Changeset 5198

Timestamp:

Dec 15, 2009, 1:56:17 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

References #1444: Implement generic BFS writers and readers/parsers

Improved error handling and error messages. Added DataWriterFactory? and two generic implementations.

Location:

trunk/src/core/net/sf/basedb/util/bfs

Files:

• AbstractDataWriterFactory.java (added)
• AnnotationWriter.java (modified) (6 diffs)
• DataWriter.java (modified) (4 diffs)
• DataWriterFactory.java (added)
• GenericBaseDataWriterFactory.java (added)
• GenericDiskDataWriterFactory.java (added)
• MetadataWriter.java (modified) (3 diffs)

trunk/src/core/net/sf/basedb/util/bfs/AnnotationWriter.java

@@ -22 +22 @@
 package net.sf.basedb.util.bfs;
 
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
 import java.io.Writer;
+import java.nio.charset.Charset;
 import java.util.HashSet;
 import java.util.Set;
@@ -39 +42 @@
 {
 
+  /**
+    Utility method for creating an annotation writer when you have an
+    output stream.
+    @param out The output stream the annotation writer should print to
+    @param filename Optional, the name of the file the output stream
+      is printing to
+  */
+  public static AnnotationWriter create(OutputStream out, String filename)
+  {
+    AnnotationWriter writer = new AnnotationWriter(
+        new OutputStreamWriter(out, Charset.forName("UTF-8")));
+    writer.setFilename(filename);
+    return writer;
+  }
+  
+  private String filename;
   private boolean hasPrintedHeaders;
   private int columnCount = -1;
@@ -53 +72 @@
   
   /**
+    Get the file name that this writer is printing to.
+    @return The file name or null if not known
+  */
+  public String getFilename()
+  {
+    return filename;
+  }
+  
+  /**
+    Set the file name that this writer is printing to.
+  */
+  public void setFilename(String filename)
+  {
+    this.filename = filename;
+  }
+
+  
+  /**
     Checks if headers has already been printed or not.
   */
@@ -87 +124 @@
     if (hasPrintedHeaders())
     {
-      throw new IllegalStateException("Headers has already been printed");
-    }
-    if (headers == null) throw new NullPointerException("headers");
+      throw new IllegalStateException("Headers has already been printed to file: " + 
+          getFilename());
+    }
+    if (headers == null) 
+    {
+      throw new NullPointerException("'headers' in file: " + getFilename());
+    }
     
     Set<String> used = new HashSet<String>();
@@ -96 +137 @@
     {
       String header = headers[i];
-      if (header == null) throw new NullPointerException("headers[" + i + "]");
+      if (header == null) 
+      {
+        throw new NullPointerException("'headers[" + i + "]' in file: " + getFilename());
+      }
       if (used.contains(header))
       {
-        throw new IllegalArgumentException("Duplicate header at index " + i + ": " + header);
+        throw new IllegalArgumentException("Duplicate header at index " + i + 
+          " in file " + getFilename() + ": " + header);
       }
       used.add(header);
@@ -127 +172 @@
     if (!hasPrintedHeaders())
     {
-      throw new IllegalStateException("Must print headers before printing data");
+      throw new IllegalStateException("Must print headers before printing data to file: " + 
+        getFilename());
     }
     if (id <= 0)
     {
-      throw new IllegalArgumentException("The id must be a positive integer");
+      throw new IllegalArgumentException("The id must be a positive integer in file: " + 
+        getFilename());
     }
     if (usedIds.contains(id))
     {
-      throw new IllegalArgumentException("Id value must be unique: " + id);
-    }
-    if (data == null) throw new NullPointerException("data");
+      throw new IllegalArgumentException("Id value must be unique in file " + 
+        getFilename() + ": " + id);
+    }
+    if (data == null) throw new NullPointerException("'data' in file: " + getFilename());
     if (data.length != columnCount)
     {
       throw new IllegalArgumentException("Data array has " + data.length + " columns; " +
-          "; expected " + columnCount);
+          "; expected " + columnCount + " in file: " + getFilename());
     }
     usedIds.add(id);

trunk/src/core/net/sf/basedb/util/bfs/DataWriter.java

@@ -43 +43 @@
 {
 
+  private String filename;
   private boolean lockedColumns;
   private int columnCount = -1;
@@ -58 +59 @@
   }
 
+  /**
+    Get the file name that this writer is printing to.
+    @return The file name or null if not known
+  */
+  public String getFilename()
+  {
+    return filename;
+  }
+
+  /**
+    Set the file name that this writer is printing to.
+  */
+  public void setFilename(String filename)
+  {
+    this.filename = filename;
+  }
+  
   /**
     Get the number of data columns. This information is only
@@ -82 +100 @@
     if (lockedColumns) 
     {
-      throw new IllegalStateException("Can't change the number of columns since data has already been written");
+      throw new IllegalStateException("Can't change the number of columns since data " +
+        "has already been written in file: " + getFilename());
     }
     this.columnCount = columns;
@@ -111 +130 @@
   {
 
-    if (data == null) throw new NullPointerException("data");
+    if (data == null) throw new NullPointerException("'data' in file: " + getFilename());
     if (columnCount <= 0) columnCount = data.length;
     if (data.length != columnCount)
     {
       throw new IllegalArgumentException("Data array has " + data.length + " columns; " +
-          "; expected " + columnCount);
+          "; expected " + columnCount + " in file: " + getFilename());
     }
     lockedColumns = true;

trunk/src/core/net/sf/basedb/util/bfs/MetadataWriter.java

@@ -22 +22 @@
 package net.sf.basedb.util.bfs;
 
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.io.Writer;
+import java.nio.charset.Charset;
 import java.util.HashSet;
 import java.util.Set;
@@ -55 +58 @@
   public static final String BOF_MARKER = "BFSformat";
 
+  /**
+    Utility method for creating a metadata writer when you have an
+    output stream.
+    @param out The output stream the metadata writer should print to
+    @param filename Optional, the name of the file the output stream
+      is printing to
+  */
+  public static MetadataWriter create(OutputStream out, String filename)
+  {
+    MetadataWriter writer = new MetadataWriter(
+        new OutputStreamWriter(out, Charset.forName("UTF-8")));
+    writer.setFilename(filename);
+    return writer;
+  }
+  
   private final EncoderDecoder encoder;
+  private String filename;
   private String subtype;
   private Set<String> usedSections;
@@ -76 +95 @@
     this.usedKeys = new HashSet<String>();
     this.encoder = new TabCrLfEncoderDecoder(true);
+  }
+  
+  /**
+    Get the file name that this writer is printing to.
+    @return The file name or null if not known
+  */
+  public String getFilename()
+  {
+    return filename;
+  }
+  
+  /**
+    Set the file name that this writer is printing to.
+  */
+  public void setFilename(String filename)
+  {
+    this.filename = filename;
   }