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From: Stefan K. <sk...@us...> - 2002-03-06 16:41:20
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf In directory usw-pr-cvs1:/tmp/cvs-serv11083/conf/jetspeed/WEB-INF/conf Modified Files: Torque.properties Log Message: modified om files Index: Torque.properties =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/Torque.properties,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** Torque.properties 5 Mar 2002 09:29:03 -0000 1.2 --- Torque.properties 6 Mar 2002 16:41:15 -0000 1.3 *************** *** 32,43 **** # SQL generated will be logged if the category # priority is set to DEBUG ! log4j.rootCategory = DEBUG, default log4j.appender.default = org.apache.log4j.FileAppender log4j.appender.default.file = ./torque.log ! log4j.appender.default.layout = org.apache.log4j.SimpleLayout ! # ------------------------------------------------------------------- ! # # D A T A B A S E S E R V I C E # --- 32,43 ---- # SQL generated will be logged if the category # priority is set to DEBUG ! log4j.rootCategory = DEBUG, default log4j.appender.default = org.apache.log4j.FileAppender log4j.appender.default.file = ./torque.log ! log4j.appender.default.layout = org.apache.log4j.SimpleLayout ! # ------------------------------------------------------------------- ! # # D A T A B A S E S E R V I C E # *************** *** 87,92 **** # adaptor. These properties are used by the DBFactory. You can add # all the drivers you want here. ! torque.database.adapter=DBOdbc, DBMM ! torque.database.adapter.DBOdbc=sun.jdbc.odbc.JdbcOdbcDriver torque.database.adapter.DBMM= torque.database.adapter.DBMM=org.gjt.mm.mysql.Driver --- 87,92 ---- # adaptor. These properties are used by the DBFactory. You can add # all the drivers you want here. ! # torque.database.adapter=DBOdbc, DBMM ! # torque.database.adapter.DBOdbc=sun.jdbc.odbc.JdbcOdbcDriver torque.database.adapter.DBMM= torque.database.adapter.DBMM=org.gjt.mm.mysql.Driver |
|
From: Stefan K. <sk...@us...> - 2002-03-06 16:41:20
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions
In directory usw-pr-cvs1:/tmp/cvs-serv11083/java/org/apache/jetspeed/modules/actions
Modified Files:
CreateNewUserAndConfirm.java
Log Message:
modified om files
Index: CreateNewUserAndConfirm.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions/CreateNewUserAndConfirm.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** CreateNewUserAndConfirm.java 1 Mar 2002 09:42:27 -0000 1.2
--- CreateNewUserAndConfirm.java 6 Mar 2002 16:41:15 -0000 1.3
***************
*** 246,256 ****
user.setLastName( data.getParameters().getString("lastname") );
user.setTitle( data.getParameters().getString("title") );
! user.setAddress( data.getParameters().getString("address") );
! user.setCity( data.getParameters().getString("city") );
! user.setState( data.getParameters().getString("state") );
! user.setZipCode( data.getParameters().getString("zipcode") );
! user.setCountry( data.getParameters().getString("country") );
! user.setWebPage( data.getParameters().getString("webpage") );
! user.setAffiliation( data.getParameters().getString("affiliation") );
user.setEmail( data.getParameters().getString("email") );
--- 246,256 ----
user.setLastName( data.getParameters().getString("lastname") );
user.setTitle( data.getParameters().getString("title") );
! //user.setAddress( data.getParameters().getString("address") );
! //user.setCity( data.getParameters().getString("city") );
! //user.setState( data.getParameters().getString("state") );
! //user.setZipCode( data.getParameters().getString("zipcode") );
! //user.setCountry( data.getParameters().getString("country") );
! //user.setWebPage( data.getParameters().getString("webpage") );
! //user.setAffiliation( data.getParameters().getString("affiliation") );
user.setEmail( data.getParameters().getString("email") );
|
|
From: Stefan K. <sk...@us...> - 2002-03-06 16:41:20
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db
In directory usw-pr-cvs1:/tmp/cvs-serv11083/conf/jetspeed/WEB-INF/db
Modified Files:
nmrshiftdb-schema.sql
Log Message:
modified om files
Index: nmrshiftdb-schema.sql
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db/nmrshiftdb-schema.sql,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** nmrshiftdb-schema.sql 6 Mar 2002 12:37:35 -0000 1.3
--- nmrshiftdb-schema.sql 6 Mar 2002 16:41:15 -0000 1.4
***************
*** 8,12 ****
(
MEASUREMENT_CONDITION_ID INTEGER NOT NULL AUTO_INCREMENT,
! TEMPERATURE FLOAT NOT NULL,
FIELD_STRENGTH INTEGER NOT NULL,
SOLVENT MEDIUMTEXT NOT NULL,
--- 8,12 ----
(
MEASUREMENT_CONDITION_ID INTEGER NOT NULL AUTO_INCREMENT,
! TEMPERATURE FLOAT NOT NULL,
FIELD_STRENGTH INTEGER NOT NULL,
SOLVENT MEDIUMTEXT NOT NULL,
***************
*** 17,21 ****
# -----------------------------------------------------------------------
! # SPECTRUM_TYPE
# -----------------------------------------------------------------------
drop table if exists SPECTRUM_TYPE;
--- 17,21 ----
# -----------------------------------------------------------------------
! # SPECTRUM_TYPE
# -----------------------------------------------------------------------
drop table if exists SPECTRUM_TYPE;
***************
*** 35,39 ****
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
);
!
# -----------------------------------------------------------------------
# SPECTRUM
--- 35,39 ----
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
);
!
# -----------------------------------------------------------------------
# SPECTRUM
***************
*** 42,49 ****
CREATE TABLE SPECTRUM
! (
SPECTRUM_ID INTEGER NOT NULL AUTO_INCREMENT,
DATE DATETIME NOT NULL,
! SPECFILE LONGBLOB NOT NULL,
SERIALIZED_SPECTRUM MEDIUMTEXT NOT NULL,
LITERATURE MEDIUMTEXT NOT NULL,
--- 42,49 ----
CREATE TABLE SPECTRUM
! (
SPECTRUM_ID INTEGER NOT NULL AUTO_INCREMENT,
DATE DATETIME NOT NULL,
! SPECFILE LONGBLOB NOT NULL,
SERIALIZED_SPECTRUM MEDIUMTEXT NOT NULL,
LITERATURE MEDIUMTEXT NOT NULL,
***************
*** 55,59 ****
MOLECULE_ID INTEGER NOT NULL,
PRIMARY KEY(SPECTRUM_ID),
! FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID),
FOREIGN KEY (MEASUREMENT_CONDITION_ID) REFERENCES MEASUREMENT_CONDITION (MEASUREMENT_CONDITION_ID),
FOREIGN KEY (SPECTRUM_TYPE_ID) REFERENCES SPECTRUM_TYPE (SPECTRUM_TYPE_ID),
--- 55,59 ----
MOLECULE_ID INTEGER NOT NULL,
PRIMARY KEY(SPECTRUM_ID),
! FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID),
FOREIGN KEY (MEASUREMENT_CONDITION_ID) REFERENCES MEASUREMENT_CONDITION (MEASUREMENT_CONDITION_ID),
FOREIGN KEY (SPECTRUM_TYPE_ID) REFERENCES SPECTRUM_TYPE (SPECTRUM_TYPE_ID),
***************
*** 64,77 ****
# SIGNAL
# -----------------------------------------------------------------------
! drop table if exists SIGNAL;
! CREATE TABLE SIGNAL
(
! SIGNAL_ID INTEGER NOT NULL AUTO_INCREMENT,
DIMENSIONALITY INTEGER NOT NULL,
SHIFT_1 FLOAT NOT NULL,
SHIFT_2 FLOAT NOT NULL,
SHIFT_3 FLOAT NOT NULL,
! SHIFT_4 FLOAT NOT NULL,
