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Revision 407

Added by Matt Jones over 24 years ago

Folded the functionality from DBWriter into DocumentImpl, continuing the
work started earlir to create a more DOM-like model for the classes, in
which a single DocumentImpl class handles both reading and writing of
documents to the database. Modified shell scripts and MetaCatServlet to
reflect these changes, and removed DBWriter.java.

Work still needs to be done on simplifying the algorith by which a Document
is created, which is currently convoluted. Will check that work in soon.

     /**
      *  '$RCSfile$'
      *    Purpose: A Class that reads in an XML text document and
      *             write its contents to a database connection using SAX
      *  Copyright: 2000 Regents of the University of California and the
      *             National Center for Ecological Analysis and Synthesis
      *    Authors: Matt Jones
      *    Release: @release@
+     *
      *   '$Author$'
      *     '$Date$'
      * '$Revision$'
      */
     package edu.ucsb.nceas.metacat;
     import java.io.*;
     import java.sql.*;
     import java.util.Stack;
     import org.xml.sax.AttributeList;
     import org.xml.sax.ContentHandler;
     import org.xml.sax.DTDHandler;
     import org.xml.sax.EntityResolver;
     import org.xml.sax.ErrorHandler;
     import org.xml.sax.InputSource;
     import org.xml.sax.XMLReader;
     import org.xml.sax.SAXException;
     import org.xml.sax.SAXParseException;
     import org.xml.sax.helpers.XMLReaderFactory;
     /**
      * A Class that reads in an XML text document and
      * write its contents to a database connection using SAX
      */
     public class DBWriter {
       private Connection	conn = null;
       private String parserName = null;
       /**
        * the main routine used to test the DBWriter utility.
        * <p>
        * Usage: java DBWriter <-f filename -a action -d docid>
+       *
        * @param filename the filename to be loaded into the database
        */
       static public void main(String[] args) {
         try {
           String filename = null;
           String action   = null;
           String docid    = null;
           for ( int i=0 ; i < args.length; ++i ) {
             if ( args[i].equals( "-f" ) ) {
               filename =  args[++i];
             } else if ( args[i].equals( "-a" ) ) {
               action =  args[++i];
             } else if ( args[i].equals( "-d" ) ) {
               docid =  args[++i];
             } else {
               System.err.println
                 ( "   args[" +i+ "] '" +args[i]+ "' ignored." );
+            }
+          }
           boolean argsAreValid = false;
           if (action != null) {
             if (action.equals("INSERT")) {
               if (filename != null) {
                 argsAreValid = true;
+              }
             } else if (action.equals("UPDATE")) {
               if ((filename != null) && (docid != null)) {
                 argsAreValid = true;
+              }
             } else if (action.equals("DELETE")) {
               if (docid != null) {
                 argsAreValid = true;
+              }
+            }
+          }
           if (!argsAreValid) {
             System.err.println("Wrong number of arguments!!!");
             System.err.println(
                   "USAGE: java DBWriter <-f filename -a action -d docid>");
             return;
+          }
           // Open a connection to the database
           MetaCatUtil   util = new MetaCatUtil();
           Connection dbconn = util.openDBConnection();
           DBWriter dbw = new DBWriter(dbconn, util.getOption("saxparser"));
           if (action.equals("DELETE")) {
             dbw.delete(docid);
             System.out.println("Document deleted: " + docid);
           } else {
             String newdocid = dbw.write(filename, action, docid);
             if ((docid != null) && (!docid.equals(newdocid))) {
               if (action.equals("INSERT")) {
                 System.out.println("New document ID generated!!! ");
               } else if (action.equals("UPDATE")) {
                 System.out.println("ERROR: Couldn't update document!!! ");
+              }
             } else if ((docid == null) && (action.equals("UPDATE"))) {
                 System.out.println("ERROR: Couldn't update document!!! ");
+            }
             System.out.println("Document processing finished for: " + filename
                   + " (" + newdocid + ")");
+          }
         } catch (AccessionNumberException ane) {
           System.out.println("ERROR: Couldn't delete document!!! ");
           System.out.println(ane.getMessage());
         } catch (Exception e) {
           System.err.println("EXCEPTION HANDLING REQUIRED");
           System.err.println(e.getMessage());
           e.printStackTrace(System.err);
+        }
+      }
       /**
