cob-cvs

[Jie B. <ba...@us...>]

Update of /cvsroot/cob/COBEditor/src/edu/iastate/ato/po
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv25786/src/edu/iastate/ato/po

Modified Files:
	DB2OBO.java 
Log Message:


Index: DB2OBO.java
===================================================================
RCS file: /cvsroot/cob/COBEditor/src/edu/iastate/ato/po/DB2OBO.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** DB2OBO.java	6 Mar 2007 22:07:35 -0000	1.2
--- DB2OBO.java	16 Aug 2007 04:01:08 -0000	1.3
***************
*** 1,16 ****
! package edu.iastate.ato.po ;
  
! import java.io.BufferedWriter ;
! import java.io.FileWriter ;
! import java.io.IOException ;
! import java.sql.Connection ;
! import java.sql.ResultSet ;
! import java.sql.SQLException ;
! import java.sql.Statement ;
! import java.util.HashMap ;
! import java.util.Map ;
! import java.util.Vector ;
  
- import edu.iastate.ato.shared.AtoConstent ;
  import edu.iastate.ato.shared.*;
  
--- 1,17 ----
! package edu.iastate.ato.po;
  
! import java.io.BufferedWriter;
! import java.io.FileWriter;
! import java.io.IOException;
! import java.sql.Connection;
! import java.sql.ResultSet;
! import java.sql.SQLException;
! import java.sql.Statement;
! import java.text.SimpleDateFormat;
! import java.util.Date;
! import java.util.HashMap;
! import java.util.Map;
! import java.util.Vector;
  
  import edu.iastate.ato.shared.*;
  
***************
*** 23,56 ****
  public class DB2OBO extends LongTask
  {
!     public static final String PROPERTY_LEADING = "![attribute]" ;
!     public static final String SCHEMA_LEADING = "![schema]" ;
  
!     String prefix ;
  
      String makeHeader(String user)
      {
!         String header = "format-version: 1.0\n" +
!             //"date: " + OntologyEdit.getTime() + "\n" +
!             "saved-by: " + user + "\n" +
!             "auto-generated-by: " + AtoConstent.APP_NAME + "\n" +
!             "default-namespace: ato\n\n" ;
!         return header ;
      }
  
      /* eg
!          [Typedef]
!          id: part_of
!          name: part of
       */
      String makeTypedef(String relation)
      {
!         return "[Typedef]\n" +
!             "id: " + relation + "\n" +
!             "name: " + relation + "\n\n" ;
      }
  
      String makeComment(String comment)
      {
!         return "comment: " + comment + "\n" ;
      }
  
--- 24,64 ----
  public class DB2OBO extends LongTask
  {
!     public static final String           PROPERTY_LEADING = "![attribute]";
!     public static final String           SCHEMA_LEADING   = "![schema]";
  
!     //date: 15:08:2007 22:12
!     final public static SimpleDateFormat dateFormat       = new SimpleDateFormat(
!                                                               "dd:MM:yyyy HH:mm");
! 
!     public static String getTime()
!     {
!         return dateFormat.format(new Date());
!     }
! 
!     String prefix;
  
      String makeHeader(String user)
      {
!         String header = "format-version: 1.0\n" + "date: "
!             + getTime() + "\n" + "saved-by: " + user + "\n"
!             + "auto-generated-by: " + AtoConstent.APP_NAME + "\n"
!             + "default-namespace: ato\n\n";
!         return header;
      }
  
      /* eg
!      [Typedef]
!      id: part_of
!      name: part of
       */
      String makeTypedef(String relation)
      {
!         return "[Typedef]\n" + "id: " + relation + "\n" + "name: " + relation
!             + "\n\n";
      }
  
      String makeComment(String comment)
      {
!         return "comment: " + comment + "\n";
      }
  
