Changeset 3876

Timestamp:

Oct 24, 2007, 4:58:42 PM (14 years ago)

Author:

Martin Svensson

Message:

References #492 Tests for webservices completed. Fixed the bugs that were found.

Location:

trunk/src

Files:

• test/TestWebservices.java (modified) (17 diffs)
• webservices/client/java/net/sf/basedb/ws/client/AbstractRPCClient.java (modified) (3 diffs)
• webservices/client/java/net/sf/basedb/ws/client/BioAssaySetClient.java (modified) (4 diffs)
• webservices/client/java/net/sf/basedb/ws/client/ExperimentClient.java (modified) (2 diffs)
• webservices/client/java/net/sf/basedb/ws/client/ProjectClient.java (modified) (3 diffs)
• webservices/client/java/net/sf/basedb/ws/client/RawBioAssayClient.java (modified) (1 diff)
• webservices/client/java/net/sf/basedb/ws/client/SessionClient.java (modified) (2 diffs)
• webservices/server/net/sf/basedb/ws/server/ArrayDesignService.java (modified) (2 diffs)
• webservices/server/net/sf/basedb/ws/server/RawBioAssayService.java (modified) (2 diffs)

trunk/src/test/TestWebservices.java

@@ -22 +22 @@
   Boston, MA  02111-1307, USA.
 */
+import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.Config;
 import net.sf.basedb.core.DataFileType;
+import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Formula;
+import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Platform;
+import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.ws.client.ArrayDesignClient;
 import net.sf.basedb.ws.client.BioAssaySetClient;
@@ -40 +47 @@
 
 import java.io.File;
+import java.util.ArrayList;
 
 /**
@@ -48 +56 @@
 {
   static boolean ok = true;
+  
+  /** 
+      @param args
+  */
   public static void main(String[] args)
   {
@@ -78 +90 @@
     TestExperiment.test_add_rawbioassay(experimentId1, rawBioAssayId1);
     TestExperiment.test_add_rawbioassay(experimentId1, rawBioAssayId2);
-    int rootBioAssaySetId1 = TestExperiment.test_create_root_bioassayset_using_calculator(experimentId1, "mean", rawBioAssayId1, rawBioAssayId2);;
+    int rootBioAssaySetId1 = TestExperiment.test_create_root_bioassayset_using_calculator(experimentId1, "mean", rawBioAssayId1, rawBioAssayId2);
     
     //Experiment with rawdata and array design stored in files.
@@ -96 +108 @@
     //Tests
     SessionClient client = test_SessionClient();
-    
-    test_ProjectClient(client, projectId);
-//    test_getRawDataInExperiment(client, experimentId1, rawBioAssayId1);
-//    test_getRawDataInExperiment(client, experimentId2, rawBioAssayId3);
-//    
-//    test_getArrayDesign(client, rawBioAssayId1);
-//    test_getArrayDesign(client, rawBioAssayId2);
-//    
-//    test_BioAssaySetClient(client, experimentId1, rootBioAssaySetId1);
-//        
-    test_Logout(client);
+    if (client != null)
+    {
+      test_ProjectClient(client, projectId);
+      test_getRawDataInExperiment(client, experimentId1, rawBioAssayId1);
+      test_getRawDataInExperiment(client, experimentId2, rawBioAssayId3);   
+      test_getArrayDesign(client, rawBioAssayId1, arrayDesignId1);
+      test_getArrayDesign(client, rawBioAssayId3, arrayDesignId2);    
+      test_BioAssaySetClient(client, experimentId1, rootBioAssaySetId1);        
+      test_Logout(client);
+    }
     
