toLowerCase() + "/" + ids.toLowerCase()
+ + (format != null ? "/" + format : ""));
- BufferedInputStream is = new BufferedInputStream(rcall.openStream());
+ InputStream is = new BufferedInputStream(rcall.openStream());
if (outFile != null)
{
FileOutputStream fio = new FileOutputStream(outFile);
{
BufferedReader br = new BufferedReader(new InputStreamReader(is));
String rtn;
- ArrayList<String> arl = new ArrayList<String>();
+ List<String> arl = new ArrayList<String>();
while ((rtn = br.readLine()) != null)
{
arl.add(rtn);
} catch (OutOfMemoryError er)
{
- System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + dbPath
+ ":\n" + ids);
throw er;
} catch (Exception ex)
{
return null;
}
- System.err.println("Unexpected exception when retrieving from " + db
+ System.err.println("Unexpected exception when retrieving from "
+ + dbPath
+ "\nQuery was : '" + ids + "'");
ex.printStackTrace(System.err);
return null;
} finally
{
- // System.err.println("Took " + (System.currentTimeMillis() - time)
- // / 1000 + " secs for one call.");
+ // System.err.println("EBIFetch took " + (System.currentTimeMillis() -
+ // time) + " ms");
}
return null;
}