SHIFT_5 FLOAT NOT NULL,
SERIALIZED_SIGNAL MEDIUMTEXT NOT NULL,
--- 64,77 ----
# SIGNAL
# -----------------------------------------------------------------------
! drop table if exists SIGNAL;
! CREATE TABLE SIGNAL
(
! SIGNAL_ID INTEGER NOT NULL AUTO_INCREMENT,
DIMENSIONALITY INTEGER NOT NULL,
SHIFT_1 FLOAT NOT NULL,
SHIFT_2 FLOAT NOT NULL,
SHIFT_3 FLOAT NOT NULL,
! SHIFT_4 FLOAT NOT NULL,
SHIFT_5 FLOAT NOT NULL,
SERIALIZED_SIGNAL MEDIUMTEXT NOT NULL,
***************
*** 101,105 ****
PRIMARY KEY(MOLECULE_ID),
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
! );
# -----------------------------------------------------------------------
--- 101,105 ----
PRIMARY KEY(MOLECULE_ID),
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
! );
# -----------------------------------------------------------------------
***************
*** 126,133 ****
(
SIGNAL_ID INTEGER NOT NULL,
! ATOM_ID INTEGER NOT NULL,
FOREIGN KEY (SIGNAL_ID) REFERENCES SIGNAL (SIGNAL_ID),
FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
! );
# -----------------------------------------------------------------------
--- 126,135 ----
(
SIGNAL_ID INTEGER NOT NULL,
! ATOM_ID INTEGER NOT NULL,
! PRIMARY KEY(SIGNAL_ID,ATOM_ID),
! INDEX(ATOM_ID),
FOREIGN KEY (SIGNAL_ID) REFERENCES SIGNAL (SIGNAL_ID),
FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
! );
# -----------------------------------------------------------------------
***************
*** 155,159 ****
BOND_ID INTEGER NOT NULL,
ATOM_ID INTEGER NOT NULL,
! FOREIGN KEY (BOND_ID) REFERENCES BOND (BOND_ID),
FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
);
--- 157,163 ----
BOND_ID INTEGER NOT NULL,
ATOM_ID INTEGER NOT NULL,
! PRIMARY KEY(BOND_ID,ATOM_ID),
! INDEX(ATOM_ID),
! FOREIGN KEY (BOND_ID) REFERENCES BOND (BOND_ID),
FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
);
***************
*** 171,175 ****
PRIMARY KEY(CHEMICAL_NAME_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
! );
# -----------------------------------------------------------------------
--- 175,179 ----
PRIMARY KEY(CHEMICAL_NAME_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
! );
# -----------------------------------------------------------------------
|
|
From: Stefan K. <sh...@us...> - 2002-03-06 14:30:07
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory usw-pr-cvs1:/tmp/cvs-serv20603 Added Files: JSX0.8.20.1.jar Log Message: Needed by the cdk |
|
From: Stefan K. <sh...@us...> - 2002-03-06 14:29:24
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory usw-pr-cvs1:/tmp/cvs-serv20123 Removed Files: JSX1.0.jar Log Message: The cdk (MDLReader) is not working with 1.0 --- JSX1.0.jar DELETED --- |
|
From: Stefan K. <sk...@us...> - 2002-03-06 12:37:38
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db
In directory usw-pr-cvs1:/tmp/cvs-serv18117
Modified Files:
nmrshiftdb-schema.sql
Log Message:
modified sql script
Index: nmrshiftdb-schema.sql
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db/nmrshiftdb-schema.sql,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** nmrshiftdb-schema.sql 28 Feb 2002 15:38:12 -0000 1.2
--- nmrshiftdb-schema.sql 6 Mar 2002 12:37:35 -0000 1.3
***************
*** 7,12 ****
CREATE TABLE MEASUREMENT_CONDITION
(
! MEASUREMENT_CONDITION_ID INTEGER NOT NULL,
! TEMPERATURE FLOAT NOT NULL,
FIELD_STRENGTH INTEGER NOT NULL,
SOLVENT MEDIUMTEXT NOT NULL,
--- 7,12 ----
CREATE TABLE MEASUREMENT_CONDITION
(
! MEASUREMENT_CONDITION_ID INTEGER NOT NULL AUTO_INCREMENT,
! TEMPERATURE FLOAT NOT NULL,
FIELD_STRENGTH INTEGER NOT NULL,
SOLVENT MEDIUMTEXT NOT NULL,
***************
*** 17,21 ****
# -----------------------------------------------------------------------
! # SPECTRUM_TYPE
# -----------------------------------------------------------------------
drop table if exists SPECTRUM_TYPE;
--- 17,21 ----
# -----------------------------------------------------------------------
! # SPECTRUM_TYPE
# -----------------------------------------------------------------------
drop table if exists SPECTRUM_TYPE;
***************
*** 23,27 ****
CREATE TABLE SPECTRUM_TYPE
(
! SPECTRUM_TYPE_ID INTEGER NOT NULL,
DIMENSIONALITY INTEGER NOT NULL,
NAME MEDIUMTEXT NOT NULL,
--- 23,27 ----
CREATE TABLE SPECTRUM_TYPE
(
! SPECTRUM_TYPE_ID INTEGER NOT NULL AUTO_INCREMENT,
DIMENSIONALITY INTEGER NOT NULL,
NAME MEDIUMTEXT NOT NULL,
***************
*** 35,39 ****
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
);
!
# -----------------------------------------------------------------------
# SPECTRUM
--- 35,39 ----
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
);
!
# -----------------------------------------------------------------------
# SPECTRUM
***************
*** 42,49 ****
CREATE TABLE SPECTRUM
! (
! SPECTRUM_ID INTEGER NOT NULL,
DATE DATETIME NOT NULL,
! SPECFILE LONGBLOB NOT NULL,
SERIALIZED_SPECTRUM MEDIUMTEXT NOT NULL,
LITERATURE MEDIUMTEXT NOT NULL,
--- 42,49 ----
CREATE TABLE SPECTRUM
! (
! SPECTRUM_ID INTEGER NOT NULL AUTO_INCREMENT,
DATE DATETIME NOT NULL,
! SPECFILE LONGBLOB NOT NULL,
SERIALIZED_SPECTRUM MEDIUMTEXT NOT NULL,
LITERATURE MEDIUMTEXT NOT NULL,
***************
*** 64,77 ****
# SIGNAL
# -----------------------------------------------------------------------
! drop table if exists SIGNAL;
! CREATE TABLE SIGNAL
(
! SIGNAL_ID INTEGER NOT NULL,
DIMENSIONALITY INTEGER NOT NULL,
SHIFT_1 FLOAT NOT NULL,
SHIFT_2 FLOAT NOT NULL,
SHIFT_3 FLOAT NOT NULL,
! SHIFT_4 FLOAT NOT NULL,
SHIFT_5 FLOAT NOT NULL,
SERIALIZED_SIGNAL MEDIUMTEXT NOT NULL,
--- 64,77 ----
# SIGNAL
# -----------------------------------------------------------------------
! drop table if exists SIGNAL;
! CREATE TABLE SIGNAL
(
! SIGNAL_ID INTEGER NOT NULL AUTO_INCREMENT,
DIMENSIONALITY INTEGER NOT NULL,
SHIFT_1 FLOAT NOT NULL,
SHIFT_2 FLOAT NOT NULL,
SHIFT_3 FLOAT NOT NULL,
! SHIFT_4 FLOAT NOT NULL,
SHIFT_5 FLOAT NOT NULL,
SERIALIZED_SIGNAL MEDIUMTEXT NOT NULL,
***************
*** 89,93 ****
CREATE TABLE MOLECULE
(
! MOLECULE_ID INTEGER NOT NULL,
DATE DATETIME NOT NULL,
STRUCTURE_FILE LONGBLOB NOT NULL,
--- 89,93 ----
CREATE TABLE MOLECULE
(
! MOLECULE_ID INTEGER NOT NULL AUTO_INCREMENT,
DATE DATETIME NOT NULL,
STRUCTURE_FILE LONGBLOB NOT NULL,
***************
*** 104,120 ****
# -----------------------------------------------------------------------
- # MOLECULE_NMRSHIFTDB_USER
- # -----------------------------------------------------------------------
- drop table if exists MOLECULE_NMRSHIFTDB_USER;
-
- CREATE TABLE MOLECULE_NMRSHIFTDB_USER
- (
- MOLECULE_ID INTEGER NOT NULL,
- USER_ID INTEGER NOT NULL,
- FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID),
- FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
- );
-
- # -----------------------------------------------------------------------
# ATOM
# -----------------------------------------------------------------------
--- 104,107 ----
***************
*** 123,127 ****
CREATE TABLE ATOM
(
! ATOM_ID INTEGER NOT NULL,
