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

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets OrderAction.java, 1.28, 1.29

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21218/src/java/org/openscience/nmrshiftdb/modules/actions/portlets

Modified Files:
	OrderAction.java 
Log Message:
this uses new cdk and new saturation stuff. should resolve a long standing problem


Index: OrderAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -r1.28 -r1.29
*** OrderAction.java	6 Oct 2006 20:12:10 -0000	1.28
--- OrderAction.java	9 Oct 2006 13:24:37 -0000	1.29
***************
*** 220,239 ****
        context.put("typesc",getTypesC());
        context.put("typesh",getTypesH());
-       Vector days=new Vector();
-       for (int i=1;i<32;i++){
-     	  days.add(new Integer(i));
-       }
-       context.put("days",days );
-       Vector months=new Vector();
-       for (int i=1;i<13;i++){
-     	  months.add(new Integer(i));
-       }
-       context.put("months",months );
-       Vector years=new Vector();
-       for (int i=2000;i<=new Date().getYear()+1900;i++){
-     	  years.add(new Integer(i));
-       }
-       context.put("years",years );
      }
    }
  
--- 220,239 ----
        context.put("typesc",getTypesC());
        context.put("typesh",getTypesH());
      }
+     Vector days=new Vector();
+     for (int i=1;i<32;i++){
+   	  days.add(new Integer(i));
+     }
+     context.put("days",days );
+     Vector months=new Vector();
+     for (int i=1;i<13;i++){
+   	  months.add(new Integer(i));
+     }
+     context.put("months",months );
+     Vector years=new Vector();
+     for (int i=2000;i<=new Date().getYear()+1900;i++){
+   	  years.add(new Integer(i));
+     }
+     context.put("years",years );
    }
  

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map DBMachineMapBuilder.java, NONE, 1.1

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv649/src/java/org/openscience/nmrshiftdb/om/map

Added Files:
	DBMachineMapBuilder.java 
Log Message:
new file


--- NEW FILE: DBMachineMapBuilder.java ---
package org.openscience.nmrshiftdb.om.map;

import java.util.*;
import java.math.*;
import org.apache.turbine.services.db.PoolBrokerService;
import org.apache.turbine.services.db.TurbineDB;
import org.apache.turbine.util.db.map.MapBuilder;
import org.apache.turbine.util.db.map.DatabaseMap;
import org.apache.turbine.util.db.map.TableMap;

/**
 */
public class DBMachineMapBuilder implements MapBuilder
{
    /** the name of this class */
    public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBMachineMapBuilder";

    /** item */
    public static String getTable( )
    {
        return "MACHINE";
    }


    /** MACHINE.MACHINE_ID */
    public static String getDBMachine_MachineId()
    {
        return getTable() + ".MACHINE_ID";
    }

    /** MACHINE.NAME */
    public static String getDBMachine_Name()
    {
        return getTable() + ".NAME";
    }

    /** MACHINE.FIELD_STRENGTH */
    public static String getDBMachine_FieldStrength()
    {
        return getTable() + ".FIELD_STRENGTH";
    }

    /**  the database map  */
    private DatabaseMap dbMap = null;

    /**
        tells us if this DatabaseMapBuilder is built so that we don't have
        to re-build it every time
    */
    public boolean isBuilt()
    {
        if ( dbMap != null )
            return true;
        return false;
    }

    /**  gets the databasemap this map builder built.  */
    public DatabaseMap getDatabaseMap()
    {
        return this.dbMap;
    }
    /** the doBuild() method builds the DatabaseMap */
    public void doBuild() throws Exception
    {
        dbMap = TurbineDB.getDatabaseMap("default");

        dbMap.addTable(getTable());
        TableMap tMap = dbMap.getTable(getTable());

                tMap.setPrimaryKeyMethod(TableMap.IDBROKERTABLE);
        


                  tMap.addPrimaryKey ( getDBMachine_MachineId(), new Integer(0) );
          
                  tMap.addColumn ( getDBMachine_Name(), new String() );
          
                  tMap.addForeignKey ( getDBMachine_FieldStrength(), new Integer(0) , "CONDITION" , "CONDITION_ID" );
          
    }

}

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om BaseDBMachine.java, NONE, 1.1 BaseDBMachinePeer.java, NONE, 1.1 DBMachine.java, NONE, 1.1 DBMachinePeer.java, NONE, 1.1

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31468/src/java/org/openscience/nmrshiftdb/om

Added Files:
	BaseDBMachine.java BaseDBMachinePeer.java DBMachine.java 
	DBMachinePeer.java 
Log Message:
new files


--- NEW FILE: BaseDBMachine.java ---
package org.openscience.nmrshiftdb.om;


import java.util.*;
import java.math.*;
import org.apache.turbine.om.*;
import org.apache.turbine.om.peer.BasePeer;
import org.apache.turbine.util.db.Criteria;
import org.apache.turbine.util.ObjectUtils;
import org.apache.turbine.util.StringUtils;
import org.apache.turbine.util.ParameterParser;
import org.apache.turbine.util.Log;
import org.apache.turbine.util.db.pool.DBConnection;

/** 
 * You should not use this class directly.  It should not even be
 * extended all references should be to DBMachine 
 */
public abstract class BaseDBMachine extends BaseObject
    implements Retrievable
{
          /** the value for the machine_id field */
    private NumberKey machine_id;
          /** the value for the name field */
    private String name;
          /** the value for the field_strength field */
    private NumberKey field_strength;
  

      /**
     * Get the MachineId
     * @return NumberKey
     */
     public NumberKey getMachineId()
     {
          return machine_id;
     }

                                                            
    /**
     * Set the value of MachineId
     */
     public void setMachineId(NumberKey v ) throws Exception
     {
  
       
        
                
          // update associated DBSample
          if (collDBSamples != null )
          {
              for (int i=0; i<collDBSamples.size(); i++)
              {
                  ((DBSample)collDBSamples.get(i))
                      .setMachine(v);
              }
          }
       

         if ( !ObjectUtils.equals(this.machine_id, v) )
        {
                       if (this.machine_id == null)
            {
                this.machine_id = new NumberKey(v);
            }
            else
            {
                this.machine_id.setValue(v);
            }
                      setModified(true);
        }
     }

     /**
    * Set the value of MachineId as a string.
    */
    public void setMachineId(String v ) throws Exception
    {
         setMachineId(new NumberKey(v));
    }
  
    /**
     * Get the Name
     * @return String
     */
     public String getName()
     {
          return name;
     }

                            
    /**
     * Set the value of Name
     */
     public void setName(String v ) 
     {
  
  

         if ( !ObjectUtils.equals(this.name, v) )
        {
                       this.name = v;
                      setModified(true);
        }
     }

  
    /**
     * Get the FieldStrength
     * @return NumberKey
     */
     public NumberKey getFieldStrength()
     {
          return field_strength;
     }

                                    
    /**
     * Set the value of FieldStrength
     */
     public void setFieldStrength(NumberKey v ) throws Exception
     {
              aDBCondition = null;
  
  

         if ( !ObjectUtils.equals(this.field_strength, v) )
        {
                       if (this.field_strength == null)
            {
                this.field_strength = new NumberKey(v);
            }
            else
            {
                this.field_strength.setValue(v);
            }
                      setModified(true);
        }
     }

     /**
    * Set the value of FieldStrength as a string.
    */
    public void setFieldStrength(String v ) throws Exception
    {
         setFieldStrength(new NumberKey(v));
    }
  

 
 
   
             
   
   
    private DBCondition aDBCondition;

    /**
     * Declares an association between this object and a DBCondition object
     *
     * @param DBCondition v
     */
    public void setDBCondition(DBCondition v) throws Exception
    {
           setFieldStrength(v.getConditionId());
           aDBCondition = v;
    }

                     
    public DBCondition getDBCondition() throws Exception
    {
        if ( aDBCondition==null && (!ObjectUtils.equals(this.field_strength, null)) )
        {
            aDBCondition = DBConditionPeer.retrieveByPK(this.field_strength);
            // The following can be used instead of the line above to
            // guarantee the related object contains a reference
            // to this object, but this level of coupling 
            // may be undesirable in many circumstances.
            // As it can lead to a db query with many results that may
            // never be used.  
            // DBCondition obj = DBConditionPeer.retrieveByPK(this.field_strength);
            // obj.addDBMachines(this);
        }
        return aDBCondition;
    }


    /**
     * Provides convenient way to set a relationship based on a 
     * ObjectKey.  e.g. 
     * <code>bar.setFooKey(foo.getPrimaryKey())</code>
     *
     */
    public void setDBConditionKey(ObjectKey key) throws Exception
    {
            setFieldStrength((NumberKey)key);        
        }

    
                
      
    /**
     * Collection to store aggregation of collDBSamples
     */
    protected Vector collDBSamples;
    /**
     * Temporary storage of collDBSamples to save a possible db hit in
     * the event objects are add to the collection, but the
     * complete collection is never requested.
     */
//    private Vector tempcollDBSamples;

    protected void initDBSamples()
    {
        if (collDBSamples == null)
            collDBSamples = new Vector();
    }

    /**
     * Method called to associate a DBSample object to this object
     * through the DBSample foreign key attribute
     *
     * @param DBSample l
     */
    public void addDBSample(DBSample l) throws Exception
    {
        /*
        if (collDBSamples == null)
        {
            if (tempcollDBSamples == null)
            {
                tempcollDBSamples = new Vector();
            }
            tempcollDBSamples.add(l);
        }
        else
        {
            collDBSamples.add(l);
        }
        */
        getDBSamples().add(l);
        l.setDBMachine((DBMachine)this);
    }

    /**
     * The criteria used to select the current contents of collDBSamples
     */
    private Criteria lastDBSamplesCriteria = null;

    /**
     * If this collection has already been initialized, returns
     * the collection. Otherwise returns the results of 
     * getDBSamples(new Criteria())
     */
    public Vector getDBSamples() throws Exception
    {
        if (collDBSamples == null)
        {
            collDBSamples = getDBSamples(new Criteria(10));
        }
        return collDBSamples;
    }

    /**
     * If this collection has already been initialized with
     * an identical criteria, it returns the collection. 
     * Otherwise if this DBMachine has previously
     * been saved, it will retrieve related DBSamples from storage.
     * If this DBMachine is new, it will return
     * an empty collection or the current collection, the criteria
     * is ignored on a new object. 
     */
    public Vector getDBSamples(Criteria criteria) throws Exception
    {
        if (collDBSamples == null)
        {
            if ( isNew() ) 
            {
               collDBSamples = new Vector();       
            } 
            else
            {
                   criteria.add(DBSamplePeer.MACHINE, getMachineId() );               
                   collDBSamples = DBSamplePeer.doSelect(criteria);
            }
/*
            if (tempcollDBSamples != null)
            {
                for (int i=0; i<tempcollDBSamples.size(); i++)
                {
                    collDBSamples.add(tempcollDBSamples.get(i));
                }
                tempcollDBSamples = null;
            }
*/
        }
        else
        {
           // criteria has no effect for a new object
            if ( !isNew() ) 
            {
                // the following code is to determine if a new query is
                // called for.  If the criteria is the same as the last
                // one, just return the collection.
                   criteria.add(DBSamplePeer.MACHINE, getMachineId() );               
                   if ( !lastDBSamplesCriteria.equals(criteria)  )
                {
                    collDBSamples = DBSamplePeer.doSelect(criteria);  
                }
            }
        }
        lastDBSamplesCriteria = criteria; 

        return collDBSamples;
    }
      

        
      
      
          
                    
                
        
        
   
    /**
     * If this collection has already been initialized with
     * an identical criteria, it returns the collection. 
     * Otherwise if this DBMachine is new, it will return
     * an empty collection; or if this DBMachine has previously
     * been saved, it will retrieve related DBSamples from storage.
     */
    protected Vector getDBSamplesJoinNmrshiftdbUser(Criteria criteria) 
        throws Exception
    {
        if (collDBSamples == null)
        {
            if ( isNew() ) 
            {
               collDBSamples = new Vector();       
            } 
            else
            {
                   criteria.add(DBSamplePeer.MACHINE, getMachineId() );               
                   collDBSamples = DBSamplePeer.doSelectJoinNmrshiftdbUser(criteria);
            }
            
            
        }
        else
        {
            // the following code is to determine if a new query is
            // called for.  If the criteria is the same as the last
            // one, just return the collection.
            boolean newCriteria = true;
                   criteria.add(DBSamplePeer.MACHINE, getMachineId() );               
               if ( !lastDBSamplesCriteria.equals(criteria)  )
            {
                collDBSamples = DBSamplePeer.doSelectJoinNmrshiftdbUser(criteria);
            }
        }
        lastDBSamplesCriteria = criteria; 

        return collDBSamples;
    }
      
      
      
          
                    
                
        
        
   
    /**
     * If this collection has already been initialized with
     * an identical criteria, it returns the collection. 
     * Otherwise if this DBMachine is new, it will return
     * an empty collection; or if this DBMachine has previously
     * been saved, it will retrieve related DBSamples from storage.
     */
    protected Vector getDBSamplesJoinDBCondition(Criteria criteria) 
        throws Exception
    {
        if (collDBSamples == null)
        {
            if ( isNew() ) 
            {
               collDBSamples = new Vector();       
            } 
            else
            {
                   criteria.add(DBSamplePeer.MACHINE, getMachineId() );               
                   collDBSamples = DBSamplePeer.doSelectJoinDBCondition(criteria);
            }
            
            
        }
        else
        {
            // the following code is to determine if a new query is
            // called for.  If the criteria is the same as the last
            // one, just return the collection.
            boolean newCriteria = true;
                   criteria.add(DBSamplePeer.MACHINE, getMachineId() );               
               if ( !lastDBSamplesCriteria.equals(criteria)  )
            {
                collDBSamples = DBSamplePeer.doSelectJoinDBCondition(criteria);
            }
        }
        lastDBSamplesCriteria = criteria; 

        return collDBSamples;
    }
      
      
         
          
                    
                
        
        
       
      
      
          
                    
                
        
        
   
    /**
     * If this collection has already been initialized with
     * an identical criteria, it returns the collection. 
     * Otherwise if this DBMachine is new, it will return
     * an empty collection; or if this DBMachine has previously
     * been saved, it will retrieve related DBSamples from storage.
     */
    protected Vector getDBSamplesJoinDBMolecule(Criteria criteria) 
        throws Exception
    {
        if (collDBSamples == null)
        {
            if ( isNew() ) 
            {
               collDBSamples = new Vector();       
            } 
            else
            {
                   criteria.add(DBSamplePeer.MACHINE, getMachineId() );               
                   collDBSamples = DBSamplePeer.doSelectJoinDBMolecule(criteria);
            }
            
            
        }
        else
        {
            // the following code is to determine if a new query is
            // called for.  If the criteria is the same as the last
            // one, just return the collection.
            boolean newCriteria = true;
                   criteria.add(DBSamplePeer.MACHINE, getMachineId() );               
               if ( !lastDBSamplesCriteria.equals(criteria)  )
            {
                collDBSamples = DBSamplePeer.doSelectJoinDBMolecule(criteria);
            }
        }
        lastDBSamplesCriteria = criteria; 

        return collDBSamples;
    }
     



     
    
    private static Vector fieldNames_ = null;

    /**
     * Generate a list of field names.
     */
    public static synchronized List getFieldNames()
    {
      if (fieldNames_ == null)
      {
        fieldNames_ = new Vector();
            fieldNames_.add("MachineId");
            fieldNames_.add("Name");
            fieldNames_.add("FieldStrength");
          }
      return fieldNames_;
    }

    /**
     * Retrieves a field from the object by name passed in
     * as a String.
     */
    public Object getByName(String name)
    {
            if (name.equals("MachineId"))
	{
	  	    return getMachineId();
	  	}
            if (name.equals("Name"))
	{
	  	    return getName();
	  	}
            if (name.equals("FieldStrength"))
	{
	  	    return getFieldStrength();
	  	}
            return null; 
    }
    /**
     * Retrieves a field from the object by name passed in
     * as a String.  The String must be one of the static
     * Strings defined in this Class' Peer.
     */
    public Object getByPeerName(String name)
    {
            if (name.equals(DBMachinePeer.MACHINE_ID ))
	    {
	  	    return getMachineId();
	  	}
            if (name.equals(DBMachinePeer.NAME ))
	    {
	  	    return getName();
	  	}
            if (name.equals(DBMachinePeer.FIELD_STRENGTH ))
	    {
	  	    return getFieldStrength();
	  	}
            return null; 
    }

    /**
     * Retrieves a field from the object by Position as specified
     * in the xml schema.  Zero-based.
     */
    public Object getByPosition(int pos)
    {
            if ( pos == 0 )
	{
	  	    return getMachineId();
	  	}
            if ( pos == 1 )
	{
	  	    return getName();
	  	}
            if ( pos == 2 )
	{
	  	    return getFieldStrength();
	  	}
                return null; 
    }

     	

    /**
     * Stores the object in the database.  If the object is new,
     * it inserts it; otherwise an update is performed.
     */
    public void save() throws Exception
    {
             save(DBMachinePeer.getMapBuilder()
                .getDatabaseMap().getName());
     }

    /**
     * Stores the object in the database.  If the object is new,
     * it inserts it; otherwise an update is performed.
     */
    public void save(String dbName) throws Exception
    {
        DBConnection dbCon = null;
         try
        {
            dbCon = BasePeer.beginTransaction(dbName);
            save(dbCon);
        }
        catch(Exception e)
        {
            BasePeer.rollBackTransaction(dbCon);
            throw e;
        }
        BasePeer.commitTransaction(dbCon);

     }

      // flag to prevent endless save loop, if this object is referenced
    // by another object which falls in this transaction.
    private boolean alreadyInSave = false;
      /**
     * Stores the object in the database.  If the object is new,
     * it inserts it; otherwise an update is performed.  This method
     * is meant to be used as part of a transaction, otherwise use
     * the save() method and the connection details will be handled
     * internally
     */
    public void save(DBConnection dbCon) throws Exception
    {
        if (!alreadyInSave)
      {
        alreadyInSave = true;
          if (isModified())
        {
            if (isNew())
            {
                DBMachinePeer.doInsert((DBMachine)this, dbCon);
                setNew(false);
            }
            else
            {
                DBMachinePeer.doUpdate((DBMachine)this, dbCon);
            }
        }

                                    
                
          if (collDBSamples != null )
          {
              for (int i=0; i<collDBSamples.size(); i++)
              {
                  ((DBSample)collDBSamples.get(i)).save(dbCon);
              }
          }
                  alreadyInSave = false;
      }
      }


                        
    
    

        /** 
     * Set the PrimaryKey using ObjectKey.
     *
     * @param ObjectKey machine_id
     */
    public void setPrimaryKey(ObjectKey machine_id) 
        throws Exception {
         setMachineId((NumberKey)machine_id);
    }

    /** 
     * Set the PrimaryKey using a String.
     */
    public void setPrimaryKey(String key) throws Exception
    {
        setMachineId(new NumberKey(key) );
    }



    /** 
     * returns an id that differentiates this object from others
     * of its class.
     */
    public ObjectKey getPrimaryKey() 
    {
        return getMachineId();
    }

 
    /** 
     * get an id that differentiates this object from others
     * of its class.
     */
    public String getQueryKey() 
    {
        if (getPrimaryKey() == null)
        {
            return "";
        }
        else
        {
            return getPrimaryKey().toString();
        }
    }

    /** 
     * set an id that differentiates this object from others
     * of its class.
     */
    public void setQueryKey(String key) 
        throws Exception
    {
        setPrimaryKey(key);
    }

    /**
     * Makes a copy of this object.  
     * It creates a new object filling in the simple attributes.
     * It then fills all the association collections and sets the
     * related objects to isNew=true.
     */
    public DBMachine copy() throws Exception
    {
        DBMachine copyObj = new DBMachine();
        copyObj.setMachineId(machine_id);
        copyObj.setName(name);
        copyObj.setFieldStrength(field_strength);


                                    
                
         List v = copyObj.getDBSamples();
         for (int i=0; i<v.size(); i++)
         {
             ((Persistent)v.get(i)).setNew(true);
         }
              
            copyObj.setMachineId((NumberKey)null);
                    return copyObj;
    }
}


--- NEW FILE: BaseDBMachinePeer.java ---
package org.openscience.nmrshiftdb.om;

import java.util.*;
import java.math.*;
import java.sql.*;
import com.workingdogs.village.*;
import org.apache.turbine.om.*;
import org.apache.turbine.om.peer.*;
import org.apache.turbine.util.*;
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.services.db.TurbineDB;
import org.apache.turbine.util.TurbineException;

// Local classes
import org.openscience.nmrshiftdb.om.map.*;

/**
 */
public abstract class BaseDBMachinePeer 
    extends BasePeer
{

    /** the mapbuilder for this class */
    private static final DBMachineMapBuilder mapBuilder = 
        (DBMachineMapBuilder)getMapBuilder(DBMachineMapBuilder.CLASS_NAME);

    /** the table name for this class */
    public static final String TABLE_NAME = mapBuilder.getTable();

    /** 
     * @return the map builder for this peer
     */
    public static MapBuilder getMapBuilder()
    {
       return(mapBuilder);
    }

    /** the column name for the MACHINE_ID field */
    public static final String MACHINE_ID = mapBuilder.getDBMachine_MachineId();
    /** the column name for the NAME field */
    public static final String NAME = mapBuilder.getDBMachine_Name();
    /** the column name for the FIELD_STRENGTH field */
    public static final String FIELD_STRENGTH = mapBuilder.getDBMachine_FieldStrength();

 
    /** number of columns for this peer */
    public static final int numColumns =  3;

    /** A class that can be returned by this peer. */
    protected static final String CLASSNAME_DEFAULT = 
        "org.openscience.nmrshiftdb.om.DBMachine";

    /** A class that can be returned by this peer. */
    protected static final Class CLASS_DEFAULT = initClass();

    /** Initialization method for static CLASS_DEFAULT attribute */
    private static Class initClass()
    {
        Class c = null;
        try
        { 
            c = Class.forName(CLASSNAME_DEFAULT);
        }
        catch (Exception e)
        {
            Log.error("A FATAL ERROR has occurred which should not" +
                "have happened under any circumstance.  Please notify" +
                "Turbine and give as many details as possible including the " +
                "error stacktrace.", e);
        }
        return c;
    }


    /**
     * Get the list of objects for a ResultSet.  Please not that your
     * resultset MUST return columns in the right order.  You can use
     * getFieldNames() in BaseObject to get the correct sequence.
     */
    public static Vector resultSet2Objects (java.sql.ResultSet results) throws Exception
    {
        QueryDataSet qds = null;
        Vector rows = null;
        try
        {
            qds = new QueryDataSet( results );
            rows = getSelectResults( qds );
        }
        finally
        {
            if (qds != null) qds.close();
        }

        return populateObjects (rows);

    }



    /** Method to do inserts */
    public static ObjectKey doInsert( Criteria criteria ) throws Exception
    {
                                                           return BasePeer.doInsert( criteria );
    }

    /** 
     * Method to do inserts.  This method is to be used during a transaction,
     * otherwise use the doInsert(Criteria) method.  It will take care of 
     * the connection details internally. 
     */
    public static ObjectKey doInsert( Criteria criteria, DBConnection dbCon ) 
        throws Exception
    {
                                                           return BasePeer.doInsert( criteria, dbCon );
    }

    /** Add all the columns needed to create a new object */
    public static void addSelectColumns (Criteria criteria) throws Exception
    {
            criteria.addSelectColumn( MACHINE_ID );
            criteria.addSelectColumn( NAME );
            criteria.addSelectColumn( FIELD_STRENGTH );
        }


    /** 
     * Create a new object of type cls from a resultset row starting
     * from a specified offset.  This is done so that you can select
     * other rows than just those needed for this object.  You may
     * for example want to create two objects from the same row.
     */
    public static DBMachine row2Object (Record row, 
                                              int offset, 
                                              Class cls ) 
        throws Exception
    {
        DBMachine obj = (DBMachine)cls.newInstance();
        populateObject(row, offset, obj);
                    obj.setModified(false);
                obj.setNew(false);

        return obj;
    }

    /** 
     * Populates an object from a resultset row starting
     * from a specified offset.  This is done so that you can select
     * other rows than just those needed for this object.  You may
     * for example want to create two objects from the same row.
     */
    public static void populateObject (Record row, 
                                       int offset, 
                                       DBMachine obj ) 
        throws Exception
    {
                                                        obj.setMachineId(
                new NumberKey(row.getValue(offset+0).asBigDecimal()));
                                                                            obj.setName(row.getValue(offset+1).asString());
                                                                            obj.setFieldStrength(
                new NumberKey(row.getValue(offset+2).asBigDecimal()));
                                        }

