Changeset 3063

Timestamp:

Jan 15, 2007, 4:12:31 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

Now get info about CEL and CDF file for affymetrix experiments. Inlcude shared experiments
and raw bioassays in queries.

Location:

branches/webservices/src

Files:

• clients/web/net/sf/basedb/clients/web/taglib/Page.java (modified) (1 diff)
• test/TestWebservices.java (modified) (2 diffs)
• webservices/client/java/net/sf/basedb/ws/client/ExperimentClient.java (modified) (2 diffs)
• webservices/client/java/net/sf/basedb/ws/info/RawBioAssayInfo.java (added)
• webservices/server/net/sf/basedb/ws/server/ExperimentService.java (modified) (4 diffs)

branches/webservices/src/clients/web/net/sf/basedb/clients/web/taglib/Page.java

@@ -235 +235 @@
     return sc;
   }
-
   
   public void setPageContext(PageContext pageContext)

branches/webservices/src/test/TestWebservices.java

@@ -27 +27 @@
 import net.sf.basedb.ws.client.SessionClient;
 import net.sf.basedb.ws.info.ItemInfo;
+import net.sf.basedb.ws.info.RawBioAssayInfo;
 
 
@@ -194 +195 @@
     {
       ExperimentClient experimentClient = new ExperimentClient(client);
-      ItemInfo[] rawBioAssays = experimentClient.getRawBioAssays(experimentId);
+      RawBioAssayInfo[] rawBioAssays = experimentClient.getRawBioAssays(experimentId);
       if (rawBioAssays != null)
       {
-        for (ItemInfo p : rawBioAssays)
+        for (RawBioAssayInfo p : rawBioAssays)
         {
-          write(p.getId() + "\t" + p.getName());
+          write(p.getId() + "\t" + p.getName() + "\t" + p.getCelFileUrl() + "\t" + p.getCdfFileUrl());
         }
       }

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

@@ -25 +25 @@
 
 import net.sf.basedb.ws.info.ItemInfo;
+import net.sf.basedb.ws.info.RawBioAssayInfo;
 
 import org.apache.axis2.AxisFault;
@@ -49 +50 @@
   }
   
-  public ItemInfo[] getRawBioAssays(int experimentId)
+  public RawBioAssayInfo[] getRawBioAssays(int experimentId)
     throws AxisFault
   {
     RPCServiceClient service = getService();
-    ItemInfo[] result = invokeBlocking("getRawBioAssays", ItemInfo[].class, session.getId(), experimentId);
+    RawBioAssayInfo[] result = invokeBlocking("getRawBioAssays", RawBioAssayInfo[].class, session.getId(), experimentId);
     return result;
   }

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

@@ -27 +27 @@
 import java.util.List;
 
+
+import net.sf.basedb.core.Affymetrix;
+import net.sf.basedb.core.ArrayDesign;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Experiment;
+import net.sf.basedb.core.File;
+import net.sf.basedb.core.Include;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.SessionControl;
+import net.sf.basedb.core.Type;
+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.info.ItemInfo;
+import net.sf.basedb.ws.info.RawBioAssayInfo;
 
 public class ExperimentService
@@ -48 +58 @@
     {
       ItemQuery<Experiment> query = Experiment.getQuery();
+      query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
+      query.restrict(Restrictions.eq(Hql.property("rawDataType"), 
+        Expressions.parameter("rawDataType", "affymetrix", Type.STRING)));
       for (Experiment experiment : query.list(dc))
       {
@@ -61 +74 @@
   }
   
-  public ItemInfo[] getRawBioAssays(String ID, int experimentId)
+  public RawBioAssayInfo[] getRawBioAssays(String ID, int experimentId)
   {
     SessionControl sc = getSessionControl(ID);
     DbControl dc = sc.newDbControl();
-    List<ItemInfo> rawBioAssays = new LinkedList<ItemInfo>();
+    List<RawBioAssayInfo> rawBioAssays = new LinkedList<RawBioAssayInfo>();
     try
     {
       Experiment experiment = Experiment.getById(dc, experimentId);
       ItemQuery<RawBioAssay> query = experiment.getRawBioAssays();
+      query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
       for (RawBioAssay rba : query.list(dc))
       {
-        rawBioAssays.add(new ItemInfo(rba));
+        RawBioAssayInfo rbaInfo = new RawBioAssayInfo(rba);
+        File celFile = Affymetrix.getCelFile(rba);
+        ArrayDesign design = rba.getArrayDesign();
+        File cdfFile = Affymetrix.getCdfFile(design);
+        String root = 
+          "/filemanager/files/download/-" + ID + "-";
+        
+        rbaInfo.setCelFileUrl(root + celFile.getPath().toString());
+        rbaInfo.setCdfFileUrl(root + cdfFile.getPath().toString());
+        rawBioAssays.add(rbaInfo);
       }
       
@@ -80 +103 @@
       if (dc != null) dc.close();
     }
-    ItemInfo[] ii = new ItemInfo[rawBioAssays.size()];
+    RawBioAssayInfo[] ii = new RawBioAssayInfo[rawBioAssays.size()];
     return rawBioAssays.toArray(ii);