Changeset 3554

Timestamp:

Jul 12, 2007, 4:28:12 PM (16 years ago)

Author:

Johan Enell

Message:

Fixes #671, References #590

Test for BioAssaySetExporter? added which highlighted some bug in the BASEfile export. Additional tests for the BASEfile should be added and for the other formats.

Location:

trunk/src

Files:

• plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (1 diff)
• plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (8 diffs)
• test/TestBioAsssaySetExporter.java (added)
• test/TestFlatFileParser.java (modified) (2 diffs)

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -1154 +1154 @@
     ffp.setHeaderRegexp(Pattern.compile("(.*?)\\t(.*)"));
     ffp.setDataHeaderRegexp(Pattern.compile("%"));
+    ffp.setDataFooterRegexp(Pattern.compile("^$"));
     ffp.setDataSplitterRegexp(Pattern.compile("\\t"));
+    ffp.setUseNullIfEmpty(false);
 
     ffp.setInputStream(stream, Config.getCharset());

trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -312 +312 @@
     }
     out.println("columns\tid\tname" + annotationString);
-    out.println("annotationColumns" + annotationString);
+    out.println("annotationColumns" + (annotationString.length() == 0 ? "\t" : annotationString));
     out.println("%");
     for (BioAssay ba : bas.getBioAssays().list(dc))
@@ -339 +339 @@
         out.println("section\t"+parameters.get("section"));
         keys = keys.subList(1, keys.size());
+      }
+      else
+      {
+        out.println("section\tsettings");
       }
       if (keys.contains("section"))
@@ -451 +455 @@
     }
     out.println();
-    out.println("count\t" + bas.getNumReporters()); //TODO: count number of column/position
+    out.println("count\t" + query.count(dc)); //TODO: count number of column/position
     out.println("%");
     
@@ -481 +485 @@
     Integer prevPos = null;
     HashMap<Short, String> spotValues = new HashMap<Short, String>();
-    String reporter = null;
     while (iterator.hasNext())
     {
@@ -487 +490 @@
       Integer currentPos = r.getInt(posIndex);
       
-      if (prevPos != null && !currentPos.equals(prevPos))
-      {
+      if (!currentPos.equals(prevPos))
+      {
+        // Print spot fields
+        if (!spotValues.isEmpty())
+        {
+          String separator = "";
+          for (Short col : columnNo)
+          {
+            String spot = spotValues.get(col);
+            if (spot != null)
+            {
+              out.print(separator);
+              out.print(spot);
+            }
+            else
+            {
+              out.print(tabs);
+            }
+            separator = "\t";
+          }
+          out.println();
+          spotValues.clear();
+        }
+        
         //Print reporter fields
-        out.print(reporter);
-        
-        //Print spot fields
-        String separator = "";
-        for (Short col : columnNo)
-        {
-          String spot = spotValues.get(col);
-          if (spot != null)
-          {
-            out.print(separator);
-            out.print(spot);
-          }
-          else
-          {
-            out.print(tabs);
-          }
-          separator = "\t";
-        }
-        out.println();
-        
-        reporter = null;
-        spotValues = new HashMap<Short, String>();
-      }
-
-      if (reporter == null)
-      {
-        reporter = "";
         for (int i = 0; i < reporterIndex.size(); ++i)
         {
           String field = r.getString(reporterIndex.get(i));
-          reporter += field == null ? "" : field;
-          reporter += "\t";
+          out.print((field == null ? "" : field) + "\t");
         }
       }
@@ -533 +530 @@
       }
       spotValues.put(r.getShort(colIndex), spot);
-      prevPos = r.getInt(posIndex);
+      prevPos = currentPos;
+    }
+    
+    // Print the last spot fields
+    if (!spotValues.isEmpty())
+    {
+      String separator = "";
+      for (Short col : columnNo)
+      {
+        String spot = spotValues.get(col);
+        if (spot != null)
+        {
+          out.print(separator);
+          out.print(spot);
+        }
+        else
+        {
+          out.print(tabs);
+        }
+        separator = "\t";
+      }
+      out.println();
+      spotValues.clear();
     }
   }
@@ -842 +861 @@
     List<QueryItem> items = new ArrayList<QueryItem>();
     items.add(new QueryItem("rep.id", "Reporter (internal id)", "reporter", "rep('id')"));
+    items.add(new QueryItem("rep.position", "Position", "position", "pos()"));
     items.add(new QueryItem("rep.name", "Reporter Name", "name", "rep('name')"));
     items.add(new QueryItem("rep.externalId", "Reporter ID", "externalId", "rep('externalId')"));
@@ -859 +879 @@
   {
     List<QueryItem> items = new ArrayList<QueryItem>();
-    items.add(new QueryItem("position", "Position", "position", "pos()"));
     int channels = bas.getRawDataType().getChannels(); 
     for (int channel = 1; channel <= channels; ++channel)

trunk/src/test/TestFlatFileParser.java

@@ -8 +8 @@
 import net.sf.basedb.util.parser.FlatFileParser;
 import net.sf.basedb.util.parser.Mapper;
+import net.sf.basedb.util.parser.FlatFileParser.Line;
 
 /*
@@ -197 +198 @@
     }
   }
+
+  public static void testHeaderLine(Line line, String name, String value) throws Exception
+  {
+    if (!line.type().equals(FlatFileParser.LineType.HEADER))
+      throw new Exception("Line is no header: "+line.toString());
+    if (!line.name().equals(name))
+      throw new Exception("Cant find name '"+name+"' in line '"+line.line()+"'");
+    if (!line.value().equals(value))
+      throw new Exception("Cant find value '"+value+"' in line '"+line.line()+"'");
+  }
+
+  public static void testLine(Line line, String name) throws Exception
+  {
+    if (!line.line().equals(name))
+      throw new Exception("Line '"+line.line()+"' doesnt match '"+name+"'");
+  }
+
+  public static void testSection(Line line, String name) throws Exception
+  {
+    if (!line.type().equals(FlatFileParser.LineType.SECTION))
+      throw new Exception("Line is no section: "+line.toString());
+    if (!line.name().equals(name))
+      throw new Exception("Cant find sectionname '"+name+"' in line '"+line.line()+"'");
+  }
 }