    /** Method to do selects */
    public static Vector doSelect( Criteria criteria ) throws Exception
    {
        return populateObjects( doSelectVillageRecords(criteria) ); 
    }


    /** Method to do selects within a transaction */
    public static Vector doSelect( Criteria criteria, 
                                   DBConnection dbCon ) 
        throws Exception
    {
        return populateObjects( doSelectVillageRecords(criteria, dbCon) ); 
    }

    /** 
     * Grabs the raw Village records to be formed into objects.
     * This method handles connections internally.  The Record objects
     * returned by this method should be considered readonly.  Do not
     * alter the data and call save(), your results may vary, but are
     * certainly likely to result in hard to track MT bugs.
     */
    public static Vector doSelectVillageRecords( Criteria criteria ) 
        throws Exception
    {
            if (criteria.getSelectColumns().size() == 0)
        {
            addSelectColumns ( criteria );
        }

                                               
        // BasePeer returns a Vector of Value (Village) arrays.  The array
        // order follows the order columns were placed in the Select clause.
        return BasePeer.doSelect(criteria);
    }


    /** 
     * Grabs the raw Village records to be formed into objects.
     * This method should be used for transactions 
     */
    public static Vector doSelectVillageRecords( Criteria criteria, 
                                                 DBConnection dbCon ) 
        throws Exception
    {
        if (criteria.getSelectColumns().size() == 0)
        {
            addSelectColumns ( criteria );
        }

                                               
        // BasePeer returns a Vector of Value (Village) arrays.  The array
        // order follows the order columns were placed in the Select clause.
        return BasePeer.doSelect(criteria, dbCon);
    }

    /** 
     * The returned vector will contain objects of the default type or
     * objects that inherit from the default.
     */
    public static Vector populateObjects(Vector records) 
        throws Exception
    {
        Vector results = new Vector(records.size());

        // populate the object(s)
        for ( int i=0; i<records.size(); i++ )
        {
            Record row = (Record)records.elementAt(i);
            results.add(DBMachinePeer.row2Object(row, 1,
                DBMachinePeer.getOMClass()));
        }
        return results;
    }
 

    /** 
     * The class that the Peer will make instances of. 
     * If the BO is abstract then you must implement this method
     * in the BO.
     */
    public static Class getOMClass() 
        throws Exception
    {
            return CLASS_DEFAULT;
        }


    /**
     * Method to do updates. 
     *
     * @param Criteria object containing data that is used to create the UPDATE statement.
     */
    public static void doUpdate(Criteria criteria) throws Exception
    {
            Criteria selectCriteria = new
            Criteria(mapBuilder.getDatabaseMap().getName(), 2);
                                selectCriteria.put( MACHINE_ID, criteria.remove(MACHINE_ID) );
                                                                     BasePeer.doUpdate( selectCriteria, criteria );
    }

    /** 
     * Method to do updates.  This method is to be used during a transaction,
     * otherwise use the doUpdate(Criteria) method.  It will take care of 
     * the connection details internally. 
     *
     * @param Criteria object containing data that is used to create the UPDATE statement.
     */
    public static void doUpdate(Criteria criteria, DBConnection dbCon) throws Exception
    {
            Criteria selectCriteria = new
            Criteria(mapBuilder.getDatabaseMap().getName(), 2);
                                selectCriteria.put( MACHINE_ID, criteria.remove(MACHINE_ID) );
                                                                     BasePeer.doUpdate( selectCriteria, criteria, dbCon );
     }

    /** 
     * Method to do deletes.
     *
     * @param Criteria object containing data that is used DELETE from database.
     */
     public static void doDelete(Criteria criteria) throws Exception
     {
                                                            BasePeer.doDelete ( criteria );
     }

    /** 
     * Method to do deletes.  This method is to be used during a transaction,
     * otherwise use the doDelete(Criteria) method.  It will take care of 
     * the connection details internally. 
     *
     * @param Criteria object containing data that is used DELETE from database.
     */
     public static void doDelete(Criteria criteria, DBConnection dbCon) throws Exception
     {
                                                            BasePeer.doDelete ( criteria, dbCon );
     }

    /** Method to do inserts */
    public static void doInsert( DBMachine obj ) throws Exception
    {
                obj.setPrimaryKey(doInsert(buildCriteria(obj)));
                obj.setNew(false);
    }

    /**
     * @param obj the data object to update in the database.
     */
    public static void doUpdate(DBMachine obj) throws Exception
    {
        doUpdate(buildCriteria(obj));
    }
    /**
     * @param obj the data object to delete in the database.
     */
    public static void doDelete(DBMachine obj) throws Exception
    {
        doDelete(buildCriteria(obj));
    }

    /** 
     * Method to do inserts.  This method is to be used during a transaction,
     * otherwise use the doInsert(DBMachine) method.  It will take 
     * care of the connection details internally. 
     *
     * @param obj the data object to insert into the database.
     */
    public static void doInsert( DBMachine obj, DBConnection dbCon) throws Exception
    {
                obj.setPrimaryKey(doInsert(buildCriteria(obj), dbCon));
                obj.setNew(false);
    }

    /**
     * Method to do update.  This method is to be used during a transaction,
     * otherwise use the doUpdate(DBMachine) method.  It will take 
     * care of the connection details internally. 
     *
     * @param obj the data object to update in the database.
     */
    public static void doUpdate(DBMachine obj, DBConnection dbCon) throws Exception
    {
        doUpdate(buildCriteria(obj), dbCon);
    }
    /**
     * Method to delete.  This method is to be used during a transaction,
     * otherwise use the doDelete(DBMachine) method.  It will take 
     * care of the connection details internally. 
     *
     * @param obj the data object to delete in the database.
     */
    public static void doDelete(DBMachine obj, DBConnection dbCon) throws Exception
    {
        doDelete(buildCriteria(obj), dbCon);
    }

    /** Build a Criteria object from the data object for this peer */
    public static Criteria buildCriteria( DBMachine obj )
    {
        Criteria criteria = new Criteria();
                            if ( !obj.isNew() )
                       criteria.add( MACHINE_ID, obj.getMachineId() );
                                criteria.add( NAME, obj.getName() );
                                criteria.add( FIELD_STRENGTH, obj.getFieldStrength() );
                return criteria;
    }

    /** 
     * Retrieve a single object by pk
     *
     * @param ObjectKey pk
     */
    public static DBMachine retrieveByPK( ObjectKey pk )
        throws Exception
    {
        DBConnection db = null;
        DBMachine retVal = null;
       try
        {
           db = TurbineDB.getConnection( mapBuilder.getDatabaseMap().getName() );
           retVal = retrieveByPK( pk, db );
        }
        finally
        {
           if (db != null)
              TurbineDB.releaseConnection(db);
        }
        return(retVal);
    }

    /** 
     * Retrieve a single object by pk
     *
     * @param ObjectKey pk
     * @param DBConnection dbcon
     */
    public static DBMachine retrieveByPK( ObjectKey pk, DBConnection dbcon )
        throws Exception
    {

        Criteria criteria = new Criteria();
            criteria.add( MACHINE_ID, pk );
        Vector v = doSelect(criteria, dbcon);
        if ( v.size() != 1)
        {
            throw new Exception("Failed to select one and only one row.");
        }
        else
        {
            return (DBMachine)v.firstElement();
        }
    }



 

     
        
                       
     
          


   /**
    * selects a collection of DBMachine objects pre-filled with their
    * DBCondition objects.
    */
    protected static Vector doSelectJoinDBCondition(Criteria c)
        throws Exception
    {
         c.setDbName(mapBuilder.getDatabaseMap().getName());

        DBMachinePeer.addSelectColumns(c);
        int offset = numColumns + 1;
        DBConditionPeer.addSelectColumns(c);


                  c.addJoin(DBMachinePeer.FIELD_STRENGTH,
            DBConditionPeer.CONDITION_ID);
     



                                                       
        Vector rows = BasePeer.doSelect(c);
        Vector results = new Vector();

        for (int i=0; i<rows.size(); i++)
        {
            Record row = (Record)rows.elementAt(i);

            Class omClass = DBMachinePeer.getOMClass();

            DBMachine obj1 = (DBMachine)DBMachinePeer
                .row2Object( row, 1, omClass);


             omClass = DBConditionPeer.getOMClass();
            DBCondition obj2 = (DBCondition)DBConditionPeer
                .row2Object(row, offset, omClass);
            
            boolean newObject = true;
            for (int j=0; j<results.size(); j++)
            {
                DBMachine temp_obj1 = (DBMachine)results.elementAt(j);
                DBCondition temp_obj2 = temp_obj1.getDBCondition();
                if ( temp_obj2.getPrimaryKey().equals(obj2.getPrimaryKey() ) )
                {
                    newObject = false;
                    temp_obj2.addDBMachine(obj1);
                    break;
                }
            }
            if (newObject)
            {
                obj2.initDBMachines();
                obj2.addDBMachine(obj1);
            }
            results.add(obj1);

        }

        return results;
    }
    

  


    /** 
     * Returns the TableMap related to this peer.  This method is not 
     * needed for general use but a specific application could have a
     * need.
     */
    protected static TableMap getTableMap()
    {
        return mapBuilder.getDatabaseMap().getTable(TABLE_NAME);
    }     
 

}


--- NEW FILE: DBMachine.java ---
package org.openscience.nmrshiftdb.om;


// JDK classes
import java.util.*;

// Turbine classes
import org.apache.turbine.om.*;
import org.apache.turbine.om.peer.BasePeer;
import org.apache.turbine.util.db.Criteria;
import org.apache.turbine.util.ObjectUtils;
import org.apache.turbine.util.StringUtils;
import org.apache.turbine.util.ParameterParser;
import org.apache.turbine.util.Log;
import org.apache.turbine.util.db.pool.DBConnection;

/** 
  * 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 DBMachine 
    extends org.openscience.nmrshiftdb.om.BaseDBMachine
    implements Persistent
{
}




--- NEW FILE: DBMachinePeer.java ---
package org.openscience.nmrshiftdb.om;

// JDK classes
import java.util.*;

// Village classes
import com.workingdogs.village.*;

// Turbine classes
import org.apache.turbine.om.peer.*;
import org.apache.turbine.util.*;
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 DBMachinePeer 
    extends org.openscience.nmrshiftdb.om.BaseDBMachinePeer
{
}

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/sql nmrshiftdb-schema.sql, 1.79, 1.80

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/sql
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28569/src/sql

Modified Files:
	nmrshiftdb-schema.sql 
Log Message:
orders now assigned to spectrometers


Index: nmrshiftdb-schema.sql
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/nmrshiftdb-schema.sql,v
retrieving revision 1.79
retrieving revision 1.80
diff -C2 -r1.79 -r1.80
*** nmrshiftdb-schema.sql	11 Sep 2006 14:21:16 -0000	1.79
--- nmrshiftdb-schema.sql	6 Oct 2006 20:12:11 -0000	1.80
***************
*** 812,815 ****
--- 812,829 ----
    
