Changeset 5076

Timestamp:

Aug 25, 2009, 11:15:41 AM (13 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1362: Validate the number of raw data spots against the number of array design features

Location:

trunk

Files:

• src/core/net/sf/basedb/util/overview/GenericOverview.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/OverviewContext.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/OverviewUtil.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/ValidationOptions.java (modified) (6 diffs)
• src/core/net/sf/basedb/util/overview/Validator.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/validator/RawBioAssayValidator.java (modified) (4 diffs)
• www/common/overview/index.jsp (modified) (2 diffs)
• www/common/overview/options.jsp (modified) (5 diffs)

trunk/src/core/net/sf/basedb/util/overview/GenericOverview.java

@@ -294 +294 @@
     Get the validation options currently in use.
   */
+  @Override
   public ValidationOptions getValidationOptions()
   {

trunk/src/core/net/sf/basedb/util/overview/OverviewContext.java

@@ -68 +68 @@
   public Project getProject();
 
+  /**
+    Get the validation options that are currently in effect.
+    @since 2.13
+  */
+  public ValidationOptions getValidationOptions();
+  
   /**
     Store an auxilliary object in the overview cache. This is a service

trunk/src/core/net/sf/basedb/util/overview/OverviewUtil.java

@@ -130 +130 @@
           Arrays.asList(new Validator[]
           {
-            Validator.NONMATHCING_ARRAYDESIGN, Validator.MULTIPLE_ARRAYDESIGNS, 
+            Validator.NONMATHCING_ARRAYDESIGN, Validator.NONMATCHING_SPOTCOUNT,
+            Validator.MULTIPLE_ARRAYDESIGNS, 
             Validator.INCORRECT_PROTOCOLTYPE, Validator.INCORRECT_SOFTWARETYPE,
             Validator.INCORRECT_HARDWARETYPE, Validator.INCORRECT_ARRAY_NUM,

trunk/src/core/net/sf/basedb/util/overview/ValidationOptions.java

@@ -44 +44 @@
     Maps Validator ID to severity.
   */
-  private Map<String, Severity> options;
+  private Map<String, Severity> severities;
+  
+  /**
+    Other options. Key is validator ID + key
+  */
+  private Map<String, String> options;
   
   /**
@@ -62 +67 @@
   public ValidationOptions(Preset preset)
   {
-    this.options = new HashMap<String, Severity>();
+    this.severities = new HashMap<String, Severity>();
+    this.options = new HashMap<String, String>();
     if (preset != null) loadFromPreset(preset, true);
   }
@@ -75 +81 @@
   public Severity getSeverity(Validator validator)
   {
-    Severity option = options.get(validator.getId());
+    Severity option = severities.get(validator.getId());
     if (option == null) option = validator.getDefaultSeverity();
     return option;
@@ -89 +95 @@
     if (severity == null)
     {
-      options.remove(validator.getId());
+      severities.remove(validator.getId());
     }
     else
     {
-      options.put(validator.getId(), severity);
+      severities.put(validator.getId(), severity);
+    }
+  }
+  
+  /**
+    Get the configured option for a validator rule.
+    
+    @param validator The validator
+    @param key The key (name) of the option
+    @param defaultValue The default value in case there is no configured value
+    @return The value of the option
+    @since 2.13
+  */
+  public String getOption(Validator validator, String key, String defaultValue)
+  {
+    String value =  options.get(validator.getId() + "+" + key);
+    if (value == null) value = defaultValue;
+    return value;
+  }
+  
+  /**
+    Set an option for a validator rule.
+    
+    @param validator The validator
+    @param key The key (name) of the option
+    @param value The value to set or null to remove the value
+    @since 2.13
+  */
+  public void setOption(Validator validator, String key, String value)
+  {
+    key = validator.getId() + "+" + key;
+    if (value == null)
+    {
+      options.remove(key);
+    }
+    else
+    {
+      options.put(key, value);
     }
   }
@@ -109 +152 @@
   public void loadFromPreset(Preset preset, boolean clearFirst)
   {
-    if (clearFirst) options.clear();
+    if (clearFirst) 
+    {
+      severities.clear();
+      options.clear();
+    }
     for (Map.Entry<String, String> entry : preset)
     {
-      options.put(entry.getKey(), Severity.valueOf(entry.getValue()));
+      String key = entry.getKey();
+      String value = entry.getValue();
+      if (key.contains("+"))
+      {
+        options.put(key, value);
+      }
+      else
+      {
+        severities.put(key, Severity.valueOf(value));
+      }
     }
   }
@@ -123 +179 @@
   public void saveToPreset(net.sf.basedb.core.Presets.Preset preset)
   {
-    for (Map.Entry<String, Severity> entry : options.entrySet())
+    for (Map.Entry<String, Severity> entry : severities.entrySet())
     {
       preset.setSetting(entry.getKey(), entry.getValue().name());
+    }
+    for (Map.Entry<String, String> entry : options.entrySet())
+    {
+      preset.setSetting(entry.getKey(), entry.getValue());
     }
   }