     //Standard test:Delete/cleanup
@@ -150 +161 @@
     BioAssaySetClient basClient = new BioAssaySetClient(client);
     ExperimentClient experimentClient = new ExperimentClient(client);
-        
+    DbControl dc = null;    
     try
     {
@@ -177 +188 @@
       else
       {
-        File receivedFile = null;
-        String[] reporterFields = {};
-        String[] spotFields = {};
+      
+        dc = TestUtil.getDbControl();
+        BioAssaySet bas = BioAssaySet.getById(dc, bioAssaySetId);
+        
+        ArrayList<String> rep = new ArrayList<String>();
+        rep.add("rep.id");
+        rep.add("rep.name");
+        rep.add("rep.position");
+        
+        ArrayList<String> spot = new ArrayList<String>();
+        ItemQuery<Formula> ratio = Formula.getQuery(Formula.Type.COLUMN_EXPRESSION, bas.getRawDataType());
+        ratio.restrict(Restrictions.eq(Hql.property("name"), Expressions.string("Ratio, ch1 / ch2")));
+        if (ratio.count(dc) < 1)
+        {
+          throw new Exception("Cant find formula 'Ratio, ch1 / ch2'");
+        }
+        spot.add("intensity1");
+        spot.add("raw.row");
+        spot.add("raw.col");
+        spot.add("raw.flags");
+        spot.add("frm."+ratio.list(dc).get(0).getId());
+
+        String[] reporterFields = new String[rep.size()];
+        String[] spotFields = new String[spot.size()];
         boolean mergeReporters = false;
+        
         for (String format : exportFormats)
         {
-          System.out.print("BioAssaySet being downloaded in format " + format + "...");
+          File receivedFile = null;
+          System.out.print("--Download BioAssaySet in file format " + format + "...");
           receivedFile = basClient.downloadBioAssaySet(
-              bioAssaySetId, format, format, reporterFields, spotFields, mergeReporters);
+              bioAssaySetId, format, format, rep.toArray(reporterFields), spot.toArray(spotFields), mergeReporters);
           if (receivedFile == null)
           {
@@ -205 +239 @@
       t.printStackTrace();
       ok = false;
+    }
+    finally
+    {
+      if (dc != null)dc.close();
     }
   }
@@ -220 +258 @@
       @param arrayDesignId Id of the ArrayDesign to test with
    */
-  static void test_getArrayDesign(SessionClient client, int rawBioAssayId)
-  {
-    if (client == null || rawBioAssayId == 0) return;
+  static void test_getArrayDesign(SessionClient client, int rawBioAssayId, int arrayDesignId)
+  {
+    if (client == null || rawBioAssayId == 0 || arrayDesignId == 0) return;
     ArrayDesignClient arrayDesignClient = new ArrayDesignClient(client);
-    RawBioAssayClient rawClient = new RawBioAssayClient(client);
-    
+    RawBioAssayClient rawClient = new RawBioAssayClient(client);    
     ArrayDesignInfo designInfo = null;
     
     try
     {         
-      designInfo = rawClient.getArrayDesign(rawBioAssayId);
+      designInfo = rawClient.getArrayDesign(rawBioAssayId);     
     }
     catch (Throwable t)
@@ -240 +277 @@
     if (designInfo != null)
     {
-      int arrayDesignId = designInfo.getId();
       try
       {
@@ -246 +282 @@
         DataFileTypeInfo[] fileTypes = arrayDesignClient.getDataFileTypes(arrayDesignId, new QueryOptions());
         
-        
         if (hasDownloadableData && fileTypes.length > 0)
         {
+          System.out.print("--Download of array design file....");
           File receivedFile = arrayDesignClient.downloadArrayDesignByType(arrayDesignId, fileTypes[0], fileTypes[0].getName());
-          receivedFile.delete();
+          if (receivedFile != null)
+          {
+            receivedFile.delete();
+            write("OK");
+          }
+          else throw new Exception("Download file FAILED");
         }
         else
         {
           File receivedFile = arrayDesignClient.downloadArrayDesignByType(arrayDesignId, null, "nullFile");
-          if (receivedFile != null) write("--ArrayDesignClient download data FAILED");
+          if (receivedFile != null) throw new Exception("Received a file though the array design doesn't have any downloadable data");
         }
-        
-        write ("--Test of ArrayDesignClient OK");
       }
       catch (Throwable t)
@@ -267 +306 @@
       }
     }
+    else write ("--No info about the Raw BioAssay was received");
+    write ("--Test of ArrayDesignClient OK");
   }
   
