Changeset 363

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Timestamp:
05/21/10 01:02:38 (21 months ago)
Author:
rodche
Message:

"Mavenized" are 6 modules: org.bridgedb, org.bridgedb.bio, org.bridgedb.webservice.bridgerest, org.bridgedb.webservice.biomart, org.bridgedb.webservice.cronos, org.bridgedb.webservice.picr, and examples; organisms.txt and datasources.txt - moved to org.bridgedb.bio/resources/org/bridgedb/bio (ant build.xml ajusted accordingly). Upgraded org.bridgedb.webservice.cronos with the new WSDL and code generation by maven plugin.

Location:
trunk
Files:
33 added
3 removed
20 modified
2 copied

Legend:

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Added
Removed

  • trunk

    • Property svn:ignore

      •  

        old new  
        11pub 
         2 
         3.settings 
         4 
         5.classpath 
         6 
         7.project 

  • trunk/README.txt

    r261 r363  
    66 
    77        ant 
     8         
     9or (experimental, makes not all jars) -  
     10 
     11        mvn clean install 
    812 
    913Library dependencies 

  • trunk/benchmarking/test/org/bridgedb/benchmarking/TestAll.java

    r317 r363  
    1212import org.bridgedb.rdb.construct.DBConnectorDerbyServer; 
    1313 
    14 import buildsystem.Measure; 
     14//import buildsystem.Measure; 
    1515 
    1616public class TestAll extends Base 
    1717{ 
    18         private Measure measure; 
     18        //private Measure measure; 
    1919         
    2020        @Override public void setUp() 
    2121        { 
    22                 measure = new Measure("bridgedb_timing.txt"); 
     22                //measure = new Measure("bridgedb_timing.txt"); 
    2323        } 
    2424 

  • trunk/examples

    • Property svn:ignore set to
      target

  • trunk/examples/src/org/bridgedb/examples/CounterExampleWithoutBridgedb.java

    r268 r363  
    22 
    33import java.io.IOException; 
    4 import java.net.URL; 
    5 import java.util.HashSet; 
    6 import java.util.Set; 
    74 
    85import javax.xml.rpc.ServiceException; 
    96 
    107import org.bridgedb.webservice.cronos.CronosWS; 
    11 import org.bridgedb.webservice.cronos.CronosWSServiceLocator; 
    12 import org.json.JSONException; 
     8import org.bridgedb.webservice.cronos.CronosWSService; 
    139 
    14 import synergizer.SynergizerClient; 
     10//import org.json.JSONException; 
     11//import synergizer.SynergizerClient; 
    1512 
    1613/* 
    … …  
    3734                // using the Cronos service directly 
    3835                // Call Web Service Operation 
    39                 CronosWSServiceLocator locator = new CronosWSServiceLocator(); 
    40                 CronosWS port = locator.getCronosWSPort(); 
     36                //CronosWSServiceLocator locator = new CronosWSServiceLocator(); 
     37                //CronosWS port = locator.getCronosWSPort(); 
     38                CronosWSService service = new CronosWSService(); 
     39                CronosWS port = service.getCronosWSPort(); 
    4140                 
    4241                String organismCode = "hsa"; 
    … …  
    5453        } 
    5554         
     55        /* 
    5656        public void mapSynergizer(String id) throws IOException, JSONException 
    5757        { 
    … …  
    7171         } 
    7272        } 
     73        */ 
    7374         
    74         public static void main(String args[]) throws ServiceException, IOException, JSONException 
     75        public static void main(String args[]) throws Exception 
    7576        { 
    7677                CounterExampleWithoutBridgedb main = new CounterExampleWithoutBridgedb(); 
    … …  
    7879                String id = "3643"; 
    7980                main.mapCronos(id); 
    80                 main.mapSynergizer(id); 
     81                //main.mapSynergizer(id); 
    8182        } 
    8283} 

  • trunk/org.bridgedb

    • Property svn:ignore set to
      target

  • trunk/org.bridgedb.bio

    • Property svn:ignore set to
      target

  • trunk/org.bridgedb.bio/build.xml

    r325 r363  
    2323                   <classpath refid="class.path"/> 
    2424        </javac> 
    25     <copy file="../resources/datasources.txt" 
     25    <copy file="resources/org/bridgedb/bio/datasources.txt" 
    2626          todir="build/org/bridgedb/bio" /> 
    27     <copy file="../resources/organisms.txt" 
     27    <copy file="resources/org/bridgedb/bio/organisms.txt" 
    2828          todir="build/org/bridgedb/bio" /> 
    2929  </target> 

  • trunk/org.bridgedb.bio/src/org/bridgedb/bio/Organism.java

    r308 r363  
    2828 * Still work in progress, currently not used everywhere it could be used. 
    2929 * <p> 
    30  * TODO: this class will move to the org.bridgedb.bio package in the future. 
    31  * <p>  
    3230 * TODO: make extensible 
    3331 */ 

  • trunk/org.bridgedb.rdb/test/org/bridgedb/rdb/Test2.java

    r317 r363  
    3636public class Test2 extends TestCase  
    3737{ 
    38         //TODO 
    3938        private static final String GDB_HUMAN =  
    4039                System.getProperty ("user.home") + File.separator +  

  • trunk/org.bridgedb.webservice.biomart

    • Property svn:ignore set to
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  • trunk/org.bridgedb.webservice.biomart/src/org/bridgedb/webservice/biomart/BiomartStub.java

    r308 r363  
    260260                                || displayName.endsWith("Accession") 
    261261                                || name.endsWith("id") 
    262                                 || name.endsWith("accession"))) { 
     262                                || name.endsWith("accession") 
     263                                || name.endsWith("ensembl_gene"))) { 
    263264                        result.add(name); 
    264265                } 

