nmrshiftdb-devel — For developers of the NMRShiftDB software and admins of an NMRShiftDB node

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om BaseAtoms.java,1.1,NONE BaseAtomsPeer.java,1.1,NONE BaseBonds.java,1.1,NONE BaseBondsAtomsPeer.java,1.1,NONE BaseBondsPeer.java,1.1,NONE BaseMeasurementConditionsPeer.java,1.1,NONE

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory usw-pr-cvs1:/tmp/cvs-serv7654

Removed Files:
	BaseAtoms.java BaseAtomsPeer.java BaseBonds.java 
	BaseBondsAtomsPeer.java BaseBondsPeer.java 
	BaseMeasurementConditionsPeer.java 
Log Message:
removed om files


--- BaseAtoms.java DELETED ---

--- BaseAtomsPeer.java DELETED ---

--- BaseBonds.java DELETED ---

--- BaseBondsAtomsPeer.java DELETED ---

--- BaseBondsPeer.java DELETED ---

--- BaseMeasurementConditionsPeer.java DELETED ---

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om Bonds.java,1.1,NONE BondsAtoms.java,1.1,NONE BondsAtomsPeer.java,1.1,NONE BondsPeer.java,1.1,NONE MeasurementConditions.java,1.1,NONE MeasurementConditionsPeer.java,1.1,NONE SignalAtoms.java,1.1,NONE SignalAtomsPeer.java,1.1,NONE

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory usw-pr-cvs1:/tmp/cvs-serv5129

Removed Files:
	Bonds.java BondsAtoms.java BondsAtomsPeer.java BondsPeer.java 
	MeasurementConditions.java MeasurementConditionsPeer.java 
	SignalAtoms.java SignalAtomsPeer.java 
Log Message:
removed om files
----------------------------------------------------------------------


--- Bonds.java DELETED ---

--- BondsAtoms.java DELETED ---

--- BondsAtomsPeer.java DELETED ---

--- BondsPeer.java DELETED ---

--- MeasurementConditions.java DELETED ---

--- MeasurementConditionsPeer.java DELETED ---

--- SignalAtoms.java DELETED ---

--- SignalAtomsPeer.java DELETED ---

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om BaseNmrshiftdbUser.java,1.1,1.2 BaseNmrshiftdbUserPeer.java,1.1,1.2 NmrshiftdbUserPeer.java,1.4,1.5 BaseCanonicalName.java,1.1,NONE BaseCanonicalNamePeer.java,1.1,NONE BaseChemicalName.java,1.1,NONE BaseChemicalNamePeer.java,1.1,NONE BaseMolecule.java,1.1,NONE BaseMoleculeNmrshiftdbUser.java,1.1,NONE BaseMoleculeNmrshiftdbUserPeer.java,1.1,NONE BaseMoleculePeer.java,1.1,NONE BaseSignal.java,1.1,NONE BaseSignalPeer.java,1.1,NONE BaseSpectrum.java,1.1,NONE BaseSpectrumPeer.java,1.1,NONE BaseSpectrumType.java,1.1,NONE BaseSpectrumTypePeer.java,1.1,NONE CanonicalName.java,1.1,NONE CanonicalNamePeer.java,1.1,NONE ChemicalName.java,1.1,NONE ChemicalNamePeer.java,1.1,NONE Molecule.java,1.1,NONE MoleculeNmrshiftdbUser.java,1.1,NONE MoleculeNmrshiftdbUserPeer.java,1.1,NONE MoleculePeer.java,1.1,NONE Signal.java,1.1,NONE SignalPeer.java,1.1,NONE Spectrum.java,1.1,NONE SpectrumPeer.java,1.1,NONE SpectrumType.java,1.1,NONE SpectrumTypePeer.java,1.1,NONE

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory usw-pr-cvs1:/tmp/cvs-serv3929

Modified Files:
	BaseNmrshiftdbUser.java BaseNmrshiftdbUserPeer.java 
	NmrshiftdbUserPeer.java 
Removed Files:
	BaseCanonicalName.java BaseCanonicalNamePeer.java 
	BaseChemicalName.java BaseChemicalNamePeer.java 
	BaseMolecule.java BaseMoleculeNmrshiftdbUser.java 
	BaseMoleculeNmrshiftdbUserPeer.java BaseMoleculePeer.java 
	BaseSignal.java BaseSignalPeer.java BaseSpectrum.java 
	BaseSpectrumPeer.java BaseSpectrumType.java 
	BaseSpectrumTypePeer.java CanonicalName.java 
	CanonicalNamePeer.java ChemicalName.java ChemicalNamePeer.java 
	Molecule.java MoleculeNmrshiftdbUser.java 
	MoleculeNmrshiftdbUserPeer.java MoleculePeer.java Signal.java 
	SignalPeer.java Spectrum.java SpectrumPeer.java 
	SpectrumType.java SpectrumTypePeer.java 
Log Message:
removed om files
: ----------------------------------------------------------------------


Index: BaseNmrshiftdbUser.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseNmrshiftdbUser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** BaseNmrshiftdbUser.java	27 Feb 2002 12:34:55 -0000	1.1
--- BaseNmrshiftdbUser.java	28 Feb 2002 13:41:29 -0000	1.2
***************
*** 17,21 ****
   * extended all references should be to NmrshiftdbUser 
   */
! public abstract class BaseNmrshiftdbUser extends TurbineUserAdapter
      implements Retrievable
  {
--- 17,21 ----
   * extended all references should be to NmrshiftdbUser 
   */
! public abstract class BaseNmrshiftdbUser extends org.apache.jetspeed.om.dbpsml.TurbineUser
      implements Retrievable
[...1376 lines suppressed...]
          }
!         lastMoleculeNmrshiftdbUsersCriteria = criteria; 
  
!         return collMoleculeNmrshiftdbUsers;
      }
        
--- 847,859 ----
              // one, just return the collection.
              boolean newCriteria = true;
!                    criteria.add(DBMoleculeNmrshiftdbUserPeer.USER_ID, getUserId() );               
!                if ( !lastDBMoleculeNmrshiftdbUsersCriteria.equals(criteria)  )
              {
!                 collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.doSelectJoinDBMolecule(criteria);
              }
          }
!         lastDBMoleculeNmrshiftdbUsersCriteria = criteria; 
  
!         return collDBMoleculeNmrshiftdbUsers;
      }
        

Index: BaseNmrshiftdbUserPeer.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseNmrshiftdbUserPeer.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** BaseNmrshiftdbUserPeer.java	27 Feb 2002 12:34:55 -0000	1.1
--- BaseNmrshiftdbUserPeer.java	28 Feb 2002 13:41:29 -0000	1.2
***************
*** 20,25 ****
   */
  public abstract class BaseNmrshiftdbUserPeer 
!     extends TurbineUserPeerAdapter
! {
   
      /** number of columns for this peer */
--- 20,25 ----
   */
  public abstract class BaseNmrshiftdbUserPeer 
!     extends org.apache.jetspeed.om.dbpsml.TurbineUserPeer
! {
   
      /** number of columns for this peer */

Index: NmrshiftdbUserPeer.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/NmrshiftdbUserPeer.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -r1.4 -r1.5
*** NmrshiftdbUserPeer.java	27 Feb 2002 14:44:08 -0000	1.4
--- NmrshiftdbUserPeer.java	28 Feb 2002 13:41:29 -0000	1.5
***************
*** 1,3 ****
! package org.openscience.nmrshiftdb.om;
  
  // JDK classes
--- 1,3 ----
! package org.openscience.nmrshiftdb.om;
  
  // JDK classes
***************
*** 5,9 ****
  
  // Village classes
! import com.workingdogs.village.*;
  
  // Turbine classes
--- 5,9 ----
  
  // Village classes
! import com.workingdogs.village.*;
  
  // Turbine classes
***************
*** 12,62 ****
  import org.apache.turbine.util.db.*;
  import org.apache.turbine.util.db.map.*;
! import org.apache.turbine.util.db.pool.DBConnection;
! import org.apache.turbine.om.ObjectKey;
! import org.apache.turbine.services.db.TurbineDB;
! 
! // Local classes
! import org.openscience.nmrshiftdb.om.map.*;
! 
! /**
!   *  You should add additional methods to this class to meet the
!   *  application requirements.  This class will only be generated as
!   *  long as it does not already exist in the output directory.
!   */
! public class NmrshiftdbUserPeer
!     extends org.openscience.nmrshiftdb.om.BaseNmrshiftdbUserPeer
! {
! 	public static NmrshiftdbUser retrieveByPK(ObjectKey pk) throws Exception
! 	{
! 		DBConnection db = null;
! 		NmrshiftdbUser retVal = null;
! 		try
! 		{
! 			db = TurbineDB.getConnection(getMapBuilder().getDatabaseMap().getName());
! 			retVal = retrieveByPK(pk, db);
! 		}
! 		finally
! 		{
! 			if(db != null)
! 			{
! 				TurbineDB.releaseConnection(db);
! 			}
! 		}
! 		return(retVal);
! 	}
! 
! 	public static NmrshiftdbUser retrieveByPK(ObjectKey pk, DBConnection dbcon) throws Exception
! 	{
! 		Criteria criteria = new Criteria();
! 		criteria.add(USER_ID, pk);
! 		Vector v = doSelect(criteria, dbcon);
! 		if(v.size() != 1)
! 		{
! 			throw new Exception("Failed to select one and only one row.");
! 		}
! 		else
! 		{
! 			return(NmrshiftdbUser)v.firstElement();
! 		}
! 	}
! }
--- 12,28 ----
  import org.apache.turbine.util.db.*;
  import org.apache.turbine.util.db.map.*;
! import org.apache.turbine.util.db.pool.DBConnection;
! 
! // Local classes
! import org.openscience.nmrshiftdb.om.map.*;
! 
! /** 
!   *  You should add additional methods to this class to meet the
!   *  application requirements.  This class will only be generated as
!   *  long as it does not already exist in the output directory.
!   */
! public class NmrshiftdbUserPeer 
!     extends org.openscience.nmrshiftdb.om.BaseNmrshiftdbUserPeer
! {
! }
! 

--- BaseCanonicalName.java DELETED ---

--- BaseCanonicalNamePeer.java DELETED ---

--- BaseChemicalName.java DELETED ---

--- BaseChemicalNamePeer.java DELETED ---

--- BaseMolecule.java DELETED ---

--- BaseMoleculeNmrshiftdbUser.java DELETED ---

--- BaseMoleculeNmrshiftdbUserPeer.java DELETED ---

--- BaseMoleculePeer.java DELETED ---

--- BaseSignal.java DELETED ---

--- BaseSignalPeer.java DELETED ---

--- BaseSpectrum.java DELETED ---

--- BaseSpectrumPeer.java DELETED ---

--- BaseSpectrumType.java DELETED ---

--- BaseSpectrumTypePeer.java DELETED ---

--- CanonicalName.java DELETED ---

--- CanonicalNamePeer.java DELETED ---

--- ChemicalName.java DELETED ---

--- ChemicalNamePeer.java DELETED ---

--- Molecule.java DELETED ---

--- MoleculeNmrshiftdbUser.java DELETED ---

--- MoleculeNmrshiftdbUserPeer.java DELETED ---

--- MoleculePeer.java DELETED ---

--- Signal.java DELETED ---

--- SignalPeer.java DELETED ---

--- Spectrum.java DELETED ---

--- SpectrumPeer.java DELETED ---

--- SpectrumType.java DELETED ---

--- SpectrumTypePeer.java DELETED ---

[Nmrshiftdb-devel] CVS: nmrshiftdb/lib vecmath1.2-1.14.jar,1.2,1.3

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib
In directory usw-pr-cvs1:/tmp/cvs-serv1439

Added Files:
	vecmath1.2-1.14.jar 
Log Message:
Needed by CDK

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om NmrshiftdbUserPeer.java,1.3,1.4

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory usw-pr-cvs1:/tmp/cvs-serv939/openscience/nmrshiftdb/om

Modified Files:
	NmrshiftdbUserPeer.java 
Log Message:
modified NmrshiftdbUserPeer.java


Index: NmrshiftdbUserPeer.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/NmrshiftdbUserPeer.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** NmrshiftdbUserPeer.java	27 Feb 2002 14:39:20 -0000	1.3
--- NmrshiftdbUserPeer.java	27 Feb 2002 14:44:08 -0000	1.4
***************
*** 33,37 ****
  		try
  		{
! 			db = TurbineDB.getConnection(getMapBuilder().getDatebaseMap().getName());
  			retVal = retrieveByPK(pk, db);
  		}
--- 33,37 ----
  		try
  		{
! 			db = TurbineDB.getConnection(getMapBuilder().getDatabaseMap().getName());
  			retVal = retrieveByPK(pk, db);
  		}

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om NmrshiftdbUserPeer.java,1.2,1.3

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory usw-pr-cvs1:/tmp/cvs-serv31787/openscience/nmrshiftdb/om

Modified Files:
	NmrshiftdbUserPeer.java 
Log Message:
added NmrshiftdbUserPeer.java


Index: NmrshiftdbUserPeer.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/NmrshiftdbUserPeer.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** NmrshiftdbUserPeer.java	27 Feb 2002 14:37:01 -0000	1.2
--- NmrshiftdbUserPeer.java	27 Feb 2002 14:39:20 -0000	1.3
***************
*** 5,9 ****
  
  // Village classes
! import com.workingdogs.village.*;
  
  // Turbine classes
--- 5,9 ----
  
  // Village classes
! import com.workingdogs.village.*;
  
  // Turbine classes
***************
*** 33,37 ****
  		try
  		{
! 			db = TurbineDB.getConnection(getMapBuilder().getDatebaseMAP().getName());
  			retVal = retrieveByPK(pk, db);
  		}
--- 33,37 ----
  		try
  		{
! 			db = TurbineDB.getConnection(getMapBuilder().getDatebaseMap().getName());
  			retVal = retrieveByPK(pk, db);
  		}

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om NmrshiftdbUserPeer.java,1.1,1.2

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory usw-pr-cvs1:/tmp/cvs-serv31002/openscience/nmrshiftdb/om

Modified Files:
	NmrshiftdbUserPeer.java 
Log Message:
modified NmrshiftdbUserPeer.java


Index: NmrshiftdbUserPeer.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/NmrshiftdbUserPeer.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** NmrshiftdbUserPeer.java	27 Feb 2002 12:34:55 -0000	1.1
--- NmrshiftdbUserPeer.java	27 Feb 2002 14:37:01 -0000	1.2
***************
*** 1,3 ****
! package org.openscience.nmrshiftdb.om;
  
  // JDK classes
--- 1,3 ----
! package org.openscience.nmrshiftdb.om;
  
  // JDK classes
***************
*** 12,28 ****
  import org.apache.turbine.util.db.*;
  import org.apache.turbine.util.db.map.*;
! import org.apache.turbine.util.db.pool.DBConnection;
! 
! // Local classes
! import org.openscience.nmrshiftdb.om.map.*;
! 
! /** 
!   *  You should add additional methods to this class to meet the
!   *  application requirements.  This class will only be generated as
!   *  long as it does not already exist in the output directory.
!   */
! public class NmrshiftdbUserPeer 
!     extends org.openscience.nmrshiftdb.om.BaseNmrshiftdbUserPeer
! {
! }
! 
--- 12,62 ----
  import org.apache.turbine.util.db.*;
  import org.apache.turbine.util.db.map.*;
! import org.apache.turbine.util.db.pool.DBConnection;
! import org.apache.turbine.om.ObjectKey;
! import org.apache.turbine.services.db.TurbineDB;
! 
! // Local classes
! import org.openscience.nmrshiftdb.om.map.*;
! 
! /**
!   *  You should add additional methods to this class to meet the
!   *  application requirements.  This class will only be generated as
!   *  long as it does not already exist in the output directory.
!   */
! public class NmrshiftdbUserPeer
!     extends org.openscience.nmrshiftdb.om.BaseNmrshiftdbUserPeer
! {
! 	public static NmrshiftdbUser retrieveByPK(ObjectKey pk) throws Exception
! 	{
! 		DBConnection db = null;
! 		NmrshiftdbUser retVal = null;
! 		try
! 		{
! 			db = TurbineDB.getConnection(getMapBuilder().getDatebaseMAP().getName());
! 			retVal = retrieveByPK(pk, db);
! 		}
! 		finally
! 		{
! 			if(db != null)
! 			{
! 				TurbineDB.releaseConnection(db);
! 			}
! 		}
! 		return(retVal);
! 	}
! 
! 	public static NmrshiftdbUser retrieveByPK(ObjectKey pk, DBConnection dbcon) throws Exception
! 	{
! 		Criteria criteria = new Criteria();
! 		criteria.add(USER_ID, pk);
! 		Vector v = doSelect(criteria, dbcon);
! 		if(v.size() != 1)
! 		{
! 			throw new Exception("Failed to select one and only one row.");
! 		}
! 		else
! 		{
! 			return(NmrshiftdbUser)v.firstElement();
! 		}
! 	}
! }

[Nmrshiftdb-devel] CVS: nmrshiftdb/lib cdk.jar,NONE,1.1

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib
In directory usw-pr-cvs1:/tmp/cvs-serv24639

Added Files:
	cdk.jar 
Log Message:
The cdk jar


--- NEW FILE: cdk.jar ---
PK


















[...1290 lines suppressed...]







4





€˜
cÒná


L

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/util IntTriple.java,NONE,1.1 SubmittingData.java,NONE,1.1

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util
In directory usw-pr-cvs1:/tmp/cvs-serv21784

Added Files:
	IntTriple.java SubmittingData.java 
Log Message:
They were in utils before


--- NEW FILE: IntTriple.java ---
package org.openscience.nmrshiftdb.util;

public class IntTriple{
	public int value1;
	public int value2;
	public int value3;
	
	public String toString(){
		return(new String(""+value1+" "+value2+" "+value3));
	}
}

--- NEW FILE: SubmittingData.java ---
package org.openscience.nmrshiftdb.util;

import java.util.*;

public class SubmittingData{
	String molecule="";
	ArrayList signalstable=new ArrayList();

	public void setMolecule(String mol){
		molecule=mol;
	}
	
	public String getMolecule(){
		return(molecule);
	}
	
	public void setSignalstable(ArrayList al){
		signalstable=al;
	}
	
	public ArrayList getSignalstable(){
		return(signalstable);
	}
	
	public void addToSignalstable(Object signal){
		signalstable.add(signal);
	}
}

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/utils/gaussian AbInitioDataset.java,1.1.1.1,NONE GaussianParser.java,1.1.1.1,NONE

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/utils/gaussian
In directory usw-pr-cvs1:/tmp/cvs-serv19030

Removed Files:
	AbInitioDataset.java GaussianParser.java 
Log Message:



--- AbInitioDataset.java DELETED ---

--- GaussianParser.java DELETED ---

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/utils/gaussian NMRReference.java,1.1.1.1,NONE

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/utils/gaussian
In directory usw-pr-cvs1:/tmp/cvs-serv19536

Removed Files:
	NMRReference.java 
Log Message:



--- NMRReference.java DELETED ---

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/lib jetspeed-1.3a2-release.jar,1.2,1.3

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/lib
In directory usw-pr-cvs1:/tmp/cvs-serv14784

Added Files:
	jetspeed-1.3a2-release.jar 
Log Message:
added jetspeed-1.3a2-release.jar

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/lib jetspeed-1.3a2-release.jar,1.1,NONE

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/lib
In directory usw-pr-cvs1:/tmp/cvs-serv14283

Removed Files:
	jetspeed-1.3a2-release.jar 
Log Message:
removed jetspeed-1.3a2-release.jar


--- jetspeed-1.3a2-release.jar DELETED ---

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/lib jetspeed-1.3a2-release.jar,NONE,1.1

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/lib
In directory usw-pr-cvs1:/tmp/cvs-serv12617

Added Files:
	jetspeed-1.3a2-release.jar 
Log Message:
added jetspeed-1.3a2-release.jar


--- NEW FILE: jetspeed-1.3a2-release.jar ---
PK
JÛvè»õpL÷…;mˌ÷q|J,ї‘¢'õh¿¶ÓVČá´mÆÂm	1k:gõqÁš¸‰=
”-
ŠS†½Á“^VóiñµÝ
|͉CAIEv¤"†Õ%dsQ=Ö­[¦øv;}v¿™Rpc®=;;•4Œžð IÖn3j¤ãÄFoŽò3µÚÐã´³¸/פY5µcm9D»ÛœýPaÍae ÉŒ›öJú£F|N“^[NÑèíY0Öæœ.ÇKfʦd_\à&´ˆ»Pt+˜ñ鉪e¤Ò1›’¯ÍåÇÞd"ž2«sˆ¦mXº°Ì)ÖꎈYÏމ¥¶Æ{œ?ÕØ5’¶™ˆ+¨rÄÆ
;Ü®ÇzրÑC®ÉÌàôŠ\™Â󹃵¹ƒ¶¥Ç©Ò²Ã]™·Ü¹Ó	)cÊ:ƒgxÑøÞÍ'ç9¶Cú¹8’+E“Ì:¢`ùB'±¸ÇHE-ÓuL±{â”óÇôkgvŠ`›Ê˜0álÂ4:Ã푻¸é1;ß;Sç„R9Rƒ½f\™w‹þÎDڊkMn3ó#h‰ªáF,×ðE4*¨œ -hX‹[4|
71õ‘4£iŽ›'ªúõTUÄ0âU†“14ÄñmWÞ8ÉJÃ2Ü  ±ß¶“áðàà`ò%fd`I41ÎÆ=‡m#e[Fým
…Íø®´i
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[...3068 lines suppressed...]



















åÊ!

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html NewAccount.vm,NONE,1.1

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html
In directory usw-pr-cvs1:/tmp/cvs-serv9812

Added Files:
	NewAccount.vm 
Log Message:
added NewAccount.vm


--- NEW FILE: NewAccount.vm ---
<div align="left">
    <center>
    <table cellpadding="4" cellspacing="0" border="1" class=INPUTFORM>
    <tr>      
      <td>
        <p>
        <h2>$l10n.NEWACCOUNT_TITLE</h2>
        <p>$l10n.NEWACCOUNT_NOTICE<br />
          #if ( $config.getBoolean("newuser.approval.enable") == "false" )
            #if ( $config.getBoolean("newuser.confirm.enable") == "true" )
                $l10n.NEWACCOUNT_CONFIRMATION
            #end
          #else
              $l10n.NEWACCOUNT_APPROVAL<br />
          #end
          <b>$l10n.NEWACCOUNT_INFOEMAILMSG</b>
        </p>
#if ($data.Message)
        <b>$data.Message</b>
        <p />
#end
  <form accept-charset="UTF-8, ISO-8859-1" method="POST" action="$link.setPage("ConfirmRegistration")" enctype="application/x-www-form-urlencoded">
  <input name="$jlink.ActionKey" type="hidden" value="CreateNewUserAndConfirm" />

        <center>
        <table cellpadding="0" cellspacing="0" border="0">
          <tr>
            <td> $l10n.USERFORM_USERNAMEMSG </td>
            <td align=right><input name="username" type="TEXT" value="$!data.Parameters.getString("username")" /> </td>
          </tr>
          <tr>
            <td> $l10n.USERFORM_PASSWORDMSG </td>
            <td align=right><input name="password" type="PASSWORD" value="" /> </td>
          </tr>
          <tr>
            <td> $l10n.USERFORM_PASSWORDCONFIRMMSG </td>
            <td align=right><input name="password_confirm" type="PASSWORD" value="" /> </td>
          </tr>
          <tr>
            <td colspan="2"> <hr size="1" noshade /> </td>
          </tr>
          <tr>
            <td> $l10n.USERFORM_FIRSTNAMEMSG </td>
            <td align=right><input name="firstname" type="TEXT" value="$!data.Parameters.getString("firstname")" /> </td> 
          </tr>
          <tr>
            <td> $l10n.USERFORM_LASTNAMEMSG </td>
            <td align=right><input name="lastname" type="TEXT" value="$!data.Parameters.getString("lastname")" /> </td>
          </tr>
	  <tr>
            <td> Title: </td>
            <td align=right><input name="title" type="TEXT" value="$!data.Parameters.getString("title")" /> </td>
          </tr>
	  <tr>
            <td> Address: </td>
            <td align=right><input name="address" type="TEXT" value="$!data.Parameters.getString("address")" /> </td>
          </tr>
	  <tr>
            <td> City: </td>
            <td align=right><input name="city" type="TEXT" value="$!data.Parameters.getString("city")" /> </td>
          </tr>
	  <tr>
            <td> State: </td>
            <td align=right><input name="state" type="TEXT" value="$!data.Parameters.getString("state")" /> </td>
          </tr>
	  <tr>
            <td> ZIP Code: </td>
            <td align=right><input name="zipcode" type="TEXT" value="$!data.Parameters.getString("zipcode")" /> </td>
          </tr>
	  <tr>
            <td> Country: </td>
            <td align=right><input name="country" type="TEXT" value="$!data.Parameters.getString("country")" /> </td>
          </tr>
          <tr>
            <td> $l10n.USERFORM_EMAILMSG </td>
            <td align=right><input name="email" type="TEXT" value="$!data.Parameters.getString("email")" /> </td>
          </tr>
	  <tr>
            <td> Web Page: </td>
            <td align=right><input name="webpage" type="TEXT" value="$!data.Parameters.getString("webpage")" /> </td>
          </tr>
	  <tr>
            <td> Affiliation: </td>
            <td align=right><input name="affiliation" type="TEXT" value="$!data.Parameters.getString("affiliation")" /> </td>
          </tr>
          <tr>
            <td colspan=2>&nbsp;</td>
          </tr> 
          <tr>
            <td align=left><input name="submit1" type="reset" value="$l10n.USERFORM_RESET" class="BUTON"/></td>
            <td align=right><input name="submit2" type="submit" value="$l10n.USERFORM_CREATE" class="BUTON"/></td>
          </tr>
        </table>
        </center>
      </td>
    </table>
    </center>
  </form>
</div>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html - New directory

