X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=9f6bc65a8524b5a3a20a4da12cd352c49313bfc4;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=623a586159359d821951ead58c186def55da383c;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 623a586..9f6bc65 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,30 +1,37 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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;
/**
@@ -54,7 +61,7 @@ public class EBIFetchClient
public String[] getSupportedDBs()
{
// TODO - implement rest call for dbfetch getSupportedDBs
- throw new Error("Not yet implemented");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
/**
@@ -65,7 +72,7 @@ public class EBIFetchClient
public String[] getSupportedFormats()
{
// TODO - implement rest call for dbfetch getSupportedFormats
- throw new Error("Not yet implemented");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
/**
@@ -76,18 +83,32 @@ public class EBIFetchClient
public String[] getSupportedStyles()
{
// TODO - implement rest call for dbfetch getSupportedStyles
- throw new Error("Not yet implemented");
+ 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,
+ String ext)
throws OutOfMemoryError
{
File outFile = null;
try
{
- outFile = File.createTempFile("jalview", ".xml");
+ outFile = File.createTempFile("jalview", ext);
outFile.deleteOnExit();
- fetchData(ids, f, s, outFile);
+ fetchData(ids, format, s, outFile);
if (outFile.length() == 0)
{
outFile.delete();
@@ -104,20 +125,20 @@ public class EBIFetchClient
*
* @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
@@ -165,18 +186,29 @@ public class EBIFetchClient
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);
@@ -193,7 +225,7 @@ public class EBIFetchClient
{
BufferedReader br = new BufferedReader(new InputStreamReader(is));
String rtn;
- ArrayList arl = new ArrayList();
+ List arl = new ArrayList();
while ((rtn = br.readLine()) != null)
{
arl.add(rtn);
@@ -203,7 +235,7 @@ public class EBIFetchClient
} 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)
@@ -213,16 +245,16 @@ public class EBIFetchClient
{
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;
}
}
-