Changeset 3972

Timestamp:

Nov 15, 2007, 12:49:51 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #492: Web services

Added ServicesUtil?.listToInfo() method for generic conversion of items to info objects

Location:

trunk/src

Files:

• core/net/sf/basedb/core/BioAssaySet.java (modified) (2 diffs)
• info/net/sf/basedb/info/BioAssaySetInfo.java (modified) (3 diffs)
• test/TestWebservices.java (modified) (2 diffs)
• webservices/server/net/sf/basedb/ws/server/ArrayDesignService.java (modified) (5 diffs)
• webservices/server/net/sf/basedb/ws/server/ExperimentService.java (modified) (6 diffs)
• webservices/server/net/sf/basedb/ws/server/ProjectService.java (modified) (3 diffs)
• webservices/server/net/sf/basedb/ws/server/RawBioAssayService.java (modified) (7 diffs)
• webservices/server/net/sf/basedb/ws/server/ServicesUtil.java (modified) (3 diffs)

trunk/src/core/net/sf/basedb/core/BioAssaySet.java

@@ -347 +347 @@
     @since 2.5
    */
-  public BioAssaySetInfo toInfo(BioAssaySetInfo info, DbControl dc)
+  public BioAssaySetInfo toInfo(BioAssaySetInfo info)
   {
     super.toInfo(info);   
@@ -354 +354 @@
     info.setNumReporters(this.getNumReporters());
     info.setNumSpots(this.getNumSpots());
-    
-    ItemQuery<BioAssay> query = this.getBioAssays();    
-    List<BioAssay> bioas = null;
-    int[] basIds;;
-    try
-    {
-      bioas = query.list(dc);
-      basIds = new int[bioas.size()];
-    }
-    catch (PermissionDeniedException pex)
-    {
-      basIds = new int[0];
-    }     
-    for (int i=0; i<basIds.length; i++)
-    {
-      basIds[i] = bioas.get(i).getId();
-    }   
-    info.setBioAssayIds(basIds);
-    
     return info;
   }

trunk/src/info/net/sf/basedb/info/BioAssaySetInfo.java

@@ -37 +37 @@
 public class BioAssaySetInfo 
   extends BasicItemInfo
-    implements NameableInfo, Serializable
+  implements NameableInfo, Serializable
 {
   private static final long serialVersionUID = -1192040975292178464L;
@@ -44 +44 @@
   private int numReporters = 0;
   private int numSpots = 0;
-  private int[] bioAssayIds;
   
   /**
@@ -86 +85 @@
   }
 
-  /** 
-      @param bioAssayIds The bioAssayIds to set.
-  */
-  public void setBioAssayIds(int[] bioAssayIds)
-  {
-    this.bioAssayIds = bioAssayIds;
-  }
-
-  /** 
-    @return Returns the bioAssayIds.
-  */
-  public int[] getBioAssayIds()
-  {
-    return bioAssayIds;
-  }
-
   public String getDescription()
   {   

trunk/src/test/TestWebservices.java

@@ -292 +292 @@
         if (hasDownloadableData && fileTypes.length > 0)
         {
-          System.out.print("--Download of array design file....");
+          System.out.print("--Download of " + fileTypes[0].getName() + " for array design....");
           File receivedFile = new File(fileTypes[0].getName());
           OutputStream out = new FileOutputStream(receivedFile);
@@ -373 +373 @@
       if (hasDownloadableData && fileTypes.length > 0)
       {
-        System.out.print("--Download of raw data file for RawBioAssay....");
+        System.out.print("--Download of " + fileTypes[0].getName() + " for RawBioAssay....");
         File receivedFile = new File(fileTypes[0].getName());
         OutputStream out = new FileOutputStream(receivedFile);