SYMBOL MEDIUMTEXT NOT NULL,
SERIALIZED_ATOM MEDIUMTEXT NOT NULL,
--- 110,114 ----
CREATE TABLE ATOM
(
! ATOM_ID INTEGER NOT NULL AUTO_INCREMENT,
SYMBOL MEDIUMTEXT NOT NULL,
SERIALIZED_ATOM MEDIUMTEXT NOT NULL,
***************
*** 142,146 ****
FOREIGN KEY (SIGNAL_ID) REFERENCES SIGNAL (SIGNAL_ID),
FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
! );
# -----------------------------------------------------------------------
--- 129,133 ----
FOREIGN KEY (SIGNAL_ID) REFERENCES SIGNAL (SIGNAL_ID),
FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
! );
# -----------------------------------------------------------------------
***************
*** 151,158 ****
CREATE TABLE BOND
(
! BOND_ID INTEGER NOT NULL,
DEGREE INTEGER NOT NULL,
SERIALIZED_BOND MEDIUMTEXT NOT NULL,
! MOLECULE_ID INTEGER NOT NULL,
PRIMARY KEY(BOND_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
--- 138,145 ----
CREATE TABLE BOND
(
! BOND_ID INTEGER NOT NULL AUTO_INCREMENT,
DEGREE INTEGER NOT NULL,
SERIALIZED_BOND MEDIUMTEXT NOT NULL,
! MOLECULE_ID INTEGER NOT NULL,
PRIMARY KEY(BOND_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
***************
*** 168,172 ****
BOND_ID INTEGER NOT NULL,
ATOM_ID INTEGER NOT NULL,
! FOREIGN KEY (BOND_ID) REFERENCES BOND (BOND_ID),
FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
);
--- 155,159 ----
BOND_ID INTEGER NOT NULL,
ATOM_ID INTEGER NOT NULL,
! FOREIGN KEY (BOND_ID) REFERENCES BOND (BOND_ID),
FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
);
***************
*** 179,183 ****
CREATE TABLE CHEMICAL_NAME
(
! CHEMICAL_NAME_ID INTEGER NOT NULL,
NAME MEDIUMTEXT NOT NULL,
MOLECULE_ID INTEGER NOT NULL,
--- 166,170 ----
CREATE TABLE CHEMICAL_NAME
(
! CHEMICAL_NAME_ID INTEGER NOT NULL AUTO_INCREMENT,
NAME MEDIUMTEXT NOT NULL,
MOLECULE_ID INTEGER NOT NULL,
***************
*** 193,197 ****
CREATE TABLE CANONICAL_NAME
(
! CANONICAL_NAME_ID INTEGER NOT NULL,
NAME MEDIUMTEXT NOT NULL,
TYPE MEDIUMTEXT NOT NULL,
--- 180,184 ----
CREATE TABLE CANONICAL_NAME
(
! CANONICAL_NAME_ID INTEGER NOT NULL AUTO_INCREMENT,
NAME MEDIUMTEXT NOT NULL,
TYPE MEDIUMTEXT NOT NULL,
***************
*** 211,213 ****
-
--- 198,199 ----
|
|
From: Stefan K. <sk...@us...> - 2002-03-06 12:35:37
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/lib In directory usw-pr-cvs1:/tmp/cvs-serv17716 Modified Files: jetspeed-1.3a2-release.jar Log Message: modified jetspeed jar Index: jetspeed-1.3a2-release.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/lib/jetspeed-1.3a2-release.jar,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 Binary files /tmp/cvs9EJWIj and /tmp/cvseZJwsA differ |
|
From: Stefan K. <sh...@us...> - 2002-03-05 09:29:09
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf In directory usw-pr-cvs1:/tmp/cvs-serv29878/src/conf/jetspeed/WEB-INF/conf Modified Files: Torque.properties TurbineResources.properties Log Message: New Version Index: Torque.properties =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/Torque.properties,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** Torque.properties 15 Feb 2002 11:01:15 -0000 1.1 --- Torque.properties 5 Mar 2002 09:29:03 -0000 1.2 *************** *** 54,58 **** torque.database.default=nmrshiftdb torque.database.nmrshiftdb.driver = org.gjt.mm.mysql.Driver ! torque.database.nmrshiftdb.url = jdbc:mysql://10.10.11.63/nmrshiftdb torque.database.nmrshiftdb.username = turbine torque.database.nmrshiftdb.password = turbine --- 54,58 ---- torque.database.default=nmrshiftdb torque.database.nmrshiftdb.driver = org.gjt.mm.mysql.Driver ! torque.database.nmrshiftdb.url = jdbc:mysql://10.10.11.63:3306/nmrshiftdb torque.database.nmrshiftdb.username = turbine torque.database.nmrshiftdb.password = turbine *************** *** 97,98 **** --- 97,100 ---- torque.database.idbroker.cleverquantity=true + + Index: TurbineResources.properties =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/TurbineResources.properties,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** TurbineResources.properties 27 Feb 2002 13:25:52 -0000 1.3 --- TurbineResources.properties 5 Mar 2002 09:29:03 -0000 1.4 *************** *** 163,167 **** database.default.driver=org.gjt.mm.mysql.Driver ! database.default.url=jdbc:mysql://10.10.11.63:3306/nmrshiftdb database.default.username=turbine database.default.password=turbine --- 163,167 ---- database.default.driver=org.gjt.mm.mysql.Driver ! database.default.url=jdbc:mysql://10.10.11.24:3306/nmrshiftdb database.default.username=turbine database.default.password=turbine *************** *** 973,974 **** --- 973,975 ---- include = NMRShiftDBResources.properties + |
|
From: Stefan K. <sh...@us...> - 2002-03-05 09:29:08
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util
In directory usw-pr-cvs1:/tmp/cvs-serv29878/src/java/org/openscience/nmrshiftdb/util
Modified Files:
IntTriple.java SubmittingData.java
Log Message:
New Version
Index: IntTriple.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/IntTriple.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** IntTriple.java 27 Feb 2002 14:08:52 -0000 1.1
--- IntTriple.java 5 Mar 2002 09:29:04 -0000 1.2
***************
*** 1,11 ****
package org.openscience.nmrshiftdb.util;
! public class IntTriple{
public int value1;
public int value2;
! public int value3;
!
! public String toString(){
! return(new String(""+value1+" "+value2+" "+value3));
}
}
--- 1,33 ----
package org.openscience.nmrshiftdb.util;
! /**
! *Description of the Class
! *
! * @author shk3
! * @created 4. März 2002
! */
! public class IntTriple {
! /**
! *Shift
! */
public int value1;
+ /**
+ *Intensity
+ */
public int value2;
! /**
! *Atom assigned, -1==none
! */
! public int value3 = -1;
!
!
! /**
! *Description of the Method
! *
! * @return Description of the Returned Value
! */
! public String toString() {
! return (new String("" + value1 + " " + value2 + " " + value3));
}
}
+
Index: SubmittingData.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/SubmittingData.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** SubmittingData.java 28 Feb 2002 15:45:29 -0000 1.2
--- SubmittingData.java 5 Mar 2002 09:29:04 -0000 1.3
***************
*** 3,64 ****
import java.util.*;
! public class SubmittingData{
! String molecule="";
! ArrayList signalstable=new ArrayList();
! String solvent="";
! int fieldStrength=0;
! long temperature=0;
! String chemName="";
! public void setChemName(String chemName){
! this.chemName=chemName;
}
!
! public String getChemName(){
! return(chemName);
}
! public void setTemperature(long temperature){
! this.temperature=temperature;
}
!
! public long getTemperature(){
! return(temperature);
}
! public void setFieldStrength(int fieldStrength){
! this.fieldStrength=fieldStrength;
}
!
! public int getFieldStrength(){
! return(fieldStrength);
}
! public void setSolvent(String sol){
! solvent=sol;
}
!
! public String getSolvent(){
! return(solvent);
}
! public void setMolecule(String mol){
! molecule=mol;
}
!