***************
*** 59,81 ****
      String makeTerm_Property(String prop, String value)
      {
!         if(OntologySchema.isOBOProperty(prop))
          {
!         	if ("def".equals(prop.trim())){
!         		value = "\"" + value.replaceAll("\"","'") + "\"";
!         		return prop + ": " + value;
!         	}
!         	else if ("def_xref".equals(prop.trim()))
!         	{	return "[" +value + "]"; // also see exportTerms        	
!         	}
!         	else if (OntologySchema.isSynonymProperty(prop))       		
!         	{
!         		return prop + ": \"" + value + "\" []\n" ;
!         	}
!         	else
!         		return prop + ": " + value + "\n" ;
          }
          else
          { // treate it as comment
!             return PROPERTY_LEADING + prop + ": " + value + "\n" ;
          }
      }
--- 67,84 ----
      String makeTerm_Property(String prop, String value)
      {
!         if (OntologySchema.isOBOProperty(prop))
          {
!             if (prop.contains("synonym") || prop.equals("def"))
!             {
!                 // e.g. related_synonym: "aa" []
!                 value = value.replaceAll("\"", "");
!                 return prop + ": \"" + value + "\" []\n";
!             }
!             else
!             return prop + ": " + value + "\n";
          }
          else
          { // treate it as comment
!             return PROPERTY_LEADING + prop + ": " + value + "\n";
          }
      }
***************
*** 84,94 ****
      public String addPrefix(String id)
      {
!         if(prefix != null && prefix.trim().length() > 0)
          {
!             return prefix + ":" + id ;
          }
          else
          {
!             return id ;
          }
      }
--- 87,97 ----
      public String addPrefix(String id)
      {
!         if (prefix != null && prefix.trim().length() > 0)
          {
!             return prefix + ":" + id;
          }
          else
          {
!             return id;
          }
      }
***************
*** 98,107 ****
          String parent_name)
      {
!         String str = "relationship: " + relation + " " + addPrefix(parent_id) ;
!         if(parent_name != null)
          {
!             str += " ! " + parent_name ;
          }
!         return str + "\n" ;
      }
  
--- 101,110 ----
          String parent_name)
      {
!         String str = "relationship: " + relation + " " + addPrefix(parent_id);
!         if (parent_name != null)
          {
!             str += " ! " + parent_name;
          }
!         return str + "\n";
      }
  
***************
*** 110,119 ****
          String parent_name)
      {
!         String str = "relationship: " + relation + " " + parent_id ;
!         if(parent_name != null)
          {
!             str += " ! " + parent_name ;
          }
!         return str + "\n" ;
      }
  
--- 113,122 ----
          String parent_name)
      {
!         String str = "relationship: " + relation + " " + parent_id;
!         if (parent_name != null)
          {
!             str += " ! " + parent_name;
          }
!         return str + "\n";
      }
  
***************
*** 130,156 ****
          try
          {
!             BufferedWriter out = new BufferedWriter(new FileWriter(fileName)) ;
  
              // prepare data structures
!             this.prefix = withPrefix ? OntologySchema.getPrefix(db) : null ;
!             packageNameCache.clear() ;
  
              // 1.  make header
!             out.write(makeHeader(user)) ;
  
              // 2. make schema
!             exportSchema(db, out) ;
  
              // 3. export package
!             exportPackages(db, out) ;
  
              // 4. write term by term
!             exportTerms(db, out) ;
  
!             out.close() ;
!         }
!         catch(IOException ex)
!         {
          }
      }
  
--- 133,158 ----
          try
          {
!             BufferedWriter out = new BufferedWriter(new FileWriter(fileName));
  
              // prepare data structures
!             this.prefix = withPrefix ? OntologySchema.getPrefix(db) : null;
!             packageNameCache.clear();
  
              // 1.  make header
!             out.write(makeHeader(user));
  
              // 2. make schema
!             exportSchema(db, out);
  
              // 3. export package
!             exportPackages(db, out);
  
              // 4. write term by term
!             exportTerms(db, out);
  
!             out.close();
          }
+         catch (IOException ex)
+         {}
      }
  
***************
*** 162,348 ****
       * @since 2005-08-24
       */
!     private void exportPackages(Connection db, BufferedWriter out) throws
!         IOException
      {
!         String sql = "SELECT oid, pid, comment, author, modified FROM package" ;
          try
          {
!             Statement stmt = db.createStatement() ;
!             ResultSet resultSet = stmt.executeQuery(sql) ;
  
!             while(resultSet.next())
              {
!                 String oid = resultSet.getString("oid") ;
!                 String pid = resultSet.getString("pid") ;
!                 String comment = resultSet.getString("comment") ;
!                 String author = resultSet.getString("author") ;
!                 String modified = resultSet.getString("modified") ;
  
                  // don't export GlobalPackage
!                 if(pid.equals(Package.GlobalPkg))
                  {
!                     continue ;
                  }
  
!                 out.write("[Package]\n") ;
                  // write the comments
!                 String str = "id: " + pid + "\n" ;
!                 str += "name: " + (comment == null ? "" : comment) + "\n" ;
!                 out.write(str) ;
!                 str = makeTerm_Property("author", author) ;
!                 out.write(str) ;
!                 str = makeTerm_Property("modified", modified) ;
!                 out.write(str) ;
  
                  //SELECT DISTINCT relation, package.pid AS parent, package.comment AS parent_name
                  //FROM pkg_relation, package WHERE pkg_relation.p1 = '116329' AND pkg_relation.p2 = package.oid
  