  # -----------------------------------------------------------------------
+ # MACHINE
+ # -----------------------------------------------------------------------
+ drop table if exists MACHINE;
+ 
+ CREATE TABLE MACHINE
+ (
+     MACHINE_ID INTEGER NOT NULL,
+     NAME VARCHAR (20) NOT NULL,
+     FIELD_STRENGTH INTEGER NOT NULL,
+     PRIMARY KEY(MACHINE_ID),
+     FOREIGN KEY (FIELD_STRENGTH) REFERENCES CONDITION (CONDITION_ID),
+ );
+ 
+ # -----------------------------------------------------------------------
  # SAMPLE
  # -----------------------------------------------------------------------
***************
*** 822,826 ****
      USER_ID INTEGER NOT NULL,
      SOLVENT INTEGER NOT NULL,
!     FIELD_STRENGTH INTEGER NOT NULL,
      PROBABLE_STRUCTURE INTEGER,
      DATE DATETIME NOT NULL,
--- 836,840 ----
      USER_ID INTEGER NOT NULL,
      SOLVENT INTEGER NOT NULL,
!     MACHINE INTEGER NOT NULL,
      PROBABLE_STRUCTURE INTEGER,
      DATE DATETIME NOT NULL,
***************
*** 833,840 ****
      FOREIGN KEY (USER_ID) REFERENCES TURBINE_USER (USER_ID),
      FOREIGN KEY (SOLVENT) REFERENCES CONDITION (CONDITION_ID),
!     FOREIGN KEY (FIELD_STRENGTH) REFERENCES CONDITION (CONDITION_ID),
      FOREIGN KEY (PROBABLE_STRUCTURE) REFERENCES MOLECULE (MOLECULE_ID),
!     INDEX USER_ID_INDEX (USER_ID)
!    
  );  
  
--- 847,853 ----
      FOREIGN KEY (USER_ID) REFERENCES TURBINE_USER (USER_ID),
      FOREIGN KEY (SOLVENT) REFERENCES CONDITION (CONDITION_ID),
!     FOREIGN KEY (MACHINE) REFERENCES MACHINE (MACHINE_ID),
      FOREIGN KEY (PROBABLE_STRUCTURE) REFERENCES MOLECULE (MOLECULE_ID),
!     INDEX USER_ID_INDEX (USER_ID)   
  );  
  

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.40, 1.41 worker-order.vm, 1.19, 1.20

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28569/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm worker-order.vm 
Log Message:
orders now assigned to spectrometers


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -r1.40 -r1.41
*** user-order.vm	6 Oct 2006 14:27:48 -0000	1.40
--- user-order.vm	6 Oct 2006 20:12:11 -0000	1.41
***************
*** 132,136 ****
                      </select>
          #else
!           : $sample.getDBConditionRelatedBySolvent().getValue()
          #end
          <br>
--- 132,136 ----
                      </select>
          #else
!           : $sample.getDBCondition().getValue()
          #end
          <br>
***************
*** 191,203 ****
          #end
          <br>
!         Field Strength
          #if($submitorshow=="submit")
            : <select name="fstrengths" size="1" onChange="document.restform.elements['fstrength'].value=''">
            #foreach($existingcondition in $fstrengths)
!             <option value="$existingcondition.getConditionId()" #if($strength==$existingcondition.getValue()) selected #end>$existingcondition.getValue()</option>
            #end
            </select>
          #else
!           : $sample.getDBConditionRelatedByFieldStrength().getValue()
          #end
          <br>
--- 191,203 ----
          #end
          <br>
!         Spectrometer 
          #if($submitorshow=="submit")
            : <select name="fstrengths" size="1" onChange="document.restform.elements['fstrength'].value=''">
            #foreach($existingcondition in $fstrengths)
!             <option value="$existingcondition.getMachineId()" #if($strength==$existingcondition.getMachineId()) selected #end>$existingcondition.getName() ($existingcondition.getDBCondition().getValue() Mhz)</option>
            #end
            </select>
          #else
!           : $sample.getDBMachine().getName() ($sample.getDBMachine().getDBCondition().getValue()
          #end
          <br>

Index: worker-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -r1.19 -r1.20
*** worker-order.vm	6 Oct 2006 13:00:05 -0000	1.19
--- worker-order.vm	6 Oct 2006 20:12:11 -0000	1.20
***************
*** 8,67 ****
          #else
            The following orders for your labgroup wait to be fullfilled:
!           <table border="3" rules="cols"><tr><td align="left" valign="top">
!           <table>
!           	<tr><th>250 MHz</th></tr>
!             #foreach($sample in $openorders250)
!               #set($greyorwhite=$velocityCount%2)
!               <tr 
!               #if($greyorwhite==0)
!                 bgcolor="#D3D3D3" 
!               #end
!               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
!             #end
!           </table></td><td align="left" valign="top">
!           <table>
!           	<tr><th>300 MHz</th></tr>
!             #foreach($sample in $openorders300)
!               #set($greyorwhite=$velocityCount%2)
!               <tr 
!               #if($greyorwhite==0)
!                 bgcolor="#D3D3D3" 
!               #end
!               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
!             #end
!           </table></td><td align="left" valign="top">
!           <table>
!           	<tr><th>400 MHz</th></tr>
!             #foreach($sample in $openorders400)
!               #set($greyorwhite=$velocityCount%2)
!               <tr 
!               #if($greyorwhite==0)
!                 bgcolor="#D3D3D3" 
!               #end
!               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
!             #end
!           </table></td><td align="left" valign="top">
!           <table>
!           	<tr><th>500 MHz</th></tr>
!             #foreach($sample in $openorders500)
!               #set($greyorwhite=$velocityCount%2)
!               <tr 
!               #if($greyorwhite==0)
!                 bgcolor="#D3D3D3" 
!               #end
!               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
!             #end
!           </table></td><td align="left" valign="top">
!           <table>
!           	<tr><th>600 MHz</th></tr>
!             #foreach($sample in $openorders600)
!               #set($greyorwhite=$velocityCount%2)
!               <tr 
!               #if($greyorwhite==0)
!                 bgcolor="#D3D3D3" 
!               #end
!               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
!             #end
!           </table></td></tr></table>
          #end
        </td>
--- 8,27 ----
          #else
            The following orders for your labgroup wait to be fullfilled:
!           <table border="3" rules="cols"><tr>
!           #foreach($machine in $machines)
! 	          <td align="left" valign="top">
! 	          <table>
! 	          	<tr><th>$machine.getName() ($machine.getDBCondition().getValue() Mhz)</th></tr>
! 	            #foreach($sample in $openorders.get($machine.getMachineId()))
! 	              #set($greyorwhite=$velocityCount%2)
! 	              <tr 
! 	              #if($greyorwhite==0)
! 	                bgcolor="#D3D3D3" 
! 	              #end
! 	              ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
! 	            #end
! 	          </table></td>
!           #end
! 		  </tr></table>
          #end
        </td>
***************
*** 75,83 ****
            Sample I. D.: $sample.getUsersId()<br>
            Date: $date<br>
!           Solvent: $sample.getDBConditionRelatedBySolvent().getValue()<br>
            #if($image)
              <img src="$image"><br>
            #end
!           Field Strength: $sample.getDBConditionRelatedByFieldStrength().getValue()<br>
            $sample.getWishedSpectrum()<br>
            Other nuclei (please specify): $sample.getOtherNuclei()<br>
--- 35,43 ----
            Sample I. D.: $sample.getUsersId()<br>
            Date: $date<br>
!           Solvent: $sample.getDBConditionRelated().getValue()<br>
            #if($image)
              <img src="$image"><br>
            #end
!           Spectrometer: $sample.getDBMachine() ($sample.getDBMachine().getDBCondition().getValue()<br>
            $sample.getWishedSpectrum()<br>
            Other nuclei (please specify): $sample.getOtherNuclei()<br>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map DBSampleMapBuilder.java, 1.6, 1.7

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28569/src/java/org/openscience/nmrshiftdb/om/map

Modified Files:
	DBSampleMapBuilder.java 
Log Message:
orders now assigned to spectrometers


Index: DBSampleMapBuilder.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map/DBSampleMapBuilder.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -r1.6 -r1.7
*** DBSampleMapBuilder.java	11 Sep 2006 14:21:16 -0000	1.6
--- DBSampleMapBuilder.java	6 Oct 2006 20:12:11 -0000	1.7
***************
*** 47,54 ****
      }
  
!     /** SAMPLE.FIELD_STRENGTH */
!     public static String getDBSample_FieldStrength()
      {
!         return getTable() + ".FIELD_STRENGTH";
      }
  
--- 47,54 ----
      }
  
!     /** SAMPLE.MACHINE */
!     public static String getDBSample_Machine()
      {
!         return getTable() + ".MACHINE";
      }
  
***************
*** 134,138 ****
                    tMap.addForeignKey ( getDBSample_Solvent(), new Integer(0) , "CONDITION" , "CONDITION_ID" );
            
!                   tMap.addForeignKey ( getDBSample_FieldStrength(), new Integer(0) , "CONDITION" , "CONDITION_ID" );
            
                    tMap.addForeignKey ( getDBSample_ProbableStructure(), new Integer(0) , "MOLECULE" , "MOLECULE_ID" );
--- 134,138 ----
                    tMap.addForeignKey ( getDBSample_Solvent(), new Integer(0) , "CONDITION" , "CONDITION_ID" );
            
!                   tMap.addForeignKey ( getDBSample_Machine(), new Integer(0) , "MACHINE" , "MACHINE_ID" );
            
                    tMap.addForeignKey ( getDBSample_ProbableStructure(), new Integer(0) , "MOLECULE" , "MOLECULE_ID" );

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets OrderAction.java, 1.27, 1.28 OrderFullfillAction.java, 1.23, 1.24

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28569/src/java/org/openscience/nmrshiftdb/modules/actions/portlets

Modified Files:
	OrderAction.java OrderFullfillAction.java 
Log Message:
orders now assigned to spectrometers


Index: OrderAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -r1.27 -r1.28
*** OrderAction.java	6 Oct 2006 13:00:04 -0000	1.27
--- OrderAction.java	6 Oct 2006 20:12:10 -0000	1.28
***************
*** 6,13 ****
  import java.io.StringReader;
  import java.text.SimpleDateFormat;
- import java.util.Calendar;
  import java.util.Collections;
  import java.util.Date;
- import java.util.GregorianCalendar;
  import java.util.Locale;
  import java.util.Vector;
--- 6,11 ----
***************
*** 25,28 ****
--- 23,28 ----
  import org.openscience.nmrshiftdb.om.DBCondition;
  import org.openscience.nmrshiftdb.om.DBConditionPeer;
+ import org.openscience.nmrshiftdb.om.DBMachine;
+ import org.openscience.nmrshiftdb.om.DBMachinePeer;
  import org.openscience.nmrshiftdb.om.DBRawFile;
  import org.openscience.nmrshiftdb.om.DBRawFileDBSpectrumPeer;
***************
*** 151,159 ****
          context.put("probablestructure",toshow.getProbableStructure());
        //The mol is put into the MView applet via a file
!       File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol"));
!       FileWriter out = new FileWriter(outputFile);
!       out.write(toshow.getDBMolecule().getStructureFile(1,false));
!       out.close();
!       context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName());
        //this is for the self fullfill
        if(toshow.getProcess().equals(this.SELF) && toshow.getFinished().equals("false")){
--- 151,161 ----
          context.put("probablestructure",toshow.getProbableStructure());
        //The mol is put into the MView applet via a file
!       if(!new String(toshow.getProbableStructure()+"").equals("")){
! 	      File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol"));
! 	      FileWriter out = new FileWriter(outputFile);
! 	      out.write(toshow.getDBMolecule().getStructureFile(1,false));
! 	      out.close();
! 	      context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName());
!       }
        //this is for the self fullfill
        if(toshow.getProcess().equals(this.SELF) && toshow.getFinished().equals("false")){
***************
*** 214,230 ****
        crit.add(DBConditionPeer.CONDITION_TYPE_ID,"2");
        context.put("solvents", DBConditionPeer.doSelect(crit));
!       Vector strengths=new Vector();
!       crit.add(DBConditionPeer.CONDITION_TYPE_ID,"3");
!       crit.add(DBConditionPeer.VALUE,"250");
!       strengths.addAll(DBConditionPeer.doSelect(crit));
!       crit.add(DBConditionPeer.VALUE,"300");
!       strengths.addAll(DBConditionPeer.doSelect(crit));
!       crit.add(DBConditionPeer.VALUE,"400");
!       strengths.addAll(DBConditionPeer.doSelect(crit));
!       crit.add(DBConditionPeer.VALUE,"500");
!       strengths.addAll(DBConditionPeer.doSelect(crit));
!       crit.add(DBConditionPeer.VALUE,"600");
!       strengths.addAll(DBConditionPeer.doSelect(crit));
!       context.put("fstrengths", strengths);
        context.put("data",data);
        context.put("typesc",getTypesC());
--- 216,220 ----
        crit.add(DBConditionPeer.CONDITION_TYPE_ID,"2");
        context.put("solvents", DBConditionPeer.doSelect(crit));
!       context.put("fstrengths", DBMachinePeer.doSelect(new Criteria()));
        context.put("data",data);
        context.put("typesc",getTypesC());
***************
*** 293,301 ****
          solvent=(DBCondition)DBConditionPeer.doSelect(crit).get(0);
        }
!       sample.setDBConditionRelatedBySolvent(solvent);
        Criteria crit=new Criteria();
!       crit.add(DBConditionPeer.CONDITION_ID,data.getParameters().get("fstrengths"));
!       DBCondition fstrength=(DBCondition)DBConditionPeer.doSelect(crit).get(0);
!       sample.setDBConditionRelatedByFieldStrength(fstrength);
        String molecule = data.getParameters().get("MolTxt");
        Molecule mol = (Molecule) new MDLReader(new StringReader(molecule)).read(new Molecule());
--- 283,291 ----
          solvent=(DBCondition)DBConditionPeer.doSelect(crit).get(0);
        }
!       sample.setDBCondition(solvent);
        Criteria crit=new Criteria();
!       crit.add(DBMachinePeer.MACHINE_ID,data.getParameters().get("fstrengths"));
!       DBMachine fstrength=(DBMachine)DBMachinePeer.doSelect(crit).get(0);
!       sample.setDBMachine(fstrength);
        String molecule = data.getParameters().get("MolTxt");
        Molecule mol = (Molecule) new MDLReader(new StringReader(molecule)).read(new Molecule());
***************
*** 341,344 ****
--- 331,335 ----
            context.put("care",sample.getSpecialCare());
            context.put("nuclei",wishedSpectrum);
+           context.put("strength",fstrength.getMachineId());
            if(mol!= null && mol.getAtomCount()>0){
    	        //The mol is put into the MView applet via a file