@@ -320 +361 @@
       if (hasDownloadableData && fileTypes.length > 0)
       {
-        System.out.print("--Downloading raw data file for RawBioAssay....");
+        System.out.print("--Download of raw data file for RawBioAssay....");
         File receivedFile = rawClient.downloadRawDataByType(rawBioAssayId, fileTypes[0], fileTypes[0].getName());
         if (receivedFile != null)
@@ -329 +370 @@
         else write("FAILED");
       }
+      write ("--Test of RawBioAssayClient OK");
     }
     catch(Throwable t)
@@ -341 +383 @@
   static void test_ProjectClient(SessionClient client, int projectId)
   {
-    if (client == null) return;
+    if (client == null || projectId == 0) return;
     
     ProjectClient projectClient = new ProjectClient(client);
@@ -347 +389 @@
     {
       //Tests ProjectClient.getProjects(QueryOptions qOpt)
-      ProjectInfo[] infos = projectClient.getProjects(new QueryOptions());
-      if (infos != null && infos.length > 0)
+      QueryOptions qOpt = new QueryOptions();
+      qOpt.setRestrictionWithPrefix("$id="+projectId, "$");
+      ProjectInfo[] infos = projectClient.getProjects(qOpt);
+      if (!(infos != null && infos.length > 0))
       {       
-        write("--" + infos.length + " projects were received.");
+        throw new Exception("No project was received");
       }
       
       //Tests ProjectClient.setActive(int projectId)
-      projectClient.setActive(projectId);
-      write("--Active project has been changed.");
+      projectClient.setActive(projectId);     
       write("--Test of ProjectClient OK");
     }   
@@ -385 +428 @@
     {
       write("--Create/login session FAILED");
-      t.printStackTrace();
-      ok = false;
+      write("--Skipping webservices test.");
+      return null;
     }
     try
     {
       client.refreshSession(client.getId());
-      write("--Refresh session OK \tSession will timeout after: " + client.getSessionTimeOut() + " minutes");
+      write("--Refresh session OK \tSession timeout set to: " + client.getSessionTimeOut() + " minutes");
     }
     catch(Throwable t)

trunk/src/webservices/client/java/net/sf/basedb/ws/client/AbstractRPCClient.java

@@ -39 +39 @@
 import org.apache.axis2.rpc.client.RPCServiceClient;
 
+/**
+  Abstract class for RPCServiceClients in web services.
+  Holds information about the service to use
+  and gives different ways of   
+    @author Martin
+    @version 2.5
+ */
 public abstract class AbstractRPCClient 
 {
@@ -48 +55 @@
   }
   
+  @SuppressWarnings("unchecked")
   protected Object[] invokeBlocking(String operation, Object[] args, Class[] returnTypes)
     throws AxisFault
@@ -73 +81 @@
     OMElement response = getService().invokeBlocking(getOperation(operation), args);
     OMElement fileElement = response.getFirstElement();
-    OMElement dataElement = fileElement.getFirstElement();    
+    OMElement dataElement = fileElement.getFirstElement();  
+    if (dataElement == null) return null;
     OMText node = (OMText) dataElement.getFirstOMChild();
     node.setBinary(true);

trunk/src/webservices/client/java/net/sf/basedb/ws/client/BioAssaySetClient.java

@@ -33 +33 @@
 
 /**
-  
+  Web service client for BioAssaySetService in BASE.
+  {@link net.sf.basedb.ws.server.BioAssaySetService}
     @author Martin
     @version 2.5
@@ -42 +43 @@
   private final SessionClient session;
   
+  /**
+    Creates new BioAssayClient for a session.
+      @param session Active session.
+   */
   public BioAssaySetClient(SessionClient session)
   {
@@ -48 +53 @@
   }
   
+  /**
+    Calls the BioAssaySetService and gets the available formats to export
+    a BioAssaySet from BASE in.
+      @return An array with the formats. 
+      @throws AxisFault If communication with the service fails.
+   */
   public String[] getExportFormats()
     throws AxisFault
   {
-    RPCServiceClient service = getService();
     String[] formats = invokeBlocking("getExportFormats", String[].class, session.getId());
     return formats;
   }
   