trunk/src/core/net/sf/basedb/util/overview/Validator.java

@@ -438 +438 @@
       "array design as of the associated hybridization.",
       "Array design mismatch", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if the number of raw data spots 
+    are the same as the number of features (given a certain threshold).
+    Default severity level is WARNING.
+  */
+  public static final Validator NONMATCHING_SPOTCOUNT = new Validator(
+      "misc.nonmatchingspotcount", "Raw spots <> features",
+      "Checks if the number of raw data spots matches the number of " +
+      "array design features. A threshold can be given as either an " +
+      "absolute number or as a percentage.",
+      "Raw spots <> features", Severity.WARNING
     );
 

trunk/src/core/net/sf/basedb/util/overview/validator/RawBioAssayValidator.java

@@ -25 +25 @@
 import java.util.Map;
 
+import net.sf.basedb.core.ArrayDesign;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Hybridization;
@@ -31 +32 @@
 import net.sf.basedb.core.RawDataType;
 import net.sf.basedb.core.Scan;
+import net.sf.basedb.util.Values;
 import net.sf.basedb.util.overview.Fix;
 import net.sf.basedb.util.overview.OverviewContext;
@@ -43 +45 @@
   <li>Two raw bioassays from the same scan uses the same array index: 
     {@link Validator#DUPLICATE_ARRAY_NUM}
+  <li>The number of raw data spots is different from the number of
+    features on the array design: {@link Validator#NONMATCHING_SPOTCOUNT}.
   </ul>
 
@@ -129 +133 @@
     {}
     
+    if (rba.hasArrayDesign() && rba.hasData())
+    {
+      try
+      {
+        ArrayDesign design = rba.getArrayDesign();
+        String threshold = context.getValidationOptions().getOption(
+            Validator.NONMATCHING_SPOTCOUNT, "threshold", "5%");
+        
+        int numDbSpots = rba.getNumDbSpots();
+        int numDbFeatures = design.getNumDbFeatures();
+        int numFileSpots = rba.getNumFileSpots();
+        int numFileFeatures = design.getNumFileFeatures();
+        int maxDbDelta = 0;
+        int maxFileDelta = 0;
+        if (threshold.endsWith("%"))
+        {
+          int percentage = Values.getInt(threshold.substring(0, threshold.length()-1));
+          if (numDbFeatures > 0) maxDbDelta = (numDbFeatures * percentage) / 100;
+          if (numFileFeatures > 0) maxFileDelta = (numFileFeatures * percentage) / 100;
+        }
+        else
+        {
+          maxDbDelta = Values.getInt(threshold);
+          maxFileDelta = maxDbDelta;
+        }
+        
+        
+        if (numDbSpots > 0 && Math.abs(numDbFeatures - numDbSpots) > maxDbDelta)
+        {
+          context.createFailure(Validator.NONMATCHING_SPOTCOUNT, node, 
+            "Raw spots (db) <> features by more than " + threshold + ": " + 
+            numDbSpots  + "<>" + numDbFeatures);
+        }
+        if (numFileSpots > 0 && Math.abs(numFileFeatures - numFileSpots) > maxFileDelta)
+        {
+          context.createFailure(Validator.NONMATCHING_SPOTCOUNT, node, 
+            "Raw spots (file) <> features by more than " + threshold + ": " + 
+            numFileSpots  + "<>" + numFileFeatures);
+        }
+        
+      }
+      catch (Exception ex)
+      {}
+    }
   }
 