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html
In directory usw-pr-cvs1:/tmp/cvs-serv9466/html

Log Message:
Directory /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html added to the repository

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens - New directory

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens
In directory usw-pr-cvs1:/tmp/cvs-serv9232/screens

Log Message:
Directory /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens added to the repository

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/db nmrshiftdb-schema.sql,NONE,1.1 populate-mysql.sql,NONE,1.1 turbine-schema.sql,NONE,1.1 jetspeed.script,1.1,1.2

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db
In directory usw-pr-cvs1:/tmp/cvs-serv7919

Modified Files:
	jetspeed.script 
Added Files:
	nmrshiftdb-schema.sql populate-mysql.sql turbine-schema.sql 
Log Message:
added sql script files


--- NEW FILE: nmrshiftdb-schema.sql ---

# -----------------------------------------------------------------------
# MEASUREMENT_CONDITIONS
# -----------------------------------------------------------------------
drop table if exists MEASUREMENT_CONDITIONS;

CREATE TABLE MEASUREMENT_CONDITIONS
(
    MEASUREMENT_CONDITIONS_ID INTEGER NOT NULL,
    TEMPERATURE FLOAT NOT NULL,
    FIELD_STRENGTH INTEGER NOT NULL,
    SOLVENT MEDIUMTEXT NOT NULL,
    USER_ID INTEGER NOT NULL,
    PRIMARY KEY(MEASUREMENT_CONDITIONS_ID),
    FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
);

# -----------------------------------------------------------------------
# SPECTRUM_TYPE
# -----------------------------------------------------------------------
drop table if exists SPECTRUM_TYPE;

CREATE TABLE SPECTRUM_TYPE
(
    SPECTRUM_TYPE_ID INTEGER NOT NULL,
    DIMENSIONALITY INTEGER NOT NULL,
    NAME MEDIUMTEXT NOT NULL,
    ISOTOPE_1 MEDIUMTEXT NOT NULL,
    ISOTOPE_2 MEDIUMTEXT NOT NULL,
    ISOTOPE_3 MEDIUMTEXT NOT NULL,
    ISOTOPE_4 MEDIUMTEXT NOT NULL,
    ISOTOPE_5 MEDIUMTEXT NOT NULL,
    USER_ID INTEGER NOT NULL,
    PRIMARY KEY(SPECTRUM_TYPE_ID),
    FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
);

# -----------------------------------------------------------------------
# SPECTRUM
# -----------------------------------------------------------------------
drop table if exists SPECTRUM;

CREATE TABLE SPECTRUM
(
    SPECTRUM_ID INTEGER NOT NULL,
    DATE DATETIME NOT NULL,
    SPECFILE LONGBLOB NOT NULL,
    SERIALIZED_SPECTRUM MEDIUMTEXT NOT NULL,
    LITERATURE MEDIUMTEXT NOT NULL,
    REVIEW_FLAG MEDIUMTEXT NOT NULL,
    USER_ID INTEGER NOT NULL,
    MEASUREMENT_CONDITIONS_ID INTEGER NOT NULL,
    SPECTRUM_TYPE_ID INTEGER NOT NULL,
    MOLECULE_ID INTEGER NOT NULL,
    PRIMARY KEY(SPECTRUM_ID),
    FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID),
    FOREIGN KEY (MEASUREMENT_CONDITIONS_ID) REFERENCES MEASUREMENT_CONDITIONS (MEASUREMENT_CONDITIONS_ID),
    FOREIGN KEY (SPECTRUM_TYPE_ID) REFERENCES SPECTRUM_TYPE (SPECTRUM_TYPE_ID),
    FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);

# -----------------------------------------------------------------------
# SIGNAL
# -----------------------------------------------------------------------
drop table if exists SIGNAL;

CREATE TABLE SIGNAL
(
    SIGNAL_ID INTEGER NOT NULL,
    DIMENSIONALITY INTEGER NOT NULL,
    SHIFT_1 FLOAT NOT NULL,
    SHIFT_2 FLOAT NOT NULL,
    SHIFT_3 FLOAT NOT NULL,
    SHIFT_4 FLOAT NOT NULL,
    SHIFT_5 FLOAT NOT NULL,
    SERIALIZED_SIGNAL MEDIUMTEXT NOT NULL,
    SPECTRUM_TYPE_ID INTEGER NOT NULL,
    PRIMARY KEY(SIGNAL_ID),
    FOREIGN KEY (SPECTRUM_TYPE_ID) REFERENCES SPECTRUM_TYPE (SPECTRUM_TYPE_ID)
);

# -----------------------------------------------------------------------
# MOLECULE
# -----------------------------------------------------------------------
drop table if exists MOLECULE;

CREATE TABLE MOLECULE
(
    MOLECULE_ID INTEGER NOT NULL,
    DATE DATETIME NOT NULL,
    STRUCTURE_FILE LONGBLOB NOT NULL,
    MOLECULAR_FORMULA MEDIUMTEXT NOT NULL,
    SERIALIZED_MOLECULE MEDIUMTEXT NOT NULL,
    CAS_NUMBER MEDIUMTEXT NOT NULL,
    NMRSHIFTDB_NUMBER MEDIUMTEXT NOT NULL,
    MOLECULAR_WEIGHT FLOAT NOT NULL,
    USER_ID INTEGER NOT NULL,
    PRIMARY KEY(MOLECULE_ID),
    FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
);

# -----------------------------------------------------------------------
# MOLECULE_NMRSHIFTDB_USER
# -----------------------------------------------------------------------
drop table if exists MOLECULE_NMRSHIFTDB_USER;

CREATE TABLE MOLECULE_NMRSHIFTDB_USER
(
    MOLECULE_ID INTEGER NOT NULL,
    USER_ID INTEGER NOT NULL,
    FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID),
    FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
);

# -----------------------------------------------------------------------
# ATOMS
# -----------------------------------------------------------------------
drop table if exists ATOMS;

CREATE TABLE ATOMS
(
    ATOMS_ID INTEGER NOT NULL,
    SYMBOL MEDIUMTEXT NOT NULL,
    SERIALIZED_ATOMS MEDIUMTEXT NOT NULL,
    MOLECULE_ID INTEGER NOT NULL,
    PRIMARY KEY(ATOMS_ID),
    FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);

# -----------------------------------------------------------------------
# SIGNAL_ATOMS
# -----------------------------------------------------------------------
drop table if exists SIGNAL_ATOMS;

CREATE TABLE SIGNAL_ATOMS
(
    SIGNAL_ID INTEGER NOT NULL,
    ATOMS_ID INTEGER NOT NULL,
    FOREIGN KEY (SIGNAL_ID) REFERENCES SIGNAL (SIGNAL_ID),
    FOREIGN KEY (ATOMS_ID) REFERENCES ATOMS (ATOMS_ID)
);

# -----------------------------------------------------------------------
# BONDS
# -----------------------------------------------------------------------
drop table if exists BONDS;

CREATE TABLE BONDS
(
    BONDS_ID INTEGER NOT NULL,
    DEGREE INTEGER NOT NULL,
    SERIALIZED_BONDS MEDIUMTEXT NOT NULL,
    MOLECULE_ID INTEGER NOT NULL,
    PRIMARY KEY(BONDS_ID),
    FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);

# -----------------------------------------------------------------------
# BONDS_ATOMS
# -----------------------------------------------------------------------
drop table if exists BONDS_ATOMS;

CREATE TABLE BONDS_ATOMS
(
    BONDS_ID INTEGER NOT NULL,
    ATOMS_ID INTEGER NOT NULL,
    FOREIGN KEY (BONDS_ID) REFERENCES BONDS (BONDS_ID),
    FOREIGN KEY (ATOMS_ID) REFERENCES ATOMS (ATOMS_ID)
);

# -----------------------------------------------------------------------
# CHEMICAL_NAME
# -----------------------------------------------------------------------
drop table if exists CHEMICAL_NAME;

CREATE TABLE CHEMICAL_NAME
(
    CHEMICAL_NAME_ID INTEGER NOT NULL,
    NAME MEDIUMTEXT NOT NULL,
    MOLECULE_ID INTEGER NOT NULL,
    PRIMARY KEY(CHEMICAL_NAME_ID),
    FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);

# -----------------------------------------------------------------------
# CANONICAL_NAME
# -----------------------------------------------------------------------
drop table if exists CANONICAL_NAME;

CREATE TABLE CANONICAL_NAME
(
    CANONICAL_NAME_ID INTEGER NOT NULL,
    NAME MEDIUMTEXT NOT NULL,
    TYPE MEDIUMTEXT NOT NULL,
    MOLECULE_ID INTEGER NOT NULL,
    PRIMARY KEY(CANONICAL_NAME_ID),
    FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);
  