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

@@ -34 +34 @@
 import net.sf.basedb.info.DataFileTypeInfo;
 import net.sf.basedb.info.QueryOptions;
-
-import java.util.LinkedList;
-import java.util.List;
 
 import org.apache.axiom.om.OMElement;
@@ -74 +71 @@
     {
       ArrayDesign design = ArrayDesign.getById(dc, arrayDesignId);
-      DataFileType type = DataFileType.getByExternalId(dc, dataFileType);
       if (design.hasFileSet())
       {
         FileSet fileSet = design.getFileSet();
+        DataFileType type = DataFileType.getByExternalId(dc, dataFileType);
         if (fileSet.hasMember(type))
         {
@@ -128 +125 @@
     SessionControl sc = getSessionControl(ID);
     DbControl dc = sc.newDbControl();
-    List<DataFileTypeInfo> types = new LinkedList<DataFileTypeInfo>();
     
     try
@@ -136 +132 @@
       {
         FileSet fileSet = design.getFileSet();
-        ItemQuery<FileSetMember> query = fileSet.getMembers();        
-        if (qOpt != null) util.getConfiguredItemQuery(query, qOpt);
-        for (FileSetMember fsm : query.list(dc))
-        {
-          DataFileTypeInfo dftInfo = new DataFileTypeInfo();
-          dftInfo = fsm.getDataFileType().toInfo(dftInfo);
-          types.add(dftInfo);
-        }
+        ItemQuery<DataFileType> query = fileSet.getMemberTypes();       
+        query = util.getConfiguredItemQuery(query, qOpt);
+        return util.listToInfo(query.list(dc), DataFileTypeInfo.class);
       }
     }
@@ -150 +141 @@
       if (dc != null) dc.close();
     }
-    DataFileTypeInfo[] dataFileTypeInfos = new DataFileTypeInfo[types.size()];
-    return types.toArray(dataFileTypeInfos);
+    return new DataFileTypeInfo[0];
   }
 }

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

@@ -69 +69 @@
       ItemQuery<Experiment> query= Experiment.getQuery();   
       query = util.getConfiguredItemQuery(query, qOpt);
-      
-      for (Experiment experiment : query.list(dc))
-      {
-        ExperimentInfo expInfo = new ExperimentInfo();
-        experiment.toInfo(expInfo);
-        experiments.add(expInfo);
-      }
+      return util.listToInfo(query.list(dc), ExperimentInfo.class);
     }
     finally
@@ -81 +75 @@
       if (dc != null) dc.close();
     }
-    ExperimentInfo[] ii = new ExperimentInfo[experiments.size()];   
-    return experiments.toArray(ii);
   }
   
@@ -95 +87 @@
   public BioAssaySetInfo[] getBioAssaySets(String ID, int experimentId, QueryOptions qOpt)
   {
-    List<BioAssaySetInfo> bioAssaySetsInfo = new LinkedList<BioAssaySetInfo>();
     SessionControl sc = getSessionControl(ID);
     DbControl dc = sc.newDbControl();
-    
     try
     {
       Experiment experiment = Experiment.getById(dc, experimentId);
       ItemQuery<BioAssaySet> query = experiment.getBioAssaySets();
-      query = qOpt != null ? util.getConfiguredItemQuery(query, qOpt) : query;
-      
-      for (BioAssaySet bas : query.list(dc))
-      {
-        BioAssaySetInfo basInfo = new BioAssaySetInfo();
-        bas.toInfo(basInfo, dc);        
-        bioAssaySetsInfo.add(basInfo);
-      }
+      query = util.getConfiguredItemQuery(query, qOpt);
+      return util.listToInfo(query.list(dc), BioAssaySetInfo.class);
     }
     finally
@@ -116 +100 @@
       if (dc != null) dc.close();
     }
-    
-    BioAssaySetInfo[] ii = new BioAssaySetInfo[bioAssaySetsInfo.size()];
-    return bioAssaySetsInfo.toArray(ii);
   }
   