trunk/www/common/overview/index.jsp

@@ -96 +96 @@
       }
     }
+    options.setOption(Validator.NONMATCHING_SPOTCOUNT, "threshold", request.getParameter("threshold"));
     options.saveToPreset(presets.getDefault());
     OverviewUtil.saveValidationPresets(sc);
@@ -112 +113 @@
       }
     }
+    preset.setSetting(Validator.NONMATCHING_SPOTCOUNT.getId() + "+threshold", 
+        request.getParameter("threshold"));
     OverviewUtil.saveValidationPresets(sc);
     forward = "options.jsp";

trunk/www/common/overview/options.jsp

@@ -50 +50 @@
 final DbControl dc = sc.newDbControl();
 final String presetName = Values.getStringOrNull(request.getParameter("presetName"));
+final boolean resetToDefault = Values.getBoolean(request.getParameter("resetToDefault"));
 try
 {
   Presets presets = OverviewUtil.getValidationPresets(sc);
-  ValidationOptions options = presetName == null ? 
-    new ValidationOptions() : 
-    new ValidationOptions(presets.getPreset(presetName));
+  ValidationOptions options = null;
+  if (resetToDefault)
+  {
+    options = new ValidationOptions();
+  }
+  else if (presetName == null)
+  {
+    options = new ValidationOptions(presets.getDefault());
+  }
+  else
+  {
+    options = new ValidationOptions(presets.getPreset(presetName));
+  }
   Map<String, List<Validator>> validators = OverviewUtil.getValidators();
   %>
@@ -128 +139 @@
     var frm = document.forms['options'];
     var selected = frm.presets[frm.presets.selectedIndex].value;
-    if (selected != '---')
-    {
-      location.href = 'options.jsp?ID=<%=ID%>&presetName='+escape(selected);
+    if (selected == '')
+    {
+      location.href = 'options.jsp?ID=<%=ID%>&resetToDefault=1';
+    }
+    else if (selected != '---')
+    {
+      location.href = 'options.jsp?ID=<%=ID%>&presetName='+encodeURIComponent(selected);
     }
   }
@@ -208 +223 @@
             />&nbsp;<b><%=HTML.encodeTags(title)%></b></a>&nbsp;&nbsp;
           </td>
-          <td style="padding-top: 6px;">
+          <td style="padding-top: 6px;" colspan="3">
             <select name="setall.<%=grp%>" onchange="setAllOnChange(<%=grp%>, this)">
             <option value="">- set all in this group -
@@ -243 +258 @@
               image="<%=hasNext ? "joust/big/join.gif" : "joust/big/joinbottom.gif"%>" 
               /><%=HTML.encodeTags(validator.getTitle())%>&nbsp;&nbsp;</td>
-            <td>
+            <td colspan="3">
             <select id="select.<%=grp%>.<%=vld%>" name="<%=validatorId%>">
               <%
@@ -254 +269 @@
               %>
             </select>
+            <%
+            if (validator == Validator.NONMATCHING_SPOTCOUNT)
+            {
+              %>
+              Threshold:
+              <input type="text" class="text" 
+                name="threshold" 
+                title="Threshold, as a percentage or an absolute value" 
+                size="8"
+                value="<%=HTML.encodeTags(options.getOption(validator, "threshold", "5%"))%>" >
+              <%
+            }
+            %>
             </td>
           </tr>