Changeset 1520 for trunk

Timestamp:

02/09/10 18:26:36 (17 months ago)

Author:

Stephen Rankin

Message:

Added save results feature and single file checking (NXDL). Update of Javadocs. ref#236.

Location:

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate

Files:

• BulkLoadFilesFrame.java (modified) (4 diffs)
• CheckNexusFileType.java (modified) (6 diffs)
• FileActions.java (moved) (moved from trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/FileLoadingActions.java) (10 diffs)
• NXLoadFilesDialog.form (modified) (1 diff)
• NXLoadFilesDialog.java (modified) (6 diffs)
• NXNodeMapper.java (modified) (12 diffs)
• NXschematron.java (modified) (6 diffs)
• NXvalidate.java (modified) (1 diff)
• NXvalidateFrame.form (modified) (2 diffs)
• NXvalidateFrame.java (modified) (11 diffs)
• TextPaneStyle.java (modified) (2 diffs)
• ValidatorUtils.java (modified) (3 diffs)
• exceptions/NXvalidateException.java (modified) (1 diff)
• resources/nxvalidate.properties (modified) (1 diff)

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/BulkLoadFilesFrame.java

@@ -45 +45 @@
     private File nxdlFile = null;
     private ArrayList<String> dataFileList = null;
-    private FileLoadingActions fileLoadingActions = null;
+    private FileActions fileLoadingActions = null;
     private boolean badFiles = false;
     private ResourceBundle bundle = null;
     private ArrayList<String> dataFileSelectedList = null;
+    private CheckNexusFileType check = null;
 
     /** Creates new form BulkLoadFilesFrame */
-    public BulkLoadFilesFrame(FileLoadingActions fileLoadingActions) {
+    public BulkLoadFilesFrame(FileActions fileLoadingActions) {
         initComponents();
         this.fileLoadingActions = fileLoadingActions;
         bundle = ResourceBundle.getBundle(
                 "org/nexusformat/nxvalidate/resources/nxvalidate");
+        check = new CheckNexusFileType();
 
     }
@@ -63 +65 @@
         bundle = ResourceBundle.getBundle(
                 "org/nexusformat/nxvalidate/resources/nxvalidate");
+        check = new CheckNexusFileType();
     }
 
@@ -213 +216 @@
             if (returnVal == jFileChooser1.APPROVE_OPTION) {
                 nxdlFile = jFileChooser1.getSelectedFile();
-                nxdcFileNameTextField.setText(nxdlFile.getAbsolutePath());
-                nxdcFileNameTextField.setToolTipText(nxdlFile.getAbsolutePath());
+
+                if(check.checkNXDLFile(nxdlFile)){
+
+                    nxdcFileNameTextField.setText(nxdlFile.getAbsolutePath());
+                    nxdcFileNameTextField.setToolTipText(nxdlFile.getAbsolutePath());
+
+                } else{
+                    nxdlFile = null;
+                    problemOptionPane.showMessageDialog(this,
+                        bundle.getString("notNXDLFileMessage"));
+                }
+
+               
             } else {
                 nxdlFile = null;
@@ -253 +267 @@
 
     private void updateTable() throws FileNotFoundException, IOException {
-
-
-        CheckNexusFileType check = new CheckNexusFileType();
 
         DefaultTableModel tableModel = new DefaultTableModel(new Object[][]{

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/CheckNexusFileType.java

@@ -56 +56 @@
             builder = factory.newDocumentBuilder();
         } catch (ParserConfigurationException ex) {
-            Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.SEVERE, null, ex);
+            Logger.getLogger(CheckNexusFileType.class.getName()).log(
+                    Level.SEVERE, null, ex);
         }
     }
@@ -68 +69 @@
      * @throws IOException
      */
-    public boolean checkNexusFile(File file) throws FileNotFoundException, IOException {
-
-        if (checkHDF5(file)) {
-            return true;
-        } else if (checkHDF4(file)) {
-            return true;
-        } else if (checkNexusXML(file)) {
-            return true;
-        }
-
+    public boolean checkNexusFile(File file) {
+        try {
+            if (checkHDF5(file)) {
+                return true;
+            } else if (checkHDF4(file)) {
+                return true;
+            } else if (checkNexusXML(file)) {
+                return true;
+            }
+        } catch (FileNotFoundException ex) {
+            Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.SEVERE, null, ex);
+        } catch (IOException ex) {
+            Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.SEVERE, null, ex);
+        }
         return false;
-
     }
 