Index: OrderFullfillAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -r1.23 -r1.24
*** OrderFullfillAction.java	6 Oct 2006 13:00:04 -0000	1.23
--- OrderFullfillAction.java	6 Oct 2006 20:12:10 -0000	1.24
***************
*** 6,10 ****
  import java.util.Collections;
  import java.util.Comparator;
! import java.util.Date;
  import java.util.Vector;
  import java.util.zip.ZipOutputStream;
--- 6,10 ----
  import java.util.Collections;
  import java.util.Comparator;
! import java.util.HashMap;
  import java.util.Vector;
  import java.util.zip.ZipOutputStream;
***************
*** 19,24 ****
  import org.apache.turbine.util.db.Criteria;
  import org.apache.velocity.context.Context;
- import org.openscience.nmrshiftdb.om.DBConditionPeer;
  import org.openscience.nmrshiftdb.om.DBLabGroupPeer;
  import org.openscience.nmrshiftdb.om.DBRawFile;
  import org.openscience.nmrshiftdb.om.DBSample;
--- 19,25 ----
  import org.apache.turbine.util.db.Criteria;
  import org.apache.velocity.context.Context;
  import org.openscience.nmrshiftdb.om.DBLabGroupPeer;
+ import org.openscience.nmrshiftdb.om.DBMachine;
+ import org.openscience.nmrshiftdb.om.DBMachinePeer;
  import org.openscience.nmrshiftdb.om.DBRawFile;
  import org.openscience.nmrshiftdb.om.DBSample;
***************
*** 52,55 ****
--- 53,59 ----
    private void buildOrderContext(Context context, RunData data) throws Exception{
      Criteria crit=new Criteria();
+     Vector machines=DBMachinePeer.doSelect(crit);
+     context.put("machines",machines);
+     crit=new Criteria();
      crit.addJoin(DBSamplePeer.USER_ID,NmrshiftdbUserPeer.USER_ID);
      crit.addJoin(NmrshiftdbUserPeer.LABGROUP,DBLabGroupPeer.LABGROUP_ID);
***************
*** 57,73 ****
      crit.add(DBSamplePeer.FINISHED, "false");
      crit.add(DBSamplePeer.PROCESS,OrderAction.WORKER);
-     crit.addJoin(DBSamplePeer.FIELD_STRENGTH, DBConditionPeer.CONDITION_ID);
-     crit.add(DBConditionPeer.CONDITION_TYPE_ID,"3");
-     crit.add(DBConditionPeer.VALUE,"250");
      crit.addDescendingOrderByColumn(DBSamplePeer.DATE);
!     context.put("openorders250",DBSamplePeer.doSelect(crit));
!     crit.add(DBConditionPeer.VALUE,"300");
!     context.put("openorders300",DBSamplePeer.doSelect(crit));
!     crit.add(DBConditionPeer.VALUE,"400");
!     context.put("openorders400",DBSamplePeer.doSelect(crit));
!     crit.add(DBConditionPeer.VALUE,"500");
!     context.put("openorders500",DBSamplePeer.doSelect(crit));
!     crit.add(DBConditionPeer.VALUE,"600");
!     context.put("openorders600",DBSamplePeer.doSelect(crit));
      context.put("data", data);
      context.put("submitorshow","submit");
--- 61,71 ----
      crit.add(DBSamplePeer.FINISHED, "false");
      crit.add(DBSamplePeer.PROCESS,OrderAction.WORKER);
      crit.addDescendingOrderByColumn(DBSamplePeer.DATE);
!     HashMap openorders=new HashMap();
!     for(int i=0;i<machines.size();i++){
!     	crit.add(DBSamplePeer.MACHINE,((DBMachine)machines.get(i)).getMachineId());
!     	openorders.put(((DBMachine)machines.get(i)).getMachineId(),DBSamplePeer.doSelect(crit));
!     }
!     context.put("openorders",openorders);
      context.put("data", data);
      context.put("submitorshow","submit");

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates homeportlet.vm, 1.43, 1.44

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17181/src/vmtemplates

Modified Files:
	homeportlet.vm 
Log Message:
some changes


Index: homeportlet.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/homeportlet.vm,v
retrieving revision 1.43
retrieving revision 1.44
diff -C2 -r1.43 -r1.44
*** homeportlet.vm	6 Oct 2006 13:00:05 -0000	1.43
--- homeportlet.vm	6 Oct 2006 14:27:48 -0000	1.44
***************
*** 9,13 ****
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/links.html">Links</a><br>
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/faq.html">FAQ</a><br>
!       <a href="mailto:$!config.getString("mail.support")" tabindex="4">Contact</a><br>
        #if ($data.User.hasLoggedIn())
  	      <a href="$link.setAction("LogoutUser")">$l10n.TOP_LOGOUT</a><br>
--- 9,13 ----
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/links.html">Links</a><br>
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/faq.html">FAQ</a><br>
!       <a href="mailto:$email" tabindex="4">Contact</a><br>
        #if ($data.User.hasLoggedIn())
  	      <a href="$link.setAction("LogoutUser")">$l10n.TOP_LOGOUT</a><br>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/navigations/html top.vm, 1.25, 1.26

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/navigations/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17181/src/conf/jetspeed/WEB-INF/templates/vm/navigations/html

Modified Files:
	top.vm 
Log Message:
some changes


Index: top.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/navigations/html/top.vm,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -r1.25 -r1.26
*** top.vm	23 Sep 2006 16:02:13 -0000	1.25
--- top.vm	6 Oct 2006 14:27:47 -0000	1.26
***************
*** 23,26 ****
--- 23,27 ----
        <td align=center class=MENUBUTTON><a href="$link.setPage("EditAccount");jsessionid=$data.getSession().getId()">Personal Page ($data.User.UserName)</a></td>
        <td align=center class=MENUBUTTON><NOBR>&nbsp;&nbsp;<a href="$link.setPage("ResetInterface")" tabindex="4">Reset User Interface</a>&nbsp;&nbsp;</NOBR></td>
+       <td align=center class=MENUBUTTON><a href="$link.setAction("LogoutUser")">$l10n.TOP_LOGOUT</a></td>
      </tr>
      </table>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.39, 1.40

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17181/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm 
Log Message:
some changes


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -r1.39 -r1.40
*** user-order.vm	6 Oct 2006 13:00:05 -0000	1.39
--- user-order.vm	6 Oct 2006 14:27:48 -0000	1.40
***************
*** 65,69 ****
                  bgcolor="#D3D3D3" 
                #end
!               ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
            </table>
--- 65,69 ----
                  bgcolor="#D3D3D3" 
                #end
!               ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a> ($sample.getDate())</td></tr>
              #end
            </table>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons BuildHomeDaemon.java, 1.51, 1.52

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17181/src/java/org/openscience/nmrshiftdb/daemons

Modified Files:
	BuildHomeDaemon.java 
Log Message:
some changes


Index: BuildHomeDaemon.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/BuildHomeDaemon.java,v
retrieving revision 1.51
retrieving revision 1.52
diff -C2 -r1.51 -r1.52
*** BuildHomeDaemon.java	23 Aug 2006 14:04:55 -0000	1.51
--- BuildHomeDaemon.java	6 Oct 2006 14:27:47 -0000	1.52
***************
*** 98,101 ****
--- 98,102 ----
        }
        //lets make a Context and put thedata into it
+       context.put("email",GeneralUtils.getAdminEmail(servcon));
        context.put("users", users);
        context.put("url","portal");

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/util UrlTool.java, 1.16, 1.17

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17181/src/java/org/openscience/nmrshiftdb/util

Modified Files:
	UrlTool.java 
Log Message:
some changes


Index: UrlTool.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/UrlTool.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -r1.16 -r1.17
*** UrlTool.java	22 May 2006 12:48:46 -0000	1.16
--- UrlTool.java	6 Oct 2006 14:27:48 -0000	1.17
***************
*** 5,8 ****
--- 5,9 ----
  import java.io.StringWriter;
  import java.net.URL;
+ import java.sql.ResultSet;
  import java.util.HashMap;
  import java.util.List;
***************
*** 31,34 ****
--- 32,36 ----
  import org.openscience.nmrshiftdb.om.DBLabGroupPeer;
  import org.openscience.nmrshiftdb.om.DBMoleculePeer;
+ import org.openscience.nmrshiftdb.om.NmrshiftdbUser;
  import org.openscience.nmrshiftdb.om.NmrshiftdbUserPeer;
  
***************
*** 158,163 ****
    public String getResetMessage() throws Exception {
      try{
!       NmrshiftdbUserPeer.executeStatement("update JETSPEED_USER_PROFILE set PROFILE =(select DISTINCT PROFILE from JETSPEED_ANON_PROFILE where MEDIA_TYPE ='html' and LANGUAGE ='en' and PAGE='default.psml') where USER_NAME ='" + data.getUser().getUserName() + "' and MEDIA_TYPE='html';");
!       return ("The user interface has been reset to initial configuration!");
      }catch(Exception ex){
        return(GeneralUtils.logError(ex,"reset user interface user "+data.getUser().getUserName(),data,true));
--- 160,173 ----
    public String getResetMessage() throws Exception {
      try{
!     	if(((NmrshiftdbUser)data.getUser()).isLabgroupUser(data)){
!     		Vector rs=NmrshiftdbUserPeer.executeQuery("select DISTINCT PROFILE from JETSPEED_USER_PROFILE where MEDIA_TYPE ='html' and PAGE='default.psml' and  USER_NAME='testuser'");
!        		NmrshiftdbUserPeer.executeStatement("update JETSPEED_USER_PROFILE set PROFILE ='"+((Record)rs.get(0)).getValue(1)+"' where USER_NAME ='" + data.getUser().getUserName() + "' and MEDIA_TYPE='html';");
!     	}else if(((NmrshiftdbUser)data.getUser()).isLabgroupUser(data)){
!     		Vector rs=NmrshiftdbUserPeer.executeQuery("select DISTINCT PROFILE from JETSPEED_USER_PROFILE where MEDIA_TYPE ='html' and PAGE='default.psml' and  USER_NAME='testworker'");
!     		NmrshiftdbUserPeer.executeStatement("update JETSPEED_USER_PROFILE set PROFILE ='"+((Record)rs.get(0)).getValue(1)+"' where USER_NAME ='" + data.getUser().getUserName() + "' and MEDIA_TYPE='html';");
!     	}else{
!     	    NmrshiftdbUserPeer.executeStatement("update JETSPEED_USER_PROFILE set PROFILE =(select DISTINCT PROFILE from JETSPEED_ANON_PROFILE where MEDIA_TYPE ='html' and LANGUAGE ='en' and PAGE='default.psml') where USER_NAME ='" + data.getUser().getUserName() + "' and MEDIA_TYPE='html';");
!     	}
!     	return ("The user interface has been reset to initial configuration!");
      }catch(Exception ex){
        return(GeneralUtils.logError(ex,"reset user interface user "+data.getUser().getUserName(),data,true));