! public String getMolecule(){
! return(molecule);
}
!
! public void setSignalstable(ArrayList al){
! signalstable=al;
}
!
! public ArrayList getSignalstable(){
! return(signalstable);
}
!
! public void addToSignalstable(Object signal){
signalstable.add(signal);
}
}
--- 3,149 ----
import java.util.*;
! /**
! *This class is used for holding the data of a molecule and an assigned spectrum in the session while the user is doing the sumbmit
! *
! * @author shk3
! * @created 4. März 2002
! */
! public class SubmittingData {
! String molecule = "";
! ArrayList signalstable = new ArrayList();
! String solvent = "";
! int fieldStrength = 0;
! long temperature = 0;
! String chemName = "";
!
! /**
! *Sets the chemName attribute of the SubmittingData object
! *
! * @param chemName The new chemName value
! */
! public void setChemName(String chemName) {
! this.chemName = chemName;
}
!
!
! /**
! *Sets the temperature attribute of the SubmittingData object
! *
! * @param temperature The new temperature value
! */
! public void setTemperature(long temperature) {
! this.temperature = temperature;
}
!
! /**
! *Sets the fieldStrength attribute of the SubmittingData object
! *
! * @param fieldStrength The new fieldStrength value
! */
! public void setFieldStrength(int fieldStrength) {
! this.fieldStrength = fieldStrength;
}
!
!
! /**
! *Sets the solvent attribute of the SubmittingData object
! *
! * @param sol The new solvent value
! */
! public void setSolvent(String sol) {
! solvent = sol;
}
!
! /**
! *Sets the molecule attribute of the SubmittingData object
! *
! * @param mol The new molecule value
! */
! public void setMolecule(String mol) {
! molecule = mol;
}
!
!
! /**
! *Sets the signalstable attribute of the SubmittingData object
! *
! * @param al The new signalstable value
! */
! public void setSignalstable(ArrayList al) {
! signalstable = al;
}
!
! /**
! *Gets the chemName attribute of the SubmittingData object
! *
! * @return The chemName value
! */
! public String getChemName() {
! return (chemName);
}
!
!
! /**
! *Gets the temperature attribute of the SubmittingData object
! *
! * @return The temperature value
! */
! public long getTemperature() {
! return (temperature);
}
!
! /**
! *Gets the fieldStrength attribute of the SubmittingData object
! *
! * @return The fieldStrength value
! */
! public int getFieldStrength() {
! return (fieldStrength);
}
!
!
! /**
! *Gets the solvent attribute of the SubmittingData object
! *
! * @return The solvent value
! */
! public String getSolvent() {
! return (solvent);
}
!
!
! /**
! *Gets the molecule attribute of the SubmittingData object
! *
! * @return The molecule value
! */
! public String getMolecule() {
! return (molecule);
}
!
!
! /**
! *Gets the signalstable attribute of the SubmittingData object
! *
! * @return The signalstable value
! */
! public ArrayList getSignalstable() {
! return (signalstable);
}
!
!
! /**
! *Adds a feature to the ToSignalstable attribute of the SubmittingData object
! *
! * @param signal The feature to be added to the ToSignalstable attribute
! */
! public void addToSignalstable(Object signal) {
signalstable.add(signal);
}
}
+
|
|
From: Stefan K. <sh...@us...> - 2002-03-05 09:29:08
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets
In directory usw-pr-cvs1:/tmp/cvs-serv29878/src/java/org/openscience/nmrshiftdb/portlets
Modified Files:
SubmitPortlet.java
Log Message:
New Version
Index: SubmitPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -r1.6 -r1.7
*** SubmitPortlet.java 28 Feb 2002 15:45:29 -0000 1.6
--- SubmitPortlet.java 5 Mar 2002 09:29:04 -0000 1.7
***************
*** 9,12 ****
--- 9,15 ----
import org.apache.jetspeed.util.servlet.*;
import org.apache.turbine.om.*;
+ import org.apache.turbine.util.*;
+
+ import org.apache.torque.*;
import java.util.*;
***************
*** 25,30 ****
* Description of the Class
*
! *@author Stefan Kuhn
! *@created 18. Februar 2002
*/
public class SubmitPortlet extends AbstractPortlet {
--- 28,33 ----
* Description of the Class
*
! * @author Stefan Kuhn
! * @created 18. Februar 2002
*/
public class SubmitPortlet extends AbstractPortlet {
***************
*** 32,290 ****
* Gets the content attribute of the ResultPortlet object
*
! *@param runData Created by turbine
! *@return The content to be displayed as the portlet
*/
public ConcreteElement getContent(RunData runData) {
HttpServletRequest req = runData.getRequest();
String action = req.getParameter("nmrshiftdbaction");
! HttpSession session= req.getSession();
! SubmittingData subData = (SubmittingData)session.getAttribute("subData");
! String messages="";//Here all sort of error messages are appended
! String returnValue="";
//Create new SubmittingData object in case there is none in the session, i. e. no submission currently going on
! if(subData==null){
! subData=new SubmittingData();
! session.setAttribute("subData",subData);
}
//User submittet new values for the spectrum
! if(action!=null&&action.equals("submitSpectrumForAssignment")){
! String spectrum=req.getParameter("spectrum")+'\n';
! char[] charSpectrum=spectrum.toCharArray();
! String shift="";
! String intensity="";
! ArrayList numberSpectrum=new ArrayList();
! boolean addingShift=true;
//The string is parsed
! for(int i=0;i<charSpectrum.length;i++){
! if(charSpectrum[i]==';'){
! intensity="";
! addingShift=false;
! }
! else{
! if(charSpectrum[i]=='\n'){
! IntTriple figures=new IntTriple();
! if(shift.trim()!=""){
! try{
! figures.value1=(new Integer(shift.trim())).intValue();
! if(intensity.trim()=="")
! figures.value2=0;
! else
! figures.value2=(new Integer(intensity.trim())).intValue();
numberSpectrum.add(figures);
}
! catch(NumberFormatException ex){
! messages+="Your input included wrong characters!<br>";
! }
! shift="";
! addingShift=true;
}
- }
- else{
- if(addingShift)shift=shift+charSpectrum[i];
- else intensity=intensity+charSpectrum[i];
}
}
}
//Values added to the signals table
! for(int i=0;i<numberSpectrum.size();i++){
subData.addToSignalstable(numberSpectrum.get(i));
}
! returnValue=submitPage(messages, subData);
}
//User submitted new assignments
! if(action!=null&&action.equals("submitAssignments")){
! for(int i=0;i<subData.getSignalstable().size();i++){
! ((IntTriple)subData.getSignalstable().get(i)).value3=new Integer(req.getParameter("atomSelect"+i).trim()).intValue();
}
! returnValue=submitPage(messages, subData);
}
//User submitted a molecule in marvin
! if(action!=null&&action.equals("submitMolecule")){
subData.setMolecule(req.getParameter("MolTxt"));
! returnValue=submitPage(messages, subData);
}
//User submitted the whole input
! if(action!=null&&action.equals("submitForConfirm")){
subData.setSolvent(req.getParameter("solvent"));
subData.setChemName(req.getParameter("chemName"));
! String fieldStrengthStr=req.getParameter("fieldStrength");
! String temperatureStr=req.getParameter("temperature");
! try{
! int fieldStrength=Integer.parseInt(fieldStrengthStr);
subData.setFieldStrength(fieldStrength);
}
! catch(NumberFormatException ex){
! messages+="Your field strength is not a decimal figure!";
! }
! try{
! long temp=Long.parseLong(temperatureStr);
subData.setTemperature(temp);
}
! catch(NumberFormatException ex){
! messages+="Your temperature is not a decimal figure!";
}
- if(messages=="")//Show confirm screen
- returnValue="Here the data should be reapeated!<form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitSpectrumForDB\"><input type=\"submit\" value=\"Write to Database\"></form>";
- else//Display message and show input screen again
- returnValue=submitPage(messages, subData);
}
//User submittet confirm screen
! if(action!=null&&action.equals("submitSpectrumForDB")){
! MDLReader mdlreader=new MDLReader(new StringReader(subData.getMolecule()));
! Molecule mol;
! try{
! mol=(Molecule)mdlreader.read(new Molecule());