        * construct a new instance of the class to write an XML file to the database
+       *
        * @param conn the database connection to which to write the XML file
        * @param parserName the name of a SAX2 compliant parser class
        */
       public DBWriter(Connection conn, String parserName) {
         this.conn = conn;
         this.parserName = parserName;
+      }
       /**
        * Insert XML stream to the database
+       *
        * @param xml the xml stream to be loaded into the database
        */
       public String write( Reader xml, String action, String docid )
                     throws Exception, IOException, SQLException,
                            ClassNotFoundException, SAXException, SAXParseException {
         try {
             XMLReader parser = initializeParser(action, docid);
             conn.setAutoCommit(false);
             parser.parse(new InputSource(xml));
             conn.commit();
             conn.setAutoCommit(true);
             return docid;
           } catch (SAXParseException e) {
             conn.rollback();
             throw e;
           } catch (SAXException e) {
             // If its a problem with the accession number its ok, just the
             // accession number was regenerated
             AccessionNumberGeneratedException ang = null;
             try {
               Exception embedded = e.getException();
               if ((embedded != null) &&
                   (embedded instanceof AccessionNumberGeneratedException)) {
                 ang = (AccessionNumberGeneratedException)e.getException();
+              }
             } catch (ClassCastException cce) {
               // Do nothing and just fall through to the ang != null test
+            }
             if (ang != null) {
               conn.commit();
               conn.setAutoCommit(true);
               return (ang.getMessage());
             } else {
               conn.rollback();
               throw e;
+            }
           } catch (Exception e) {
             conn.rollback();
             throw e;
+          }
+      }
       /**
        * Insert an XML file to the database
+       *
        * @param filename the filename to be loaded into the database
        */
       public String write( String filename, String action, String docid )
                     throws Exception, IOException, SQLException,
                            ClassNotFoundException, SAXException, SAXParseException {
          return write(new FileReader(new File(filename).toString()), action, docid);
+      }
       private XMLReader initializeParser(String action, String docid) {
         XMLReader parser = null;
         //
         // Set up the SAX document handlers for parsing
         //
         try {
           ContentHandler chandler   = new DBSAXHandler(conn, action, docid);
           EntityResolver dbresolver = new DBEntityResolver(conn,
                                           (DBSAXHandler)chandler);
           DTDHandler dtdhandler     = new DBDTDHandler(conn);
           // Get an instance of the parser
           parser = XMLReaderFactory.createXMLReader(parserName);
           // Turn off validation
           parser.setFeature("http://xml.org/sax/features/validation", false);
           // Set Handlers in the parser
           parser.setProperty("http://xml.org/sax/properties/declaration-handler",
                              chandler);
           parser.setProperty("http://xml.org/sax/properties/lexical-handler",
                              chandler);
           parser.setContentHandler((ContentHandler)chandler);
           parser.setEntityResolver((EntityResolver)dbresolver);
           parser.setDTDHandler((DTDHandler)dtdhandler);
           parser.setErrorHandler((ErrorHandler)chandler);
         } catch (Exception e) {
            System.err.println(e.toString());
+        }
         return parser;
+      }
       /**
        * Delete an XML file from the database (actually, just make it a revision
        * in the xml_revisions table)
+       *
        * @param docid the ID of the document to be deleted from the database
        */
       public void delete( String docid )
                       throws IOException, SQLException,
                              ClassNotFoundException, AccessionNumberException {
         String newdocid = AccessionNumber.generate(docid, "DELETE");
         conn.setAutoCommit(false);
         // Copy the record to the xml_revisions table
         DocumentImpl document = new DocumentImpl(conn);
         document.saveDocument( docid );
         // Now delete it from the xml_documents table
         Statement stmt = conn.createStatement();
         stmt.execute("DELETE FROM xml_index WHERE docid LIKE '" + docid + "'");
         stmt.execute("DELETE FROM xml_documents WHERE docid LIKE '" + docid + "'");
         stmt.close();
         conn.commit();
+      }
+    }