-  public File downloadBioAssaySet(int bioAssaySetId, String filePath, String format, String[] reporterFields, String[] spotFields, boolean mergeReporters) 
+  /**
+    Call the service in BioAssaySetService that exports a bioassay set and
+    then sends it as a file. 
+      @param bioAssaySetId Id of the bioAssay set to export
+      @param filePath Abstract file path to give to the received file.
+      @param format Export format to use when exporting the bioassay set
+      @param reporterFields Reporter fields to include in the export
+      @param spotFields Spot fields to include in the export
+      @param mergeReporters If the reporters should be merged or not.
+      @return A file at the specified path
+      @throws AxisFault If communication with services fails.
+      @throws IOException If accessing the file files.
+   */
+  public File downloadBioAssaySet(int bioAssaySetId, String filePath, String format, 
+      String[] reporterFields, String[] spotFields, boolean mergeReporters) 
     throws AxisFault, IOException
   {
@@ -74 +98 @@
         spotFields,
         mergeReporters
-      );  
-    
+      );      
     return receivedFile;
   }

trunk/src/webservices/client/java/net/sf/basedb/ws/client/ExperimentClient.java

@@ -30 +30 @@
 
 import org.apache.axis2.AxisFault;
-import org.apache.axis2.rpc.client.RPCServiceClient;
 
+/**
+  Webservice client for Experiment.
+  Call services in {@link net.sf.basedb.ws.server.ExperimentService}
+    @author Martin
+    @version 2.5
+ */
 public class ExperimentClient 
   extends AbstractRPCClient 
-{
-  
+{ 
   private final SessionClient session;
   
+  /**
+    Creates a new client in active session
+      @param session The active session
+   */
   public ExperimentClient(SessionClient session)
   {
@@ -44 +52 @@
   }
   
+  /**
+    Gets info about experiments that are available in the logged in session.
+      @param qOpt Options to put on the query that gets the experiments.
+      @return An array with info object for each experiment that was found. 
+      @throws AxisFault If communication with web service fails.
+   */
   public ExperimentInfo[] getExperiments(QueryOptions qOpt)
     throws AxisFault
   {
-    RPCServiceClient service = getService();
     ExperimentInfo[] result = invokeBlocking("getExperiments", ExperimentInfo[].class, session.getId(), qOpt);
     return result;
   }
   
+  /**
+    Gets info about raw bioassays used in an experiment.    
+      @param experimentId Id of experiment to get raw bioassays from.
+      @param qOpt Options to put on the query that gets the raw bioassays.
+      @return An array with info object about each raw bioassay that was found.
+      @throws AxisFault If communication with web services fails.
+   */
   public RawBioAssayInfo[] getRawBioAssays(int experimentId, QueryOptions qOpt)
     throws AxisFault
   {
-    RPCServiceClient service = getService();
     RawBioAssayInfo[] result = invokeBlocking("getRawBioAssays", RawBioAssayInfo[].class, session.getId(), experimentId, qOpt);
     return result;
   }
   
+  /**
+    Gets info about bioassay sets in an experiment
+      @param experimentId Id of the experiment to get the bioassay sets from
+      @param qOpt Options to put on the query that gets the bioassay sets.
+      @return An array with info about each bioassay set found by the query.
+      @throws AxisFault If communication with web services fails.
+   */
   public BioAssaySetInfo[] getBioAssaySets(int experimentId, QueryOptions qOpt)
     throws AxisFault
   {
-    RPCServiceClient service = getService();
     BioAssaySetInfo[] result = invokeBlocking("getBioAssaySets", BioAssaySetInfo[].class, session.getId(), experimentId, new QueryOptions());
     return result;
-  }
-  
+  } 
 }

trunk/src/webservices/client/java/net/sf/basedb/ws/client/ProjectClient.java

@@ -28 +28 @@
 
 import org.apache.axis2.AxisFault;
-import org.apache.axis2.rpc.client.RPCServiceClient;
 
+/**
+  Web service client for project in BASE.
+  Calls services in {@link net.sf.basedb.ws.server.ProjectService}
+    @author Martin
+    @version 2.5
+ */
 public class ProjectClient 
   extends AbstractRPCClient 
 {
-  
   private final SessionClient session;
   