  
  
  
  
  
  
  
  
  
  
  

--- NEW FILE: populate-mysql.sql ---
INSERT INTO TURBINE_PERMISSION VALUES(1,'view',NULL);
INSERT INTO TURBINE_PERMISSION VALUES(2,'customize',NULL);
INSERT INTO TURBINE_PERMISSION VALUES(3,'maximize',NULL);
INSERT INTO TURBINE_PERMISSION VALUES(4,'minimize',NULL);
INSERT INTO TURBINE_PERMISSION VALUES(5,'personalize',NULL);
INSERT INTO TURBINE_PERMISSION VALUES(6,'info',NULL);
INSERT INTO TURBINE_PERMISSION VALUES(7,'close',NULL);
INSERT INTO TURBINE_PERMISSION VALUES(8,'detach',NULL);
INSERT INTO TURBINE_ROLE VALUES(1,'user',NULL);
INSERT INTO TURBINE_ROLE VALUES(2,'admin',NULL);
INSERT INTO TURBINE_GROUP VALUES(1,'Jetspeed',NULL);
INSERT INTO TURBINE_GROUP VALUES(2,'apache',NULL);
INSERT INTO TURBINE_USER VALUES(1,'admin','jetspeed','Raphael','Admin','','','','','','','','','ra...@ap...','CONFIRMED',NULL,NULL,NULL,'aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000037708000000050000000274000a4c4153545f4c4f47494e7372000e6a6176612e7574696c2e44617465686a81014b5974190300007870770800000000000000007874000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b0200007870000000a778');
INSERT INTO TURBINE_USER VALUES(2,'turbine','turbine','David','Turbine','','','','','','','','','ta...@ap...','CONFIRMED',NULL,NULL,NULL,'aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000037708000000050000000274000a4c4153545f4c4f47494e7372000e6a6176612e7574696c2e44617465686a81014b5974190300007870770800000000000000007874000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000007478');
INSERT INTO TURBINE_USER VALUES(100,'con','con','con','con','','','','','','','','','shk3@localhost','CONFIRMED',NULL,NULL,'2002-02-12 17:20:05.073','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000001278');
INSERT INTO TURBINE_USER VALUES(110,'rev','rev','rev','rev','','','','','','','','','shk3@localhost','CONFIRMED',NULL,NULL,'2002-02-12 17:20:36.49','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000000d78');
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(1,1);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(1,2);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(1,3);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(1,4);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(1,5);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(1,6);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,1);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,2);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,3);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,4);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,5);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,6);
INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,7);
INSERT INTO TURBINE_USER_GROUP_ROLE VALUES(0,1,1);
INSERT INTO TURBINE_USER_GROUP_ROLE VALUES(1,1,1);
INSERT INTO TURBINE_USER_GROUP_ROLE VALUES(1,1,2);
INSERT INTO ID_TABLE VALUES(1,'TURBINE_PERMISSION',100,10);
INSERT INTO ID_TABLE VALUES(2,'TURBINE_ROLE',120,10);
INSERT INTO ID_TABLE VALUES(3,'TURBINE_GROUP',100,10);
INSERT INTO ID_TABLE VALUES(4,'TURBINE_USER',120,10);
INSERT INTO ID_TABLE VALUES(5,'TURBINE_SCHEDULED_JOB',100,10);
INSERT INTO ID_TABLE VALUES(6,'TURBINE_ROLE_PERMISSION',100,10);
INSERT INTO ID_TABLE VALUES(7,'TURBINE_USER_GROUP_ROLE',100,10);



--- NEW FILE: turbine-schema.sql ---

# -----------------------------------------------------------------------
# TURBINE_PERMISSION
# -----------------------------------------------------------------------
drop table if exists TURBINE_PERMISSION;

CREATE TABLE TURBINE_PERMISSION
(
    PERMISSION_ID INTEGER NOT NULL,
    PERMISSION_NAME VARCHAR (99) NOT NULL,
    OBJECTDATA MEDIUMBLOB,
    PRIMARY KEY(PERMISSION_ID),
    UNIQUE (PERMISSION_NAME),
);

# -----------------------------------------------------------------------
# TURBINE_ROLE
# -----------------------------------------------------------------------
drop table if exists TURBINE_ROLE;

CREATE TABLE TURBINE_ROLE
(
    ROLE_ID INTEGER NOT NULL,
    ROLE_NAME VARCHAR (99) NOT NULL,
    OBJECTDATA MEDIUMBLOB,
    PRIMARY KEY(ROLE_ID),
    UNIQUE (ROLE_NAME),
);

# -----------------------------------------------------------------------
# TURBINE_GROUP
# -----------------------------------------------------------------------
drop table if exists TURBINE_GROUP;

CREATE TABLE TURBINE_GROUP
(
    GROUP_ID INTEGER NOT NULL,
    GROUP_NAME VARCHAR (99) NOT NULL,
    OBJECTDATA MEDIUMBLOB,
    PRIMARY KEY(GROUP_ID),
    UNIQUE (GROUP_NAME),
);

# -----------------------------------------------------------------------
# TURBINE_ROLE_PERMISSION
# -----------------------------------------------------------------------
drop table if exists TURBINE_ROLE_PERMISSION;

CREATE TABLE TURBINE_ROLE_PERMISSION
(
    ROLE_ID INTEGER NOT NULL,
    PERMISSION_ID INTEGER NOT NULL,
    PRIMARY KEY(ROLE_ID,PERMISSION_ID),
    INDEX(PERMISSION_ID),
    FOREIGN KEY (ROLE_ID) REFERENCES TURBINE_ROLE (ROLE_ID),
    FOREIGN KEY (PERMISSION_ID) REFERENCES TURBINE_PERMISSION (PERMISSION_ID),
);

# -----------------------------------------------------------------------
# TURBINE_USER
# -----------------------------------------------------------------------
drop table if exists TURBINE_USER;

CREATE TABLE TURBINE_USER
(
    USER_ID INTEGER NOT NULL,
    LOGIN_NAME VARCHAR (32) NOT NULL,
    PASSWORD_VALUE VARCHAR (32) NOT NULL,
    FIRST_NAME VARCHAR (99) NOT NULL,
    LAST_NAME VARCHAR (99) NOT NULL,
    TITLE VARCHAR (99),
    ADDRESS VARCHAR (99) NOT NULL,
    CITY VARCHAR (99) NOT NULL,
    STATE VARCHAR (99),
    ZIP_CODE VARCHAR (99) NOT NULL,
    COUNTRY VARCHAR (99) NOT NULL,
    WEB_PAGE VARCHAR (99),
    AFFILIATION VARCHAR (99),
    EMAIL VARCHAR (99) NOT NULL,
    CONFIRM_VALUE VARCHAR (99),
    MODIFIED TIMESTAMP,
    CREATED TIMESTAMP,
    LAST_LOGIN TIMESTAMP,
    OBJECTDATA MEDIUMBLOB,
    PRIMARY KEY(USER_ID),
    UNIQUE (LOGIN_NAME),
);

# -----------------------------------------------------------------------
# TURBINE_USER_GROUP_ROLE
# -----------------------------------------------------------------------
drop table if exists TURBINE_USER_GROUP_ROLE;

CREATE TABLE TURBINE_USER_GROUP_ROLE
(
    USER_ID INTEGER NOT NULL,
    GROUP_ID INTEGER NOT NULL,
    ROLE_ID INTEGER NOT NULL,
    PRIMARY KEY(USER_ID,GROUP_ID,ROLE_ID),
    INDEX(GROUP_ID,ROLE_ID),
    INDEX(ROLE_ID),
    FOREIGN KEY (USER_ID) REFERENCES TURBINE_USER (USER_ID),
    FOREIGN KEY (GROUP_ID) REFERENCES TURBINE_GROUP (GROUP_ID),
    FOREIGN KEY (ROLE_ID) REFERENCES TURBINE_ROLE (ROLE_ID),
);

# -----------------------------------------------------------------------
# TURBINE_SCHEDULED_JOB
# -----------------------------------------------------------------------
drop table if exists TURBINE_SCHEDULED_JOB;

CREATE TABLE TURBINE_SCHEDULED_JOB
(
    JOB_ID INTEGER NOT NULL,
    SECOND INTEGER default -1 NOT NULL,
    MINUTE INTEGER default -1 NOT NULL,
    HOUR INTEGER default -1 NOT NULL,
    WEEK_DAY INTEGER default -1 NOT NULL,
    DAY_OF_MONTH INTEGER default -1 NOT NULL,
    TASK VARCHAR (99) NOT NULL,
    EMAIL VARCHAR (99),
    PROPERTY MEDIUMBLOB,
    PRIMARY KEY(JOB_ID),
);

