Changeset 3984

Timestamp:

Nov 20, 2007, 2:02:22 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

References #827: Add more web services methods

Added example code for downloading raw data files

Location:

trunk/src

Files:

• core/net/sf/basedb/core/RawBioAssay.java (modified) (1 diff)
• examples/webservices/README (modified) (2 diffs)
• examples/webservices/build.xml (modified) (2 diffs)
• examples/webservices/src/net/sf/basedb/ws/example/Main.java (modified) (7 diffs)

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

@@ -430 +430 @@
   {
     super.toTransferable(info);
-    info.setArrayDesignId(this.getArrayDesign().getId());
+    ArrayDesign ad = getArrayDesign();
+    info.setArrayDesignId(ad == null ? 0 : ad.getId());
     info.setPlatformId(this.getPlatform().getId());
     info.setRawDataTypeId(this.getRawDataType().getId());

trunk/src/examples/webservices/README

@@ -26 +26 @@
   Your password for the BASE web server.
 
+* download.dir
+  Set this option to a valid directory path to enable download of raw data from 
+  all raw bioassays. NOTE! Be careful with this option if you have a lot of data.
+  All files from all raw bioassay will be downloaded!
+
 From the command line type:
 
@@ -36 +41 @@
 ant -Dservices.url=http://localhost/base/services 
  -Dservices.login=mylogin -Dservices.password=mypassword
+ -Ddownload.dir=.
 
 

trunk/src/examples/webservices/build.xml

@@ -11 +11 @@
   <property name="services.login" value="root" />
   <property name="services.password" value="root" />
+  <!-- set this to a valid directory to enable download of raw data from raw bioassays -->
+  <property name="download.dir" value="" />
   
   <!-- variables for compiling -->
@@ -49 +51 @@
       <arg value="${services.login}" />
       <arg value="${services.password}" />
+      <arg value="${download.dir}" />
       <classpath>
         <path refid="classpath" />

trunk/src/examples/webservices/src/net/sf/basedb/ws/example/Main.java

@@ -24 +24 @@
 package net.sf.basedb.ws.example;
 
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
 import org.apache.axis2.AxisFault;
 
+import net.sf.basedb.info.DataFileTypeInfo;
 import net.sf.basedb.info.ExperimentInfo;
 import net.sf.basedb.info.ProjectInfo;
 import net.sf.basedb.info.QueryOptions;
+import net.sf.basedb.info.RawBioAssayInfo;
 import net.sf.basedb.info.VersionInfo;
 import net.sf.basedb.ws.client.ExperimentClient;
 import net.sf.basedb.ws.client.ProjectClient;
+import net.sf.basedb.ws.client.RawBioAssayClient;
 import net.sf.basedb.ws.client.SessionClient;
 
@@ -45 +54 @@
   
   This class will connect to the BASE server as specified in the 
-  <code>servicesUrl</code>, login, list all projects and experiments
-  the the user has access to and then logout again.
+  <code>servicesUrl</code>, login, list all projects, experiments
+  and raw bioassays the user has access to. It may optionally download
+  data files associated with a raw bioassay. The final step is to logout
+  again.
 
   @author nicklas
@@ -57 +68 @@
   public static void main(String[] args)
   {
-    if (args.length != 3) 
+    if (args.length < 3 || args.length > 4) 
     {
       showUsage();
@@ -65 +76 @@
     String username = args[1];
     String password = args[2];
+    String directory = args.length >= 4 ? args[3] : null;
+    
 
     Main main = new Main();
@@ -78 +91 @@
       main.listExperiments();
       System.out.println("------------");
+      main.listRawBioassays(directory);
+      System.out.println("------------");
       main.logout();
     }
@@ -89 +104 @@
   private static void showUsage()
   {
-    System.out.println("Usage: Main <url> <login> <password>");
-    System.out.println("       url      : The URL to the BASE webservices server");
-    System.out.println("       login    : The login for an existing user account on the BASE server");
-    System.out.println("       password : The password for the account");
+    System.out.println("Usage: Main <url> <login> <password> [directory]");
+    System.out.println("       url       : The URL to the BASE webservices server");
+    System.out.println("       login     : The login for an existing user account on the BASE server");
+    System.out.println("       password  : The password for the account");
+    System.out.println("       directory : Optional; if specified all raw bioassay data files will be downloaded to this directory");
   }
   
@@ -196 +212 @@
   }
   
+  /**
+    List all raw bioassays that the logged in user is has access to. For
+    each raw bioassay, list it's datafiles and download those to the specified
+    directory. If no directory is specified the download is disabled.
+  */
+  public void listRawBioassays(String directory)
+    throws AxisFault
+  {
+    RawBioAssayClient rc = new RawBioAssayClient(session);
+    RawBioAssayInfo[] rawBioAssays = rc.getRawBioAssays(new QueryOptions());
+    
+    File downloadDir = directory != null ? new File(directory) : null;
+    boolean doDownload = downloadDir != null && downloadDir.isDirectory();
+    
+    if (rawBioAssays == null || rawBioAssays.length == 0)
+    {
+      System.out.println("No raw bioassays found.");
+    }
+    else
+    {
+      System.out.println(rawBioAssays.length + " raw bioassays found");
+      int i = 0;
+      while (i < rawBioAssays.length)
+      {
+        RawBioAssayInfo info = rawBioAssays[i];
+        ++i;
+        System.out.println( i + ". " + info.getName() + " [id=" + info.getId() + "]");
+
+        listDataFiles(rc, info, doDownload ? downloadDir : null);
+      }
+    }
+  }
+
+  /**
+    List all datafiles for a given raw bioassay and download them if a 
+    download directory is given.
+  */
+  public void listDataFiles(RawBioAssayClient rc, RawBioAssayInfo info, File downloadDir)
+    throws AxisFault
+  {
+    DataFileTypeInfo[] files = rc.getDataFileTypes(info.getId(), new QueryOptions());
+    if (files == null || files.length == 0)
+    {
+      System.out.println("   No data files found.");
+    }
+    else
+    {
+      for (DataFileTypeInfo fileType : files)
+      {
+        System.out.print("   " + fileType.getName());
+        if (downloadDir != null)
+        {
+          String extension = fileType.getExtension() == null ? "" : "." + fileType.getExtension();
+          File downloadTo = new File(downloadDir, info.getName() + extension);
+          try
+          {
+            InputStream in = rc.downloadRawDataByType(info.getId(), fileType.getExternalId());
+            OutputStream out = new FileOutputStream(downloadTo);
+            copy(in, out);
+            out.close();
+            in.close();
+            System.out.print("; Download --> " + downloadTo);
+          }
+          catch (IOException ex)
+          {
+            System.out.print("; Download failed: " + ex.getMessage());
+          }
+        }
+        System.out.println("");
+      }
+    } 
+  }
+  
+  /**
+    Copy from InputStream to OutputStream
+  */
+  public long copy(InputStream in, OutputStream out)
+    throws IOException
+  {
+    int bytes = 0;
+    long totalBytes = 0;
+    byte[] buffer = new byte[1024];
+    while (bytes != -1) // -1 = end of stream
+    {
+      bytes = in.read(buffer, 0, buffer.length);
+      if (bytes > 0)
+      {
+        totalBytes += bytes;
+        out.write(buffer, 0, bytes);
+      }
+    }
+    return totalBytes;
+  }
+
   
 }