@@ -89 +93 @@
      * @throws IOException
      */
-    public boolean checkHDF5(File file) throws FileNotFoundException, IOException {
+    public boolean checkHDF5(File file) throws FileNotFoundException,
+                                               IOException {
 
         byte[] b = new byte[7];
@@ -121 +126 @@
      * @throws IOException
      */
-    public boolean checkHDF4(File file) throws FileNotFoundException, IOException {
+    public boolean checkHDF4(File file) throws FileNotFoundException,
+                                               IOException {
 
         byte[] b = new byte[4];
@@ -148 +154 @@
      * @throws IOException
      */
-    private boolean checkNexusXML(File file) throws FileNotFoundException, IOException {
+    private boolean checkNexusXML(File file) {
 
         boolean result = false;
@@ -186 +192 @@
 
     }
+
+    /**
+     * Checks to see if a file is a Nexus definition file and returns true if
+     * it is.
+     * @param file the input file to check.
+     * @return boolean which is true if the file is a Nexus definition file.
+     * @throws FileNotFoundException
+     * @throws IOException
+     */
+    public boolean checkNXDLFile(File file) {
+
+        boolean result = false;
+
+        try {
+            Document resultsDoc = builder.parse(file);
+            if (resultsDoc.getDocumentElement().getNodeName().equals("definition")) {
+                result = true;
+            }
+        } catch (SAXException ex) {
+            //Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.INFO,
+            //        "SAXException: " + file.getAbsolutePath(), ex);
+            return result;
+        } catch (MalformedByteSequenceException ex) {
+           // Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.INFO,
+            //        "MalformedByteSequenceException: " + file.getAbsolutePath(), ex);
+            return result;
+        } catch (ConnectException ex) {
+            //Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.INFO,
+            //        "ConnectException: " + file.getAbsolutePath(), ex);
+            return result;
+        } catch (MalformedURLException ex) {
+            //Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.INFO,
+            //        "MalformedURLException: " + file.getAbsolutePath(), ex);
+            return result;
+        } catch (FileNotFoundException ex) {
+            //Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.INFO,
+            //        "FileNotFoundException: " + file.getAbsolutePath(), ex);
+            return result;
+        } catch (IOException ex) {
+            //Logger.getLogger(CheckNexusFileType.class.getName()).log(Level.INFO,
+             //       "IOException: " + file.getAbsolutePath(), ex);
+            return result;
+        }
+
+        return result;
+
+    }
+
 }

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/FileActions.java

@@ -21 +21 @@
  * For further information, see <http://www.neutron.anl.gov/NeXus/>
  *
- * FileLoadingActions.java
+ * FileActions.java
  *
  */
@@ -27 +27 @@
 
 import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
 import java.util.ArrayList;
+import java.util.Enumeration;
 import java.util.ResourceBundle;
 import org.w3c.dom.Document;
@@ -44 +49 @@
  * @author Stephen Rankin
  */
-public class FileLoadingActions implements Runnable {
+public class FileActions implements Runnable {
 
     private File nxsFile = null;
@@ -51 +56 @@
     private File resultsFile = null;
     private File nxconvertFile = null;
+    private File saveDirectory = null;
     private DocumentBuilderFactory factory = null;
     private DocumentBuilder builder = null;
@@ -71 +77 @@
     private boolean isNotBulk = false;
 
-    public FileLoadingActions(NXvalidateFrame frame, JTree jTree,
+    public FileActions(NXvalidateFrame frame, JTree jTree,
             DocumentBuilder builder, NXReducedToTree domTree,
             NXNodeMapper root) {
@@ -134 +140 @@
     public void setDataFileList(ArrayList<String> dataFileList) {
         this.dataFileList = dataFileList;
+    }
+
+    public File getSaveDirectory() {
+        return saveDirectory;
+    }
+
+    public void setSaveDirectory(File saveDirectory) {
+        this.saveDirectory = saveDirectory;
     }
 
