Changeset 4055

Timestamp:

Dec 12, 2007, 9:20:25 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #800: Make the Illumina importer accept tab as data delimiter and comma as numeric decimal separator

File:

• branches/2.5-stable/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java (modified) (7 diffs)

branches/2.5-stable/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java

@@ -86 +86 @@
 import net.sf.basedb.util.parser.FlatFileParser.Data;
 import net.sf.basedb.util.parser.FlatFileParser.Line;
+import net.sf.basedb.util.parser.FlatFileParser.LineType;
 
 /**
@@ -128 +129 @@
     ));
   
+  
   private static final PluginParameter<String> invalidColumnsErrorParameter = new PluginParameter<String>(
       "invalidColumnsError",
@@ -251 +253 @@
         storeValue(job, request, fileParameter);
         storeValue(job, request, ri.getParameter(CHARSET));
+        storeValue(job, request, ri.getParameter(DECIMAL_SEPARATOR));
         
         // Associations
@@ -300 +303 @@
     Create a FlatFileParser that can parse Illumina data files:
     <ul>
-    <li>Data splitter: ,
+    <li>Data splitter: (,|\t)
     <li>Header regexp: (.+)=(.*?),*
-    <li>Data header: TargetId,.*
+    <li>Data header: TargetID(,|\t).*
     </ul>
+    NOTE! To begin with we support both comma and tab as column splitter but
+    later on (in {@link #isImportable(FlatFileParser)}) when we know which one is actually
+    used, we change this in the parser. We need to do this since numbers may
+    use comma as decimal separator.
   */
   @Override
@@ -309 +316 @@
     throws BaseException
   {
+    String separator = "(,|\\t)";
     FlatFileParser ffp = new FlatFileParser();
-    ffp.setDataSplitterRegexp(Pattern.compile(","));
-    ffp.setDataHeaderRegexp(Pattern.compile("TargetID,.*"));
+    ffp.setDataSplitterRegexp(Pattern.compile(separator));
+    ffp.setDataHeaderRegexp(Pattern.compile("TargetID"+separator + ".*"));
     ffp.setHeaderRegexp(Pattern.compile("(.+)=(.*?),*"));
     return ffp;
   }
   /**
-    @return Always "dot"
+    @return As specified by job parameter or "dot" if not
   */
   @Override
   protected String getDecimalSeparator()
   {
-    return "dot";
+    String separator = super.getDecimalSeparator();
+    if (separator == null) separator = "dot";
+    return separator;
   }
 
@@ -333 +343 @@
   {
     String firstLine = ffp.getLineCount() >= 1 ? ffp.getLine(0).line() : null;
-    return firstLine != null && firstLine.contains("Illumina") ;
+    boolean isIllumina = firstLine != null && firstLine.contains("Illumina");
+    if (isIllumina)
+    {
+      String separator = ",";
+      FlatFileParser.Line lastLine = ffp.getLine(ffp.getLineCount()-1);
+      if (lastLine.type() == LineType.DATA_HEADER)
+      {
+        int firstTab = lastLine.line().indexOf("\t");
+        if (firstTab > 0 && firstTab < lastLine.line().indexOf(","))
+        {
+          separator = "\\t";
+        }
+        ffp.setDataSplitterRegexp(Pattern.compile(separator));
+      }
+    }
+    return isIllumina;
   }
   
@@ -592 +617 @@
         parameters.add(fileParameter);
         parameters.add(getCharsetParameter(null, null, null));
+        parameters.add(getDecimalSeparatorParameter(null, null, (String)job.getValue(DECIMAL_SEPARATOR)));
   
         // parameters for scan, protocol and software