!                 sql =
!                     "SELECT DISTINCT relation, package.pid AS parent, package.comment AS parent_name" +
!                     " FROM pkg_relation, package WHERE pkg_relation.p1 = '" +
!                     oid + "' AND pkg_relation.p2 = package.oid" ;
                  //Debug.systrace(this,sql);
!                 Statement stmt2 = db.createStatement() ;
!                 ResultSet resultSet2 = stmt2.executeQuery(sql) ;
!                 while(resultSet2.next())
                  {
!                     String relation = resultSet2.getString("relation") ;
!                     String parent = resultSet2.getString("parent") ;
!                     String parent_name = resultSet2.getString("parent_name") ;
  
!                     str = makePackageRelation(relation, parent, parent_name) ;
!                     out.write(str) ;
                  }
!                 out.write("\n") ;
              } // end of a package
          }
!         catch(SQLException ex)
          {
!             ex.printStackTrace() ;
          }
  
      }
  
!     Map<String, String> packageNameCache = new HashMap() ;
      private String getPackageName(Connection db, String pkg_oid)
      {
          // read the cache
!         String pkgName = packageNameCache.get(pkg_oid) ;
!         if(pkgName == null)
          {
              // not yet in cache
!             pkgName = DbPackage.read(db, pkg_oid).pid ;
!             packageNameCache.put(pkg_oid, pkgName) ;
          }
!         return pkgName ;
      }
  
      void exportTerms(Connection db, BufferedWriter out)
      {
!         String sql =
!             "SELECT oid, id, name, slm, package, author, modified, is_obsolete FROM term" ;
          try
          {
!             System.out.println(sql) ;
  
!             Statement stmt = db.createStatement() ;
!             ResultSet resultSet = stmt.executeQuery(sql) ;
  
!             while(resultSet.next())
              {
!                 String oid = resultSet.getString("oid") ;
!                 String id = resultSet.getString("id") ;
!                 String name = resultSet.getString("name") ;
!                 String author = resultSet.getString("author") ;
!                 String modified = resultSet.getString("modified") ;
!                 String is_obsolete = resultSet.getString("is_obsolete") ;
!                 String package_oid = resultSet.getString("package") ;
!                 String slm = resultSet.getString("slm") ;
  
!                 out.write("[Term]\n") ;
  
                  // write the basic information
!                 String str = "id: " + addPrefix(id) + "\n" ;
!                 str += "name: " + (name == null ? "" : name) + "\n" ;
!                 out.write(str) ;
!                 if(is_obsolete.equalsIgnoreCase("true"))
                  {
!                     str = "is_obsolete: true\n" ;
!                     out.write(str) ;
                  }
!                 str = makeTerm_Property("author", author) ;
!                 out.write(str) ;
!                 str = makeTerm_Property("modified", modified) ;
!                 out.write(str) ;
                  // write package membership
!                 str = getPackageName(db, package_oid) ; // package id
!                 str = makeTerm_Property("package", str) ;
!                 out.write(str) ;
!                 str = makeTerm_Property("slm", slm) ;
!                 out.write(str) ;
  
                  // write the property details
!                 sql = "SELECT attribute, value FROM details WHERE term = '" +
!                     oid + "'" ;
!                 Statement stmt1 = db.createStatement() ;
!                 ResultSet resultSet1 = stmt1.executeQuery(sql) ;
!                 
!                 String def = null, def_xref = null;
!                 
!                 while(resultSet1.next())
                  {
!                     String attribute = resultSet1.getString("attribute") ;
!                     String value = resultSet1.getString("value") ;
  
!                     if(value != null && value.trim().length() > 0)
                      {
!                         str = makeTerm_Property(attribute, value) ;
!                         
!                         if ("def_xref".equals(attribute.trim()))
!                         	def_xref = str;
!                         else if ("def".equals(attribute.trim())) 
!                         	def = str;
!                         else
!                         
!                         out.write(str) ;
                      }
                  }
!                 if (def != null)
!                 {
!                 	if (def_xref != null)
!                 	{
!                 		out.write(def + " " + def_xref + "\n");
!                 	}
!                 	else
!                 	{
!                 		out.write(def + "\n");
!                 	}
!                 	//out.write("def is not null \n") ;
!                 }
                  //SELECT DISTINCT relation, term.id AS parent, term.name AS parent_name
!                 //FROM relation WHERE id = '59056' AND relation.pid = term.oid
!                 sql =
!                     "SELECT DISTINCT relation, term.id AS parent, term.name AS parent_name FROM relation, term " +
!                     "WHERE relation.id = '" + oid + "' AND relation.pid = term.oid" ;
!                 Statement stmt2 = db.createStatement() ;
!                 ResultSet resultSet2 = stmt2.executeQuery(sql) ;
!                 
!                 while(resultSet2.next())
!                 {                	
!                     String relation = resultSet2.getString("relation") ;
!                     String parent = resultSet2.getString("parent") ;
!                     String parent_name = resultSet2.getString("parent_name") ;
  