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets OrderAction.java, 1.26, 1.27 OrderFullfillAction.java, 1.22, 1.23

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv13604/src/java/org/openscience/nmrshiftdb/modules/actions/portlets

Modified Files:
	OrderAction.java OrderFullfillAction.java 
Log Message:
the time for the done orders can be set


Index: OrderAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -r1.26 -r1.27
*** OrderAction.java	23 Sep 2006 22:10:44 -0000	1.26
--- OrderAction.java	6 Oct 2006 13:00:04 -0000	1.27
***************
*** 5,10 ****
--- 5,14 ----
  import java.io.FileWriter;
  import java.io.StringReader;
+ import java.text.SimpleDateFormat;
+ import java.util.Calendar;
  import java.util.Collections;
  import java.util.Date;
+ import java.util.GregorianCalendar;
+ import java.util.Locale;
  import java.util.Vector;
  import java.util.zip.ZipOutputStream;
***************
*** 99,104 ****
      Vector v=DBSamplePeer.doSelect(crit);
      Vector v3=new Vector();
      for(int i=0;i<v.size();i++){
!       sql="select distinct SAMPLE.SAMPLE_ID from SAMPLE join RAW_FILE using(SAMPLE_ID) left join RAW_FILE_SPECTRUM using (RAW_FILE_ID) where SAMPLE.SAMPLE_ID ="+((DBSample)v.get(i)).getSampleId()+" and RAW_FILE_SPECTRUM.SPECTRUM_ID is null";
        Vector v4=DBSamplePeer.executeQuery(sql);
        if(v4.size()>0)
--- 103,122 ----
      Vector v=DBSamplePeer.doSelect(crit);
      Vector v3=new Vector();
+     SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd", Locale.US);
+     Date end=(Date)data.getSession().getAttribute("end");
+     if(end==null){
+     	end=new Date();
+     	data.getSession().setAttribute("end",end);
+     }
+     Date start=(Date)data.getSession().getAttribute("start");
+     if(start==null){
+     	long millis=System.currentTimeMillis();
+     	start=new Date(millis-(7*24*60*60*1000));
+     	data.getSession().setAttribute("start",start);
+     }
+     context.put("start",start);
+     context.put("end",end);
      for(int i=0;i<v.size();i++){
!       sql="select distinct SAMPLE.SAMPLE_ID from SAMPLE join RAW_FILE using(SAMPLE_ID) left join RAW_FILE_SPECTRUM using (RAW_FILE_ID) where SAMPLE.SAMPLE_ID ="+((DBSample)v.get(i)).getSampleId()+" and RAW_FILE_SPECTRUM.SPECTRUM_ID is null and SAMPLE.DATE>='"+formatter.format(start)+"' and SAMPLE.DATE<='"+formatter.format(end)+"'";
        Vector v4=DBSamplePeer.executeQuery(sql);
        if(v4.size()>0)
***************
*** 212,217 ****
--- 230,272 ----
        context.put("typesc",getTypesC());
        context.put("typesh",getTypesH());
+       Vector days=new Vector();
+       for (int i=1;i<32;i++){
+     	  days.add(new Integer(i));
+       }
+       context.put("days",days );
+       Vector months=new Vector();
+       for (int i=1;i<13;i++){
+     	  months.add(new Integer(i));
+       }
+       context.put("months",months );
+       Vector years=new Vector();
+       for (int i=2000;i<=new Date().getYear()+1900;i++){
+     	  years.add(new Integer(i));
+       }
+       context.put("years",years );
      }
    }
+ 
+   
+   public void doChangedates(RunData data, Context context) throws Exception {
+ 	    try{
+ 	    	Date start=new Date();
+ 	    	start.setDate(Integer.parseInt(data.getParameters().get("fromday")));
+ 	    	start.setMonth(Integer.parseInt(data.getParameters().get("frommonth"))-1);
+ 	    	start.setYear(Integer.parseInt(data.getParameters().get("fromyear"))-1900);
+ 	    	data.getSession().setAttribute("start",start);
+ 	    	Date end=new Date();
+ 	    	end.setDate(Integer.parseInt(data.getParameters().get("today")));
+ 	    	end.setMonth(Integer.parseInt(data.getParameters().get("tomonth"))-1);
+ 	    	end.setYear(Integer.parseInt(data.getParameters().get("toyear"))-1900);
+ 	    	data.getSession().setAttribute("end",end);
+ 	    	buildOrderContext(context,data);
+ 	    }
+ 	    catch(Exception ex){
+ 	    	ex.printStackTrace();
+ 	      GeneralUtils.logError(ex,"guestbook/doentry",data,true);
+ 	    }
+ 	}
+ 
    
    

Index: OrderFullfillAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -r1.22 -r1.23
*** OrderFullfillAction.java	23 Sep 2006 22:10:44 -0000	1.22
--- OrderFullfillAction.java	6 Oct 2006 13:00:04 -0000	1.23
***************
*** 6,9 ****
--- 6,10 ----
  import java.util.Collections;
  import java.util.Comparator;
+ import java.util.Date;
  import java.util.Vector;
  import java.util.zip.ZipOutputStream;
***************
*** 138,141 ****
--- 139,143 ----
    }
    
+   
    public void doSubmitdelete(RunData data, Context context) throws Exception {
  	    try{

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates homeportlet.vm, 1.42, 1.43

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv13604/src/vmtemplates

Modified Files:
	homeportlet.vm 
Log Message:
the time for the done orders can be set


Index: homeportlet.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/homeportlet.vm,v
retrieving revision 1.42
retrieving revision 1.43
diff -C2 -r1.42 -r1.43
*** homeportlet.vm	23 Sep 2006 16:02:13 -0000	1.42
--- homeportlet.vm	6 Oct 2006 13:00:05 -0000	1.43
***************
*** 8,12 ****
        <a href="http://almost.cubic.uni-koeln.de/nmrshiftdb.names.html">Static name list</a><br>
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/links.html">Links</a><br>
!       <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/faq.html">FAQ</a><br><br>
        <a href="mailto:$!config.getString("mail.support")" tabindex="4">Contact</a><br>
        #if ($data.User.hasLoggedIn())
--- 8,12 ----
        <a href="http://almost.cubic.uni-koeln.de/nmrshiftdb.names.html">Static name list</a><br>
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/links.html">Links</a><br>
!       <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/faq.html">FAQ</a><br>
        <a href="mailto:$!config.getString("mail.support")" tabindex="4">Contact</a><br>
        #if ($data.User.hasLoggedIn())

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb AdminPanel.java, 1.232, 1.233

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv13604/src/java/org/openscience/nmrshiftdb

Modified Files:
	AdminPanel.java 
Log Message:
the time for the done orders can be set


Index: AdminPanel.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/AdminPanel.java,v
retrieving revision 1.232
retrieving revision 1.233
diff -C2 -r1.232 -r1.233
*** AdminPanel.java	29 Aug 2006 16:10:04 -0000	1.232
--- AdminPanel.java	6 Oct 2006 13:00:04 -0000	1.233
***************
*** 35,42 ****
--- 35,45 ----
  import libsvm.svm_train;
  
+ import org.apache.jetspeed.services.JetspeedSecurity;
+ import org.apache.jetspeed.services.rundata.DefaultJetspeedRunData;
  import org.apache.log4j.Category;
  import org.apache.log4j.FileAppender;
  import org.apache.log4j.SimpleLayout;
  import org.apache.turbine.om.NumberKey;
+ import org.apache.turbine.om.security.User;
  import org.apache.turbine.services.db.TurbineDB;
  import org.apache.turbine.util.Log;
***************
*** 994,1003 ****
  	  DBConnection dbconn = TurbineDB.getConnection();
  	  Statement stmt = dbconn.createStatement();
! 	  ResultSet rs = stmt.executeQuery("select SPECTRUM_ID, COMMENT from SPECTRUM;");
  	  FileOutputStream fos=new FileOutputStream("/tmp/gr.sql");
  	  while (rs.next()) {
  		  fos.write(new String("update SPECTRUM set COMMENT='"+GeneralUtils.escape(rs.getString(2))+"' where SPECTRUM_ID="+rs.getInt(1)+";\r\n").getBytes());
  	  }
! 	  fos.close();
  	  /*ResultSet rs = stmt.executeQuery("select MOLECULE_ID from MOLECULE;");
  	  int errors=0;
--- 997,1013 ----
  	  DBConnection dbconn = TurbineDB.getConnection();
  	  Statement stmt = dbconn.createStatement();
! 	  ResultSet rs = stmt.executeQuery("select LOGIN_NAME,FIRST_NAME,LAST_NAME,ADDRESS,CITY from TURBINE_USER where FIRST_NAME=LAST_NAME;");
! 	  while (rs.next()){
! 		  if (warn(rs.getString(2)+" "+rs.getString(3)+" "+rs.getString(4)+" "+rs.getString(5)+" delete?", new BufferedReader(new InputStreamReader(System.in)))) {
!           	User user = JetspeedSecurity.getUser(rs.getString(1));
!         	JetspeedSecurity.removeUser(user, new DefaultJetspeedRunData());
! 		  }
! 	  }
! 	  /*ResultSet rs = stmt.executeQuery("select SPECTRUM_ID, COMMENT from SPECTRUM;");
  	  FileOutputStream fos=new FileOutputStream("/tmp/gr.sql");
  	  while (rs.next()) {
  		  fos.write(new String("update SPECTRUM set COMMENT='"+GeneralUtils.escape(rs.getString(2))+"' where SPECTRUM_ID="+rs.getInt(1)+";\r\n").getBytes());
  	  }
! 	  fos.close();*/
  	  /*ResultSet rs = stmt.executeQuery("select MOLECULE_ID from MOLECULE;");
  	  int errors=0;

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.38, 1.39 worker-order.vm, 1.18, 1.19

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv13604/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm worker-order.vm 
Log Message:
the time for the done orders can be set


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -r1.38 -r1.39
*** user-order.vm	23 Sep 2006 22:10:44 -0000	1.38
--- user-order.vm	6 Oct 2006 13:00:05 -0000	1.39
***************
*** 69,72 ****
--- 69,107 ----
            </table>
          #end
+         <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration">
+         	Show orders from
+         	<select name="fromday" size="1">
+   	          #foreach($day in $days)
+     	        <option value="$day" #if($day==$start.getDate()) selected #end>$day</option>
+         	  #end
+           	</select>
+         	<select name="frommonth" size="1">
+   	          #foreach($day in $months)
+     	        <option value="$day" #if($day==$start.getMonth()+1) selected #end>$day</option>
+         	  #end
+           	</select>
+         	<select name="fromyear" size="1">
+   	          #foreach($day in $years)
+     	        <option value="$day" #if($day==$start.getYear()+1900) selected #end>$day</option>
+         	  #end
+           	</select>
+         	to 
+         	<select name="today" size="1">
+   	          #foreach($day in $days)
+     	        <option value="$day" #if($day==$end.getDate()) selected #end>$day</option>
+         	  #end
+           	</select>
+         	<select name="tomonth" size="1">
+   	          #foreach($day in $months)
+     	        <option value="$day" #if($day==$end.getMonth()+1) selected #end>$day</option>
+         	  #end
+           	</select>
+         	<select name="toyear" size="1">
+   	          #foreach($day in $years)
+     	        <option value="$day" #if($day==$end.getYear()+1900) selected #end>$day</option>
+         	  #end
+           	</select>
+ 	        <input type="submit" name="eventSubmit_doChangedates" value="Change dates"/>
+         </form>
        </td>
      </tr>