     import java.io.PrintWriter;
     import java.util.TreeSet;
     import java.io.*;
     import java.util.Stack;
     import org.xml.sax.AttributeList;
     import org.xml.sax.ContentHandler;
     import org.xml.sax.DTDHandler;
     import org.xml.sax.EntityResolver;
     import org.xml.sax.ErrorHandler;
     import org.xml.sax.InputSource;
     import org.xml.sax.XMLReader;
     import org.xml.sax.SAXException;
     import org.xml.sax.SAXParseException;
     import org.xml.sax.helpers.XMLReaderFactory;
     /**
      * A class that represents an XML document. It can be created with a simple
      * document identifier from a database connection.
      * document identifier from a database connection.  It also will write an
      * XML text document to a database connection using SAX.
      */
     public class DocumentImpl {
       private Connection conn = null;
       private MetaCatUtil util = null;
       private String docid = null;
       private String docname = null;
       private String doctype = null;
-...
       private long rootnodeid;
       private ElementNode rootNode = null;
       private String doctitle = null;
       private String parserName = null;
       /**
        * Constructor, creates document from database connection, used
-...
         this.docid = docid;
         writeDocumentToDB(action);
+      }
       /**
        * Construct a new document instance, used for deleting documents
+       *
-...
       public DocumentImpl (Connection conn)
+      {
         this.conn = conn;
         this.util = new MetaCatUtil();
         this.parserName = util.getOption("saxparser");
+      }
       /**
-...
+      }
       /**
        * main routine used for testing.
        * <p>
        * Usage: java DocumentImpl <docid>
        * Write an XML file to the database, given a filename
+       *
        * @param docid the id number of the document to display
        * @param filename the filename to be loaded into the database
        * @param action the action to be performed (INSERT OR UPDATE)
        * @param docid the docid to use for the INSERT OR UPDATE
        */
       static public void main(String[] args) {
          if (args.length < 1)
+         {
             System.err.println("Wrong number of arguments!!!");
             System.err.println("USAGE: java DocumentImpl <docid>");
             return;
          } else {
       public String write( String filename, String action, String docid )
                     throws Exception, IOException, SQLException,
                            ClassNotFoundException, SAXException, SAXParseException {
          return write(new FileReader(new File(filename).toString()), action, docid);
+      }
       /**
        * Write an XML file to the database, given a Reader
+       *
        * @param xml the xml stream to be loaded into the database
        * @param action the action to be performed (INSERT OR UPDATE)
        * @param docid the docid to use for the INSERT OR UPDATE
        */
       public String write( Reader xml, String action, String docid )
                     throws Exception, IOException, SQLException,
                            ClassNotFoundException, SAXException, SAXParseException {
         try {
             XMLReader parser = initializeParser(action, docid);
             conn.setAutoCommit(false);
             parser.parse(new InputSource(xml));
             conn.commit();
             conn.setAutoCommit(true);
             return docid;
           } catch (SAXParseException e) {
             conn.rollback();
             throw e;
           } catch (SAXException e) {
             // If its a problem with the accession number its ok, just the
             // accession number was regenerated
             AccessionNumberGeneratedException ang = null;
             try {
               String docid = args[0];
               // Open a connection to the database
               MetaCatUtil   util = new MetaCatUtil();
               Connection dbconn = util.openDBConnection();
               DocumentImpl xmldoc = new DocumentImpl( dbconn, docid );
               System.out.println(xmldoc.toString());
             } catch (McdbException me) {
               me.toXml(new PrintWriter(System.err));
             } catch (Exception e) {
               System.err.println("EXCEPTION HANDLING REQUIRED");
               System.err.println(e.getMessage());
               e.printStackTrace(System.err);
               Exception embedded = e.getException();
               if ((embedded != null) &&
                   (embedded instanceof AccessionNumberGeneratedException)) {
                 ang = (AccessionNumberGeneratedException)e.getException();
+              }
             } catch (ClassCastException cce) {
               // Do nothing and just fall through to the ang != null test
+            }
+         }
             if (ang != null) {
               conn.commit();
               conn.setAutoCommit(true);
               return (ang.getMessage());
             } else {
               conn.rollback();
               throw e;
+            }
           } catch (Exception e) {
             conn.rollback();
             throw e;
+          }
+      }
       /**
        * Delete an XML file from the database (actually, just make it a revision
        * in the xml_revisions table)
+       *
        * @param docid the ID of the document to be deleted from the database
        */
       public void delete( String docid )
                       throws IOException, SQLException,
                              ClassNotFoundException, AccessionNumberException {
         String newdocid = AccessionNumber.generate(docid, "DELETE");
         conn.setAutoCommit(false);
         // Copy the record to the xml_revisions table
         DocumentImpl document = new DocumentImpl(conn);
         document.archiveDocRevision( docid );
         // Now delete it from the xml_documents table
         Statement stmt = conn.createStatement();
         stmt.execute("DELETE FROM xml_index WHERE docid LIKE '" + docid + "'");
         stmt.execute("DELETE FROM xml_documents WHERE docid LIKE '" + docid + "'");
         stmt.close();
         conn.commit();
+      }
       /** creates SQL code and inserts new document into DB connection */
