Changeset 3919

Timestamp:

Nov 6, 2007, 4:49:15 PM (15 years ago)

Author:

Martin Svensson

Message:

References #492 Modified the download methods to eliminate the problems with hardcoded filenames. WSDL files are now generated in misc/wsdl.

Location:

trunk

Files:

• build.xml (modified) (3 diffs)
• src/webservices/server/net/sf/basedb/ws/server/AbstractRPCService.java (modified) (3 diffs)
• src/webservices/server/net/sf/basedb/ws/server/ArrayDesignService.java (modified) (4 diffs)
• src/webservices/server/net/sf/basedb/ws/server/BaseFileDataSource.java (added)
• src/webservices/server/net/sf/basedb/ws/server/BioAssaySetService.java (modified) (5 diffs)
• src/webservices/server/net/sf/basedb/ws/server/RawBioAssayService.java (modified) (5 diffs)

trunk/build.xml

@@ -145 +145 @@
       <fileset dir="${dist}" defaultexcludes="no" />
       <fileset dir="bin/jar" defaultexcludes="no" />
+      <fileset dir="misc/wsdl" defaultexcludes="no" />
       <fileset dir="www/WEB-INF/lib" defaultexcludes="no" />
       <fileset dir="www/WEB-INF/classes" defaultexcludes="no" />
@@ -848 +849 @@
     <property name="webservices.build" location="${build}/webservices" 
       description="Location of compiled files" />
+    <property name="webservices.wsdlpath" location="misc/wsdl"
+      description="Location of created wsdl-files" />
     <path id="webservices.classpath" description="Class path for compiling webservices">
       <path refid="core.classpath"/>
@@ -904 +907 @@
         classpath="${webservices.build};${core.build}"
         className="net.sf.basedb.ws.server.@{serviceClassName}"
-        outputLocation="${webservices.build}/wsdl"      
+        outputLocation="${webservices.wsdlpath}"      
         serviceName="@{serviceClassName}"
         outputFileName="@{serviceClassName}.wsdl"

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

@@ -27 +27 @@
 import net.sf.basedb.core.SessionControl;
 
-import java.io.File;
-
 import javax.activation.DataHandler;
-import javax.activation.FileDataSource;
+import javax.activation.DataSource;
 
 import org.apache.axiom.om.OMAbstractFactory;
@@ -84 +82 @@
       InputStream in = dataHandler.getInputStream();<br>
      </code>
-      @param file File to be attached. 
+      @param dataSource A DataSource to be attached to an OMElement. 
       @param elementName The name to call the element by.
       @return OMElement where the file is attached to.
    */
-  protected OMElement attachFile(File file, String elementName)
+  protected OMElement attachFile(DataSource dataSource, String elementName)
   {
     OMFactory messageFactory = OMAbstractFactory.getOMFactory();
@@ -94 +92 @@
     OMElement fileElement = messageFactory.createOMElement(elementName, nameSpace);
     
-    FileDataSource fileDataSource = new FileDataSource(file);
-    DataHandler dataHandler = new DataHandler(fileDataSource);
+    DataHandler dataHandler = new DataHandler(dataSource);
     OMText node = messageFactory.createOMText(dataHandler, true);   
     fileElement.addChild(node);

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

@@ -27 +27 @@
 import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileSet;
 import net.sf.basedb.core.FileSetMember;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.SessionControl;
-import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.ws.info.DataFileTypeInfo;
 import net.sf.basedb.ws.info.QueryOptions;
 
-import java.io.File;
-import java.io.FileOutputStream;
 import java.util.LinkedList;
 import java.util.List;
@@ -59 +57 @@
   
   /**
-    Returns array design file of a certain type.
+    Returns array design file of a certain type, attached to an OMElement.
       @param ID Used to identify an active session with.
       @param arrayDesignId Id of the array design the file is associated with.
@@ -70 +68 @@
   {
     if (ID == null || typeInfo == null) return null;
-    File arrayDesignFile = null;
+    
     SessionControl sc = getSessionControl(ID);
     DbControl dc = sc.newDbControl();
@@ -82 +80 @@
         FileSet fileSet = design.getFileSet();
         FileSetMember member = fileSet.getMember(type);
-        FileOutputStream fos = null;
-        try
-        {
-          arrayDesignFile = new File(member.getFile().getName());
-          fos = new FileOutputStream(arrayDesignFile);  
-          FileUtil.copy(member.getFile().getDownloadStream(0), fos);
-          fos.close();
-        }
-        catch (Throwable th)
-        {
-          arrayDesignFile = null;
-        }
+        File file = member.getFile();
+        BaseFileDataSource source = new BaseFileDataSource(member.getFile());
+        return attachFile(source, file.getName());
       }
+      else return null;
     }
     finally
     {
       if (dc != null) dc.close();
-    }
-    if (arrayDesignFile == null ) return null;
-    return attachFile(arrayDesignFile, arrayDesignFile.getName());
+    }   
   }
   

