ApiClientTester.java

//---------------------------------------------------
// ApiClientTester.java
// 
// Project: PDBe API Framework 
// Module:  Java Client for PDBe API Webservice (SOAP) Server 
//
// 
// SOAP User Layer
// Last updated: 25 February 2004 10:17
// (C) Siamak Sobhany
//---------------------------------------------------
// 



package msd_soap_service_pkg;
import java.*;
import java.lang.*;
import java.util.*;
import java.net.URL;
import org.apache.axis.client.Call;
import org.apache.axis.client.Stub;
import org.apache.axis.client.Service;
import org.apache.axis.encoding.XMLType;
import org.apache.axis.utils.Options;
import org.apache.axis.AxisFault;
import javax.xml.namespace.QName;
import org.apache.axis.message.SOAPBodyElement;
import org.apache.axis.message.*;
import msd_soap_types.*;
import com.google.soap.search.*;
import org.apache.axis.message.SOAPHeaderElement;

public class ApiClientTester
{
    public static void main(java.lang.String [] args) throws Exception  {
      try {
                long start = System.currentTimeMillis();
        // Make a service
        Msd_soap_service api_service = new Msd_soap_serviceLocator();
        // Now use the service to get a stub which implements the SDI.
        Msd_soap_servicePortType api_port = api_service.getmsd_soap_service();
        org.apache.axis.client.Stub stubs = (org.apache.axis.client.Stub) api_port;
        //stubs.setUsername("amichie");
                //stubs.setPassword("alex220104");
                stubs.setUsername("geoff");
                stubs.setPassword("cc12345678");
        // Make the actual call
                java.lang.String sessionName="MyJavaSession";
        java.lang.String connName="MyJavaConnection";
                java.lang.String queryName="MyJavaQuery";
                java.lang.String resName="MyJavaResult";
                int otl_buf=50;
        java.lang.String sessionID = "my_java_session_number";
                java.lang.String sqlSSMQuery = "select s.target_id from ssm_out_tab s where s.session_id = '" + sessionID + "'";
                java.lang.String stm= "select e.entry_id, e.accession_code from entry e, author a where e.res_val <= 2.5 and e.entry_id = a.entry_id " +
                "and a.last_name = 'HENRICK' and e.accession_code in ( " + sqlSSMQuery + ")";
                                
                java.lang.String ssmQuery ="<SSMInput>" +
        "<program>" +                                                           
                  "SSM v1.38 // 30/06/2003 // by Eugene B. Krissinel," +                
                  "European Bioinformatics Institute, Hinxton, Cambridge CB1 9SD, UK" + 
                "</program>" +                                                          
                "<query>" +                                                             
                "<type>PDB entry</type>" +                                              
                "<pdbcode>9xia</pdbcode>" +                                             
                "</query>" +                                                            
                "<target>" +                                                            
                "<type>PDB archive</type>" +                                            
                "</target>" +                                                           
                "<selection>" +                                                         
                "<type>Chain(s)</type>" +                                               
                "<chains>*(all)</chains>" +                                             
                "</selection>" +                                                        
                "<percent1>70</percent1>" +                                             
                "<percent2>70</percent2>" +                                             
                "<sepchains>Yes</sepchains>" +                                          
                "<connectivity>Yes</connectivity>" +                                    
                "<bestmatch>Yes</bestmatch>" +                                          
                "<uniquematch>Yes</uniquematch>" +                                      
                "<precision>Normal</precision>" +                                       
                "<sorting>RMSD</sorting>" +                                             
                "</SSMInput>";                                                                              
        
                java.lang.Object[] inputArray = new java.lang.Object[2];
            inputArray[0]= ssmQuery;
                inputArray[1]= sessionID;
            int numOfParams = 2;
       try {
                api_port.msdSSM(numOfParams, inputArray);
                System.out.println("msdSSM() method Called successfully.");
           
                int ic =1;
                do { 
                   String faultstr="OK";
                   AxisFault f2 = new AxisFault();
                   try {
                        api_port.msdSSMParser(1, sessionID);
                   } catch (AxisFault f1){
                         faultstr = f1.getFaultString();
                         f2 = f1;
                         } // end catch
                         if(faultstr.equals("Result fille not ready")){
                          System.out.println("\nXML File not ready...retry: "+ ic);
                         } else if(faultstr.equals("XML SSM file will not be ready in less than 15 minutes."))
                                 {ic = -2;
                                 }else{
                                 ic  = -1;
                                 }
                         
                        if (ic == -2)
            { System.out.println("msdSSMParser() method call failed.");
              System.out.println(faultstr);
                          if (f2 instanceof java.rmi.RemoteException) {
               throw (java.rmi.RemoteException)f2;
              }
                    }
          long time = System.currentTimeMillis()+ 10000;
           long tempTime = System.currentTimeMillis();
                   while (time > tempTime) { // wait...
             tempTime=System.currentTimeMillis(); 
                         //System.out.println(".");
                   }
                 ++ic;
         } while (ic > 0);
        
         
                int c = api_port.msdConnect(connName);
                int r = api_port.msdResultset(connName, queryName, resName);
                int q = api_port.msdQuery(connName, queryName, resName, stm);
                System.out.println("\nConnect: " + c + "\nResult: " + r + "\nQuery: "+ q + " : "+ stm + "\n");
                int result3 = api_port.msdExecQuery(connName, queryName, resName, otl_buf);
                if (result3 == 0)
                {System.out.println("\nmsdExecQuery Executed: " + result3 + "\n"); 
                
                //java.lang.Object[] result3 = api_port.msdGetResult(connName, queryName, resName);
                msd_soap_types.Resultset result4 = api_port.msdGetResult(connName, queryName, resName);
                
                  java.lang.Object[] dataSet = result4.getR();
                  java.util.List res = Arrays.asList(dataSet);
                  int m = res.size();
         
                  java.lang.Object[] record = (java.lang.Object[])dataSet[0];
                  java.util.List rec = Arrays.asList(record);
                  int n = rec.size();
                  for (int j=0;j<m;j++) // java.lang.reflect.Array.getLength(rs.value.getParam())
                   { //field = (msd_soap_service.Map)result.value.getParam(j);
                     //if (result[j].equals (null))
                     //break;
                 
                   record = (java.lang.Object[])dataSet[j];
                  //if (record == null)
                  //j=-1;else{
                  System.out.println("Column " + j + " started...\n");
                        
                        for (int i=0;i<n;i++)
              {   //java.lang.Object obj = java.lang.reflect.Array.get(result.value.getParam(), i);
                          //obj.getClass().isArray()
                          //record = (msd_soap_service.Item)field.getItem(i);
                         //if (record[i]==null)
                         //i=-1;else
                         //column[i].toString();
                         
                         System.out.println("Value[" + j + "," + i + "] = " +  record[i]  + "\n"); // column[i] rs.value.getParam(i) 
                 
                   } //end for
        
                
                  } //end for
                int stts = api_port.msdEndQueryPack(queryName, resName);
                System.out.println("\nmsdEndQueryPack status: " + stts + "\n");
                stts = api_port.msdEndConnect(connName);
                System.out.println("\nmsdEndSession status: " + stts + "\n"); 
                stts = api_port.msdEndSession(sessionName);
                System.out.println("\nmsdEndSession status: " + stts + "\n"); 

                }else{
                System.out.println("\nmsdExecQuery Failed. " + result3 + "\n");}
                long finish = System.currentTimeMillis();
            long time = finish-start;
            System.out.println("Time taken = "+ time + " milliseconds.");
                //System.out.println("java.lang.reflect.Array.getLength(rs.value.getParam()) = " + java.lang.reflect.Array.getLength(rs.value.getParam()));
      } // end try
      catch (AxisFault f){
                 System.out.println(f.getFaultString());
          }
          } catch (Exception e) {
            System.err.println(e.toString());
            e.printStackTrace();
      }
        String clientKey = "fGeTRvdQFHLfeNjYlcoRt13M6mKs4SgT";
    String directive = "search";
    String directiveArg = "KIM HENRICK and 9xia";
    
    // Create a Google Search object, set our authorization key
    GoogleSearch s = new GoogleSearch();
    s.setKey(clientKey);

    // Depending on user input, do search or cache query, then print out result
    try {
      if (directive.equalsIgnoreCase("search")) {
        s.setQueryString(directiveArg);
        GoogleSearchResult r = s.doSearch();
        System.out.println("Google Search Results:");
        System.out.println("======================");
        System.out.println(r.toString());
      } else if (directive.equalsIgnoreCase("cached")) {
        System.out.println("Cached page:");
        System.out.println("============");
        byte [] cachedBytes = s.doGetCachedPage(directiveArg);
        // Note - this conversion to String should be done with reference
        // to the encoding of the cached page, but we don't do that here.
        String cachedString = new String(cachedBytes);
        System.out.println(cachedString);
      } else if (directive.equalsIgnoreCase("spell")) {
        System.out.println("Spelling suggestion:");
        String suggestion = s.doSpellingSuggestion(directiveArg);
        System.out.println(suggestion);
      } else {
                System.err.println("Usage:  " + 
                       " <client-key>" +
                       " (search <query> | cached <url> | spell <phrase>)");
        System.exit(1);
      }
    } catch (GoogleSearchFault f) {
      System.out.println("The call to the Google Web APIs failed:");
      System.out.println(f.toString());
    }

    }}

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