! }
! catch(Throwable ex){
! ex.printStackTrace();
}
//Add molecule to DB
! Criteria crit=new Criteria();
! crit.add(MoleculePeer.SERIALIZED_MOLECULE,serializeObject(mol));
! crit.add(MoleculePeer.DATE,(java.sql.Date)new java.util.Date());
! NumberKey nkMol=(NumberKey)MoleculePeer.doInsert(crit);
! //Add spectrum to DB
! crit=new Criteria();
! crit.add(SpectrumPeer.MOLECULE_ID,nkMol.getValue());
! crit.add(SpectrumPeer.REVIEW_FLAG, 'n');
! NumberKey nkSpectrum=(NumberKey)SpectrumPeer.doInsert(crit);
! //Add atoms to db
! Atom[] atoms=mol.getAtoms();
! NumberKey[] nkAtom=new NumberKey[atoms.length];
! for(int i=0; i<atoms.length;i++){
! crit=new Criteria();
! crit.add(AtomsPeer.SYMBOL,atoms[i].getSymbol());
! crit.add(AtomsPeer.SERIALIZED_ATOMS,serializeObject(atoms[i]));
! crit.add(AtomsPeer.MOLECULE_ID,nkMol.getValue());
! nkAtom[i]=(NumberKey)AtomsPeer.doInsert(crit);
! }
! //Add bonds to db
! Bond[] bonds=mol.getBonds();
! NumberKey[] nkBond=new NumberKey[bonds.length];
! for(int i=0; i<bonds.length;i++){
! crit=new Criteria();
! crit.add(BondsPeer.DEGREE,bonds[i].getOrder());
! crit.add(BondsPeer.SERIALIZED_BONDS,serializeObject(bonds[i]));
! crit.add(BondsPeer.MOLECULE_ID,nkMol.getValue());
! nkBond[i]=(NumberKey)BondsPeer.doInsert(crit);
! //Add bonds-atoms relationship to DB
! Atoms[] neighbourAtoms=bonds[i].getAtoms();
! for(int k=0;k<neighbourAtoms.length;k++){
! crit=new Criteria();
! crit.add(BondsAtomsPeer.BONDS_ID,nkBond[i].getValue());
! crit.add(BondsAtomsPeer.ATOMS_ID,nkAtom[mol.getAtomNumber(neighbourAtoms[k])].getValue());
}
! }
! //add signals to DB
! NumberKey[] nkSignal=new NumberKey[subData.getSignalstable().size()];
! for(int i=0;i<subData.getSignalstable().size();i++){
! crit=new Criteria();
! crit.add(SignalPeer.DIMENSIONALITY,1);
! crit.add(SignalPeer.SHIFT_1,((IntTriple)subData.getSignalstable().get(i)).value1);
! crit.add(SignalPeer.SPECTRUM_ID,nkSpectrum.getValue());
! //The serialized signal is not used at the moment //Intensity still missing
! //crit.add(SignalPeer.INTENSITY,((IntTriple)subData.getSignalstable[i]).value2);
! nkSignal[i]=(NumberKey)SignalPeer.doInsert(crit);
! crit=new Criteria();
! crit.add(SignalAtomsPeer.SIGNAL_ID,nkSignal[i].getValue());
! crit.add(SignalAtomsPeer.ATOMS_ID,nkAtom[((IntTriple)subData.getSignalstable().get(i)).value3].getValue());
! NumberKey nk=(NumberKey)SignalAtomsPeer.doInsert(crit);
}
session.removeAttribute("subData");
! returnValue="Your spectrum has been submitted and will be reviewed shortly! Thanks for your contribution!";
}
! if(action==null)returnValue=submitPage(messages,subData);
! return(new StringElement(returnValue));
}
!
! private String serializeObject(Object o){
! StringWriter strWriter=new StringWriter();
! ObjOut out=new ObjOut(false,strWriter);
! out.writeObject(o);
! return(strWriter.toString());
! }
!
/**
* Puts together the submit page
*
! *@param messages Collected messages for the user
! *@param subData submittingData object from session
! *@return The content to be displayed as the portlet
*/
! private String submitPage(String messages, SubmittingData subData){
! String returnValue="";
! int tableSize;//the number of rows the table for the assignments will have (10 is minimum)
! if(subData.getSignalstable().size()<10)
! tableSize=10;
! else
! tableSize=subData.getSignalstable().size()+2;
//The return string is put together (better would be a jsp, butthat's not working
! returnValue+="<p><bold>"+messages+"</bold></p>";
! returnValue+="<table border=\"3\"><tr><th>Draw your structure</th><th colspan=\"3\">Here the assignment which will be uploaded</th><th>Enter your spectral data here</th></tr><tr><td rowspan=\"";
! returnValue+=tableSize+"\">Click to draw your molecule!<br>";
! returnValue+="<script LANGUAGE=\"JavaScript1.1\" SRC=\"/jetspeed/nmrshiftdb/marvin.js\"></script>\n";
! returnValue+="<script LANGUAGE=\"JavaScript1.1\">\n";
! returnValue+="<!--\n";
! returnValue+="function exportMol(format) {\n";
! returnValue+="if(document.MSketch != null) {\n";
! returnValue+="var s = document.MSketch.getMol(format);\n";
! returnValue+="s = unix2local(s);\n";
! returnValue+="document.MolForm.MolTxt.value=s;\n";
! returnValue+="} else {\n";
! returnValue+="alert(\"Cannot import molecule: no JavaScript to Java communication in your browser.\");\n";
! returnValue+="}\n";
! returnValue+="}\n";
! returnValue+="function unselectandselect(b){\n";
! returnValue+="document.MView.selectAllAtoms(0,false);\n";
! returnValue+="document.MView.selectAtom(0,b,true);\n";
! returnValue+="}\n";
! returnValue+="msketch_name = \"MSketch\";\n";
! returnValue+="msketch_begin(\"/jetspeed/nmrshiftdb\", 100, 300);\n";
! returnValue+="msketch_param(\"autoscale\", \"true\");\n";
! returnValue+="msketch_param(\"detach\", \"hide\");\n";
! returnValue+="msketch_param(\"menubar\",\"false\");\n";
! returnValue+="msketch_end();\n";
! returnValue+="mview_name = \"MView\";\n";
! returnValue+="mview_begin(\"/jetspeed/nmrshiftdb\", 300, 300);\n";
//The mol is put into the MView applet via a file (Problem: If two people write at the same time, the files are messed up)
File outputFile = new File("/usr/local/jakarta-tomcat-3.3a/webapps/jetspeed/nmrshiftdb/temp.mol");
! try{
! FileWriter out=new FileWriter(outputFile);
! out.write(subData.getMolecule());
! out.close();
! }
! catch(Exception e){
System.out.println(e.getMessage());
}
! if(!subData.getMolecule().equals("")){
! returnValue+="mview_param(\"mol\",\"temp.mol\");\n";
}
! returnValue+="mview_end();\n";
! returnValue+="//-->\n";
! returnValue+="</script>\n";
! returnValue+="<form action=\"/jetspeed/portal/\" method=\"post\" NAME=\"MolForm\">";
! returnValue+="<input type=\"hidden\" name=\"MolTxt\" value=\""+subData.getMolecule()+"\">";
! returnValue+="<input type=\"hidden\" name=\"nmrshiftdbaction\"value=\"submitMolecule\">";
! returnValue+="<input TYPE=\"submit\" VALUE=\"Submit molecule\" onClick=\"exportMol(\'mol\')\"></form>";
! returnValue+="</td><td>Atom No.</td><td>Shift</td><td>Intensity</td>";
! returnValue+="<td rowspan=\"";
! returnValue+=tableSize+"\"><form action=\"/jetspeed/portal/\" name=\"spectrumForm\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitSpectrumForAssignment\"><textarea name=\"spectrum\" cols=\"10\" rows=\"10\"></textarea><br><input type=\"submit\" value=\"Submit the Spectrum\"></form></td></tr>";
! returnValue+="<form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitAssignments\">";
! for(int i=0;i<subData.getSignalstable().size();i++){
! returnValue+="<tr><td><select name=\"atomSelect"+i+"\" size=\"1\" onChange=\"unselectandselect(this.value)\">";
! for(int k=0;k<subData.getSignalstable().size();k++){
! if(k==((IntTriple)subData.getSignalstable().get(i)).value3)
! returnValue+="<option selected>"+(k)+"</option>";
! else
! returnValue+="<option>"+(k)+"</option>";
}
! returnValue+="</select></td><td>"+((IntTriple)subData.getSignalstable().get(i)).value1+"</td><td>"+((IntTriple)subData.getSignalstable().get(i)).value2+"</td></tr>";
}
! returnValue+="<tr><td colspan=\"3\"><input type=\"submit\" value=\"Submit assignments\"></td></tr></form>";
! returnValue+="</table><br><form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitForConfirm\"><center>Chemical name:<input type=\"text\" name=\"chemName\"></center><br><center>Measurement conditions - temperature (in <sup>0</sup>K):<input type=\"text\" name=\"temperature\"> -Field strength:<input type=\"text\" name=\"fieldStrength\"> -Solvent:<input type=\"text\" name=\"solvent\"></center><br><center><input type=\"submit\" value=\"Write to Database\"></center></form>";
return (returnValue);
}
}
-
--- 35,349 ----
* Gets the content attribute of the ResultPortlet object
*
! * @param runData Created by turbine
! * @return The content to be displayed as the portlet
*/
public ConcreteElement getContent(RunData runData) {