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

@@ -36 +36 @@
 import java.util.Collections;
 import java.util.List;
+
+import javax.activation.FileDataSource;
 
 import org.apache.axiom.om.OMElement;
@@ -99 +101 @@
     
     String elementName = "exportFile";
+    OMElement elementWithAttachment = null;
     
     SessionControl sc = getSessionControl(ID);
@@ -113 +116 @@
       mergeReporters = mergeReporters == null ? false : mergeReporters;
       
+      exportFile =  File.createTempFile("BioAssaySetFile", null);
+      fos = new FileOutputStream(exportFile);
+      
       BioAssaySetExporter exporter = new BioAssaySetExporter();
       //Export to MeV-file format     
       if (format.equals(MEV))
-      {     
-          exportFile = new File("mevfile");
-          fos = new FileOutputStream(exportFile);
-          exporter.exportMeV(bioassayset, fos, null);
-          fos.close();
+      {             
+        exporter.exportMeV(bioassayset, fos, null);       
       }           
       //Export the data from the bioassayset as one big matrix in a BASEfile
       else if(format.equals(MATRIX_BASEFILE))
       {
-        exportFile = new File("MatrixBaseFile");
-        fos = new FileOutputStream(exportFile);
         exporter.exportBaseFileMatrix(bioassayset, fos, Collections.EMPTY_MAP, reporterFields, spotFields, mergeReporters);
-        fos.close();
       }     
       //Export the data from a bioassayset as a serial BASEfile.       
       else if (format.equals(SERIAL_BASEFILE))
       {
-        exportFile = new File("SerialBaseFile");
-        fos = new FileOutputStream(exportFile);
         exporter.exportBaseFileSerial(bioassayset, fos, Collections.EMPTY_MAP, reporterFields, spotFields, mergeReporters);
-        fos.close();
       }     
       else
@@ -142 +139 @@
         throw new BaseException("BASE web services does not support this format: " + format);
       }
+      fos.close();
+      FileDataSource source = new FileDataSource(exportFile);
+      elementWithAttachment = attachFile(source, elementName);
     }
     catch(Throwable th)
@@ -151 +151 @@
     {   
       if (dc != null) dc.close();
+      if (exportFile != null) exportFile.deleteOnExit();
     }
-    return attachFile(exportFile, elementName);   
+    
+    return elementWithAttachment;
   }
 }

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

@@ -27 +27 @@
 import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileSet;
 import net.sf.basedb.core.FileSetMember;
@@ -32 +33 @@
 import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.SessionControl;
-import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.ws.info.ArrayDesignInfo;
 import net.sf.basedb.ws.info.DataFileTypeInfo;
 import net.sf.basedb.ws.info.QueryOptions;
 
-import java.io.File;
-import java.io.FileOutputStream;
 import java.util.LinkedList;
 import java.util.List;
@@ -94 +92 @@
   {
     if (ID == null || typeInfo == null) return null;
-    File rawDataFile = null;
     SessionControl sc = getSessionControl(ID);
     DbControl dc = sc.newDbControl();
@@ -102 +99 @@
       RawBioAssay rawBioAssay = RawBioAssay.getById(dc, rawBioAssayId);
       DataFileType type = DataFileType.getByExternalId(dc, typeInfo.getExternalId());
-      if (rawBioAssay.hasFileSet());
+      if (rawBioAssay.hasFileSet())
       {
         FileSet fileSet = rawBioAssay.getFileSet(); 
         FileSetMember member = fileSet.getMember(type);
-        FileOutputStream fos = null;
-        try
-        {
-          rawDataFile = new File(member.getFile().getName());
-          fos = new FileOutputStream(rawDataFile);  
-          FileUtil.copy(member.getFile().getDownloadStream(0), fos);
-          fos.close();
-        }
-        catch (Throwable th)
-        {
-          rawDataFile = null;
-        }
+        File file = member.getFile();
+        BaseFileDataSource source = new BaseFileDataSource(file); 
+        return attachFile(source, file.getName());
       }
+      else return null;
     }
     finally
@@ -124 +113 @@
       if (dc != null) dc.close();
     }
-    if (rawDataFile == null) return null;
-    return attachFile(rawDataFile, rawDataFile.getName());
   }