jsbml-svn Mailing List for JSBML (Page 12)

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Revision: 2238
          http://sourceforge.net/p/jsbml/code/2238
Author:   niko-rodrigue
Date:     2015-04-23 14:10:42 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
added a default load of the parsers for the two other methods that were missing it. Need to do a bit of cleanup and re-factoring once we checked that it worked + added the uncertml parser to the build files and ParserManager

Modified Paths:
--------------
    trunk/build.xml
    trunk/core/build.xml
    trunk/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java
    trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java

Removed Paths:
-------------
    trunk/core/resources/META-INF/services/org.sbml.jsbml.xml.parsers.ReadingParser

Modified: trunk/build.xml
===================================================================

--- trunk/build.xml	2015-04-23 13:21:16 UTC (rev 2237)
+++ trunk/build.xml	2015-04-23 14:10:42 UTC (rev 2238)
@@ -244,6 +244,7 @@
 				<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+				<provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
 			</service>
 
 		</jar>
@@ -313,6 +314,7 @@
 				<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+				<provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
 			</service>
 		</jar>
 	</target>

Modified: trunk/core/build.xml
===================================================================
--- trunk/core/build.xml	2015-04-23 13:21:16 UTC (rev 2237)
+++ trunk/core/build.xml	2015-04-23 14:10:42 UTC (rev 2238)
@@ -348,6 +348,7 @@
 				<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+				<provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
 			</service>
 		</jar>
 	</target>

Deleted: trunk/core/resources/META-INF/services/org.sbml.jsbml.xml.parsers.ReadingParser
===================================================================
--- trunk/core/resources/META-INF/services/org.sbml.jsbml.xml.parsers.ReadingParser	2015-04-23 13:21:16 UTC (rev 2237)
+++ trunk/core/resources/META-INF/services/org.sbml.jsbml.xml.parsers.ReadingParser	2015-04-23 14:10:42 UTC (rev 2238)
@@ -1,5 +0,0 @@
-# Generated by org.mangosdk.spi.processor.SpiProcessor (0.2.4)
-# Mon, 17 Mar 2014 11:36:19 +0000
-org.sbml.jsbml.xml.parsers.MathMLStaxParser
-org.sbml.jsbml.xml.parsers.SBMLCoreParser
-org.sbml.jsbml.xml.parsers.XMLNodeReader

Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java	2015-04-23 13:21:16 UTC (rev 2237)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java	2015-04-23 14:10:42 UTC (rev 2238)
@@ -68,6 +68,14 @@
    */
   private Logger logger = Logger.getLogger(ParserManager.class);
 
+  private String[] parserDefaults = {"org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader", 
+    "org.sbml.jsbml.xml.parsers.MathMLStaxParser", "org.sbml.jsbml.xml.parsers.ArraysParser", "org.sbml.jsbml.xml.parsers.CompParser",
+    "org.sbml.jsbml.xml.parsers.DistribParser", "org.sbml.jsbml.xml.parsers.DynParser", "org.sbml.jsbml.xml.parsers.FBCParser",
+    "org.sbml.jsbml.xml.parsers.GroupsParser", "org.sbml.jsbml.xml.parsers.L3LayoutParser", "org.sbml.jsbml.xml.parsers.LayoutParser",
+    "org.sbml.jsbml.xml.parsers.MultiParser", "org.sbml.jsbml.xml.parsers.QualParser", "org.sbml.jsbml.xml.parsers.RenderParser",
+    "org.sbml.jsbml.xml.parsers.ReqParser", "org.sbml.jsbml.xml.parsers.SpatialParser", "org.sbml.jsbml.xml.parsers.XMLNodeReader", "org.sbml.jsbml.xml.parsers.SBMLCoreParser"};
+
+
   /**
    * Private constructor to make sure that we have only one {@link ParserManager} per JVM.
    */
@@ -161,13 +169,6 @@
     // prevent problems when developers are not setting properly eclipse, when jar 
     // files are not generated with 
  
-    String[] parserDefaults = {"org.sbml.jsbml.xml.parsers.SBMLCoreParser", "org.sbml.jsbml.xml.parsers.XMLNodeReader", 
-     "org.sbml.jsbml.xml.parsers.MathMLStaxParser", "org.sbml.jsbml.xml.parsers.ArraysParser", "org.sbml.jsbml.xml.parsers.CompParser",
-     "org.sbml.jsbml.xml.parsers.DistribParser", "org.sbml.jsbml.xml.parsers.DynParser", "org.sbml.jsbml.xml.parsers.FBCParser",
-     "org.sbml.jsbml.xml.parsers.GroupsParser", "org.sbml.jsbml.xml.parsers.L3LayoutParser", "org.sbml.jsbml.xml.parsers.LayoutParser",
-     "org.sbml.jsbml.xml.parsers.MultiParser", "org.sbml.jsbml.xml.parsers.QualParser", "org.sbml.jsbml.xml.parsers.RenderParser",
-     "org.sbml.jsbml.xml.parsers.ReqParser", "org.sbml.jsbml.xml.parsers.SpatialParser"};
-
     for (String parserClassName  : parserDefaults) {
       if (! classNames.contains(parserClassName)) {
         System.out.println("###DEBUG### adding parser '" + parserClassName + "' by hand");
@@ -179,7 +180,6 @@
             ReadingParser readingParser = (ReadingParser) newInstance;
             
             String packageName = "core";
-            classNames.add(readingParser.getClass().getName());
             System.out.println("###DEBUG####; class name = " + readingParser.getClass().getName());
             
             if (readingParser instanceof PackageParser) {
@@ -197,12 +197,12 @@
               }
             }
           }
-          else if (newInstance instanceof WritingParser)
+          
+          if (newInstance instanceof WritingParser)
           {
             WritingParser writingParser = (WritingParser) newInstance;
 