@@ -159 +173 @@
             //Do the validation.
             if (nxconvertFile != null) {
-                validator = new ValidatorUtils(nxconvertFile);
+                validator = new ValidatorUtils(nxsFile,nxconvertFile);
             } else {
                 dialogReportProblem.showMessageDialog(
@@ -232 +246 @@
         } catch (InterruptedException ex) {
             Logger.getLogger(
-                    NXvalidateFrame.class.getName()).log(Level.SEVERE,
+                    FileActions.class.getName()).log(Level.SEVERE,
                     null, ex);
         } catch (SAXException ex) {
             Logger.getLogger(
-                    NXvalidateFrame.class.getName()).log(Level.SEVERE,
+                    FileActions.class.getName()).log(Level.SEVERE,
                     null, ex);
         } catch (IOException ex) {
             Logger.getLogger(
-                    NXvalidateFrame.class.getName()).log(Level.SEVERE,
+                    FileActions.class.getName()).log(Level.SEVERE,
                     null, ex);
         }
@@ -316 +330 @@
         }
 
+    }
+
+    private void copy(File src, File dst) throws IOException {
+        InputStream in = new FileInputStream(src);
+        OutputStream out = new FileOutputStream(dst);
+
+        byte[] buf = new byte[1024];
+        int len;
+        while ((len = in.read(buf)) > 0) {
+            out.write(buf, 0, len);
+        }
+        in.close();
+        out.close();
+    }
+
+    public void saveResults(File directory){
+
+        NXNodeMapper tmpNode = null;
+        File tmpReduced = null;
+        File tmpResults = null;
+        Enumeration children = root.children();
+        
+        while(children.hasMoreElements()){
+
+            tmpNode = (NXNodeMapper)children.nextElement();
+            
+            if(tmpNode.getReducedFile()!=null){
+
+                tmpReduced = new File(directory.getAbsolutePath() +
+                        directory.separator + tmpNode.getReducedFile().getName());
+                tmpResults = new File(directory.getAbsolutePath() +
+                        directory.separator + tmpNode.getResultsFile().getName());
+                try{
+                    copy(tmpNode.getReducedFile(),tmpReduced);
+                    copy(tmpNode.getResultsFile(),tmpResults);
+                } catch (IOException ex) {
+                    Logger.getLogger(
+                    FileActions.class.getName()).log(Level.SEVERE, null, ex);
+                }
+            }
+        }
     }
 
@@ -336 +391 @@
         }else if (which == 5) {
             bulkValidate();
-        }
-
+        } else if (which == 6) {
+            saveResults(saveDirectory);
+        }
     }
 }

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/NXLoadFilesDialog.form

@@ -4 +4 @@
   <NonVisualComponents>
     <Component class="javax.swing.JFileChooser" name="jFileChooser1">
+    </Component>
+    <Component class="javax.swing.JOptionPane" name="messageOptionPane">
     </Component>
   </NonVisualComponents>

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/NXLoadFilesDialog.java

@@ -28 +28 @@
 
 import java.io.File;
+import java.util.ResourceBundle;
 
 /**
@@ -38 +39 @@
     private File nxdl = null;
     private boolean OKButtonUsed = false;
-
+    private CheckNexusFileType check = null;
+    private ResourceBundle bundle = null;
     /** Creates new form NXLoadFilesDialog */
     public NXLoadFilesDialog(java.awt.Frame parent, boolean modal) {
         super(parent, modal);
         initComponents();
+        check = new CheckNexusFileType();
+        bundle = ResourceBundle.getBundle(
+                "org/nexusformat/nxvalidate/resources/nxvalidate");
     }
 
@@ -55 +60 @@
 
         jFileChooser1 = new javax.swing.JFileChooser();
+        messageOptionPane = new javax.swing.JOptionPane();
         jPanel1 = new javax.swing.JPanel();
         nxsLabel = new javax.swing.JLabel();
@@ -172 +178 @@
             if (returnVal == jFileChooser1.APPROVE_OPTION) {
                 nxs = jFileChooser1.getSelectedFile();
-                nxsTextField.setText(nxs.getAbsolutePath());
-                nxsTextField.setToolTipText(nxs.getAbsolutePath());
+
+                if(check.checkNexusFile(nxs)){
+                    nxsTextField.setText(nxs.getAbsolutePath());
+                    nxsTextField.setToolTipText(nxs.getAbsolutePath());
+                } else{
+                    nxs = null;
+                    messageOptionPane.showMessageDialog(this,
+                        bundle.getString("notNXDLFileMessage"));
+                }
+
+                
             } else {
                 nxs = null;
@@ -189 +204 @@
             if (returnVal == jFileChooser1.APPROVE_OPTION) {
                 nxdl = jFileChooser1.getSelectedFile();
-                nxdcTextField.setText(nxdl.getAbsolutePath());
-                nxdcTextField.setToolTipText(nxdl.getAbsolutePath());
+
+                if(check.checkNXDLFile(nxdl)){
+                    nxdcTextField.setText(nxdl.getAbsolutePath());
+                    nxdcTextField.setToolTipText(nxdl.getAbsolutePath());
+                } else{
+                    nxdl = null;
+                    messageOptionPane.showMessageDialog(this,
+                        bundle.getString("notNXDLFileMessage"));
+                }
+                
+                
             } else {
                 nxdl = null;
@@ -247 +271 @@
     private javax.swing.JFileChooser jFileChooser1;
     private javax.swing.JPanel jPanel1;
+    private javax.swing.JOptionPane messageOptionPane;
     private javax.swing.JTextField nxdcTextField;
     private javax.swing.JLabel nxdlLabel;

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/NXNodeMapper.java

@@ -122 +122 @@
     /**
      * Set the flag that says that this node is a documents node i.e. one of the
-     * list of nodes directly under the root note that are the open NXS documents.
+     * list of nodes directly under the root node that are the open NXS documents.
      * @param isDocument a flag which is true if the node is a document node.
      */
@@ -218 +218 @@
     }
 
+    /**
+     * Initially the Nexus file is converted to a reduced (all data removed)
+     * XML document via the Nexus convert command. This method gets the
+     * W3C DOM document of the reduced XML file.
+     * @return the W3C DOM document of the reduced XML file.
+     */
     public Document getReducedDoc() {
         return reducedDoc;
     }
 
+    /**
+     * Initially the Nexus file is converted to a reduced (all data removed)
+     * XML document via the Nexus convert command. This method sets the
+     * W3C DOM document of the reduced XML file.
+     * @param reducedDoc the W3C DOM document of the reduced XML file.
+     */
     public void setReducedDoc(Document reducedDoc) {
         this.reducedDoc = reducedDoc;
     }
 
+    /**
+     * If a node in the reduced XML document fails one of the schematron tests
+     * then the node can be marked as a bad node with a boolean flag. The flag
+     * is set to true if the node failed one of the tests.
+     * @param badNode true if the node failed one of the schematron tests.
+     */
     public void setBadNode(boolean badNode) {
         this.badNode = badNode;
     }
 
+    /**
+     * If a node in the reduced XML document fails one of the schematron tests
+     * then the node can be marked as a bad node with a boolean flag. The flag
+     * is set to true if the node failed one of the tests.
+     * @return true if the node failed one of the schematron tests.
+     */
     public boolean getBadNode() {
         return badNode;
     }
 
+    /**
+     * Get the W3C DOM node corresponding to this tree node.
+     * @return the W3C DOM node corresponding to this tree node.
+     */
     public Node getDomNode() {
         return domNode;
     }
 
+    /**
+     * A convenience method to force the checking if a node is bad
+     * (failed schematron tests). Sets the flag to indicate the node is bad.
+     */
     public void checkBadNode() {
         if (!isRoot) {
@@ -247 +279 @@
     }
 
+    /**
+     * Resets the various properties of a node, i.e flag to indicate that it
+     * is a bad node, the text for the tests that failed etc.
+     */
     public void resetNode() {
 
         badNode = false;
-
         domNode.setUserData("texts", null, null);
         domNode.setUserData("tests", null, null);
@@ -258 +293 @@
     }
 
+    /**
+     * This is a list of text strings which correspond to the error message
+     * results of the schematron tests.
+     * @return list of text strings corresponding to the schematron test results.
+     */
     public ArrayList<String> getNodeTexts() {
         if (!isRoot) {
@@ -266 +306 @@
     }
 
+    /**
+     * This is a list of text strings which correspond to the schematron
+     * test descriptions.
+     * @return list of text strings corresponding to the schematron test
+     *         descriptions.
+     */
     public ArrayList<String> getNodeTests() {
         if (!isRoot) {
@@ -274 +320 @@
     }
 
+    /**
+     * This is a list of text strings which correspond to the schematron
+     * diagnostic errors.
+     * @return list of text strings corresponding to the schematron
+     *         diagnostic errors.
+     */
     public ArrayList<String> getNodeDiags() {
         if (!isRoot) {
@@ -378 +430 @@
             return root;
 
-        } else if(domNode.getParentNode()!=null ){
-
-            if(domNode.getParentNode().getNodeType() == domNode.DOCUMENT_NODE){
-
-                Document doc = (Document)domNode.getParentNode();
+        } else if (domNode.getParentNode() != null) {
+
+            if (domNode.getParentNode().getNodeType() == domNode.DOCUMENT_NODE) {
+
+                Document doc = (Document) domNode.getParentNode();
 
                 return new NXNodeMapper(domNode.getParentNode(), true,
-                    ((File)doc.getUserData("file")).getAbsolutePath());
-
-            } else{
+                        ((File) doc.getUserData("file")).getAbsolutePath());
+
+            } else {
 
                 return new NXNodeMapper(domNode.getParentNode(), false,
-                    domNode.getParentNode().getNodeName());
-            }
-        }else{
-                return null;
-        }
-        
-    }
-
+                        domNode.getParentNode().getNodeName());
+            }
+        } else {
+            return null;
+        }
+
+    }
+
+    /**
+     * Each node of the reduced XML document may have attributes associated
+     * with it, this method provides a list of the attributes. Each string
+     * contains the attribute name and the value.
+     * @return a list of the attributes and their values.
+     */
     public String[] getAttributeList() {
 
@@ -412 +470 @@
 
             for (int i = 0; i < na; ++i) {
-                atts.add(att.item(i).getNodeName() + " = " + att.item(i).getNodeValue());
+                atts.add(att.item(i).getNodeName() + " = " +
+                         att.item(i).getNodeValue());
             }
 
@@ -419 +478 @@
     }
 
+    /**
+     * Each node of the reduced XML document may have a value associated with it.
+     * This method returns that value as a string.
+     * @return the value of the XML node.
+     */
     public String getValue() {
 
@@ -445 +509 @@
 
             if (node.getNodeType() == ELEMENT_TYPE) {
-
                 nodes.add(node);
                 ++childCount;
@@ -469 +532 @@
     }
 
+    /**
+     * Returns a list of nodes that represent the Nexus documents that are open
+     * i.e. that have been reduced.
+     * @return a list of Nexus document nodes.
+     */
     public ArrayList<NXNodeMapper> getOpenNodes() {
         return documents;
     }
 
+     /**
+     * Removes the list of nodes that represent the Nexus documents that are
+     * open i.e. that have been reduced.
+     */
     public void removeAllNodes() {
         documents.clear();
     }
 
+    /**
+     * A class that represents the child nodes of a node from a
+     * reduced document. The child nodes are represented as an enumeration.
+     */
     private class children implements Enumeration {
 
@@ -482 +558 @@
         private boolean more = true;
         private Node node = null;
+        private NXNodeMapper nxNode = null;
 
         public boolean hasMoreElements() {
-            
-            if (count < children.size()) {
-                more = true;
+
+            if (isRoot) {
+
+                if (documents == null) {
+                    more = false;
+                    return more;
+                }
+
+                if (count < documents.size()) {
+                    more = true;
+                } else {
+                    more = false;
+                }
             } else {
-                more = false;
-            }
-
+
+                if (children == null) {
+                    more = false;
+                    return more;
+                }
+
+                if (count < children.size()) {
+                    more = true;
+                } else {
+                    more = false;
+                }
+
+            }
             return more;
         }
 
         public Object nextElement() {
-            
-            if (count < children.size()) {
-                node = children.get(count);
-                count++;
-                return new NXNodeMapper(node, false, node.getNodeName());
-            } else {
-                throw new NoSuchElementException();
-            }
-
+
+            if (isRoot) {
+
+                if (count < documents.size()) {
+                    nxNode = documents.get(count);
+                    count++;
+                    return nxNode;
+                } else {
+                    throw new NoSuchElementException();
+                }
+                
+            } else{
+
+                if (count < children.size()) {
+                    node = children.get(count);
+                    count++;
+                    return new NXNodeMapper(node, false, node.getNodeName());
+                } else {
+                    throw new NoSuchElementException();
+                }
+
+            }
         }
     }

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/NXschematron.java

@@ -44 +44 @@
     private File reducedNeXusFile;
     private File schematronFile;
+    private File inputNexusFile;
     private boolean keepTemp;
     private InputStream dsdlIncludeXSLTStream = null;
@@ -52 +53 @@
     //    "iso_abstract_expand.xsl", "iso_svrl_for_xslt2.xsl"};
 
-    public NXschematron(File reducedNeXusFile, File schematronFile,
+    public NXschematron(File inputNexusFile, File reducedNeXusFile, File schematronFile,
             final boolean keepTemp) {
 
         this.reducedNeXusFile = reducedNeXusFile;
         this.schematronFile = schematronFile;
+        this.inputNexusFile = inputNexusFile;
         this.keepTemp = keepTemp;
 
@@ -77 +79 @@
 
     /**
-     * Transform an XML file to somthing else given ans XSLT transformation.
+     * Transform an XML file to something else given an XSLT transformation.
      * @param inputFilename the XML input file name.
      * @param xslFilename the xslt file name.
@@ -92 +94 @@
 
     /**
-     * Transform an XML file to somthing else given ans XSLT transformation.
+     * Transform an XML file to something else given an XSLT transformation.
      * @param inputFile the XML input file
      * @param xslFile the xslt file.
@@ -178 +180 @@
 
         // Now lets validate the actual reduced file.
-        File resultsFile = File.createTempFile("result", ".xml");
+        //File resultsFile = File.createTempFile(inputNexusFile.getName() + ".result", ".xml");
+
+        //File resultsFile = File.createTempFile(inputNexusFile.getName(). + ".result", ".xml");
+
+        File resultsFile = new File(reducedNeXusFile.getName().replaceAll(".reduced", "") + ".result");
 
         if (!this.keepTemp) {
@@ -192 +198 @@
 
     public static void main(String[] args) {
-        if (args.length != 2) {
-            System.out.println("Must specify two input files");
+        if (args.length != 3) {
+            System.out.println("Must specify three input files");
             return;
         }
         try {
-            NXschematron sch = new NXschematron(
-                    new File(args[0]), new File(args[1]), false);
+            NXschematron sch = new NXschematron(new File(args[0]),
+                    new File(args[1]), new File(args[2]), false);
             File results = sch.validate();
             System.out.println(results.getAbsolutePath());

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/NXvalidate.java

@@ -191 +191 @@
             
             // create the validation setup
-            NXschematron schematron = new NXschematron(reduced,
+            NXschematron schematron = new NXschematron(file,reduced,
                     schematronFile, keepTemp);
 

