Changeset 1149

Timestamp:

Aug 25, 2009, 2:33:52 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #240: Bead summary importer should have an option to fail if the number of skipped data lines get too high

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BeadSummaryImporter.java (modified) (7 diffs)

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BeadSummaryImporter.java

@@ -87 +87 @@
 import net.sf.basedb.util.ChainedProgressReporter;
 import net.sf.basedb.util.MD5;
+import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ClassMapErrorHandler;
 import net.sf.basedb.util.error.ErrorHandler;
@@ -146 +147 @@
       "This can for example happen if an incorrect array design is used.\n\n"+
       "skip = Skip the current data line and continue\n"+
+      "auto = Skip and continue unless the threshold is reached\n" +
       "fail = Stop with an error message",
-      new StringParameterType(255, "skip", false, 1, 0, 0, 
-        Arrays.asList( new String[] { "skip", "fail"} ))
+      new StringParameterType(255, "auto", false, 1, 0, 0, 
+        Arrays.asList( new String[] { "skip", "auto", "fail"} ))
+    );
+
+  private static final PluginParameter<String> thresholdParameter = 
+    new PluginParameter<String>(
+      "featureMismatchThreshold",
+      "Probe not found: threshold",
+      "If the 'Probe not found' options is set to auto the plug-in will skip " +
+      "data lines until the threshold is reached. If the threshold is reached, the " +
+      "plug-in stops with an error message. The threshold can be given as a percentage " +
+      "or as an absolute value.",
+      new StringParameterType(255, "5%", false)
     );
   
@@ -170 +183 @@
   */
   private ClassMapErrorHandler errorHandler;
+  private boolean useAutoFeatureMismatchErrorHandling;
+  private String featureMismatchThreshold;
 
   
@@ -387 +402 @@
         storeValue(job, request, ri.getParameter(Parameters.DEFAULT_ERROR));
         storeValue(job, request, featureMismatchErrorParameter);
+        storeValue(job, request, thresholdParameter);
         storeValue(job, request, ri.getParameter(Parameters.INVALID_USE_OF_NULL_ERROR));
         storeValue(job, request, ri.getParameter(Parameters.NUMBER_FORMAT_ERROR));
@@ -547 +563 @@
       
       parameters.add(featureMismatchErrorParameter);
+      parameters.add(thresholdParameter);
       parameters.add(Parameters.invalidUseOfNullError(null, null, null));
       parameters.add(Parameters.numberFormatError(null, 
@@ -792 +809 @@
         done++;
       }
+      
+      if (useAutoFeatureMismatchErrorHandling)
+      {
+        int maxSkipped = 0;
+        if (featureMismatchThreshold == null) featureMismatchThreshold = "5%";
+        if (featureMismatchThreshold.endsWith("%"))
+        {
+          int percentage = Values.getInt(featureMismatchThreshold.substring(0, featureMismatchThreshold.length()-1));
+          maxSkipped = (numLines * percentage) / 100;
+        }
+        else
+        {
+          maxSkipped = Values.getInt(featureMismatchThreshold);
+        }
+        if (batcher.getNumSkippedMissingFeature() > maxSkipped)
+        {
+          throw new BaseException("Too many 'Not found probes'. " + 
+            batcher.getNumSkippedMissingFeature() + 
+            " > threshold (" + featureMismatchThreshold + ")");
+        }
+      }
+      
       batcher.flush();
       batcher.close();
@@ -840 +879 @@
     ErrorHandler defaultErrorHandler = new SimpleErrorHandler("skip".equals(config.getValue("defaultError")));
     errorHandler = new ClassMapErrorHandler(defaultErrorHandler);
-    addErrorHandler(ItemNotFoundException.class, 
-      createErrorHandler((String)config.getValue("featureMismatchError"), defaultErrorHandler));
+    String featureMismatchError = (String)config.getValue("featureMismatchError");
+    useAutoFeatureMismatchErrorHandling = "auto".equals(featureMismatchError);
+    if (useAutoFeatureMismatchErrorHandling)
+    {
+      addErrorHandler(ItemNotFoundException.class, 
+        createErrorHandler("skip", defaultErrorHandler));
+      featureMismatchThreshold = (String)config.getValue("featureMismatchThreshold");
+    }
+    else
+    {
+      addErrorHandler(ItemNotFoundException.class, 
+        createErrorHandler(featureMismatchError, defaultErrorHandler));
+    }
     addErrorHandler(InvalidUseOfNullException.class, 
       createErrorHandler((String)config.getValue("invalidUseOfNullError"), defaultErrorHandler));