Changeset 4362

Timestamp:

Jul 1, 2008, 4:30:32 PM (15 years ago)

Author:

Jari Häkkinen

Message:

Fixes #1074.

File:

• branches/2.7-stable/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (7 diffs)

branches/2.7-stable/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -127 +127 @@
 import java.util.TreeMap;
 import java.util.regex.Pattern;
+import java.util.regex.Matcher;
 
 /**
@@ -843 +844 @@
       Boolean mergeReporters = (Boolean) configuration.getValue(geneAveragesParameter.getName());
       
+      TreeMap<String, JobParameter> base1parametertype = getJobParameterObjectsFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName())), true);
       ListMap<String, String> parameters = new ListMap<String, String>();
       for (PluginParameter<?> pp : getJobParametersFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName())), true))
@@ -848 +850 @@
         String name = pp.getName();
         Object value = job.getValue(name);
-        parameters.put(name, value == null ? "" : value.toString());
+        String valueString = (value == null) ? "" : value.toString();
+        JobParameter jp=base1parametertype.get(name);
+        // replacing line breaks for Base1 TEXT and STRING types
+        if (jp.getType() == Base1JobParameterType.STRING ||
+            jp.getType() == Base1JobParameterType.TEXT)
+        {
+          Pattern p=Pattern.compile("\r");
+          Matcher m=p.matcher(valueString);
+          valueString = m.replaceAll("\\\\r");
+          m.usePattern(Pattern.compile("\n"));
+          m.reset(valueString);
+          valueString = m.replaceAll("\\\\n");
+        }
+        parameters.put(name, valueString);
       }
       
@@ -1010 +1025 @@
     return headers;
   }
-  
-  
+
+
   @SuppressWarnings({ "unchecked", "serial" })
-  private List<PluginParameter<?>> getJobParametersFromXML(String xml, boolean hideRemoved)
+  private TreeMap<String, JobParameter>
+    getJobParameterObjectsFromXML(String xml, boolean hideRemoved)
   {
     try
@@ -1031 +1047 @@
         }
       });
-      
-      TreeMap<Integer, PluginParameter<?>> positionParameter = new TreeMap<Integer, PluginParameter<?>>();
+
+      TreeMap<String, JobParameter> pars= new TreeMap<String, JobParameter>();
       while (it.hasNext())
       {
@@ -1039 +1055 @@
         if (!jp.isRemoved())
         {
+          if (pars.containsKey(jp.getName()))
+          {
+            throw new BaseException("Duplicate parameter at position "+jp.getPosition());
+          }
+          pars.put(jp.getName(), jp);
+        }
+      }
+      return pars;
+    }
+    catch (JDOMException e1)
+    {
+      throw new BaseException(e1.getCause());
+    }
+    catch (IOException e1)
+    {
+      throw new BaseException(e1);
+    }
+  }
+
+
+  @SuppressWarnings({ "unchecked", "serial" })
+  private List<PluginParameter<?>> getJobParametersFromXML(String xml, boolean hideRemoved)
+  {
+    try
+    {
+      String doctype = "<!DOCTYPE jobparameters SYSTEM \"base1-plugin-configuration-file.dtd\">";
+      Document doc = XMLUtil.getValidatedXml(doctype+xml, dtdFile);
+      Iterator<Element> it = doc.getDescendants(new Filter()
+      {
+        public boolean matches(Object o)
+        {
+          if (o instanceof Element)
+          {
+            Element e = (Element) o;
+            return e.getName().equals("parameter");
+          }
+          return false;
+        }
+      });
+      
+      TreeMap<Integer, PluginParameter<?>> positionParameter = new TreeMap<Integer, PluginParameter<?>>();
+      while (it.hasNext())
+      {
+        Element e = it.next();
+        JobParameter jp = new JobParameter(e);
+        if (!jp.isRemoved())
+        {
           if (positionParameter.containsKey(jp.getPosition()))
           {
@@ -1057 +1120 @@
     }
   }
-  
-  
+
+
   /**
     Creates a boolean from a string.