  • trunk/org.bridgedb.webservice.biomart/src/org/bridgedb/webservice/biomart/util/Dataset.java

    r308 r363  
    160160             
    161161            // only add attributes listed as "feature_page" 
    162             if ("feature_page".equals(page)) 
     162            // and "homologs" 
     163            if ("feature_page".equals(page) || "homologs".equals(page)) 
    163164                attributes.put(parts[0], new Attribute( 
    164165                        parts[0], displayName, description, page)); 

  • trunk/org.bridgedb.webservice.biomart/test/org/bridgedb/webservice/biomart/TestBiomart.java

    r308 r363  
    2424import org.bridgedb.Xref; 
    2525import org.bridgedb.webservice.biomart.util.BiomartClient; 
    26 import buildsystem.Measure; 
     26//import buildsystem.Measure; 
    2727 
    2828import java.io.File; 

  • trunk/org.bridgedb.webservice.bridgerest

    • Property svn:ignore set to
      target

  • trunk/org.bridgedb.webservice.cronos

    • Property svn:ignore set to
      target

  • trunk/org.bridgedb.webservice.cronos/WSREADME.txt

    r308 r363  
    66----------------------------------- 
    77 
    8 http://mips.helmholtz-muenchen.de/CronosWSService/CronosWS?WSDL 
    9  
     8http://mips.helmholtz-muenchen.de/genre/proj/cronos/CronosWSService.wsdl 
     9[http://mips.helmholtz-muenchen.de/CronosWSService/CronosWS?WSDL - doesn't not work for xjc] 
    1010 
    1111Supported Methods: 

  • trunk/org.bridgedb.webservice.cronos/src/org/bridgedb/webservice/cronos/IDMapperCronos.java

    r308 r363  
    11package org.bridgedb.webservice.cronos; 
    22 
    3 import java.rmi.RemoteException; 
    43import java.util.Arrays; 
    54import java.util.Collection; 
    … …  
    87import java.util.Map; 
    98import java.util.Set; 
    10  
    11 import javax.xml.rpc.ServiceException; 
    129 
    1310import org.bridgedb.bio.BioDataSource; 
    … …  
    128125                {       // Call Web Service Operation 
    129126 
    130                         CronosWSServiceLocator locator = new CronosWSServiceLocator(); 
    131                         port = locator.getCronosWSPort(); 
    132                         info.put("WSPortAddress", locator.getCronosWSPortAddress()); 
    133                         info.put("WSDDServiceName", locator.getCronosWSPortWSDDServiceName()); 
    134                         info.put("WSDLDocumentLocation", "" + locator.getWSDLDocumentLocation()); 
    135                 } 
    136                 catch (ServiceException ex) 
     127                        //CronosWSServiceLocator locator = new CronosWSServiceLocator(); 
     128                        CronosWSService service = new CronosWSService(); 
     129                        port = service.getCronosWSPort(); //locator.getCronosWSPort(); 
     130                        //info.put("WSPortAddress", locator.getCronosWSPortAddress()); 
     131                        //info.put("WSDDServiceName", locator.getCronosWSPortWSDDServiceName()); 
     132                        //info.put("WSDLDocumentLocation", "" + locator.getWSDLDocumentLocation()); 
     133                        info.put("WSPortAddress", service.WSDL_LOCATION.toString()); 
     134                        info.put("WSDDServiceName", service.getServiceName().toString()); 
     135                        info.put("WSDLDocumentLocation", service.WSDL_LOCATION.toString()); 
     136                } 
     137                catch (Exception ex) 
    137138                { 
    138139                        throw new IDMapperException (ex); 
    … …  
    215216                                } 
    216217                        } 
    217                 } catch (RemoteException e) { 
     218                } catch (Exception e) { 
    218219                        throw new IDMapperException(e); 
    219220                } 

  • trunk/org.bridgedb.webservice.picr

    • Property svn:ignore set to
      target

  • trunk/org.bridgedb/test/org/bridgedb/TestFile.java

    r308 r363  
    1717package org.bridgedb; 
    1818 
    19 import buildsystem.Measure; 
     19//import buildsystem.Measure; 
    2020 
    2121import java.io.File; 
    … …  
    3838public class TestFile extends TestCase  
    3939{ 
    40         private Measure measure; 
     40        //private Measure measure; 
    4141         
    4242        private static final File YEAST_IDS = new File ("test-data/yeast_id_mapping.txt"); 
    … …  
    4848        @Override public void setUp() 
    4949        { 
    50                 measure = new Measure("bridgedb_timing.txt"); 
     50                //measure = new Measure("bridgedb_timing.txt"); 
    5151        } 
    5252         
    … …  
    7171                long delta = end - start; 
    7272                System.out.println (delta); 
    73                 measure.add ("timing::text file non-transitive", "" + delta, "msec"); 
     73                //measure.add ("timing::text file non-transitive", "" + delta, "msec"); 
    7474 
    7575                Set<Xref> expected = new HashSet<Xref>(); 
    … …  
    115115                long delta = end - start; 
    116116                System.out.println (delta); 
    117                 measure.add ("timing::text file transitive", "" + delta, "msec"); 
     117                //measure.add ("timing::text file transitive", "" + delta, "msec"); 
    118118 
    119119                System.out.println (mapXrefs);