HttpServletRequest req = runData.getRequest();
String action = req.getParameter("nmrshiftdbaction");
! HttpSession session = req.getSession();
! SubmittingData subData = (SubmittingData) session.getAttribute("subData");
! String messages = "";
! //Here all sort of error messages are appended
! String returnValue = "";
//Create new SubmittingData object in case there is none in the session, i. e. no submission currently going on
! if (subData == null) {
! subData = new SubmittingData();
! session.setAttribute("subData", subData);
}
//User submittet new values for the spectrum
! if (action != null && action.equals("submitSpectrumForAssignment")) {
! String spectrum = req.getParameter("spectrum") + '\n';
! char[] charSpectrum = spectrum.toCharArray();
! String shift = "";
! String intensity = "";
! ArrayList numberSpectrum = new ArrayList();
! boolean addingShift = true;
//The string is parsed
! for (int i = 0; i < charSpectrum.length; i++) {
! if (charSpectrum[i] == ';') {
! intensity = "";
! addingShift = false;
! } else {
! if (charSpectrum[i] == '\n') {
! IntTriple figures = new IntTriple();
! if (shift.trim() != "") {
! try {
! figures.value1 = (new Integer(shift.trim())).intValue();
! if (intensity.trim() == "") {
! figures.value2 = 0;
! } else {
! figures.value2 = (new Integer(intensity.trim())).intValue();
! }
numberSpectrum.add(figures);
+ } catch (NumberFormatException ex) {
+ messages += "Your input included wrong characters!<br>";
}
! shift = "";
! addingShift = true;
! }
! } else {
! if (addingShift) {
! shift = shift + charSpectrum[i];
! } else {
! intensity = intensity + charSpectrum[i];
}
}
}
}
//Values added to the signals table
! for (int i = 0; i < numberSpectrum.size(); i++) {
subData.addToSignalstable(numberSpectrum.get(i));
}
! returnValue = submitPage(messages, subData);
}
//User submitted new assignments
! if (action != null && action.equals("submitAssignments")) {
! for (int i = 0; i < subData.getSignalstable().size(); i++) {
! if (req.getParameter("atomSelect" + i).equals("none")) {
! ((IntTriple) subData.getSignalstable().get(i)).value3 = -1;
! } else {
! ((IntTriple) subData.getSignalstable().get(i)).value3 = new Integer(req.getParameter("atomSelect" + i).trim()).intValue();
! }
}
! returnValue = submitPage(messages, subData);
}
//User submitted a molecule in marvin
! if (action != null && action.equals("submitMolecule")) {
subData.setMolecule(req.getParameter("MolTxt"));
! returnValue = submitPage(messages, subData);
}
//User submitted the whole input
! if (action != null && action.equals("submitForConfirm")) {
subData.setSolvent(req.getParameter("solvent"));
subData.setChemName(req.getParameter("chemName"));
! String fieldStrengthStr = req.getParameter("fieldStrength");
! String temperatureStr = req.getParameter("temperature");
! try {
! int fieldStrength = Integer.parseInt(fieldStrengthStr);
subData.setFieldStrength(fieldStrength);
+ } catch (NumberFormatException ex) {
+ messages += "Your field strength is not a decimal figure!";
}
! try {
! long temp = Long.parseLong(temperatureStr);
subData.setTemperature(temp);
+ } catch (NumberFormatException ex) {
+ messages += "Your temperature is not a decimal figure!";
}
! if (messages == "") {
! //Show confirm screen
! returnValue = "Here the data should be reapeated!<form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitSpectrumForDB\"><input type=\"submit\" value=\"Write to Database\"></form>";
! } else {
! //Display message and show input screen again
! returnValue = submitPage(messages, subData);
}
}
//User submittet confirm screen
! if (action != null && action.equals("submitSpectrumForDB")) {
! //Log.debug(subData.getMolecule());
! MDLReader mdlreader = new MDLReader(new StringReader(subData.getMolecule()));
! Molecule mol = new Molecule();
! try {
! mol = (Molecule) mdlreader.read(new Molecule());
! } catch (Throwable ex) {
! Log.debug("Fehler1: " + ex.getMessage());
! StringWriter strWr = new StringWriter();
! PrintWriter prWr = new PrintWriter(strWr);
! ex.printStackTrace(prWr);
! Log.debug(strWr.toString());
}
//Add molecule to DB
! try {
! //Torque.init("/usr/local/jakarta-tomcat-3.3a/webapps/jetspeed/WEB-INF/conf/Torque.properties");
! org.apache.turbine.util.db.pool.DBConnection dbconn=org.apache.turbine.services.db.TurbineDB.getConnection();
! System.err.println(dbconn);
! Criteria crit = new Criteria();
! DBMolecule mol2 = new DBMolecule();
! mol2.setDate(new Date());
! //mol2.save();
! //crit.add(DBMoleculePeer.SERIALIZED_MOLECULE,"serializeObject(mol)");
! //crit.add(DBMoleculePeer.DATE,(java.sql.Date)new java.util.Date());
! //crit.add(DBMoleculePeer.CAS_NUMBER,45);
! mol2.save(dbconn);
! System.err.println("juhu");
! NumberKey nkMol = new NumberKey();
! Log.debug("after insert molecule");
! //Add chemical name to DB
! crit = new Criteria();
! crit.add(DBChemicalNamePeer.MOLECULE_ID, nkMol.getValue());
! crit.add(DBChemicalNamePeer.NAME, subData.getChemName());
! //Add spectrum to DB
! crit = new Criteria();
! crit.add(DBSpectrumPeer.MOLECULE_ID, nkMol.getValue());
! crit.add(DBSpectrumPeer.REVIEW_FLAG, 'n');
! NumberKey nkSpectrum = (NumberKey) DBSpectrumPeer.doInsert(crit);
! //Add atoms to db
! Atom[] atoms = mol.getAtoms();
! NumberKey[] nkAtom = new NumberKey[atoms.length];
! for (int i = 0; i < atoms.length; i++) {
! crit = new Criteria();
! crit.add(DBAtomPeer.SYMBOL, atoms[i].getSymbol());
! crit.add(DBAtomPeer.SERIALIZED_ATOM, serializeObject(atoms[i]));
! crit.add(DBAtomPeer.MOLECULE_ID, nkMol.getValue());
! nkAtom[i] = (NumberKey) DBAtomPeer.doInsert(crit);
}
! //Add bonds to db
! Bond[] bonds = mol.getBonds();
! NumberKey[] nkBond = new NumberKey[bonds.length];
! for (int i = 0; i < bonds.length; i++) {
! crit = new Criteria();
! crit.add(DBBondPeer.DEGREE, bonds[i].getOrder());
! crit.add(DBBondPeer.SERIALIZED_BOND, serializeObject(bonds[i]));
! crit.add(DBBondPeer.MOLECULE_ID, nkMol.getValue());
! nkBond[i] = (NumberKey) DBBondPeer.doInsert(crit);
! //Add bonds-atoms relationship to DB
! Atom[] neighbourAtoms = bonds[i].getAtoms();
! for (int k = 0; k < neighbourAtoms.length; k++) {
! crit = new Criteria();
! crit.add(DBBondDBAtomPeer.BOND_ID, nkBond[i].getValue());
! crit.add(DBBondDBAtomPeer.ATOM_ID, nkAtom[mol.getAtomNumber(neighbourAtoms[k])].getValue());
! Object o = DBBondDBAtomPeer.doInsert(crit);
! }
! }
! //add signals to DB
! NumberKey[] nkSignal = new NumberKey[subData.getSignalstable().size()];
! for (int i = 0; i < subData.getSignalstable().size(); i++) {
! crit = new Criteria();
! crit.add(DBSignalPeer.DIMENSIONALITY, 1);
! crit.add(DBSignalPeer.SHIFT_1, ((IntTriple) subData.getSignalstable().get(i)).value1);
! crit.add(DBSignalPeer.SPECTRUM_ID, nkSpectrum.getValue());
! //The serialized signal is not used at the moment //Intensity still missing
! //crit.add(SignalPeer.INTENSITY,((IntTriple)subData.getSignalstable[i]).value2);
! nkSignal[i] = (NumberKey) DBSignalPeer.doInsert(crit);
! crit = new Criteria();
! crit.add(DBSignalDBAtomPeer.SIGNAL_ID, nkSignal[i].getValue());
! crit.add(DBSignalDBAtomPeer.ATOM_ID, nkAtom[((IntTriple) subData.getSignalstable().get(i)).value3].getValue());
! NumberKey nk = (NumberKey) DBSignalDBAtomPeer.doInsert(crit);
! }
! } catch (Exception ex) {
! Log.debug("Fehler2: " + ex.getMessage());
! StringWriter strWr = new StringWriter();
! PrintWriter prWr = new PrintWriter(strWr);
! ex.printStackTrace(prWr);
! Log.debug(strWr.toString());
}
session.removeAttribute("subData");
! returnValue = "Your spectrum has been submitted and will be reviewed shortly! Thanks for your contribution! For a new submit <a heref=\"http://localhost:8080/jetspeed/portal/pane0/Submit\">click here</a>";
! }
! if (action == null) {
! returnValue = submitPage(messages, subData);
}
! return (new StringElement(returnValue));
}
!
