/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\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
+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
-public class EBIFetchClient {\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
- public EBIFetchClient() {\r
- try {\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
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
- public String[] getSupportedDBs() {\r
- try {\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
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
return null;\r
}\r
}\r
\r
- public String[] getSupportedFormats() {\r
- try {\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
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
return null;\r
}\r
}\r
\r
- public String[] getSupportedStyles() {\r
- try {\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
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
return null;\r
}\r
}\r
\r
- public String[] fetchData(String ids, String f, String s) {\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
+ 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
+ if (f != null)\r
+ {\r
format = f;\r
}\r
\r
- if (s != null) {\r
+ if (s != null)\r
+ {\r
style = s;\r
}\r
\r
return (String[]) call.invoke(new Object[] { ids, format, style });\r
- } catch (Exception ex) {\r
- return null;\r
}\r
- }\r
-\r
- public String fetchDataFile(String arg, String f, String s) {\r
- if (f != null) {\r
- format = f;\r
- }\r
-\r
- if (s != null) {\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
- Object ret = call.invoke(new Object[] { arg, format, style });\r
-\r
- if (null == ret) {\r
- System.err.println("Received null ");\r
- throw new AxisFault("", "Received null", null, null);\r
- }\r
-\r
- if (ret instanceof String) {\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
- //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
- 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
- return receivedfileName;\r
- } else if (arg.equalsIgnoreCase("interpro")) {\r
- return receivedfileName;\r
- } else {\r
- System.err.println(receivedfileName);\r
- }\r
- } catch (Exception ex) {\r
- ex.printStackTrace();\r
+ catch (Exception ex)\r
+ {\r
+ return null;\r
}\r
-\r
- return "ERROR";\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff