-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.io;\r
-\r
-import org.apache.axis.AxisFault;\r
-import org.apache.axis.client.*;\r
-import org.apache.axis.encoding.XMLType;\r
-import org.apache.axis.encoding.ser.JAFDataHandlerDeserializerFactory;\r
-import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;\r
-\r
-import java.io.*;\r
-\r
-import javax.activation.DataHandler;\r
-\r
-import javax.xml.namespace.QName;\r
-import javax.xml.rpc.ParameterMode;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class EBIFetchClient\r
-{\r
- Call call;\r
- String format = "default";\r
- String style = "raw";\r
-\r
- /**\r
- * Creates a new EBIFetchClient object.\r
- */\r
- public EBIFetchClient()\r
- {\r
- try\r
- {\r
- call = (Call) new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/ws/services/Dbfetch"));\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedDBs()\r
- {\r
- try\r
- {\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- return (String[]) call.invoke(new Object[] { });\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedFormats()\r
- {\r
- try\r
- {\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- return (String[]) call.invoke(new Object[] { });\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedStyles()\r
- {\r
- try\r
- {\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- return (String[]) call.invoke(new Object[] { });\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ids DOCUMENT ME!\r
- * @param f DOCUMENT ME!\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String[] fetchData(String ids, String f, String s)\r
- {\r
- // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;\r
- // max 50 ids can be added at one time\r
- try\r
- {\r
- call.setOperationName(new QName("urn:Dbfetch", "fetchData"));\r
- call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- if (f != null)\r
- {\r
- format = f;\r
- }\r
-\r
- if (s != null)\r
- {\r
- style = s;\r
- }\r
-\r
- return (String[]) call.invoke(new Object[] { ids, format, style });\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param arg DOCUMENT ME!\r
- * @param f DOCUMENT ME!\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String fetchDataFile(String arg, String f, String s)\r
- {\r
- if (f != null)\r
- {\r
- format = f;\r
- }\r
-\r
- if (s != null)\r
- {\r
- style = s;\r
- }\r
-\r
- call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));\r
- call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
-\r
- QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");\r
- call.registerTypeMapping(javax.activation.DataSource.class,\r
- qnameAttachment, JAFDataHandlerSerializerFactory.class,\r
- JAFDataHandlerDeserializerFactory.class);\r
-\r
- call.setReturnType(qnameAttachment);\r
-\r
- try\r
- {\r
- Object ret = call.invoke(new Object[] { arg, format, style });\r
-\r
- if (null == ret)\r
- {\r
- System.err.println("Received null ");\r
- throw new AxisFault("", "Received null", null, null);\r
- }\r
-\r
- if (ret instanceof String)\r
- {\r
- System.err.println("Received problem response from server: " +\r
- ret);\r
- throw new AxisFault("", (String) ret, null, null);\r
- }\r
-\r
- if (!(ret instanceof DataHandler))\r
- {\r
- //The wrong type of object that what was expected.\r
- System.err.println("Received problem response from server:" +\r
- ret.getClass().getName());\r
- throw new AxisFault("",\r
- "Received problem response from server:" +\r
- ret.getClass().getName(), null, null);\r
- }\r
-\r
- //Still here, so far so good.\r
- DataHandler rdh = (DataHandler) ret;\r
-\r
- //From here we'll just treat the data resource as file.\r
- String receivedfileName = rdh.getName(); //Get the filename.\r
-\r
- if (receivedfileName == null)\r
- {\r
- System.err.println("Could not get the file name.");\r
- throw new AxisFault("", "Could not get the file name.", null,\r
- null);\r
- }\r
-\r
- if (arg.equalsIgnoreCase("medline"))\r
- {\r
- return receivedfileName;\r
- }\r
- else if (arg.equalsIgnoreCase("interpro"))\r
- {\r
- return receivedfileName;\r
- }\r
- else\r
- {\r
- System.err.println(receivedfileName);\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- return "ERROR";\r
- }\r
-}\r
+/*
+ * 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
+ * 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.
+ *
+ * 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
+ */
+package jalview.io;
+
+import java.io.*;
+import java.util.*;
+import javax.xml.namespace.*;
+import javax.xml.rpc.*;
+
+import org.apache.axis.client.Call;
+import org.apache.axis.client.Service;
+import org.apache.axis.encoding.*;
+
+/**
+ * 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;
+ }
+ }
+
+ /**
+ * 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;
+ }
+ }
+
+ /**
+ * 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;
+ }
+ }
+
+ public static void main(String[] args)
+ {
+ EBIFetchClient ebi = new EBIFetchClient();
+ String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
+ "xml", null);
+
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter("out.xml"));
+
+ for (int i = 0; i < result.length; i++)
+ {
+ out.println(result[i]);
+ }
+ out.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ }
+
+ public File fetchDataAsFile(String ids, String f, String s)
+ {
+ String[] data = fetchData(ids, f, s);
+ File outFile = null;
+ try
+ {
+ outFile = File.createTempFile("jalview", ".xml");
+ outFile.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ int index = 0;
+ while (index < data.length)
+ {
+ out.println(data[index]);
+ index++;
+ }
+ out.close();
+ }
+ 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)
+ {
+ // Need to split
+ // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
+
+ StringTokenizer queries = new StringTokenizer(ids, ";");
+ String db = null;
+ StringBuffer querystring = null;
+ while (queries.hasMoreTokens())
+ {
+ String query = queries.nextToken();
+ int p;
+ if ( (p = query.indexOf(':')) > -1 && (p + 3 < query.length()))
+ {
+ db = query.substring(0, p);
+ 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'");
+ }
+ return fetchBatch(querystring.toString(), db, f, s);
+ }
+
+ public String[] fetchBatch(String ids, String db, String f, String s)
+ {
+ // max 50 ids can be added at one time
+ 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;
+ }
+
+ if (s != null)
+ {
+ style = s;
+ }
+
+ try
+ {
+ return (String[]) call.invoke(new Object[]
+ {ids.toLowerCase(), db.toLowerCase(),
+ format, style});
+ }
+ catch (OutOfMemoryError er)
+ {
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + ":\n" +
+ ids);
+ }
+ return null;
+ }
+ 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;
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff