/src/edu/ucsb/nceas/metacat/DBQuery.java - Diff - Metacat - Ecoinformatics Redmine

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Revision 940

Added by Jing Tao over 22 years ago

A public method named getZippedPackage() and other relative private methods were add to this class. The public method can give a zip output stream if a docid and other parameters were passed to it.

     package edu.ucsb.nceas.metacat;
     import edu.ucsb.nceas.morpho.datapackage.*;
     import java.io.*;
     import java.util.Vector;
     import java.util.zip.*;
     import java.net.URL;
     import java.net.MalformedURLException;
     import java.sql.*;
-...
     import java.io.File;
     import java.io.FileWriter;
     import java.io.BufferedWriter;
     import javax.servlet.ServletOutputStream;
     /**
      * A Class that searches a relational DB for elements and
-...
       static final int ALL = 1;
       static final int WRITE = 2;
       static final int READ = 4;
       private Connection  conn = null;
       private String  parserName = null;
       private MetaCatUtil util = new MetaCatUtil();
-...
               String docid = null;
               result.append("<?xml version=\"1.0\"?>\n");
               result.append("<resultset>\n");
       // following line removed by Dan Higgins to avoid insertion of query XML inside returned XML doc
       //        result.append("  <query>" + xmlfile + "</query>\n");
               if (!showRuntime)
+              {
                 Enumeration doclist = nodelist.keys();
-...
                   document.append("<subjectdoctype>").append(subDT);
                   document.append("</subjectdoctype>");
+                }
                 document.append("<relationship>").append(MetaCatUtil.normalize(rel));
                 document.append("<relationship>").
                                               append(MetaCatUtil.normalize(rel));
                 document.append("</relationship>");
                 document.append("<object>").append(MetaCatUtil.normalize(obj));
                 document.append("</object>");
-...
         AccessControlList aclobj = new AccessControlList(conn);
         return aclobj.hasPermission("READ", user, groups, docid);
+      }
       /**
         * Get all docIds list for a data packadge
         * @param dataPackageDocid, the string in docId field of xml_relation table
         */
       private Vector getCurrentDocidListForDataPackage(String dataPackageDocid)
+      {
         Vector docIdList=new Vector();//return value
         PreparedStatement pStmt;
         ResultSet rs=null;
         String docIdInSubjectField=null;
         String docIdInObjectField=null;
         //the query stirng
         String query="SELECT subject, object from xml_relation where docId = ?";
         try
+        {
           pStmt=conn.prepareStatement(query);
           //bind the value to query
           pStmt.setString(1, dataPackageDocid);
           //excute the query
           pStmt.execute();
           //get the result set
           rs=pStmt.getResultSet();
           //process the result
           while (rs.next())
+          {
             //In order to get the whole docIds in a data packadge,
             //we need to put the docIds of subject and object field in xml_relation
             //into the return vector
             docIdInSubjectField=rs.getString(1);//the result docId in subject field
             docIdInObjectField=rs.getString(2);//the result docId in object field
             //don't put the duplicate docId into the vector
             if (!docIdList.contains(docIdInSubjectField))
+            {
               docIdList.add(docIdInSubjectField);
+            }
             //don't put the duplicate docId into the vector
             if (!docIdList.contains(docIdInObjectField))
+            {
               docIdList.add(docIdInObjectField);
+            }
           }//while
           //close the pStmt
           pStmt.close();
         }//try
         catch (SQLException e)
+        {
           util.debugMessage("Error in getDocidListForDataPackage: "
                                 +e.getMessage());
         }//catch
         return docIdList;
       }//getCurrentDocidListForDataPackadge()
       /**
        * Get all docIds list for a data packadge
        * @param dataPackageDocid, the string in docId field of xml_relation table
        */
       private Vector getOldVersionDocidListForDataPackage(String dataPackageDocid)
                                      throws SQLException, McdbException,Exception
+      {
         Vector docIdList=new Vector();//return value
         Vector tripleList=null;
         String xml=null;
         Connection dbConn=null;
         if (conn == null || conn.isClosed())
+        {
           dbConn = util.openDBConnection();
+        }
         else
+        {
           dbConn=conn;
+        }
         //initial a documentImpl object
         DocumentImpl packageDocument = new DocumentImpl(dbConn, dataPackageDocid);
         //transfer to documentImpl object to string
         xml=packageDocument.toString();
         //create a tripcollection object
         TripleCollection tripleForPackage = new
                                          TripleCollection(new StringReader(xml));
         //get the vetor of triples
         tripleList=tripleForPackage.getCollection();
         for (int i= 0; i<tripleList.size(); i++)
+        {
           //put subject docid  into docIdlist without duplicate
           if (!docIdList.contains(((Triple)tripleList.elementAt(i)).getSubject()))
+          {
             //put subject docid  into docIdlist
              docIdList.add(((Triple)tripleList.get(i)).getSubject());
+          }
           //put object docid into docIdlist without duplicate
           if (!docIdList.contains(((Triple)tripleList.elementAt(i)).getObject()))
+          {
              docIdList.add(((Triple)(tripleList.get(i))).getObject());
+          }
         }//for
         return docIdList;
       }//getDocidListForPackageInXMLRevisions()
       /**
        * Check if the docId is a data packadge id. If the id is a data packadage
        *id, it should be store in the docId fields in xml_relation table.
        *So we can use a query to get the entries which the docId equals the given
        *value. If the result is null. The docId is not a packadge id. Otherwise,
        * it is.
        * @param docId, the id need to be checked
        */
       private boolean isDataPackageId(String docId)
+      {
         boolean result=false;
         PreparedStatement pStmt;
         ResultSet rs=null;
         String query="SELECT docId from xml_relation where docId = ?";
         try
+        {
           pStmt=conn.prepareStatement(query);
           //bind the value to query
           pStmt.setString(1, docId);
           //execute the query
           pStmt.execute();
           rs=pStmt.getResultSet();
           //process the result
           if (rs.next()) //There are some records for the id in docId fields
+          {
             result=true;//It is a data packadge id
+          }
           pStmt.close();
         }//try
         catch (SQLException e)
+        {
           util.debugMessage("Error in getDocidListForDataPackadge: "
                                 +e.getMessage());
+        }
         return result;
       }//isDataPackageId()
       /**
        *Get the current Rev for a docid in xml_documents table
        * @param docId, the id need to get version numb
        * If the return value is -5, means no value in rev field for this docid
        */
       private int getCurrentRevFromXMLDoumentsTable(String docId)
+      {
         int rev=-5;
         PreparedStatement pStmt;
         ResultSet rs=null;
         String query="SELECT rev from xml_documents where docId = ?";
         try
+        {
           pStmt=conn.prepareStatement(query);
           //bind the value to query
           pStmt.setString(1, docId);
           //execute the query
           pStmt.execute();
           rs=pStmt.getResultSet();
           //process the result
           if (rs.next()) //There are some records for rev
+          {
             rev=rs.getInt(1);;//It is the version for given docid
+          }
           else
+          {
             rev=-5;
+          }
           pStmt.close();
         }//try
         catch (SQLException e)
+        {
           util.debugMessage("Error in getDocidListForDataPackadge: "
                                 +e.getMessage());
+        }
         return rev;
       }//getCurrentRevFromXMLDoumentsTable
      /**
        *put a doc into a zip output stream
        *@param docImpl, docmentImpl object which will be sent to zip output stream
        *@param zipOut, zip output stream which the docImpl will be put
        *@param packageZipEntry, the zip entry name for whole package
        */
       private void addDocToZipOutputStream(DocumentImpl docImpl,
                                     ZipOutputStream zipOut, String packageZipEntry)
                    throws ClassNotFoundException, IOException, SQLException,
                           McdbException, Exception
+      {
         byte[] byteString = null;
         ZipEntry zEntry = null;
         byteString = docImpl.toString().getBytes();
         //use docId as the zip entry's name
         zEntry = new ZipEntry(packageZipEntry+"/metadata/"+docImpl.getDocID());
         zEntry.setSize(byteString.length);
         zipOut.putNextEntry(zEntry);
         zipOut.write(byteString, 0, byteString.length);
         zipOut.closeEntry();
       }//addDocToZipOutputStream()
       /**
        *transfer a docid vetor to a documentImpl vector. The documentImpl vetor
        *inlcudes current and old version
        *@param docIdList, a vetor hold a docid list for a data package. In docid,
        *there is not version number in it.
        */
       private Vector getCurrentAllDocumentImpl( Vector docIdList)
                                   throws McdbException,Exception
+      {
         Connection dbConn=null;
         Vector documentImplList=new Vector();
         int rev=0;
         if (conn == null || conn.isClosed())
+        {
           dbConn = util.openDBConnection();
+        }
         else
+        {
           dbConn=conn;
+        }
         //for every docid in vector
         for (int i=0;i<docIdList.size();i++)
+        {
           //get newest version for this docId
           rev=getCurrentRevFromXMLDoumentsTable((String)docIdList.elementAt(i));
           //get all versions including current and old ones for one docid
           for (int j=1;j<=rev;j++)
+          {
             String docidPlusVersion=((String)docIdList.elementAt(i))
                             +util.getOption("accNumSeparator")+j;
             //create new documentImpl object
             DocumentImpl documentImplObject =
                                         new DocumentImpl(dbConn,docidPlusVersion);
             //add them to vector
             documentImplList.add(documentImplObject);
           }//for
         }//for
         return documentImplList;
+      }
       /**
        *transfer a docid vetor to a documentImpl vector. The documentImpl vetor
        *inlcudes old version
        *@param docIdList, a vetor hold a docid list for a data package. In docid,
        *there is version number in it.
        */
       private Vector getOldVersionAllDocumentImpl( Vector docIdList)
                                   throws McdbException,Exception
+      {
         Connection dbConn=null;
         Vector documentImplList=new Vector();
         String siteCode=null;
         String uniqueId=null;
         int rev=0;
         if (conn == null || conn.isClosed())
+        {
           dbConn = util.openDBConnection();
+        }
         else
+        {
           dbConn=conn;
+        }
         //for every docid in vector
         for (int i=0;i<docIdList.size();i++)
+        {
           //create a documentIdentifier object
           DocumentIdentifier identifier=
                             new DocumentIdentifier((String)docIdList.elementAt(i));
           //get newest version for this docId
           siteCode=identifier.getSiteCode();
           uniqueId=identifier.getUniqueId();
           rev=Integer.parseInt(identifier.getRev());
           //get all versions including current and old ones for one docid
           for (int j=1;j<=rev;j++)
+          {
             String docidPlusVersion=siteCode+util.getOption("accNumSeparator")+
                             uniqueId+util.getOption("accNumSeparator")+j;
             //create new documentImpl object
             DocumentImpl documentImplObject =
                                         new DocumentImpl(dbConn,docidPlusVersion);
             //add them to vector
             documentImplList.add(documentImplObject);
           }//for
         }//for
         return documentImplList;
+      }
       /**
        *put a data file into a zip output stream
        *@param docImpl, docmentImpl object which will be sent to zip output stream
        *@param zipOut, the zip output stream which the docImpl will be put
        *@param packageZipEntry, the zip entry name for whole package
        */
       private void addDataFileToZipOutputStream(DocumentImpl docImpl,
                                     ZipOutputStream zipOut, String packageZipEntry)
                    throws ClassNotFoundException, IOException, SQLException,
                           McdbException, Exception
+      {
         byte[] byteString = null;
         ZipEntry zEntry = null;
         // this is data file; add file to zip
         String filePath = util.getOption("datafilepath");
         if (!filePath.endsWith("/"))
+        {
           filePath += "/";
+        }
         String fileName = filePath + docImpl.getDocID();
         zEntry = new ZipEntry(packageZipEntry+"/data/"+docImpl.getDocID());
         zipOut.putNextEntry(zEntry);
         FileInputStream fin = null;
         try
+        {
           fin = new FileInputStream(fileName);
           byte[] buf = new byte[4 * 1024]; // 4K buffer
           int b = fin.read(buf);
           while (b != -1)
+          {
             zipOut.write(buf, 0, b);
             b = fin.read(buf);
           }//while
           zipOut.closeEntry();
         }//try
         catch (IOException ioe)
+        {
           util.debugMessage("There is an exception: "+ioe.getMessage());
         }//catch
       }//addDataFileToZipOutputStream()
       /**
        *create a html summary for data package and put it into zip output stream
        *@param docImplList, the documentImpl ojbects in data package
        *@param zipOut, the zip output stream which the html should be put
        *@param packageZipEntry, the zip entry name for whole package
        */
        private void addHtmlSummaryToZipOutputStream(Vector docImplList,
                                     ZipOutputStream zipOut, String packageZipEntry)
                                                throws Exception
+      {
         StringBuffer htmlDoc = new StringBuffer();
         ZipEntry zEntry = null;
         byte[] byteString=null;
         InputStream source;
         DBTransform xmlToHtml;
         Connection dbConn;
         //get the connection to the database
         if (conn == null || conn.isClosed())
+        {
           dbConn = util.openDBConnection();
+        }
         else
+        {
           dbConn=conn;
+        }
         //create a DBTransform ojbect
         xmlToHtml = new DBTransform(dbConn);
         //head of html
         htmlDoc.append("<html><head></head><body>");
         for (int i=0; i<docImplList.size(); i++)
+        {
           if ((((DocumentImpl)docImplList.elementAt(i)).getDoctype()).
                                                              compareTo("BIN")!=0)
           { //this is an xml file so we can transform it.
             //transform each file individually then concatenate all of the
             //transformations together.
             //for metadata xml title
             htmlDoc.append("<h2>");
             htmlDoc.append(((DocumentImpl)docImplList.elementAt(i)).getDocID());
             //htmlDoc.append(".");
             //htmlDoc.append(((DocumentImpl)docImplList.elementAt(i)).getRev());
             htmlDoc.append("</h2>");
             //do the actual transform
             StringWriter docString = new StringWriter();
             xmlToHtml.transformXMLDocument(
                             ((DocumentImpl)docImplList.elementAt(i)).toString(),
                "-//NCEAS//eml-generic//EN", "-//W3C//HTML//EN", "html", docString);
             htmlDoc.append(docString.toString());
             htmlDoc.append("<br><br><hr><br><br>");
           }//if
           else
           { //this is a data file so we should link to it in the html
             htmlDoc.append("<a href=\"");
             String dataFileName = null;
             String dataFileid =((DocumentImpl)docImplList.elementAt(i)).getDocID();
             htmlDoc.append("./data/").append(dataFileid).append("\">");
             htmlDoc.append("Data File: ");
             htmlDoc.append(dataFileid).append("</a><br>");
             htmlDoc.append("<br><hr><br>");
           }//else
         }//for
         htmlDoc.append("</body></html>");
         byteString = htmlDoc.toString().getBytes();
         zEntry = new ZipEntry(packageZipEntry+"/metadata.html");
         zEntry.setSize(byteString.length);
         zipOut.putNextEntry(zEntry);
         zipOut.write(byteString, 0, byteString.length);
         zipOut.closeEntry();
         dbConn.close();
       }//addHtmlSummaryToZipOutputStream
       /**
        * put a data packadge into a zip output stream
        * @param docId, which the user want to put into zip output stream
        * @param out, a servletoutput stream which the zip output stream will be put
        * @param user, the username of the user
        * @param groups, the group of the user
        */
       public ZipOutputStream getZippedPackage(String docIdString,
                         ServletOutputStream out, String user, String[] groups)
                         throws ClassNotFoundException, IOException, SQLException,
                           McdbException, NumberFormatException, Exception
+      {
         ZipOutputStream zOut = null;
         String elementDocid=null;
         DocumentImpl docImpls=null;
         Connection dbConn = null;
         Vector docIdList=new Vector();
         Vector documentImplList= new Vector();
         String packageId=null;
         String rootName="package";//the package zip entry name
         String docId=null;
         int version=-5;
         docId=MetaCatUtil.getDocIdFromString(docIdString);
         version=MetaCatUtil.getVersionFromString(docIdString);
         //get the connection to the database
         if (conn == null || conn.isClosed())
+        {
           dbConn = util.openDBConnection();
+        }
         else
+        {
           dbConn=conn;
+        }
         //check if the reqused docId is a data package id
         if (!isDataPackageId(docId))//if it is not, throw a exception
+        {
           Exception e = new Exception("The request the doc id " +docId+
                                         " is not a data package id");
           dbConn.close();
           throw e;
+        }
         else //it is a packadge id
+        {
           //store the package id
           packageId=docId;
           //If it is for current version
           if ((version ==-1)||version==getCurrentRevFromXMLDoumentsTable(packageId))
+          {
             //get current version number
             version=getCurrentRevFromXMLDoumentsTable(packageId);
             //get package zip entry name
             //it should be docId.revsion.package
             rootName=packageId+util.getOption("accNumSeparator")+version+
                                       util.getOption("accNumSeparator")+"package";
             //get the whole id list for data packadge
             docIdList=getCurrentDocidListForDataPackage(packageId);
             //get the whole documentImple object
             documentImplList=getCurrentAllDocumentImpl(docIdList);
           }//if
           else  //for an old version
+          {
             rootName=docIdString+util.getOption("accNumSeparator")+"package";
             //get the whole id list for data packadge
             docIdList=getOldVersionDocidListForDataPackage(docIdString);
             //get the whole documentImple object
             documentImplList=getOldVersionAllDocumentImpl(docIdList);
           }//else
           zOut = new ZipOutputStream(out);
           //put every element into zip output stream
           for (int i=0; i < documentImplList.size(); i++ )
+          {
             //create a docmentImpls object (represent xml doc) base on the docId
             docImpls=(DocumentImpl)documentImplList.elementAt(i);
             if ((docImpls.getDoctype()).compareTo("BIN")!=0)
+            {
               //if the docImpls is metadata
               //add metadata into zip output stream
               addDocToZipOutputStream(docImpls, zOut, rootName);
+            }
             else //if the docImpls is a data file
+            {
                //add data file into zip output stream too
                addDataFileToZipOutputStream(docImpls, zOut, rootName);
+            }
           }//for
           //add html summary file
           addHtmlSummaryToZipOutputStream(documentImplList, zOut, rootName);
           zOut.finish(); //terminate the zip file
           dbConn.close();
           return zOut;
         }//else
       }//getZippedPackage()
+    }

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Revision 940

Added by Jing Tao over 22 years ago