Index: worker-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -r1.18 -r1.19
*** worker-order.vm	23 Sep 2006 22:10:44 -0000	1.18
--- worker-order.vm	6 Oct 2006 13:00:05 -0000	1.19
***************
*** 8,12 ****
          #else
            The following orders for your labgroup wait to be fullfilled:
!           <table border="3" rules="cols">><tr><td align="left" valign="top">
            <table>
            	<tr><th>250 MHz</th></tr>
--- 8,12 ----
          #else
            The following orders for your labgroup wait to be fullfilled:
!           <table border="3" rules="cols"><tr><td align="left" valign="top">
            <table>
            	<tr><th>250 MHz</th></tr>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets OrderAction.java, 1.25, 1.26 OrderFullfillAction.java, 1.21, 1.22

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12776/src/java/org/openscience/nmrshiftdb/modules/actions/portlets

Modified Files:
	OrderAction.java OrderFullfillAction.java 
Log Message:
no arrows after files


Index: OrderAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -r1.25 -r1.26
*** OrderAction.java	21 Sep 2006 12:22:11 -0000	1.25
--- OrderAction.java	23 Sep 2006 22:10:44 -0000	1.26
***************
*** 177,180 ****
--- 177,181 ----
  	        local.add("portal/pane0/NMR+lab+administration?nmrshiftdbaction=browseto&filename="+filesindir[i].getName()+"&submitorshow=show&id="+toshow.getSampleId());
  	        files.add(local);
+ 	        local.add(new Boolean(filesindir[i].isFile()));
  	      }
  	      Collections.sort(files, new OrderFullfillAction.LocalComparator());
***************
*** 185,188 ****
--- 186,190 ----
  	          local.add("portal/pane0/NMR+lab+administration?nmrshiftdbaction=browseto&filename=..&submitorshow=show&id="+toshow.getSampleId());
  	          files.add(local);
+ 	          local.add(new Boolean(true));
  	      }
  	      context.put("files",files);
***************
*** 335,338 ****
--- 337,341 ----
  	      for(int i=0;i<v.size();i++){
  	        GeneralUtils.zipDir(((File)v.get(i)), zipout,new File(GeneralUtils.getNmrshiftdbProperty("rawfiledirectory",data)));
+ 	        GeneralUtils.alreadyAttached.clear();
  	        attachedfiles.append(((File)v.get(i)).getName()+"; ");
  	      }

Index: OrderFullfillAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -r1.21 -r1.22
*** OrderFullfillAction.java	21 Sep 2006 12:22:11 -0000	1.21
--- OrderFullfillAction.java	23 Sep 2006 22:10:44 -0000	1.22
***************
*** 122,125 ****
--- 122,126 ----
          local.add(filesindir[i].getName());
          local.add("portal/pane0/NMR+lab+administration?nmrshiftdbaction=browseto&filename="+filesindir[i].getName()+"&submitorshow=show&id="+toshow.getSampleId());
+         local.add(new Boolean(filesindir[i].isFile()));
          files.add(local);
        }
***************
*** 130,133 ****
--- 131,135 ----
            local.add("..");
            local.add("portal/pane0/NMR+lab+administration?nmrshiftdbaction=browseto&filename=..&submitorshow=show&id="+toshow.getSampleId());
+           local.add(new Boolean(true));
            files.add(local);
        }
***************
*** 168,171 ****
--- 170,174 ----
  	      for(int i=0;i<v.size();i++){
  	        GeneralUtils.zipDir(((File)v.get(i)), zipout,new File(GeneralUtils.getNmrshiftdbProperty("rawfiledirectory",data)));
+ 	        GeneralUtils.alreadyAttached.clear();
  	        attachedfiles.append(((File)v.get(i)).getName()+"; ");
  	      }

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.37, 1.38 worker-order.vm, 1.17, 1.18

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12776/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm worker-order.vm 
Log Message:
no arrows after files


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -r1.37 -r1.38
*** user-order.vm	21 Sep 2006 12:22:12 -0000	1.37
--- user-order.vm	23 Sep 2006 22:10:44 -0000	1.38
***************
*** 223,227 ****
  		      <table><tr><td>
  		      #foreach($file in $files)
! 		        <a href="$file.get(0)">$file.get(1)</a> <a href="$file.get(2)">&gt;&gt;&gt;&gt;</a><br>
  		        #set($test=$velocityCount % 50)
  			    #if($test==0)
--- 223,227 ----
  		      <table><tr><td>
  		      #foreach($file in $files)
! 		        <a href="$file.get(0)">$file.get(1)</a> #if($file.get(3)) <a href="$file.get(2)">&gt;&gt;&gt;&gt;</a> #end <br>
  		        #set($test=$velocityCount % 50)
  			    #if($test==0)

Index: worker-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -r1.17 -r1.18
*** worker-order.vm	21 Sep 2006 12:22:13 -0000	1.17
--- worker-order.vm	23 Sep 2006 22:10:44 -0000	1.18
***************
*** 97,101 ****
            <table><tr><td>
  	          #foreach($file in $files)
! 	            <a href="$file.get(0)">$file.get(1)</a> <a href="$file.get(2)">&gt;&gt;&gt;&gt;</a><br>
  		        #set($test=$velocityCount % 50)
  			    #if($test==0)
--- 97,101 ----
            <table><tr><td>
  	          #foreach($file in $files)
! 	            <a href="$file.get(0)">$file.get(1)</a> #if($file.get(3)) <a href="$file.get(2)">&gt;&gt;&gt;&gt;</a> #end <br>
  		        #set($test=$velocityCount % 50)
  			    #if($test==0)

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/util GeneralUtils.java, 1.186, 1.187

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12776/src/java/org/openscience/nmrshiftdb/util

Modified Files:
	GeneralUtils.java 
Log Message:
no arrows after files


Index: GeneralUtils.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/GeneralUtils.java,v
retrieving revision 1.186
retrieving revision 1.187
diff -C2 -r1.186 -r1.187
*** GeneralUtils.java	29 Aug 2006 16:10:05 -0000	1.186
--- GeneralUtils.java	23 Sep 2006 22:10:44 -0000	1.187
***************
*** 149,152 ****
--- 149,155 ----
    static GeneralUtils instance=new GeneralUtils();
    
+   //attention - problem with static
+   public static Vector alreadyAttached=new Vector();
+   
    /**
     *Constructor for the GeneralUtils object (private since only static methods)
***************
*** 1844,1857 ****
      	int bytesIn = 0;
      	byte[] readBuffer = new byte[2156];
!         FileInputStream fis = new FileInputStream(zipDir);
!         ZipEntry anEntry = new ZipEntry(zipDir.getPath());
!         //place the zip entry in the ZipOutputStream object
!         zos.putNextEntry(anEntry);
!         //now write the content of the file to the ZipOutputStream
!         while ((bytesIn = fis.read(readBuffer)) != -1) {
!           zos.write(readBuffer, 0, bytesIn);
          }
-         //close the Stream
-         fis.close();
      }else{
  	    //get a listing of the directory content
--- 1847,1863 ----
      	int bytesIn = 0;
      	byte[] readBuffer = new byte[2156];
!         if(!alreadyAttached.contains(zipDir.getPath())){
!         	FileInputStream fis = new FileInputStream(zipDir);
!             ZipEntry anEntry = new ZipEntry(zipDir.getPath());
!         	alreadyAttached.add(zipDir.getPath());
!         	//place the zip entry in the ZipOutputStream object
!         	zos.putNextEntry(anEntry);
!         	//now write the content of the file to the ZipOutputStream
!         	while ((bytesIn = fis.read(readBuffer)) != -1) {
!         		zos.write(readBuffer, 0, bytesIn);
!         	}
!         	//close the Stream
!         	fis.close();
          }
      }else{
  	    //get a listing of the directory content
***************
*** 1870,1885 ****
  	        continue;
  	      }
! 	      //if we reached here, the File object f was not a directory
! 	      //create a FileInputStream on top of f
! 	      FileInputStream fis = new FileInputStream(f);
! 	      ZipEntry anEntry = new ZipEntry(getRelativePath(rawdatadir,f));
! 	      //place the zip entry in the ZipOutputStream object
! 	      zos.putNextEntry(anEntry);
! 	      //now write the content of the file to the ZipOutputStream
! 	      while ((bytesIn = fis.read(readBuffer)) != -1) {
! 	        zos.write(readBuffer, 0, bytesIn);
  	      }
- 	      //close the Stream
- 	      fis.close();
  	  }
      }
--- 1876,1894 ----
  	        continue;
  	      }
! 	      if(!alreadyAttached.contains(getRelativePath(rawdatadir,f))){
! 		      //if we reached here, the File object f was not a directory
! 		      //create a FileInputStream on top of f
! 		      FileInputStream fis = new FileInputStream(f);
! 		      ZipEntry anEntry = new ZipEntry(getRelativePath(rawdatadir,f));
! 		      alreadyAttached.add(getRelativePath(rawdatadir,f));
! 		      //place the zip entry in the ZipOutputStream object
! 		      zos.putNextEntry(anEntry);
! 		      //now write the content of the file to the ZipOutputStream
! 		      while ((bytesIn = fis.read(readBuffer)) != -1) {
! 		        zos.write(readBuffer, 0, bytesIn);
! 		      }
! 		      //close the Stream
! 		      fis.close();
  	      }
  	  }
      }

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/navigations/html top.vm, 1.24, 1.25

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/navigations/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv26307/src/conf/jetspeed/WEB-INF/templates/vm/navigations/html

Modified Files:
	top.vm 
Log Message:
changes suggested by sab


Index: top.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/navigations/html/top.vm,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -r1.24 -r1.25
*** top.vm	27 Jun 2006 14:29:17 -0000	1.24
--- top.vm	23 Sep 2006 16:02:13 -0000	1.25
***************
*** 11,26 ****
      </table>
    </td>
!   <td rowspan=2><img src="images/blank.gif" width=60 height=1></td>
    <td align="left" width="100%">
      <FONT class=welcome>Welcome to NMRShiftDB</font><br/>
  ##    <sup>Logged in since:&nbsp;$!data.getUser().getLastLogin()</sup>
    </td>
-   <td align=center>
-     <table cellpadding=1 cellspacing=3 border=0 width=100%>
-     <tr>
-       <td align=center class=MENUBUTTON><NOBR>&nbsp;&nbsp;<a href="$link.setPage("ResetInterface")" tabindex="4">Reset User Interface</a>&nbsp;&nbsp;</NOBR></td><td align=center class=MENUBUTTON><NOBR>&nbsp;&nbsp;<a href="mailto:$!config.getString("mail.support")" tabindex="4">Contact</a>&nbsp;&nbsp;</NOBR></td>
-     </tr>
-     </table>
-   </td>
  </tr>
  <tr>
--- 11,19 ----
      </table>
    </td>
!   <td rowspan=3><img src="images/blank.gif" width=60 height=1></td>
    <td align="left" width="100%">
      <FONT class=welcome>Welcome to NMRShiftDB</font><br/>
  ##    <sup>Logged in since:&nbsp;$!data.getUser().getLastLogin()</sup>
    </td>
  </tr>
  <tr>
***************
*** 29,33 ****
      <tr>
        <td align=center class=MENUBUTTON><a href="$link.setPage("EditAccount");jsessionid=$data.getSession().getId()">Personal Page ($data.User.UserName)</a></td>
!       <td align=center class=MENUBUTTON><a href="$link.setAction("LogoutUser")">$l10n.TOP_LOGOUT</a></td>
      </tr>
      </table>
--- 22,26 ----
      <tr>
        <td align=center class=MENUBUTTON><a href="$link.setPage("EditAccount");jsessionid=$data.getSession().getId()">Personal Page ($data.User.UserName)</a></td>
!       <td align=center class=MENUBUTTON><NOBR>&nbsp;&nbsp;<a href="$link.setPage("ResetInterface")" tabindex="4">Reset User Interface</a>&nbsp;&nbsp;</NOBR></td>
      </tr>
      </table>
***************
*** 74,80 ****
        <td align=center class=MENUBUTTON><NOBR>&nbsp;&nbsp;<a href="$link.setPage("RememberPassword")">Forgot password?</a>&nbsp;&nbsp;</NOBR></td>
      </tr>
-     <tr>
-       <td align=center class=MENUBUTTON><NOBR>&nbsp;&nbsp;<a href="mailto:$!config.getString("mail.support")" tabindex="4">Contact</a>&nbsp;&nbsp;</NOBR></td>
-     </tr>
      </table>
    </td>
--- 67,70 ----