!                     str = makeTerm_Relation(relation, parent, parent_name) ;
!                    	out.write( str) ;
                  }
! 
!                 out.write("\n") ;
  
              }
          }
!         catch(Exception e)
          {
!             e.printStackTrace() ;
          }
  
--- 164,328 ----
       * @since 2005-08-24
       */
!     private void exportPackages(Connection db, BufferedWriter out)
!             throws IOException
      {
!         String sql = "SELECT oid, pid, comment, author, modified FROM package";
          try
          {
!             Statement stmt = db.createStatement();
!             ResultSet resultSet = stmt.executeQuery(sql);
  
!             while (resultSet.next())
              {
!                 String oid = resultSet.getString("oid");
!                 String pid = resultSet.getString("pid");
!                 String comment = resultSet.getString("comment");
!                 String author = resultSet.getString("author");
!                 String modified = resultSet.getString("modified");
  
                  // don't export GlobalPackage
!                 if (pid.equals(Package.GlobalPkg))
                  {
!                     continue;
                  }
  
!                 out.write("[Package]\n");
                  // write the comments
!                 String str = "id: " + pid + "\n";
!                 str += "name: " + (comment == null ? "" : comment) + "\n";
!                 out.write(str);
!                 str = makeTerm_Property("author", author);
!                 out.write(str);
!                 str = makeTerm_Property("modified", modified);
!                 out.write(str);
  
                  //SELECT DISTINCT relation, package.pid AS parent, package.comment AS parent_name
                  //FROM pkg_relation, package WHERE pkg_relation.p1 = '116329' AND pkg_relation.p2 = package.oid
  
!                 sql = "SELECT DISTINCT relation, package.pid AS parent, package.comment AS parent_name"
!                     + " FROM pkg_relation, package WHERE pkg_relation.p1 = '"
!                     + oid + "' AND pkg_relation.p2 = package.oid";
                  //Debug.systrace(this,sql);
!                 Statement stmt2 = db.createStatement();
!                 ResultSet resultSet2 = stmt2.executeQuery(sql);
!                 while (resultSet2.next())
                  {
!                     String relation = resultSet2.getString("relation");
!                     String parent = resultSet2.getString("parent");
!                     String parent_name = resultSet2.getString("parent_name");
  
!                     str = makePackageRelation(relation, parent, parent_name);
!                     out.write(str);
                  }
!                 out.write("\n");
              } // end of a package
          }
!         catch (SQLException ex)
          {
!             ex.printStackTrace();
          }
  
      }
  
!     Map<String, String> packageNameCache = new HashMap();
! 
      private String getPackageName(Connection db, String pkg_oid)
      {
          // read the cache
!         String pkgName = packageNameCache.get(pkg_oid);
!         if (pkgName == null)
          {
              // not yet in cache
!             pkgName = DbPackage.read(db, pkg_oid).pid;
!             packageNameCache.put(pkg_oid, pkgName);
          }
!         return pkgName;
      }
  
      void exportTerms(Connection db, BufferedWriter out)
      {
!         String sql = 
!             "SELECT oid, id, name, slm, package, author, modified, is_obsolete FROM term";
          try
          {
!             System.out.println(sql);
  
!             Statement stmt = db.createStatement();
!             ResultSet resultSet = stmt.executeQuery(sql);
  
!             while (resultSet.next())
              {
!                 String oid = resultSet.getString("oid");
!                 String id = resultSet.getString("id");
!                 String name = resultSet.getString("name");
!                 String author = resultSet.getString("author");
!                 String modified = resultSet.getString("modified");
!                 String is_obsolete = resultSet.getString("is_obsolete");
!                 String package_oid = resultSet.getString("package");
!                 String slm = resultSet.getString("slm");
  
!                 out.write("[Term]\n");
  
                  // write the basic information
!                 String str = "id: " + addPrefix(id) + "\n";
!                 str += "name: " + (name == null ? "" : name) + "\n";
!                 out.write(str);
!                 if (is_obsolete.equalsIgnoreCase("true"))
                  {
!                     str = "is_obsolete: true\n";
!                     out.write(str);
                  }
!                 str = makeTerm_Property("author", author);
!                 out.write(str);
!                 str = makeTerm_Property("modified", modified);
!                 out.write(str);
                  // write package membership
!                 str = getPackageName(db, package_oid); // package id
!                 str = makeTerm_Property("package", str);
!                 out.write(str);
!                 str = makeTerm_Property("slm", slm);
!                 out.write(str);
  