             String packageName = "core";
-            classNames.add(writingParser.getClass().getName());
             System.out.println("###DEBUG####; writer class name = " + writingParser.getClass().getName());
 
             if (writingParser instanceof PackageParser) {
@@ -309,6 +309,7 @@
   public Map<String, ReadingParser> getReadingParsers() {
 
     Map<String, ReadingParser> clonedMap = new HashMap<String, ReadingParser>();
+    List<String> classNames = new ArrayList<String>();
 
     Iterator<ReadingParser> readingParserList = ServiceLoader.load(ReadingParser.class).iterator();
 
@@ -318,6 +319,8 @@
 
         if (readingParser != null) {
 
+          classNames.add(readingParser.getClass().getName());
+          
           for (String namespaceURI : readingParser.getNamespaces()) {
             clonedMap.put(namespaceURI, readingParser);
           }
@@ -327,7 +330,42 @@
         // No need to print the message again, it is printed once in the init() method
       }
     }
+    
+    for (String parserClassName  : parserDefaults) {
+      if (! classNames.contains(parserClassName)) {
+        System.out.println("###DEBUG### getReadingParsers - adding parser '" + parserClassName + "' by hand");
+        
+        try {
+          Object newInstance = Class.forName(parserClassName).newInstance();
+          
+          if (newInstance instanceof ReadingParser) {
+            ReadingParser readingParser = (ReadingParser) newInstance;
+            
+            System.out.println("###DEBUG#### getReadingParsers -  class name = " + readingParser.getClass().getName());
+            
+            for (String namespaceURI : readingParser.getNamespaces()) {
+              clonedMap.put(namespaceURI, readingParser);
+            }
+          }
+        } catch (ClassNotFoundException e) 
+        {
+          System.out.println("###DEBUG### problem loading class '" + parserClassName + "': " + e.getMessage());
+          // e.printStackTrace();
+        }
+        catch (InstantiationException e) 
+        {
+          System.out.println("###DEBUG### problem loading class '" + parserClassName + "': " + e.getMessage());
+          // e.printStackTrace();
+        }
+        catch (IllegalAccessException e) 
+        {
+          System.out.println("###DEBUG### problem loading class '" + parserClassName + "': " + e.getMessage());
+          // e.printStackTrace();
+        }
+      }
+    }
 
+
     return clonedMap;
   }
 
@@ -339,6 +377,7 @@
   public Map<String, WritingParser> getWritingParsers() {
 
     Map<String, WritingParser> clonedMap = new HashMap<String, WritingParser>();
+    List<String> classNames = new ArrayList<String>();
 
     Iterator<ReadingParser> readingParserList = ServiceLoader.load(ReadingParser.class).iterator();
 
@@ -348,6 +387,8 @@
 
         if (readingParser != null && readingParser instanceof WritingParser) {
 
+          classNames.add(readingParser.getClass().getName());
+
           for (String namespaceURI : readingParser.getNamespaces()) {
             clonedMap.put(namespaceURI, (WritingParser) readingParser);
           }
@@ -366,6 +407,8 @@
 
         if (writingParser != null) {
 
+          classNames.add(writingParser.getClass().getName());
+
           for (String namespaceURI : writingParser.getNamespaces()) {
             clonedMap.put(namespaceURI, writingParser);
           }
@@ -376,6 +419,39 @@
       }
     }
 
+    for (String parserClassName  : parserDefaults) {
+      if (! classNames.contains(parserClassName)) {
+        System.out.println("###DEBUG### getWritingParsers - adding parser '" + parserClassName + "' by hand");
+        
+        try {
+          Object newInstance = Class.forName(parserClassName).newInstance();
+          
+          if (newInstance instanceof WritingParser) {
+            WritingParser readingParser = (WritingParser) newInstance;
+            
+            System.out.println("###DEBUG#### getWritingParsers -  class name = " + readingParser.getClass().getName());
+            
+            for (String namespaceURI : readingParser.getNamespaces()) {
+              clonedMap.put(namespaceURI, readingParser);
+            }
+          }
+        } catch (ClassNotFoundException e) 
+        {
+          System.out.println("###DEBUG### problem loading class '" + parserClassName + "': " + e.getMessage());
+          // e.printStackTrace();
+        }
+        catch (InstantiationException e) 
+        {
+          System.out.println("###DEBUG### problem loading class '" + parserClassName + "': " + e.getMessage());
+          // e.printStackTrace();
+        }
+        catch (IllegalAccessException e) 
+        {
+          System.out.println("###DEBUG### problem loading class '" + parserClassName + "': " + e.getMessage());
+          // e.printStackTrace();
+        }
+      }
+    }
 
     return clonedMap;
   }

Modified: trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java	2015-04-23 13:21:16 UTC (rev 2237)
+++ trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java	2015-04-23 14:10:42 UTC (rev 2238)
@@ -692,7 +692,7 @@
         if (!characters.isWhiteSpace()) {
           isText = true; // the characters are not only 'white spaces'
         }
-        if ((sbmlElements.peek() instanceof XMLNode) || isInsideNotes || isInsideAnnotation) {
+        if ((!sbmlElements.isEmpty() && (sbmlElements.peek() instanceof XMLNode)) || isInsideNotes || isInsideAnnotation) {
           isText = true; // We want to keep the whitespace/formatting when reading html block
         }
 

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jsbml-svn Mailing List for JSBML (Page 12)

The Java library for working with the SBML format.

jsbml-svn — SVN commit notification list for the JSBML project.