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/NXvalidateFrame.form

@@ -21 +21 @@
       </SubComponents>
     </Container>
+    <Component class="javax.swing.JFileChooser" name="jFileChooser1">
+    </Component>
     <Menu class="javax.swing.JMenuBar" name="jMenuBar1">
       <SubComponents>
@@ -42 +44 @@
             </MenuItem>
             <MenuItem class="javax.swing.JPopupMenu$Separator" name="jSeparator4">
+            </MenuItem>
+            <MenuItem class="javax.swing.JMenuItem" name="saveMenuItem">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Save Results"/>
+                <Property name="toolTipText" type="java.lang.String" value="Save results to files."/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="saveMenuItemActionPerformed"/>
+              </Events>
+            </MenuItem>
+            <MenuItem class="javax.swing.JPopupMenu$Separator" name="jSeparator7">
             </MenuItem>
             <MenuItem class="javax.swing.JMenuItem" name="closeAllMenuItem">

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/NXvalidateFrame.java

@@ -64 +64 @@
     private UserSettings settings = null;
     private File nxconvertFile = null;
+    private File saveDirectory = null;
     private boolean foundNXconvert = false;
     private MouseListener popupListener = null;
     private TextPaneStyle txtStyle = null;
-    private FileLoadingActions fileLoadingActions = null;
+    private FileActions fileLoadingActions = null;
 
     /** Creates new form NXvalidateFrame */
@@ -130 +131 @@
         txtStyle = new TextPaneStyle(jTextPane1);
 
-        fileLoadingActions = new FileLoadingActions(this, jTree1, builder, domTree, root);
+        fileLoadingActions = new FileActions(this, jTree1, builder, domTree, root);
 
     }
@@ -146 +147 @@
         treePopupMenu = new javax.swing.JPopupMenu();
         closeFileMenuItem = new javax.swing.JMenuItem();
+        jFileChooser1 = new javax.swing.JFileChooser();
         jPanel2 = new javax.swing.JPanel();
         jSplitPane1 = new javax.swing.JSplitPane();
@@ -156 +158 @@
         openFilesMenuItem = new javax.swing.JMenuItem();
         jSeparator4 = new javax.swing.JPopupMenu.Separator();
+        saveMenuItem = new javax.swing.JMenuItem();
+        jSeparator7 = new javax.swing.JPopupMenu.Separator();
         closeAllMenuItem = new javax.swing.JMenuItem();
         jSeparator5 = new javax.swing.JPopupMenu.Separator();
@@ -231 +235 @@
         fileMenu.add(jSeparator4);
 
+        saveMenuItem.setText("Save Results");
+        saveMenuItem.setToolTipText("Save results to files.");
+        saveMenuItem.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                saveMenuItemActionPerformed(evt);
+            }
+        });
+        fileMenu.add(saveMenuItem);
+        fileMenu.add(jSeparator7);
+
         closeAllMenuItem.setText("Close All Files");
         closeAllMenuItem.addActionListener(new java.awt.event.ActionListener() {
@@ -321 +335 @@
 
     private boolean loadOpenFilesDialog() {
+
+        NXLoadFilesDialog loadFile = new NXLoadFilesDialog(this, true);
+        loadFile.setModalityType(ModalityType.APPLICATION_MODAL);
+        loadFile.setVisible(true);
+        nxsFile = loadFile.getNXSFile();
+        nxdlFile = loadFile.getNXDLFile();
+        return loadFile.OKButtonUsed();
+
+    }
+
+    private boolean saveResultsFilesDialog() {
 
         NXLoadFilesDialog loadFile = new NXLoadFilesDialog(this, true);
@@ -461 +486 @@
                     dialogReportProblem.showMessageDialog(this,
                             bundle.getString("openSchemaFileMessage"));
-
-                    
                 }
             }
@@ -511 +534 @@
     private void exitAppMenuItemActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_exitAppMenuItemActionPerformed
         if (evt.getSource() == exitAppMenuItem) {
-
             this.dispose();
-
         }
     }//GEN-LAST:event_exitAppMenuItemActionPerformed
@@ -550 +571 @@
 
         if (evt.getSource() == filterMenuItem) {
-
             treeUtils.hideGoodNodes(jTree1);
-
         }
 