!
! /**
! *Returns a JSX-stylish serialized string of an object
! *
! * @param o The object to be serialized
! * @return The serialized object
! */
! private String serializeObject(Object o) {
! StringWriter strWriter = new StringWriter();
! try {
! ObjOut out = new ObjOut(false, strWriter);
! out.writeObject(o);
! } catch (IOException ex) {
! System.out.println(ex.getMessage());
! }
! return (strWriter.toString());
! }
!
!
/**
* Puts together the submit page
*
! * @param messages Collected messages for the user
! * @param subData submittingData object from session
! * @return The content to be displayed as the portlet
*/
! private String submitPage(String messages, SubmittingData subData) {
! String returnValue = "";
! int tableSize;
! //the number of rows the table for the assignments will have (10 is minimum)
! if (subData.getSignalstable().size() < 10) {
! tableSize = 10;
! } else {
! tableSize = subData.getSignalstable().size() + 2;
! }
//The return string is put together (better would be a jsp, butthat's not working
! returnValue += "<p><bold>" + messages + "</bold></p>";
! returnValue += "<table border=\"3\"><tr><th>Draw your structure</th><th colspan=\"3\">Here the assignment which will be uploaded</th><th>Enter your spectral data here</th></tr><tr><td rowspan=\"";
! returnValue += tableSize + "\">Click to draw your molecule!<br>";
! returnValue += "<script LANGUAGE=\"JavaScript1.1\" SRC=\"/jetspeed/nmrshiftdb/marvin.js\"></script>\n";
! returnValue += "<script LANGUAGE=\"JavaScript1.1\">\n";
! returnValue += "<!--\n";
! returnValue += "function exportMol(format) {\n";
! returnValue += "if(document.MSketch != null) {\n";
! returnValue += "var s = document.MSketch.getMol(format);\n";
! returnValue += "s = unix2local(s);\n";
! returnValue += "document.MolForm.MolTxt.value=s;\n";
! returnValue += "} else {\n";
! returnValue += "alert(\"Cannot import molecule: no JavaScript to Java communication in your browser.\");\n";
! returnValue += "}\n";
! returnValue += "}\n";
! returnValue += "function unselectandselect(b){\n";
! returnValue += "document.MView.selectAllAtoms(0,false);\n";
! returnValue += "document.MView.selectAtom(0,b,true);\n";
! returnValue += "}\n";
! returnValue += "msketch_mayscript = true;\n";
! returnValue += "msketch_name = \"MSketch\";\n";
! returnValue += "msketch_begin(\"/jetspeed/nmrshiftdb\", 100, 300);\n";
! returnValue += "msketch_param(\"autoscale\", \"true\");\n";
! returnValue += "msketch_param(\"detach\", \"hide\");\n";
! returnValue += "msketch_param(\"menubar\",\"false\");\n";
! returnValue += "msketch_end();\n";
! returnValue += "msview_mayscript = true;\n";
! returnValue += "mview_name = \"MView\";\n";
! returnValue += "mview_begin(\"/jetspeed/nmrshiftdb\", 300, 300);\n";
//The mol is put into the MView applet via a file (Problem: If two people write at the same time, the files are messed up)
File outputFile = new File("/usr/local/jakarta-tomcat-3.3a/webapps/jetspeed/nmrshiftdb/temp.mol");
! try {
! FileWriter out = new FileWriter(outputFile);
! out.write(subData.getMolecule());
! out.close();
! } catch (Exception e) {
System.out.println(e.getMessage());
}
! if (!subData.getMolecule().equals("")) {
! returnValue += "mview_param(\"mol\",\"temp.mol\");\n";
}
! returnValue += "mview_end();\n";
! returnValue += "//-->\n";
! returnValue += "</script>\n";
! returnValue += "<form action=\"/jetspeed/portal/\" method=\"post\" NAME=\"MolForm\">";
! returnValue += "<input type=\"hidden\" name=\"MolTxt\" value=\"" + subData.getMolecule() + "\">";
! returnValue += "<input type=\"hidden\" name=\"nmrshiftdbaction\"value=\"submitMolecule\">";
! returnValue += "<input TYPE=\"submit\" VALUE=\"Submit molecule\" onClick=\"exportMol(\'mol\')\"></form>";
! returnValue += "</td><td height=\"20\">Atom No.</td><td>Shift</td><td>Intensity</td>";
! returnValue += "<td rowspan=\"";
! returnValue += tableSize + "\" valign=\"bottom\">Enter one shift per line, the intensity<br>(optional) seperated by ;<br>like<br>56;4<br>64;6<br><form action=\"/jetspeed/portal/\" name=\"spectrumForm\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitSpectrumForAssignment\"><textarea name=\"spectrum\" cols=\"10\" rows=\"10\"></textarea><br><input type=\"submit\" value=\"Submit the Spectrum\"></form></td></tr>";
! returnValue += "<form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitAssignments\">";
! for (int i = 0; i < subData.getSignalstable().size(); i++) {
! returnValue += "<tr><td><select name=\"atomSelect" + i + "\" size=\"1\" onChange=\"unselectandselect(this.value)\">";
! if (((IntTriple) subData.getSignalstable().get(i)).value3 == -1) {
! returnValue += "<OPTION SELECTED>none</option>";
! } else {
! returnValue += "<OPTION>none</option>";
! }
! for (int k = 0; k < subData.getSignalstable().size(); k++) {
! if (k == ((IntTriple) subData.getSignalstable().get(i)).value3) {
! returnValue += "<option selected>" + (k) + "</option>";
! } else {
! returnValue += "<option>" + (k) + "</option>";
! }
}
! returnValue += "</select></td><td>" + ((IntTriple) subData.getSignalstable().get(i)).value1 + "</td><td>" + ((IntTriple) subData.getSignalstable().get(i)).value2 + "</td></tr>";
}
! returnValue += "<tr><td colspan=\"3\" valign=\"bottom\"><input type=\"submit\" value=\"Submit assignments\"></td></tr></form>";
! returnValue += "</table><br><form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitForConfirm\"><center>Chemical name:<input type=\"text\" name=\"chemName\"></center><br><center>Measurement conditions - temperature (in <sup>0</sup>K):<input type=\"text\" name=\"temperature\"> -Field strength:<input type=\"text\" name=\"fieldStrength\"> -Solvent:<input type=\"text\" name=\"solvent\"></center><br><center><input type=\"submit\" value=\"Write to Database\"></center></form>";
return (returnValue);
}
}
|
|
From: Stefan K. <sk...@us...> - 2002-03-04 16:40:20