                  // write the property details
!                 sql = "SELECT attribute, value FROM details WHERE term = '"
!                     + oid + "'";
!                 Statement stmt1 = db.createStatement();
!                 ResultSet resultSet1 = stmt1.executeQuery(sql);
!                 while (resultSet1.next())
                  {
!                     String attribute = resultSet1.getString("attribute");
!                     String value = resultSet1.getString("value");
  
!                     if (value != null && value.trim().length() > 0)
                      {
!                         str = makeTerm_Property(attribute, value);
!                         out.write(str);
                      }
                  }
! 
                  //SELECT DISTINCT relation, term.id AS parent, term.name AS parent_name
!                 //FROM relation,term WHERE relation.id = '59056' AND relation.pid = term.oid
!                 sql = "SELECT DISTINCT relation, term.id AS parent, term.name AS parent_name FROM relation, term "
!                     + "WHERE relation.id = '"
!                     + oid
!                     + "' AND relation.pid = term.oid";
!                 Statement stmt2 = db.createStatement();
!                 ResultSet resultSet2 = stmt2.executeQuery(sql);
!                 while (resultSet2.next())
!                 {
!                     String relation = resultSet2.getString("relation");
!                     String parent = resultSet2.getString("parent");
!                     String parent_name = resultSet2.getString("parent_name");
  
!                     str = makeTerm_Relation(relation, parent, parent_name);
!                     out.write(str);
                  }
!                 out.write("\n");
  
              }
          }
!         catch (Exception e)
          {
!             e.printStackTrace();
          }
  
***************
*** 350,394 ****
  
      // 2005-08-23
!     private void exportSchema(Connection db, BufferedWriter out) throws
!         IOException
      {
          // 1. write properties - if not obo property
!         Vector<String> props = OntologySchema.getTermProperties(db) ;
!         for(String attr : props)
          {
              // ![schema]term-property:unit
!             String str = SCHEMA_LEADING +
!                 OntologySchema.TERM_PROPERTY + ":" + attr + "\n" ;
!             out.write(str) ;
  
          }
          // 2. naming policy
!         String value = OntologySchema.getNamingPolicy(db) ;
!         if(value != null)
          {
!             String str = SCHEMA_LEADING + OntologySchema.NAMING_POLICY + ":" +
!                 value + "\n" ;
!             out.write(str) ;
          }
  
          // 3. prefix
!         value = OntologySchema.getPrefix(db) ;
!         if(value != null)
          {
!             String str = SCHEMA_LEADING + OntologySchema.PREFIX + ":" +
!                 value + "\n" ;
!             out.write(str) ;
          }
  
          // 4. a blank line
!         out.write("\n") ;
  
          // 5. write partial orders
          // write typedef like [Typedef]\n  id: part_of \n name: part of
!         Vector<String> relations = OntologySchema.getPartialOrders(db) ;
!         for(String relation : relations)
          {
!             String str = makeTypedef(relation) ;
!             out.write(str) ;
          }
  
--- 330,374 ----
  
      // 2005-08-23
!     private void exportSchema(Connection db, BufferedWriter out)
!             throws IOException
      {
          // 1. write properties - if not obo property
!         Vector<String> props = OntologySchema.getTermProperties(db);
!         for (String attr : props)
          {
              // ![schema]term-property:unit
!             String str = SCHEMA_LEADING + OntologySchema.TERM_PROPERTY + ":"
!                 + attr + "\n";
!             out.write(str);
  
          }
          // 2. naming policy
!         String value = OntologySchema.getNamingPolicy(db);
!         if (value != null)
          {
!             String str = SCHEMA_LEADING + OntologySchema.NAMING_POLICY + ":"
!                 + value + "\n";
!             out.write(str);
          }
  
          // 3. prefix
!         value = OntologySchema.getPrefix(db);
!         if (value != null)
          {
!             String str = SCHEMA_LEADING + OntologySchema.PREFIX + ":" + value
!                 + "\n";
!             out.write(str);
          }
  
          // 4. a blank line
!         out.write("\n");
  
          // 5. write partial orders
          // write typedef like [Typedef]\n  id: part_of \n name: part of
!         Vector<String> relations = OntologySchema.getPartialOrders(db);
!         for (String relation : relations)
          {
!             String str = makeTypedef(relation);
!             out.write(str);
          }