     }//GEN-LAST:event_filterMenuItemActionPerformed
+
+    private void saveMenuItemActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_saveMenuItemActionPerformed
+       if (evt.getSource() == saveMenuItem) {
+
+            jFileChooser1.setMultiSelectionEnabled(false);
+            jFileChooser1.setFileSelectionMode(jFileChooser1.DIRECTORIES_ONLY);
+            jFileChooser1.setApproveButtonText("Save");
+            int returnVal = jFileChooser1.showOpenDialog(this);
+
+            if (returnVal == jFileChooser1.APPROVE_OPTION) {
+
+                saveDirectory = jFileChooser1.getSelectedFile();
+
+                if(!saveDirectory.exists()){
+                    saveDirectory.mkdir();
+                }
+
+                fileLoadingActions.setSaveDirectory(saveDirectory);
+                fileLoadingActions.setWhich(6);
+                Thread thread = new Thread(fileLoadingActions);
+                thread.start();
+
+                dialogReportProblem.showMessageDialog(
+                    this,
+                    bundle.getString("savedResultsMessage"));
+
+            } else {
+                saveDirectory = null;
+            }
+
+        }
+    }//GEN-LAST:event_saveMenuItemActionPerformed
 
     /**
@@ -581 +632 @@
     private javax.swing.JMenu helpMenu;
     private javax.swing.JMenuItem helpMenuItem;
+    private javax.swing.JFileChooser jFileChooser1;
     private javax.swing.JMenuBar jMenuBar1;
     private javax.swing.JPanel jPanel2;
@@ -591 +643 @@
     private javax.swing.JPopupMenu.Separator jSeparator5;
     private javax.swing.JPopupMenu.Separator jSeparator6;
+    private javax.swing.JPopupMenu.Separator jSeparator7;
     private javax.swing.JSplitPane jSplitPane1;
     private javax.swing.JTextPane jTextPane1;
     private javax.swing.JTree jTree1;
     private javax.swing.JMenuItem openFilesMenuItem;
+    private javax.swing.JMenuItem saveMenuItem;
     private javax.swing.JMenuItem settingsMenuItem;
     private javax.swing.JMenu toolsMenu;

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/TextPaneStyle.java

@@ -130 +130 @@
             if (node.getNodeTexts() != null) {
 
-                for (int i = 0; i
-                        < node.getNodeTexts().size();
-                        ++i) {
+                for (int i = 0; i < node.getNodeTexts().size(); ++i) {
                     doc.insertString(doc.getLength(),
                             node.getNodeTexts().get(i), doc.getStyle("error"));
@@ -138 +136 @@
                     doc.insertString(doc.getLength(), newline + newline,
                             doc.getStyle("heading"));
-
-
                 }
 

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/ValidatorUtils.java

@@ -44 +44 @@
     private File nxconvertFile = null;
 
-    public ValidatorUtils(File nxconvertFile) {
+
+    public ValidatorUtils(File nxsFile, File nxconvertFile) {
 
         this.nxconvertFile = nxconvertFile;
-
+        this.nxsFile = nxsFile;
     }
 
@@ -157 +158 @@
 
             // create the validation setup
-            NXschematron schematron = new NXschematron(reduced,
+            NXschematron schematron = new NXschematron(nxsFile, reduced,
                     schematronFile, keepTemp);
 
@@ -165 +166 @@
                 Logger.getLogger(ValidatorUtils.class.getName()).log(Level.SEVERE,
                         "While creating validation report");
-                throw new NXvalidateException("While creating validation report");
+                throw new NXvalidateException("While creating validation report", e);
             }
         }

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/exceptions/NXvalidateException.java

@@ -47 +47 @@
         super(msg);
     }
+
+    public NXvalidateException(String msg, Throwable cause) {
+        super(msg,cause);
+    }
+
+    public NXvalidateException(Throwable cause) {
+        super(cause);
+    }
+
 }

trunk/applications/NXvalidate/src/org/nexusformat/nxvalidate/resources/nxvalidate.properties

@@ -22 +22 @@
 closeAllWarningMessage=Are you sure you want to close all files?
 filesNotNexusError=Some files have been detected as not being Nexus/HDF files and have been unchecked in the include column.
+savedResultsMessage=Results have been saved.
+notNXDLFileMessage=File is not a NXDL file, please select a NXDL file.
+notNexusFileMessage=File is not a Nexus file, please select a Nexus file.