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates homeportlet.vm, 1.41, 1.42

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv26307/src/vmtemplates

Modified Files:
	homeportlet.vm 
Log Message:
changes suggested by sab


Index: homeportlet.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/homeportlet.vm,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -r1.41 -r1.42
*** homeportlet.vm	23 Aug 2006 14:04:55 -0000	1.41
--- homeportlet.vm	23 Sep 2006 16:02:13 -0000	1.42
***************
*** 3,9 ****
      <td width="200">
        <h2 style="color:#0000AA">NMRShiftDB Links</h2>
-       <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=t1.html#about">About NMRShiftDB</a><br>
        <a href="http://sourceforge.net/projects/nmrshiftdb" target="_blank">Developers' page</a><br>
-       <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()">Help</a><br>
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/sponsoring.html">Sponsoring</a><br>
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/clippings">Media coverage</a><br>
--- 3,7 ----
***************
*** 11,14 ****
--- 9,16 ----
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/links.html">Links</a><br>
        <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=http://nmrshiftdb.sf.net/faq.html">FAQ</a><br><br>
+       <a href="mailto:$!config.getString("mail.support")" tabindex="4">Contact</a><br>
+       #if ($data.User.hasLoggedIn())
+ 	      <a href="$link.setAction("LogoutUser")">$l10n.TOP_LOGOUT</a><br>
+ 	  #end
        #parse("halloffame.vm")
        <h2 style="color:#0000AA">NMRShiftDB Servers</h2>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons AssignRobotDaemon.java, 1.6, 1.7

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv9931/src/java/org/openscience/nmrshiftdb/daemons

Modified Files:
	AssignRobotDaemon.java 
Log Message:
more robot stuff


Index: AssignRobotDaemon.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/AssignRobotDaemon.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -r1.6 -r1.7
*** AssignRobotDaemon.java	22 Sep 2006 15:44:55 -0000	1.6
--- AssignRobotDaemon.java	22 Sep 2006 16:30:35 -0000	1.7
***************
*** 64,67 ****
--- 64,68 ----
      private void searchfiles(File tolookin, String usersid, ZipOutputStream zipoutputstream, StringBuffer attachedfiles, File dirtoignore) throws IOException{
      	File[] filesindir=tolookin.listFiles();
+     	//System.err.println("search "+tolookin+"  "+usersid+"  "+filesindir[0].getName());
      	if(filesindir!=null){
  	    	for(int i=0;i<filesindir.length;i++){
***************
*** 88,91 ****
--- 89,93 ----
      private void addfiles(File toadd, ZipOutputStream zipoutputstream, StringBuffer attachedfiles) throws IOException{
      	File[] filesindir=toadd.listFiles();
+     	//System.err.println("add "+toadd);
      	if(filesindir!=null){
  	    	for(int i=0;i<filesindir.length;i++){
***************
*** 93,97 ****
  	    			addfiles(filesindir[i],zipoutputstream,attachedfiles);
  	    		}else if(filesindir[i].isFile()){
! 	    				zipoutputstream.putNextEntry(new ZipEntry(toadd.getName()+"/"+filesindir[i].getName()));
  	    				FileInputStream fis=new FileInputStream(filesindir[i]);
  	    				int read=0;
--- 95,99 ----
  	    			addfiles(filesindir[i],zipoutputstream,attachedfiles);
  	    		}else if(filesindir[i].isFile()){
! 	    				zipoutputstream.putNextEntry(new ZipEntry(toadd+"/"+filesindir[i].getName()));
  	    				FileInputStream fis=new FileInputStream(filesindir[i]);
  	    				int read=0;

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons AssignRobotDaemon.java, 1.5, 1.6

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv23708/src/java/org/openscience/nmrshiftdb/daemons

Modified Files:
	AssignRobotDaemon.java 
Log Message:
avoids npe (hopefully)


Index: AssignRobotDaemon.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/AssignRobotDaemon.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -r1.5 -r1.6
*** AssignRobotDaemon.java	22 Sep 2006 10:56:34 -0000	1.5
--- AssignRobotDaemon.java	22 Sep 2006 15:44:55 -0000	1.6
***************
*** 64,84 ****
      private void searchfiles(File tolookin, String usersid, ZipOutputStream zipoutputstream, StringBuffer attachedfiles, File dirtoignore) throws IOException{
      	File[] filesindir=tolookin.listFiles();
!     	for(int i=0;i<filesindir.length;i++){
!     		if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)!=0 && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..") && !filesindir[i].equals(dirtoignore)){
!     			searchfiles(filesindir[i],usersid,zipoutputstream,attachedfiles, dirtoignore);
!     		}else if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)==0){
!     			addfiles(filesindir[i], zipoutputstream, attachedfiles);
!     		}else{
!     			if(filesindir[i].getName().indexOf(usersid)==0){
!     				zipoutputstream.putNextEntry(new ZipEntry(filesindir[i].getName()));
!     				FileInputStream fis=new FileInputStream(filesindir[i]);
!     				int read=0;
!     				while((read=fis.read())!=-1){
!     					zipoutputstream.write(read);
!     				}
!     				attachedfiles.append(filesindir[i]+"; ");
!     				zipoutputstream.closeEntry();
!     			}
!     		}
      	}
      }
--- 64,86 ----
      private void searchfiles(File tolookin, String usersid, ZipOutputStream zipoutputstream, StringBuffer attachedfiles, File dirtoignore) throws IOException{
      	File[] filesindir=tolookin.listFiles();
!     	if(filesindir!=null){
! 	    	for(int i=0;i<filesindir.length;i++){
! 	    		if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)!=0 && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..") && !filesindir[i].equals(dirtoignore)){
! 	    			searchfiles(filesindir[i],usersid,zipoutputstream,attachedfiles, dirtoignore);
! 	    		}else if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)==0){
! 	    			addfiles(filesindir[i], zipoutputstream, attachedfiles);
! 	    		}else{
! 	    			if(filesindir[i].getName().indexOf(usersid)==0){
! 	    				zipoutputstream.putNextEntry(new ZipEntry(filesindir[i].getName()));
! 	    				FileInputStream fis=new FileInputStream(filesindir[i]);
! 	    				int read=0;
! 	    				while((read=fis.read())!=-1){
! 	    					zipoutputstream.write(read);
! 	    				}
! 	    				attachedfiles.append(filesindir[i]+"; ");
! 	    				zipoutputstream.closeEntry();
! 	    			}
! 	    		}
! 	    	}
      	}
      }
***************
*** 86,102 ****
      private void addfiles(File toadd, ZipOutputStream zipoutputstream, StringBuffer attachedfiles) throws IOException{
      	File[] filesindir=toadd.listFiles();
!     	for(int i=0;i<filesindir.length;i++){
!     		if(filesindir[i].isDirectory() && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..")){
!     			addfiles(filesindir[i],zipoutputstream,attachedfiles);
!     		}else{
!     				zipoutputstream.putNextEntry(new ZipEntry(toadd.getName()+"/"+filesindir[i].getName()));
!     				FileInputStream fis=new FileInputStream(filesindir[i]);
!     				int read=0;
!     				while((read=fis.read())!=-1){
!     					zipoutputstream.write(read);
!     				}
!     				attachedfiles.append(filesindir[i]+"; ");
!     				zipoutputstream.closeEntry();
!     		}
      	}
      }
--- 88,106 ----
      private void addfiles(File toadd, ZipOutputStream zipoutputstream, StringBuffer attachedfiles) throws IOException{
      	File[] filesindir=toadd.listFiles();
!     	if(filesindir!=null){
! 	    	for(int i=0;i<filesindir.length;i++){
! 	    		if(filesindir[i].isDirectory() && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..")){
! 	    			addfiles(filesindir[i],zipoutputstream,attachedfiles);
! 	    		}else if(filesindir[i].isFile()){
! 	    				zipoutputstream.putNextEntry(new ZipEntry(toadd.getName()+"/"+filesindir[i].getName()));
! 	    				FileInputStream fis=new FileInputStream(filesindir[i]);
! 	    				int read=0;
! 	    				while((read=fis.read())!=-1){
! 	    					zipoutputstream.write(read);
! 	    				}
! 	    				attachedfiles.append(filesindir[i]+"; ");
! 	    				zipoutputstream.closeEntry();
! 	    		}
! 	    	}
      	}
      }

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/conf JetspeedResources.properties, 1.23, 1.24 NMRShiftDB.properties, 1.50, 1.51

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3306/src/conf/jetspeed/WEB-INF/conf

Modified Files:
	JetspeedResources.properties NMRShiftDB.properties 
Log Message:
still the robot stuff


Index: JetspeedResources.properties
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/JetspeedResources.properties,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -r1.23 -r1.24
*** JetspeedResources.properties	11 Sep 2006 14:21:16 -0000	1.23
--- JetspeedResources.properties	22 Sep 2006 10:56:33 -0000	1.24
***************
*** 216,220 ****
  #daemon.entry=buildsdf
  daemon.entry=buildsvm
! #daemon.entry=robotdaemon
  
  daemon.feeddaemon.classname=org.apache.jetspeed.daemon.impl.FeedDaemon
--- 216,220 ----
  #daemon.entry=buildsdf
  daemon.entry=buildsvm
! daemon.entry=robotdaemon
  
  daemon.feeddaemon.classname=org.apache.jetspeed.daemon.impl.FeedDaemon

Index: NMRShiftDB.properties
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/NMRShiftDB.properties,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -r1.50 -r1.51
*** NMRShiftDB.properties	11 Sep 2006 14:21:16 -0000	1.50
--- NMRShiftDB.properties	22 Sep 2006 10:56:33 -0000	1.51
***************
*** 32,36 ****
  rawfiledirectoryuser=/home/shk3
  #A directory where raw files can be found for robot assignment
! rawfiledirectoryrobot=/home/shk3
  #A directoy where to put compressed raw files for download
  compressedfiledirectory=/home/shk3
--- 32,36 ----
  rawfiledirectoryuser=/home/shk3
  #A directory where raw files can be found for robot assignment
! rawfiledirectoryrobot=/home/shk3/packtest
  #A directoy where to put compressed raw files for download
  compressedfiledirectory=/home/shk3

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons AssignRobotDaemon.java, 1.4, 1.5

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

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3306/src/java/org/openscience/nmrshiftdb/daemons

Modified Files:
	AssignRobotDaemon.java 
Log Message:
still the robot stuff


Index: AssignRobotDaemon.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/AssignRobotDaemon.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -r1.4 -r1.5
*** AssignRobotDaemon.java	22 Sep 2006 09:26:28 -0000	1.4
--- AssignRobotDaemon.java	22 Sep 2006 10:56:34 -0000	1.5
***************
*** 64,68 ****
      private void searchfiles(File tolookin, String usersid, ZipOutputStream zipoutputstream, StringBuffer attachedfiles, File dirtoignore) throws IOException{
      	File[] filesindir=tolookin.listFiles();
-     	System.err.println("search "+tolookin+"  "+usersid+"  "+filesindir[0].getName());
      	for(int i=0;i<filesindir.length;i++){
      		if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)!=0 && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..") && !filesindir[i].equals(dirtoignore)){
--- 64,67 ----
***************
*** 86,90 ****
      
      private void addfiles(File toadd, ZipOutputStream zipoutputstream, StringBuffer attachedfiles) throws IOException{
-     	System.err.println("add "+toadd);
      	File[] filesindir=toadd.listFiles();
      	for(int i=0;i<filesindir.length;i++){
--- 85,88 ----
***************
*** 92,96 ****
      			addfiles(filesindir[i],zipoutputstream,attachedfiles);
      		}else{
!     				zipoutputstream.putNextEntry(new ZipEntry(filesindir[i].getName()));
      				FileInputStream fis=new FileInputStream(filesindir[i]);
      				int read=0;
--- 90,94 ----
      			addfiles(filesindir[i],zipoutputstream,attachedfiles);
      		}else{
!     				zipoutputstream.putNextEntry(new ZipEntry(toadd.getName()+"/"+filesindir[i].getName()));
      				FileInputStream fis=new FileInputStream(filesindir[i]);
      				int read=0;