@@ -133 +114 @@
     SessionControl sc = getSessionControl(ID);
     DbControl dc = sc.newDbControl();
-    List<RawBioAssayInfo> rawBioAssays = new LinkedList<RawBioAssayInfo>();
     try
     {
       Experiment experiment = Experiment.getById(dc, experimentId);
       ItemQuery<RawBioAssay> query = experiment.getRawBioAssays();      
-      query = qOpt != null ? util.getConfiguredItemQuery(query, qOpt) : query;
-      
-      for (RawBioAssay rba : query.list(dc))
-      {       
-        RawBioAssayInfo rbaInfo = new RawBioAssayInfo();
-        rbaInfo = rba.toInfo(rbaInfo);
-        rawBioAssays.add(rbaInfo);
-      }
-      
+      query = util.getConfiguredItemQuery(query, qOpt);
+      return util.listToInfo(query.list(dc), RawBioAssayInfo.class);
     }
     finally
@@ -152 +125 @@
       if (dc != null) dc.close();
     }
-    RawBioAssayInfo[] ii = new RawBioAssayInfo[rawBioAssays.size()];
-    return rawBioAssays.toArray(ii);
   } 
 }

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

@@ -31 +31 @@
 import net.sf.basedb.info.QueryOptions;
 
-import java.util.LinkedList;
-import java.util.List;
 
 /**
@@ -83 +81 @@
   {
     SessionControl sc = getSessionControl(ID);
-    DbControl dc = sc.newDbControl();
-    List<ProjectInfo> projects = new LinkedList<ProjectInfo>();   
+    DbControl dc = sc.newDbControl(); 
     try
     {
       ItemQuery<Project> query = Project.getQuery();
-      query = qOpt != null ? util.getConfiguredItemQuery(query, qOpt) : query;
-      
-      for (Project project : query.list(dc))
-      {
-        ProjectInfo pInfo = new ProjectInfo();
-        project.toInfo(pInfo);        
-        projects.add(pInfo);
-      }
+      query = util.getConfiguredItemQuery(query, qOpt);
+      return util.listToInfo(query.list(dc), ProjectInfo.class);
     }
     finally
@@ -101 +92 @@
       if (dc != null) dc.close();
     }
-    ProjectInfo[] ii = new ProjectInfo[projects.size()];
-    return projects.toArray(ii);
   }
 }

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

@@ -37 +37 @@
 import net.sf.basedb.info.QueryOptions;
 
-import java.util.LinkedList;
-import java.util.List;
 
 import org.apache.axiom.om.OMElement;
@@ -67 +65 @@
     SessionControl sc = getSessionControl(ID);
     DbControl dc = sc.newDbControl();
-    ArrayDesign arrayDesign = null;
+    ArrayDesignInfo info = null;
     try
     {
       RawBioAssay rawBioAssay = RawBioAssay.getById(dc, rawBioAssayId);
-      arrayDesign= rawBioAssay.getArrayDesign();
+      ArrayDesign arrayDesign = rawBioAssay.getArrayDesign();
+      if (arrayDesign != null) info = arrayDesign.toInfo(new ArrayDesignInfo());
     }
     finally
@@ -77 +76 @@
       if (dc != null) dc.close();
     }
-    
-    ArrayDesignInfo adInfo = new ArrayDesignInfo();
-    arrayDesign.toInfo(adInfo);
-    return adInfo;
+    return info;
   }
   
@@ -101 +97 @@
     {
       RawBioAssay rawBioAssay = RawBioAssay.getById(dc, rawBioAssayId);
-      DataFileType type = DataFileType.getByExternalId(dc, dataFileType);
       if (rawBioAssay.hasFileSet())
       {
         FileSet fileSet = rawBioAssay.getFileSet();
+        DataFileType type = DataFileType.getByExternalId(dc, dataFileType);
         if (fileSet.hasMember(type))
         {
@@ -156 +152 @@
     SessionControl sc = getSessionControl(ID);
     DbControl dc = sc.newDbControl();
-    List<DataFileTypeInfo> types = new LinkedList<DataFileTypeInfo>(); 
     try
     {
@@ -162 +157 @@
       if (rawBioAssay.hasFileSet())
       {     
-        ItemQuery<FileSetMember> query = rawBioAssay.getFileSet().getMembers();
-        if (qOpt != null) util.getConfiguredItemQuery(query, qOpt);
-        for (FileSetMember fsm : query.list(dc))
-        {
-          DataFileTypeInfo dftInfo = new DataFileTypeInfo();
-          fsm.getDataFileType().toInfo(dftInfo);
-          types.add(dftInfo);
-        }
+        ItemQuery<DataFileType> query = rawBioAssay.getFileSet().getMemberTypes();
+        query = util.getConfiguredItemQuery(query, qOpt);
+        return util.listToInfo(query.list(dc), DataFileTypeInfo.class);
       }
     }
@@ -176 +166 @@
       if (dc != null) dc.close();
     }
-    DataFileTypeInfo[] dataFileTypeInfo = new DataFileTypeInfo[types.size()];
-    return types.toArray(dataFileTypeInfo);
+    return new DataFileTypeInfo[0];
   }
 }

