-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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 java.io.*;\r
-\r
-import org.apache.axis.client.*;\r
-import org.apache.axis.encoding.XMLType;\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
- public static void main (String [] args)\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",\r
- "xml", null);\r
-\r
- try{\r
- java.io.PrintWriter out = new java.io.PrintWriter(\r
- new java.io.FileWriter("out.xml"));\r
-\r
-\r
- for(int i=0; i<result.length; i++)\r
- {\r
- out.println(result[i]);\r
- }\r
- out.close();\r
- }catch(Exception ex){ex.printStackTrace();}\r
-\r
- }\r
-\r
-\r
- public File fetchDataAsFile(String ids, String f, String s)\r
- {\r
- String [] data = fetchData(ids, f, s);\r
- File outFile = null;\r
- try{\r
- outFile = File.createTempFile("jalview", ".xml");\r
- outFile.deleteOnExit();\r
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
- int index=0;\r
- while( index < data.length )\r
- {\r
- out.println(data[index]);\r
- index++;\r
- }\r
- out.close();\r
- }catch(Exception ex){}\r
- return outFile;\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
- try{\r
- return (String[]) call.invoke(new Object[]\r
- {ids, format, style});\r
- }catch(OutOfMemoryError er)\r
- {\r
- System.out.println("OUT OF MEMORY LOADING PDB FILE!!");\r
- }\r
- return null;\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 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.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+
+import org.apache.axis.client.*;
+import org.apache.axis.encoding.XMLType;
+
+import javax.xml.namespace.QName;
+import javax.xml.rpc.ParameterMode;
+
+
+/**
+ * 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;
+ }
+ }
+}