       private void writeDocumentToDB(String action)
-...
             this.docid = AccessionNumber.generate(docid, "UPDATE");
             // Save the old document entry in a backup table
             saveDocument(docid);
             archiveDocRevision(docid);
             // Update the new document to reflect the new node tree
             pstmt = conn.prepareStatement(
-...
+      }
       /** Save a document entry in the xml_revisions table */
       public void saveDocument(String docid) throws SQLException {
       private void archiveDocRevision(String docid) throws SQLException {
         // First get all of the values we need
         long rnodeid = -1;
         String docname = null;
-...
         pstmt.execute();
         pstmt.close();
+      }
       /**
        * Set up the parser handlers for writing the document to the database
        */
       private XMLReader initializeParser(String action, String docid) {
         XMLReader parser = null;
         //
         // Set up the SAX document handlers for parsing
         //
         try {
           ContentHandler chandler   = new DBSAXHandler(conn, action, docid);
           EntityResolver dbresolver = new DBEntityResolver(conn,
                                           (DBSAXHandler)chandler);
           DTDHandler dtdhandler     = new DBDTDHandler(conn);
           // Get an instance of the parser
           parser = XMLReaderFactory.createXMLReader(parserName);
           // Turn off validation
           parser.setFeature("http://xml.org/sax/features/validation", false);
           // Set Handlers in the parser
           parser.setProperty("http://xml.org/sax/properties/declaration-handler",
                              chandler);
           parser.setProperty("http://xml.org/sax/properties/lexical-handler",
                              chandler);
           parser.setContentHandler((ContentHandler)chandler);
           parser.setEntityResolver((EntityResolver)dbresolver);
           parser.setDTDHandler((DTDHandler)dtdhandler);
           parser.setErrorHandler((ErrorHandler)chandler);
         } catch (Exception e) {
            System.err.println(e.toString());
+        }
         return parser;
+      }
       /**
        * the main routine used to test the DBWriter utility.
        * <p>
        * Usage: java DocumentImpl <-f filename -a action -d docid>
+       *
        * @param filename the filename to be loaded into the database
        * @param action the action to perform (READ, INSERT, UPDATE, DELETE)
        * @param docid the id of the document to process
        */
       static public void main(String[] args) {
         try {
           String filename = null;
           String action   = null;
           String docid    = null;
           for ( int i=0 ; i < args.length; ++i ) {
             if ( args[i].equals( "-f" ) ) {
               filename =  args[++i];
             } else if ( args[i].equals( "-a" ) ) {
               action =  args[++i];
             } else if ( args[i].equals( "-d" ) ) {
               docid =  args[++i];
             } else {
               System.err.println
                 ( "   args[" +i+ "] '" +args[i]+ "' ignored." );
+            }
+          }
           boolean argsAreValid = false;
           if (action != null) {
             if (action.equals("INSERT")) {
               if (filename != null) {
                 argsAreValid = true;
+              }
             } else if (action.equals("UPDATE")) {
               if ((filename != null) && (docid != null)) {
                 argsAreValid = true;
+              }
             } else if (action.equals("DELETE")) {
               if (docid != null) {
                 argsAreValid = true;
+              }
             } else if (action.equals("READ")) {
               if (docid != null) {
                 argsAreValid = true;
+              }
+            }
+          }
           if (!argsAreValid) {
             System.err.println("Wrong number of arguments!!!");
             System.err.println(
                   "USAGE: java DocumentImpl <-a INSERT> [-d docid] <-f filename>");
             System.err.println(
                   "   OR: java DocumentImpl <-a UPDATE -d docid -f filename>");
             System.err.println(
                   "   OR: java DocumentImpl <-a DELETE -d docid>");
             System.err.println(
                   "   OR: java DocumentImpl <-a READ -d docid>");
             return;
+          }
           // Open a connection to the database
           MetaCatUtil util = new MetaCatUtil();
           Connection dbconn = util.openDBConnection();
           if (action.equals("READ")) {
               DocumentImpl xmldoc = new DocumentImpl( dbconn, docid );
               System.out.println(xmldoc.toString());
           } else {
             DocumentImpl doc = new DocumentImpl(dbconn);
             if (action.equals("DELETE")) {
               doc.delete(docid);
               System.out.println("Document deleted: " + docid);
             } else {
               String newdocid = doc.write(filename, action, docid);
               if ((docid != null) && (!docid.equals(newdocid))) {
                 if (action.equals("INSERT")) {
                   System.out.println("New document ID generated!!! ");
                 } else if (action.equals("UPDATE")) {
                   System.out.println("ERROR: Couldn't update document!!! ");
+                }
               } else if ((docid == null) && (action.equals("UPDATE"))) {
                   System.out.println("ERROR: Couldn't update document!!! ");
+              }
               System.out.println("Document processing finished for: " + filename
                     + " (" + newdocid + ")");
+            }
+          }
         } catch (McdbException me) {
           me.toXml(new PrintWriter(System.err));
         } catch (AccessionNumberException ane) {
           System.out.println("ERROR: Couldn't delete document!!! ");
           System.out.println(ane.getMessage());
         } catch (Exception e) {
           System.err.println("EXCEPTION HANDLING REQUIRED");
           System.err.println(e.getMessage());
           e.printStackTrace(System.err);
+        }
+      }
+    }

                 // get a connection from the pool
                 conn = util.getConnection();
                 // write the document to the database
                 DBWriter dbw = new DBWriter(conn, saxparser);
                 DocumentImpl doc = new DocumentImpl(conn);
                 try {
                     String accNumber = docid[0];
                     if (accNumber.equals("")) {
                         accNumber = null;
+                    }
                     newdocid = dbw.write(xml, doAction, accNumber);
                     newdocid = doc.write(xml, doAction, accNumber);
                 } catch (NullPointerException npe) {
                   newdocid = dbw.write(xml, doAction, null);
                   newdocid = doc.write(xml, doAction, null);
+                }
             } catch (Exception e) {
               response.setContentType("text/html");
-...
         try {
           // get a connection from the pool
           conn = util.getConnection();
           DBWriter dbw = new DBWriter(conn, saxparser);
           DocumentImpl doc = new DocumentImpl(conn);
                                           // NOTE -- NEED TO TEST HERE
                                           // FOR EXISTENCE OF PARAM
                                           // BEFORE ACCESSING ARRAY
           try {
             dbw.delete(docid[0]);
             doc.delete(docid[0]);
             response.setContentType("text/xml");
             out.println("<?xml version=\"1.0\"?>");
             out.println("<success>");

bin/loadxml
6	6
7	7	export CPATH=$PDIR/build/metacat.jar:$PARSER:$JDBC
8	8
9		java -cp ${CPATH} edu.ucsb.nceas.metacat.DBWriter $@
	9	java -cp ${CPATH} edu.ucsb.nceas.metacat.DocumentImpl $@

bin/readxml
6	6
7	7	export CPATH=$PDIR/build/metacat.jar:$PARSER:$JDBC
8	8
9		java -cp ${CPATH} edu.ucsb.nceas.metacat.DocumentImpl $1
	9	java -cp ${CPATH} edu.ucsb.nceas.metacat.DocumentImpl $@

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Metacat

Revision 407

Added by Matt Jones over 24 years ago