# -----------------------------------------------------------------------
# ID_TABLE
# -----------------------------------------------------------------------
drop table if exists ID_TABLE;

CREATE TABLE ID_TABLE
(
    ID_TABLE_ID INTEGER NOT NULL AUTO_INCREMENT,
    TABLE_NAME VARCHAR (255) NOT NULL,
    NEXT_ID INTEGER,
    QUANTITY INTEGER,
    PRIMARY KEY(ID_TABLE_ID),
    UNIQUE (TABLE_NAME),
);
  
  
  
  
  
  
  
  

Index: jetspeed.script
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db/jetspeed.script,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** jetspeed.script	14 Feb 2002 10:05:24 -0000	1.1
--- jetspeed.script	27 Feb 2002 13:30:45 -0000	1.2
***************
*** 1,3 ****
! CREATE TABLE TURBINE_PERMISSION(PERMISSION_ID INTEGER NOT NULL IDENTITY PRIMARY KEY,PERMISSION_NAME VARCHAR NOT NULL,OBJECTDATA BINARY)
  CREATE TABLE TURBINE_ROLE(ROLE_ID INTEGER NOT NULL IDENTITY PRIMARY KEY,ROLE_NAME VARCHAR NOT NULL,OBJECTDATA BINARY)
  CREATE TABLE TURBINE_GROUP(GROUP_ID INTEGER NOT NULL IDENTITY PRIMARY KEY,GROUP_NAME VARCHAR NOT NULL,OBJECTDATA BINARY)
--- 1,3 ----
! CREATE TABLE TURBINE_PERMISSION(PERMISSION_ID INTEGER NOT NULL IDENTITY PRIMARY KEY,PERMISSION_NAME VARCHAR NOT NULL,OBJECTDATA BINARY)
  CREATE TABLE TURBINE_ROLE(ROLE_ID INTEGER NOT NULL IDENTITY PRIMARY KEY,ROLE_NAME VARCHAR NOT NULL,OBJECTDATA BINARY)
  CREATE TABLE TURBINE_GROUP(GROUP_ID INTEGER NOT NULL IDENTITY PRIMARY KEY,GROUP_NAME VARCHAR NOT NULL,OBJECTDATA BINARY)
***************
*** 53,57 ****
  CREATE ALIAS YEAR FOR "org.hsql.Library.year"
  CREATE ALIAS LEFT FOR "org.hsql.Library.left"
! CREATE ALIAS ROUNDMAGIC FOR "org.hsql.Library.roundMagic"
  CREATE ALIAS BITOR FOR "org.hsql.Library.bitor"
  CREATE ALIAS LTRIM FOR "org.hsql.Library.ltrim"
--- 53,57 ----
  CREATE ALIAS YEAR FOR "org.hsql.Library.year"
  CREATE ALIAS LEFT FOR "org.hsql.Library.left"
! CREATE ALIAS ROUNDMAGIC FOR "org.hsql.Library.roundMagic"
  CREATE ALIAS BITOR FOR "org.hsql.Library.bitor"
  CREATE ALIAS LTRIM FOR "org.hsql.Library.ltrim"
***************
*** 102,111 ****
  INSERT INTO TURBINE_USER VALUES(1,'admin','jetspeed','Jetspeed','Admin','da...@bl...','CONFIRMED',NULL,NULL,'2002-02-11 15:50:42.926','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000016178')
  INSERT INTO TURBINE_USER VALUES(140,'con','con','con','con','shk3@localhost','CONFIRMED',NULL,NULL,'2002-02-12 17:20:05.073','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000001278')
! INSERT INTO TURBINE_USER VALUES(141,'rev','rev','rev','rev','shk3@localhost','CONFIRMED',NULL,NULL,'2002-02-12 17:20:36.49','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000000d78')
! INSERT INTO TURBINE_USER VALUES(161,'c','c','c','c','c','CONFIRMED',NULL,NULL,'2002-02-08 14:41:17.353','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000000678')
! INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,1)
  INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,2)
  INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,3)
! INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,4)
  INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,5)
  INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,6)
--- 102,109 ----
  INSERT INTO TURBINE_USER VALUES(1,'admin','jetspeed','Jetspeed','Admin','da...@bl...','CONFIRMED',NULL,NULL,'2002-02-11 15:50:42.926','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000016178')
  INSERT INTO TURBINE_USER VALUES(140,'con','con','con','con','shk3@localhost','CONFIRMED',NULL,NULL,'2002-02-12 17:20:05.073','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000001278')
! INSERT INTO TURBINE_USER VALUES(141,'rev','rev','rev','rev','shk3@localhost','CONFIRMED',NULL,NULL,'2002-02-12 17:20:36.49','aced0005737200136a6176612e7574696c2e486173687461626c6513bb0f25214ae4b803000246000a6c6f6164466163746f724900097468726573686f6c6478703f400000000000027708000000030000000174000f5f6163636573735f636f756e746572737200116a6176612e6c616e672e496e746567657212e2a0a4f781873802000149000576616c7565787200106a6176612e6c616e672e4e756d62657286ac951d0b94e08b02000078700000000d78')
  INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,2)
  INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,3)
! INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,4)
  INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,5)
  INSERT INTO TURBINE_ROLE_PERMISSION VALUES(2,6)

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/conf NMRShiftDB.properties,NONE,1.1 TurbineResources.properties,1.2,1.3

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf
In directory usw-pr-cvs1:/tmp/cvs-serv6587

Modified Files:
	TurbineResources.properties 
Added Files:
	NMRShiftDB.properties 
Log Message:
added NMRShiftDB.properties


--- NEW FILE: NMRShiftDB.properties ---
EXCLUDEDDOMAINS=hotmail.com yahoo.com aol.com

Index: TurbineResources.properties
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/TurbineResources.properties,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** TurbineResources.properties	18 Feb 2002 16:47:55 -0000	1.2
--- TurbineResources.properties	27 Feb 2002 13:25:52 -0000	1.3
***************
*** 26,29 ****
--- 26,30 ----
  # A facility for system logging.
  services.LoggingService.system.destination.file=/WEB-INF/log/jetspeed.log
+ services.LoggingService.system.destination.console=false
  services.LoggingService.system.className=org.apache.turbine.services.logging.FileLogger
  services.LoggingService.system.level=DEBUG
***************
*** 61,65 ****
  services.LoggingService.rotation.file.backups=5
  services.LoggingService.rotation.className=org.apache.turbine.services.logging.Log4JavaLogger
! services.LoggingService.rotation.level=INFO
  
  # An example configuration for using *NIX syslogd with Log4Java
--- 62,66 ----
  services.LoggingService.rotation.file.backups=5
  services.LoggingService.rotation.className=org.apache.turbine.services.logging.Log4JavaLogger
! services.LoggingService.rotation.level=DEBUG
  
  # An example configuration for using *NIX syslogd with Log4Java
***************
*** 67,71 ****
  services.LoggingService.syslog.destination.syslogd.facility=LOG_DAEMON
  services.LoggingService.syslog.className=org.apache.turbine.services.logging.Log4JavaLogger
! services.LoggingService.syslog.level=INFO
  
  # An example configuration for using remote Log4Java server
--- 68,72 ----
  services.LoggingService.syslog.destination.syslogd.facility=LOG_DAEMON
  services.LoggingService.syslog.className=org.apache.turbine.services.logging.Log4JavaLogger
! services.LoggingService.syslog.level=DEBUG
  
  # An example configuration for using remote Log4Java server
***************
*** 73,80 ****
  services.LoggingService.remote.destination.remote.port=1099
  services.LoggingService.remote.className=org.apache.turbine.services.logging.Log4JavaLogger
! services.LoggingService.remote.level=INFO
  
  # An example configuration for sending error reports as email with Log4Java
! # notes: 
  # * uses 'mail.server' as SMTP server to send mail through
  # * log4j will send the email when an ERROR is logged, with
--- 74,81 ----
  services.LoggingService.remote.destination.remote.port=1099
  services.LoggingService.remote.className=org.apache.turbine.services.logging.Log4JavaLogger
! services.LoggingService.remote.level=DEBUG
  
  # An example configuration for sending error reports as email with Log4Java
! # notes:
  # * uses 'mail.server' as SMTP server to send mail through
  # * log4j will send the email when an ERROR is logged, with
***************
*** 87,91 ****
  services.LoggingService.email.destination.email.buffer.size=512
  services.LoggingService.email.className=org.apache.turbine.services.logging.Log4JavaLogger
! services.LoggingService.email.level=INFO
  
  # -------------------------------------------------------------------
--- 88,92 ----
  services.LoggingService.email.destination.email.buffer.size=512
  services.LoggingService.email.className=org.apache.turbine.services.logging.Log4JavaLogger
! services.LoggingService.email.level=DEBUG
  
