/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.*;
-import java.util.*;
-import javax.xml.namespace.*;
-import javax.xml.rpc.*;
+import jalview.datamodel.DBRefSource;
+import jalview.util.MessageManager;
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.axis.encoding.*;
+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;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class EBIFetchClient
{
- Call call;
- String format = "default";
- String style = "raw";
/**
* Creates a new EBIFetchClient object.
*/
public EBIFetchClient()
{
- try
- {
- call = (Call)new Service().createCall();
- call.setTargetEndpointAddress(new java.net.URL(
- "http://www.ebi.ac.uk/ws/services/Dbfetch"));
- }
- catch (Exception ex)
- {
- }
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String[] getSupportedDBs()
{
- try
- {
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- return (String[]) call.invoke(new Object[]
- {});
- }
- catch (Exception ex)
- {
- return null;
- }
+ // TODO - implement rest call for dbfetch getSupportedDBs
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String[] getSupportedFormats()
{
- try
- {
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- return (String[]) call.invoke(new Object[]
- {});
- }
- catch (Exception ex)
- {
- return null;
- }
+ // TODO - implement rest call for dbfetch getSupportedFormats
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String[] getSupportedStyles()
{
- try
- {
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- return (String[]) call.invoke(new Object[]
- {});
- }
- catch (Exception ex)
- {
- return null;
- }
+ // 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 extension
+ * for the temporary file to hold response
+ * @return the file holding the response
+ * @throws OutOfMemoryError
+ */
- public File fetchDataAsFile(String ids, String f, String s)
+ public File fetchDataAsFile(String ids, String format, String ext)
+ throws OutOfMemoryError
{
- String[] data = fetchData(ids, f, s);
File outFile = null;
try
{
- outFile = File.createTempFile("jalview", ".xml");
+ outFile = File.createTempFile("jalview", ext);
outFile.deleteOnExit();
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- int index = 0;
- while (index < data.length)
+ fetchData(ids, format, outFile);
+ if (outFile.length() == 0)
{
- out.println(data[index]);
- index++;
+ outFile.delete();
+ return null;
}
- out.close();
+ } catch (Exception ex)
+ {
}
- 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
+ * Fetches queries and either saves the response to a file or returns as
+ * string data
+ *
+ * @param ids
+ * @param format
+ * @param outFile
+ * @return
+ * @throws OutOfMemoryError
*/
- public String[] fetchData(String ids, String f, String s)
+ String[] fetchData(String ids, String format, File outFile)
+ throws OutOfMemoryError
{
- // Need to split
- // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
+ 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, ";");
- String db = null;
- StringBuffer querystring = null;
+ boolean appending = queryString.length() > 0;
while (queries.hasMoreTokens())
{
String query = queries.nextToken();
- int p;
- if ( (p = query.indexOf(':')) > -1)
+ int p = query.indexOf(':');
+ if (p > -1)
{
- db = query.substring(0, p);
+ 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);
}
- if (querystring == null)
- {
- querystring = new StringBuffer(query);
- }
- else
- {
- querystring.append("," + query);
- }
- }
- if (db == null)
- {
- System.err.println("Invalid Query string : '" + ids +
- "'\nShould be of form 'dbname:q1;q2;q3;q4'");
+ queryString.append(appending ? "," : "");
+ queryString.append(query);
+ appending = true;
}
- return fetchBatch(querystring.toString(), db, f, s);
+ return database;
}
- public String[] fetchBatch(String ids, String db, String f, String s)
+ /**
+ * 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
+ * @throws OutOfMemoryError
+ */
+ String[] fetchBatch(String ids, String database, String format,
+ File outFile) throws OutOfMemoryError
{
- // max 50 ids can be added at one time
+ // long time = System.currentTimeMillis();
+ String url = buildUrl(ids, database, format);
+
try
{
- //call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
- call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
- call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
- call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);
- call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
- call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- if (f != null)
- {
- format = f;
- }
+ URL rcall = new URL(url);
- if (s != null)
+ InputStream is = new BufferedInputStream(rcall.openStream());
+ if (outFile != null)
{
- style = s;
+ 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();
}
-
- try
- {
- return (String[]) call.invoke(new Object[]
- {ids.toLowerCase(), db.toLowerCase(),
- format, style});
- }
- catch (OutOfMemoryError er)
+ else
{
- System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + ":\n" +
- ids);
+ BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ String rtn;
+ List<String> arl = new ArrayList<String>();
+ while ((rtn = br.readLine()) != null)
+ {
+ arl.add(rtn);
+ }
+ return arl.toArray(new String[arl.size()]);
}
- return null;
- }
- catch (Exception ex)
+ } 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"))
+ "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
{
return null;
}
- System.err.println("Unexpected exception when retrieving from " + db +
- "\nQuery was : '" + ids + "'");
+ System.err.println("Unexpected exception when retrieving from "
+ + database + "\nQuery was : '" + ids + "'");
ex.printStackTrace(System.err);
return null;
+ } finally
+ {
+ // System.err.println("EBIFetch took " + (System.currentTimeMillis() -
+ // time) + " ms");
+ }
+ 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 = "http://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
+ + (format != null ? "&" + format : "");
+ }
+ else
+ {
+ url = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+ + database.toLowerCase() + "/" + ids.toLowerCase()
+ + (format != null ? "/" + format : "");
}
+ return url;
}
}
git://source.jalview.org / jalview.git / blobdiff