+  /**
+    Creates new ProjectClient object for an active session client.
+      @param session The active session client
+   */
   public ProjectClient(SessionClient session)
   {
@@ -42 +50 @@
   }
   
+  /**
+    Sets a project to be active.
+      @param projectId Id of the project that should be put active.
+      @throws AxisFault If communication with web services fails.
+   */
   public void setActive(int projectId)
     throws AxisFault
@@ -48 +61 @@
   }
   
+  /**
+    Gets info about each projects that are available for the active session client.
+      @param qOpt Options to put on the query that gets the project from database.
+      @return An array with a info object for each project.
+      @throws AxisFault If communication with web service fails.
+   */
   public ProjectInfo[] getProjects(QueryOptions qOpt)
     throws AxisFault
   {    
-    RPCServiceClient service = getService();
     ProjectInfo[] result = invokeBlocking("getProjects", ProjectInfo[].class, session.getId(), qOpt);
     return result;

trunk/src/webservices/client/java/net/sf/basedb/ws/client/RawBioAssayClient.java

@@ -101 +101 @@
         filePath, 
         session.getId(), 
-        rawBioAssayId
+        rawBioAssayId,
+        info
       );
     return receivedFile;

trunk/src/webservices/client/java/net/sf/basedb/ws/client/SessionClient.java

@@ -38 +38 @@
   private final String ID;
   
+  /**
+    Creates a new SessionClient to a certain URL.
+      @param url The url where web services are located.
+      @param ID Session id of a logged in session. A new session will be created if this is NULL.
+      @param externalClientId External id of the client that is registered in BASE.
+      @throws AxisFault If communication with the web service fails.
+   */
   public SessionClient(String url, String ID, String externalClientId)
     throws AxisFault
@@ -64 +71 @@
   }
   
+  /**
+    Calling the getChallenge method.
+      @return Gets a random string to use with password encryption.
+      @throws AxisFault If communication with web service fails.
+   */
   public String getChallenge()
     throws AxisFault

trunk/src/webservices/server/net/sf/basedb/ws/server/ArrayDesignService.java

@@ -69 +69 @@
         int arrayDesignId, DataFileTypeInfo typeInfo)
   {
+    if (ID == null || typeInfo == null) return null;
     File arrayDesignFile = null;
     SessionControl sc = getSessionControl(ID);
@@ -144 +145 @@
       if (design.hasFileSet())
       {
-        ItemQuery<DataFileType> query = design.getFileSet().getMemberTypes();
+        FileSet fileSet = design.getFileSet();
+        ItemQuery<FileSetMember> query = fileSet.getMembers();        
         if (qOpt != null) util.getConfiguredItemQuery(query, qOpt);
-        for (DataFileType dft : query.list(dc))
+        for (FileSetMember fsm : query.list(dc))
         {
-          types.add(new DataFileTypeInfo(dft));
+          types.add(new DataFileTypeInfo(fsm.getDataFileType()));
         }
       }

trunk/src/webservices/server/net/sf/basedb/ws/server/RawBioAssayService.java

@@ -93 +93 @@
       int rawBioAssayId, DataFileTypeInfo typeInfo)
   {
+    if (ID == null || typeInfo == null) return null;
     File rawDataFile = null;
     SessionControl sc = getSessionControl(ID);
@@ -167 +168 @@
       RawBioAssay rawBioAssay = RawBioAssay.getById(dc, rawBioAssayId);
       if (rawBioAssay.hasFileSet())
-      {
-        ItemQuery<DataFileType> query = rawBioAssay.getFileSet().getMemberTypes();
+      {     
+        ItemQuery<FileSetMember> query = rawBioAssay.getFileSet().getMembers();
         if (qOpt != null) util.getConfiguredItemQuery(query, qOpt);
-        for (DataFileType dft : query.list(dc))
+        for (FileSetMember fsm : query.list(dc))
         {
-          types.add(new DataFileTypeInfo(dft));
+          types.add(new DataFileTypeInfo(fsm.getDataFileType()));
         }
       }