  # -------------------------------------------------------------------
***************
*** 102,106 ****
  
  # -------------------------------------------------------------------
! # 
  #  M O D U L E  C A C H I N G
  #
--- 103,107 ----
  
  # -------------------------------------------------------------------
! #
  #  M O D U L E  C A C H I N G
  #
***************
*** 146,150 ****
  
  # -------------------------------------------------------------------
! # 
  #  D A T A B A S E  S E T T I N G S
  #
--- 147,151 ----
  
  # -------------------------------------------------------------------
! #
  #  D A T A B A S E  S E T T I N G S
  #
***************
*** 351,355 ****
  # -------------------------------------------------------------------
  
! database.maps.builder=org.apache.turbine.util.db.map.TurbineMapBuilder
  
  # -------------------------------------------------------------------
--- 352,357 ----
  # -------------------------------------------------------------------
  
! database.maps.builder=org.openscience.nmrshiftdb.util.db.map.TurbineMapBuilderAdapter
! # database.maps.builder=org.apache.turbine.util.db.map.TurbineMapBuilder
  
  # -------------------------------------------------------------------
***************
*** 783,787 ****
  #
  
! services.SecurityService.user.class=org.apache.turbine.om.security.TurbineUser
  
  #
--- 785,790 ----
  #
  
! services.SecurityService.user.class=org.openscience.nmrshiftdb.om.NmrshiftdbUser
! # services.SecurityService.user.class=org.apache.turbine.om.security.TurbineUser
  
  #
***************
*** 794,798 ****
  # Defalut: org.apache.turbine.om.security.peer.TurbineUserPeer
  #
! services.SecurityService.userPeer.class=org.apache.turbine.om.security.peer.TurbineUserPeer
  
  #
--- 797,803 ----
  # Defalut: org.apache.turbine.om.security.peer.TurbineUserPeer
  #
! 
! services.SecurityService.userPeer.class=org.openscience.nmrshiftdb.om.NmrshiftdbUserPeer
! # services.SecurityService.userPeer.class=org.apache.turbine.om.security.peer.TurbineUserPeer
  
  #
***************
*** 967,968 ****
--- 972,974 ----
  include = JetspeedResources.properties
  
+ include = NMRShiftDBResources.properties

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/apache/jetspeed/modules/actions CreateNewUserAndConfirm.java,NONE,1.1

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions
In directory usw-pr-cvs1:/tmp/cvs-serv3826

Added Files:
	CreateNewUserAndConfirm.java 
Log Message:
added CreateNewUserAndConfirm.java added


--- NEW FILE: CreateNewUserAndConfirm.java ---
/* ====================================================================
 * The Apache Software License, Version 1.1
 *
 * Copyright (c) 2000-2001 The Apache Software Foundation.  All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in
 *    the documentation and/or other materials provided with the
 *    distribution.
 *
 * 3. The end-user documentation included with the redistribution,
 *    if any, must include the following acknowledgment:
 *       "This product includes software developed by the
 *        Apache Software Foundation (http://www.apache.org/)."
 *    Alternately, this acknowledgment may appear in the software itself,
 *    if and wherever such third-party acknowledgments normally appear.
 *
 * 4. The names "Apache" and "Apache Software Foundation" and
 *     "Apache Jetspeed" must not be used to endorse or promote products
 *    derived from this software without prior written permission. For
 *    written permission, please contact ap...@ap....
 *
 * 5. Products derived from this software may not be called "Apache" or
 *    "Apache Jetspeed", nor may "Apache" appear in their name, without
 *    prior written permission of the Apache Software Foundation.
 *
 * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
 * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
 * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
 * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
 * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
 * SUCH DAMAGE.
 * ====================================================================
 *
 * This software consists of voluntary contributions made by many
 * individuals on behalf of the Apache Software Foundation.  For more
 * information on the Apache Software Foundation, please see
 * <http://www.apache.org/>.
 */

package org.apache.jetspeed.modules.actions;


// java.util
import java.util.Date;
import java.util.Hashtable;
import java.util.Properties;
import java.util.StringTokenizer;
import java.io.FileInputStream;
import java.lang.String;

import javax.servlet.http.*;

// turbine.modules
import org.apache.turbine.modules.Action;
import org.apache.turbine.modules.ActionLoader;

// resources
import org.apache.turbine.services.localization.Localization;
import org.apache.turbine.services.resources.TurbineResources;
import org.apache.jetspeed.services.resources.JetspeedResources;

// templates
import org.apache.turbine.services.template.TurbineTemplate;

// turbine.util
import org.apache.turbine.util.Log;
import org.apache.turbine.util.RunData;
import org.apache.turbine.util.GenerateUniqueId;
import org.apache.turbine.util.StringUtils;
import org.apache.turbine.util.DynamicURI;

// turbine.om
import org.apache.turbine.om.security.User;

// profiler
import org.apache.jetspeed.services.Profiler;

// security
import org.apache.jetspeed.services.JetspeedSecurity;
import org.apache.turbine.services.security.TurbineSecurity;
import org.apache.turbine.util.security.AccessControlList;

import org.openscience.nmrshiftdb.om.NmrshiftdbUser;
import org.openscience.nmrshiftdb.om.TurbineUserAdapter;
import org.apache.turbine.util.Log;
/**
    This action validates the form input from the NewAccount Screen.
    If it is valid, then it will check to make sure that the user account
    does not already exist. If it does, then it will show the NewAccount
    screen again. If it doesn't alread exist, then it will create the new
    user and set the CONFIRM_VALUE to be the users session id. This part should
    probably be re-done to get a better less hackable CONFIRM_VALUE, but this
    should work for now. If everything goes well, this action will send the user
    a confirmation email and then show the ConfirmRegistration screen.

    @author Jon S. Stevens <a href="mailto:jo...@cl...">jo...@cl...</a>
    @author David S. Taylor <a href="mailto:da...@bl...">da...@bl...</a>
    @author Tom Adams <a href="mailto:to...@PI...">to...@PI...</a>

*/

/**
    Changes made by the NMRShiftDB developers group:
    added the following user attributes
    - title
    - address
    - city
    - state
    - zip code
    - country
    - webpage
    - affiliation

    S.Krause - 20.02.2002

*/

public class CreateNewUserAndConfirm extends Action
{
    public void doPerform( RunData data ) throws Exception
    {
        try
        {

            String submit = "submit1";
            String str = (String) data.getUser().getTemp ( submit, "asdfasdf" );
            if ( str != null && str
                .equalsIgnoreCase( data.getParameters().getString(submit, "")) )
            {
                data.getUser().removeTemp(submit);
                data.setScreenTemplate( TurbineTemplate.getDefaultScreen() );
                return;
            }

            String pass1 = data.getParameters().getString("password", "");
            String pass2 = data.getParameters().getString("password_confirm", "");
            // make sure the passwords are not empty
            if ( (pass1.length() == 0 || pass2.length() == 0 )
                || ! pass1.equals ( pass2 ) )
            {
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_PWNOTMATCH"));
                data.setScreenTemplate("NewAccount");
                return;
            }

            String username = data.getParameters().getString("username", "");
            // make sure the username exists
            if ( username.length() == 0 )
            {
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_NOUSERNAME"));
                data.setScreenTemplate("NewAccount");
                return;
            }
	    
            String email = data.getParameters().getString("email", "");
            // make sure the email exists and test on forbidden email accounts
	    Properties emailProperties = new Properties();
	    try
	    {
	        emailProperties.load(new FileInputStream("/usr/local/jakarta-tomcat-3.3a/webapps/jetspeed/WEB-INF/conf/NMRShiftDB.properties"));
            }
	    catch(Throwable exc)
	    {}
	    StringTokenizer emailToken = new StringTokenizer(email, "@");
	    StringTokenizer emailPropsToken = new StringTokenizer(emailProperties.getProperty("EXCLUDEDDOMAINS"));
	    String emailDom = new String("");
	    boolean isExcludedDomain = false;
	    while ( emailToken.hasMoreTokens() ) 
	    {
                emailDom = emailToken.nextToken();
    	    }
	    while ( emailPropsToken.hasMoreTokens() )
	    {
		if( emailDom.equals(emailPropsToken.nextToken()) )
			isExcludedDomain = true;
	    }	    
	    if ( email.length() == 0 || isExcludedDomain )
            {
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_NOEMAIL"));
                data.setScreenTemplate("NewAccount");
                return;
            }
	    
