Changeset 3538

Timestamp:

Jun 29, 2007, 2:30:48 PM (16 years ago)

Author:

Johan Enell

Message:

Fixes #660

Added permission delete for File and read for Job

File:

• branches/2.3.2/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (7 diffs)

branches/2.3.2/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -53 +53 @@
 import net.sf.basedb.core.PositionBatcher;
 import net.sf.basedb.core.ProgressReporter;
-import net.sf.basedb.core.Reporter;
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.SpotBatcher;
@@ -95 +94 @@
 import java.util.Collection;
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.EnumSet;
 import java.util.HashMap;
@@ -102 +102 @@
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -557 +558 @@
       permissions.add(new Permissions(Item.DIRECTORY, null, EnumSet.of(Permission.CREATE, Permission.WRITE)));
       permissions.add(new Permissions(Item.EXPERIMENT, null, EnumSet.of(Permission.WRITE)));
-      permissions.add(new Permissions(Item.FILE, EnumSet.of(Permission.USE), EnumSet.of(Permission.CREATE, Permission.WRITE)));
+      permissions.add(new Permissions(Item.FILE, EnumSet.of(Permission.DELETE), EnumSet.of(Permission.CREATE, Permission.WRITE)));
+      permissions.add(new Permissions(Item.JOB, EnumSet.of(Permission.READ), null));
       permissions.add(new Permissions(Item.PLUGINCONFIGURATION, EnumSet.of(Permission.WRITE), null));
       permissions.add(new Permissions(Item.RAWBIOASSAY, null, EnumSet.of(Permission.READ)));
@@ -743 +745 @@
       Boolean mergeReporters = (Boolean) configuration.getValue(geneAveragesParameter.getName());
       
-      Map<String, String> parameters = new HashMap<String, String>();
+      TreeMap<String, String> parameters = new TreeMap<String, String>(new Comparator<String>()
+      {
+        /**
+         * To make the keys orderd by the same order they are added
+         */
+        public int compare(String o1, String o2)
+        {
+          return 1;
+        }
+      });
       for (PluginParameter<?> pp : getJobParametersFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName()))))
       {
-        String name = pp.getName();
-        Object value = job.getValue(name);
-        parameters.put(name, value == null ? "" : value.toString());
+        if (pp != null)
+        {
+          String name = pp.getName();
+          Object value = job.getValue(name);
+          parameters.put(name, value == null ? "" : value.toString());
+        }
       }
       
@@ -861 +875 @@
     try
     {
-      List<PluginParameter<?>> p = new ArrayList<PluginParameter<?>>();
       String doctype = "<!DOCTYPE jobparameters SYSTEM \"base1-plugin-configuration-file.dtd\">";
       Document doc = XMLUtil.getValidatedXml(doctype+xml, dtdFile);
@@ -876 +889 @@
         }
       });
+      
+      TreeMap<Integer, PluginParameter<?>> positionParameter = new TreeMap<Integer, PluginParameter<?>>();
       while (it.hasNext())
       {
         Element e = it.next();
         JobParameter jp = new JobParameter(e);
-        p.add(jp.getPluginParameter());
-      }
-      return p;
+        if (positionParameter.containsKey(jp.getPosition()))
+        {
+          throw new BaseException("Duplicate parameter at position "+jp.getPosition());
+        }
+        positionParameter.put(jp.getPosition(), jp.getPluginParameter());
+      }
+      return new ArrayList<PluginParameter<?>>(positionParameter.values());
     }
     catch (JDOMException e1)