Changeset 3637

Timestamp:

Aug 7, 2007, 11:17:37 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #710: Allow subclasses to AbstractFlatFileParser? to participate in auto-detection of file format

Location:

trunk

Files:

• doc/src/docbook/developerdoc/plugin_developer.xml (modified) (3 diffs)
• src/plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/PrintMapFlatFileImporter.java (modified) (1 diff)

trunk/doc/src/docbook/developerdoc/plugin_developer.xml

@@ -1778 +1778 @@
    try
    {
+      ffp.nextSection();
       FlatFileParser.LineType result = ffp.parseHeaders();
-      return result != FlatFileParser.LineType.UNKNOWN;
+      if (result == FlatFileParser.LineType.UNKNOWN)
+      {
+         return false;
+      }
+      else
+      {
+         return isImportable(ffp);
+      }
    }
    catch (IOException ex)
@@ -1937 +1945 @@
       <listitem>
         <para>
-        Implement the <methodname>Plugin.getAbout()</methodname> and 
-        <methodname>Plugin.getMainType()</methodname> methods. See
+        Implement the <methodname>Plugin.getAbout()</methodname> method. See
         <xref linkend="plugin_developer.api.interfaces.plugin" /> for more information.
         </para>
@@ -2054 +2061 @@
    ffp.setMinDataColumns(12);
    return ffp;
+}
+</programlisting>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected</modifier>
+            <type>boolean</type>
+            <methodname>isImportable</methodname>
+            <methodparam>
+              <type>FlatFileParser</type>
+              <parameter>ffp</parameter>
+            </methodparam>
+            <exceptionname>IOException</exceptionname>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+          This method is called from the <methodname>isImportable(InputStream)</methodname>
+          method, AFTER <methodname>FlatFileParser.nextSection()</methodname> and
+          <methodname>FlatFileParser.parseHeaders()</methodname> has been called
+          a single time and if the <methodname>parseHeaders</methodname> method didn't
+          stop on an unknown line. The default implementation of this method always returns
+          TRUE, since obviously some data has been found. A subclass may override this method
+          if it wants to do more checks, for example, make that a certain header is present
+          with a certain value. It may also continut parsing the file. Here is a code example from
+          the <classname>PrintMapFlatFileImporter</classname> which checks if a 
+          <constant>FormatName</constant> header is present and contains either 
+          <constant>TAM</constant> or <constant>MwBr</constant>.
+          </para>
+          
+          <programlisting>
+/**
+   Check that the file is a TAM or MwBr file.
+   @return TRUE if a FormatName header is present and contains "TAM" or "MwBr", FALSE
+      otherwise
+*/
+@Override
+protected boolean isImportable(FlatFileParser ffp)
+{
+   String formatName = ffp.getHeader("FormatName");
+   return formatName != null &amp;&amp; 
+      (formatName.contains("TAM") || formatName.contains("MwBr"));
 }
 </programlisting>

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

@@ -493 +493 @@
     FlatFileParser ffp = getInitializedFlatFileParser();
     ffp.setInputStream(in, getCharset());
+    ffp.setDefaultNumberFormat(getNumberFormat());
     try
     {
+      ffp.nextSection();
       FlatFileParser.LineType result = ffp.parseHeaders();
-      return result != FlatFileParser.LineType.UNKNOWN;
+      if (result == FlatFileParser.LineType.UNKNOWN)
+      {
+        return false;
+      }
+      else
+      {
+        return isImportable(ffp);
+      }
     }
     catch (IOException ex)
@@ -657 +666 @@
 
   /**
+    This method is called by the {@link #isImportable(InputStream)} method after
+    {@link FlatFileParser#nextSection()} and {@link FlatFileParser#parseHeaders()}
+    has been called and if data has been found. Thus, the default implementation of this
+    method always returns TRUE. Subclasses may override this method to do more checks, for
+    example to make sure certain headers are present or parse more data from the file.
+    
+    @param ffp The FlatFileParser object used to parse the file
+    @return Always TRUE
+    @since 2.4
+   */
+  protected boolean isImportable(FlatFileParser ffp)
+    throws IOException
+  {
+    return true;
+  }
+  
+  /**
     Called just before parsing of the file begins. A subclass
     may override this method if it needs to initialise some

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

@@ -321 +321 @@
   }
 
+  /**
+    Check that the first line contains the text "Illumina"
+    @return TRUE if the first line contains "Illumina", FALSE
+      otherwise
+  */
+  @Override
+  protected boolean isImportable(FlatFileParser ffp)
+  {
+    String firstLine = ffp.getLineCount() >= 1 ? ffp.getLine(0).line() : null;
+    return firstLine != null && firstLine.contains("Illumina") ;
+  }
   
   @Override

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

@@ -275 +275 @@
     -------------------------------------------
   */
+  /**
+    Check that the file is a TAM or MwBr file.
+    @return TRUE if a FormatName header is present and contains "TAM" or "MwBr", FALSE
+      otherwise
+  */
+  @Override
+  protected boolean isImportable(FlatFileParser ffp)
+  {
+    String formatName = ffp.getHeader("FormatName");
+    return formatName != null && (formatName.contains("TAM") || formatName.contains("MwBr"));
+  }
 
   /**