	    String title = data.getParameters().getString("title", "");
	    String address = data.getParameters().getString("address", "");
	    if ( address.length() == 0 )
            {
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_NOADDRESS"));
                data.setScreenTemplate("NewAccount");
                return;
            }
	    String city = data.getParameters().getString("city", "");
	    if ( city.length() == 0 )
            {
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_NOCITY"));
                data.setScreenTemplate("NewAccount");
                return;
            }
	    String state = data.getParameters().getString("state", "");
	    String zipcode = data.getParameters().getString("zipcode", "");
	    if ( zipcode.length() == 0 )
            {
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_NOZIPCODE"));
                data.setScreenTemplate("NewAccount");
                return;
            }
	    String country = data.getParameters().getString("country", "");
	    if ( country.length() == 0 )
            {
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_NOCOUNTRY"));
                data.setScreenTemplate("NewAccount");
                return;
            }
	    String webpage = data.getParameters().getString("webpage", "");
	    String affiliation = data.getParameters().getString("affiliation", "");

            String CHNAME = Localization.getString("CREATENEWUSERANDCONFIRM_DUPLICATEMSG");

            if (!JetspeedSecurity.accountExists(username))
            {
                Date now = new Date();
		
		NmrshiftdbUser user = (NmrshiftdbUser) JetspeedSecurity.getUserInstance();
		
		user.setUserName( username );
                user.setPassword( pass1 );
                user.setCreateDate(now);
                user.setLastLogin(new Date(0));
                user.setFirstName( data.getParameters().getString("firstname") );
                user.setLastName( data.getParameters().getString("lastname") );
                user.setTitle( data.getParameters().getString("title") );
                user.setAddress( data.getParameters().getString("address") );
                user.setCity( data.getParameters().getString("city") );
                user.setState( data.getParameters().getString("state") );
                user.setZipCode( data.getParameters().getString("zipcode") );
                user.setCountry( data.getParameters().getString("country") );
                user.setWebPage( data.getParameters().getString("webpage") );
                user.setAffiliation( data.getParameters().getString("affiliation") );
                user.setEmail( data.getParameters().getString("email") );

                createUser(user, data);

                // create a unique confirmation string for the new user
                String confirmValue = GenerateUniqueId.getIdentifier();

                // allow for disabling of email for configurations without a mail server
                boolean newUserNotification = JetspeedResources.getBoolean("newuser.notification.enable", false);
                boolean newUserApproval = JetspeedResources.getBoolean("newuser.approval.enable", false);
                boolean enableMail = JetspeedResources.getBoolean("newuser.confirm.email.enable", false);
                if (false == enableMail)
                    confirmValue = JetspeedResources.CONFIRM_VALUE;

                if (true == newUserApproval)
                    confirmValue = JetspeedResources.CONFIRM_VALUE_PENDING;

                user.setConfirmed( confirmValue );

                // Store the user object.
                data.setUser(user);

                JetspeedSecurity.addUser(user, pass1, data);
                if (!enableMail && !newUserApproval)
                {
                  user.setHasLoggedIn(new Boolean (true));
                  user.setLastLogin(new Date(0));
                }
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_CREATE"));
                if (enableMail || newUserNotification || newUserApproval)
                {
                    data.setUser(TurbineSecurity.getAnonymousUser());
                    data.getParameters().add("username", username);
                    data.getParameters().add("password", pass1);
                    if ( ! newUserApproval )
                    {
                        ActionLoader.getInstance().exec(data, "SendConfirmationEmail");
                        data.setScreenTemplate("ConfirmRegistration");
                    }
                    else
                    {
                        data.setScreenTemplate("NewUserAwaitingAcceptance");
                    }
                    // FIXME: Should notification be set when request is made, or when
                    //        user is accepted?
                    if ( newUserNotification )
                    {
                        ActionLoader.getInstance().exec(data, "SendNewUserNotificationEmail");
                    }
                }
                else
                {
                    bypassConfirmMail(data, username, pass1);
                }

            }
            else // username exists. show the screen again.
            {
                data.setMessage(Localization.getString("CREATENEWUSERANDCONFIRM_CHOOSENEWNAME"));
                data.setScreenTemplate("NewAccount");
                // set the username to be the CHNAME string so that it is
                // clear that this needs to be replaced
                data.getParameters().add("username", CHNAME);
            }
        }
        catch (Exception e)
        {
          Log.error("CreateNewUserAndConfirm",e);
          data.setMessage(e.toString());
          data.setStackTrace(StringUtils.stackTrace(e), e);
          data.setScreenTemplate("Error");
        }
    }

    /**
     * createUser creates a new user.
     * Subclasses can override this method - adding additional user property settings as needed.
     * The default implementation does nothing.
     *
     * @param user the new user that has been created
     * @param data the current RunData instance
     *
     * @throws Exception passed up from JetspeedSecurity
     */
    protected void createUser(User user, RunData data) throws Exception
    {
    }

    /**
     * bypassConfirmMail allows configurations to bypass sending the confirmation email
     * The new user is logged on and then redirected to the home page
     *
     * @param data Turbine information.
     * @param username The user's username.
     * @param password The user's password.
     */
    private void bypassConfirmMail(RunData data, String username, String password)
    {
        User usr = null;
        try
        {
          // Authenticate the user and get the object.
          usr = JetspeedSecurity.getAuthenticatedUser( username, password );

          // Store the user object.
          data.setUser(usr);

          // Mark the user as being logged in.
          usr.setHasLoggedIn(new Boolean(true));

          // Set the last_login date in the database.
          usr.updateLastLogin();

          AccessControlList acl = data.getACL();
          if ( acl == null )
          {
              acl = JetspeedSecurity.getACL( data.getUser() );
              data.getSession().setAttribute( AccessControlList.SESSION_KEY,
                                          (Object)acl );
          }
          data.setACL(acl);
          data.save();

          // bring logged on user to homepage with internal redirect
          //data.setScreenTemplate(TurbineTemplate.getDefaultScreen());
          //data.setScreenTemplate("Home");
          DynamicURI duri = new DynamicURI (data);
          duri.addPathInfo(JetspeedResources.PATH_TEMPLATE_KEY, "Home");
          data.getResponse().sendRedirect(duri.toString());

        }
        catch ( Exception e )
        {
            Log.error(e);
            data.setMessage(e.toString());
            data.setStackTrace(StringUtils.stackTrace(e), e);
            data.setScreenTemplate("Error");
        }
      }


}

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/apache/jetspeed/modules/actions - New directory

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions
In directory usw-pr-cvs1:/tmp/cvs-serv3603/actions

Log Message:
Directory /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions added to the repository

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/map AtomsMapBuilder.java,1.1,NONE BondsAtomsMapBuilder.java,1.1,NONE BondsMapBuilder.java,1.1,NONE CanonicalNameMapBuilder.java,1.1,NONE ChemicalNameMapBuilder.java,1.1,NONE MeasurementConditionsMapBuilder.java,1.1,NONE MoleculeMapBuilder.java,1.1,NONE MoleculeTurbineUserMapBuilder.java,1.1,NONE SignalAtomsMapBuilder.java,1.1,NONE SignalMapBuilder.java,1.1,NONE SpectrumMapBuilder.java,1.1,NONE SpectrumTypeMapBuilder.java,1.1,NONE TurbineUserMapBuilder.java,1.1,NONE

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/map
In directory usw-pr-cvs1:/tmp/cvs-serv3471

Removed Files:
	AtomsMapBuilder.java BondsAtomsMapBuilder.java 
	BondsMapBuilder.java CanonicalNameMapBuilder.java 
	ChemicalNameMapBuilder.java 
	MeasurementConditionsMapBuilder.java MoleculeMapBuilder.java 
	MoleculeTurbineUserMapBuilder.java SignalAtomsMapBuilder.java 
	SignalMapBuilder.java SpectrumMapBuilder.java 
	SpectrumTypeMapBuilder.java TurbineUserMapBuilder.java 
Log Message:
Best to go for these


--- AtomsMapBuilder.java DELETED ---

--- BondsAtomsMapBuilder.java DELETED ---

--- BondsMapBuilder.java DELETED ---

--- CanonicalNameMapBuilder.java DELETED ---

--- ChemicalNameMapBuilder.java DELETED ---

--- MeasurementConditionsMapBuilder.java DELETED ---

--- MoleculeMapBuilder.java DELETED ---

--- MoleculeTurbineUserMapBuilder.java DELETED ---

--- SignalAtomsMapBuilder.java DELETED ---

--- SignalMapBuilder.java DELETED ---

--- SpectrumMapBuilder.java DELETED ---

--- SpectrumTypeMapBuilder.java DELETED ---

--- TurbineUserMapBuilder.java DELETED ---

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/apache/jetspeed/modules - New directory

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules
In directory usw-pr-cvs1:/tmp/cvs-serv3428/modules

Log Message:
Directory /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules added to the repository

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/apache/jetspeed - New directory

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed
In directory usw-pr-cvs1:/tmp/cvs-serv3334/jetspeed

Log Message:
Directory /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed added to the repository

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/apache - New directory

[Stefan K. <sk...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache
In directory usw-pr-cvs1:/tmp/cvs-serv3112/apache

Log Message:
Directory /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache added to the repository