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

@@ -28 +28 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.info.BasicItemInfo;
 import net.sf.basedb.info.QueryOptions;
 
-import java.util.ArrayList;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.EnumSet;
 import java.util.List;
+import java.util.Set;
 
 /**
   A utility class for common methods in the web services.
-    @author Martin
+    @author Martin, Nicklas
     @version 2.5
  */
@@ -50 +54 @@
    */
   @SuppressWarnings("unchecked")
-  protected <T extends BasicItem> ItemQuery<T> getConfiguredItemQuery(ItemQuery<T> query, QueryOptions qOpt)
+  public <T extends BasicItem> ItemQuery<T> getConfiguredItemQuery(ItemQuery<T> query, QueryOptions qOpt)
   {   
-    List<Include> includes = new ArrayList<Include>();
-    qOpt = qOpt == null ? new QueryOptions() : qOpt;
+    Set<Include> includes = EnumSet.noneOf(Include.class);
+    if (qOpt == null) qOpt = new QueryOptions();
     if (qOpt.getIncludeMine()) includes.add(Include.MINE);
     if (qOpt.getIncludeShared()) includes.add(Include.SHARED);
@@ -62 +66 @@
     query.include(includes);
     if (qOpt.getRestriction() != null)
-    { 
-      query.restrict(Hql.restriction(qOpt.getRestriction(), qOpt.getRestrictionPrefix()));      
-    }   
+    {
+      query.restrict(Hql.restriction(qOpt.getRestriction(), qOpt.getRestrictionPrefix()));
+    }
     return query;
   }
+  
+  /**
+    Convert a list of objects to an array of info objects
+    objects. This method uses reflection to find the correct method. For this
+    to work there are a few requirements:
+    
+    <ul>
+    <li>The list must contain objects of the same class only.
+    <li>The class for the objects in the list must contain a method
+      with the name "toInfo".
+    <li>The "toInfo" method must take an object of the specified
+      info class as the single parameter.
+    <li>The "toInfo" method must return the same object that was
+      passed to it.
+    </ul>
+    
+    See for example: {@link net.sf.basedb.core.Experiment#toInfo(net.sf.basedb.info.ExperimentInfo)}
+    
+    <p>
+    Note that this method is not limited to BasicItem object. It will work with
+    any kind of object as long as the above requirements are fulfilled.
+    
+    @param list A list of BasicItem objects or one of the subclasses
+    @param clazz The class of the BasicItemInfo that is matching the BasicItem:s
+      in the list
+    @return An array info objects of the specified class
+  */
+  @SuppressWarnings("unchecked")
+  public <T> T[] listToInfo(List<?> list, Class<T> clazz)
+  {
+    T[] result = (T[])java.lang.reflect.Array.newInstance(clazz, list.size());
+    int i = 0;
+    Method toInfo = null;
+    try
+    {
+      for (Object o : list)
+      {
+        if (toInfo == null) toInfo = o.getClass().getDeclaredMethod("toInfo", clazz);
+        result[i] = clazz.newInstance();
+        toInfo.invoke(o, result[i]);
+        ++i;
+      }
+    }
+    catch (NoSuchMethodException ex)
+    {
+      throw new RuntimeException(ex);
+    }
+    catch (InstantiationException ex)
+    {
+      throw new RuntimeException(ex);
+    }
+    catch (IllegalAccessException ex)
+    {
+      throw new RuntimeException(ex);
+    }
+    catch (InvocationTargetException ex)
+    {
+      throw new RuntimeException(ex);
+    }
+    return result;
+  }
+  
 }