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/lib In directory usw-pr-cvs1:/tmp/cvs-serv2242 Modified Files: jetspeed-1.3a2-release.jar Log Message: use a newer jetspeed version Index: jetspeed-1.3a2-release.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/lib/jetspeed-1.3a2-release.jar,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 Binary files /tmp/cvs7INNAr and /tmp/cvsKjLuPP differ |
|
From: Stefan K. <sk...@us...> - 2002-03-01 14:22:59
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc
In directory usw-pr-cvs1:/tmp/cvs-serv17202
Modified Files:
entrel_020228_ls_A4.gd
Log Message:
updated entrel diagram
Index: entrel_020228_ls_A4.gd
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/entrel_020228_ls_A4.gd,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** entrel_020228_ls_A4.gd 28 Feb 2002 15:47:33 -0000 1.1
--- entrel_020228_ls_A4.gd 1 Mar 2002 14:22:55 -0000 1.2
***************
*** 4,8 ****
{ GeneratedFrom TGD-version-2.01 }
{ WrittenBy stefan }
! { WrittenOn "Thu Feb 28 15:30:55 2002" }
}
--- 4,8 ----
{ GeneratedFrom TGD-version-2.01 }
{ WrittenBy stefan }
! { WrittenOn "Fri Mar 1 15:22:06 2002" }
}
***************
*** 1622,1628 ****
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{ Color "black" }
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--- 4422,4426 ----
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|
|
From: Stefan K. <sk...@us...> - 2002-03-01 10:21:34
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db
In directory usw-pr-cvs1:/tmp/cvs-serv21745
Modified Files:
turbine-schema.sql
Log Message:
errors corrected
Index: turbine-schema.sql
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db/turbine-schema.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** turbine-schema.sql 27 Feb 2002 13:30:45 -0000 1.1
--- turbine-schema.sql 1 Mar 2002 10:10:12 -0000 1.2
***************
*** 1,3 ****
!
# -----------------------------------------------------------------------
# TURBINE_PERMISSION
--- 1,3 ----
!
# -----------------------------------------------------------------------
# TURBINE_PERMISSION
***************
*** 11,15 ****
OBJECTDATA MEDIUMBLOB,
PRIMARY KEY(PERMISSION_ID),
! UNIQUE (PERMISSION_NAME),
);
--- 11,15 ----
OBJECTDATA MEDIUMBLOB,
PRIMARY KEY(PERMISSION_ID),
! UNIQUE (PERMISSION_NAME)
);
***************
*** 25,29 ****
OBJECTDATA MEDIUMBLOB,
PRIMARY KEY(ROLE_ID),
! UNIQUE (ROLE_NAME),
);
--- 25,29 ----
OBJECTDATA MEDIUMBLOB,
PRIMARY KEY(ROLE_ID),
! UNIQUE (ROLE_NAME)
);
***************
*** 39,43 ****
OBJECTDATA MEDIUMBLOB,
PRIMARY KEY(GROUP_ID),
! UNIQUE (GROUP_NAME),
);
--- 39,43 ----
OBJECTDATA MEDIUMBLOB,
PRIMARY KEY(GROUP_ID),
! UNIQUE (GROUP_NAME)
);
***************
*** 54,58 ****
INDEX(PERMISSION_ID),
FOREIGN KEY (ROLE_ID) REFERENCES TURBINE_ROLE (ROLE_ID),
! FOREIGN KEY (PERMISSION_ID) REFERENCES TURBINE_PERMISSION (PERMISSION_ID),
);
--- 54,58 ----
INDEX(PERMISSION_ID),
FOREIGN KEY (ROLE_ID) REFERENCES TURBINE_ROLE (ROLE_ID),
! FOREIGN KEY (PERMISSION_ID) REFERENCES TURBINE_PERMISSION (PERMISSION_ID)
);
***************
*** 84,88 ****
OBJECTDATA MEDIUMBLOB,
PRIMARY KEY(USER_ID),
! UNIQUE (LOGIN_NAME),
);
--- 84,88 ----
OBJECTDATA MEDIUMBLOB,
PRIMARY KEY(USER_ID),
! UNIQUE (LOGIN_NAME)
);
***************
*** 102,106 ****
FOREIGN KEY (USER_ID) REFERENCES TURBINE_USER (USER_ID),
FOREIGN KEY (GROUP_ID) REFERENCES TURBINE_GROUP (GROUP_ID),
! FOREIGN KEY (ROLE_ID) REFERENCES TURBINE_ROLE (ROLE_ID),
);
--- 102,106 ----
FOREIGN KEY (USER_ID) REFERENCES TURBINE_USER (USER_ID),
FOREIGN KEY (GROUP_ID) REFERENCES TURBINE_GROUP (GROUP_ID),
! FOREIGN KEY (ROLE_ID) REFERENCES TURBINE_ROLE (ROLE_ID)
);
***************
*** 110,114 ****
drop table if exists TURBINE_SCHEDULED_JOB;
! CREATE TABLE TURBINE_SCHEDULED_JOB
(
JOB_ID INTEGER NOT NULL,
--- 110,114 ----
drop table if exists TURBINE_SCHEDULED_JOB;
! CREATE TABLE TURBINE_SCHEDULED_JOB
(
JOB_ID INTEGER NOT NULL,
***************
*** 121,126 ****
EMAIL VARCHAR (99),
PROPERTY MEDIUMBLOB,
! PRIMARY KEY(JOB_ID),
! );
# -----------------------------------------------------------------------
--- 121,126 ----
EMAIL VARCHAR (99),
PROPERTY MEDIUMBLOB,
! PRIMARY KEY(JOB_ID)
! );
# -----------------------------------------------------------------------
***************
*** 136,140 ****
QUANTITY INTEGER,
PRIMARY KEY(ID_TABLE_ID),
! UNIQUE (TABLE_NAME),
);
--- 136,140 ----
QUANTITY INTEGER,
PRIMARY KEY(ID_TABLE_ID),
! UNIQUE (TABLE_NAME)
);
|
|
From: Stefan K. <sk...@us...> - 2002-03-01 09:42:31
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory usw-pr-cvs1:/tmp/cvs-serv15745/org/openscience/nmrshiftdb/om
Modified Files:
BaseDBMeasurementCondition.java BaseDBMolecule.java
BaseDBSpectrum.java BaseDBSpectrumType.java
BaseNmrshiftdbUser.java BaseNmrshiftdbUserPeer.java
NmrshiftdbUserPeer.java
Log Message:
modified om files, extended some entities
Index: BaseDBMeasurementCondition.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBMeasurementCondition.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** BaseDBMeasurementCondition.java 28 Feb 2002 15:37:05 -0000 1.1
--- BaseDBMeasurementCondition.java 1 Mar 2002 09:42:27 -0000 1.2
***************
*** 1,8 ****
! 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;
--- 1,8 ----
! 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;
***************
*** 11,15 ****
import org.apache.turbine.util.ParameterParser;
import org.apache.turbine.util.Log;
! import org.apache.turbine.util.db.pool.DBConnection;
/**
--- 11,16 ----
import org.apache.turbine.util.ParameterParser;
import org.apache.turbine.util.Log;
! import org.apache.turbine.util.db.pool.DBConnection;
! import org.apache.turbine.om.ObjectKey;
/**
***************
*** 60,64 ****
}
}
!
if ( !ObjectUtils.equals(this.measurement_condition_id, v) )
--- 61,65 ----
}
}
!
if ( !ObjectUtils.equals(this.measurement_condition_id, v) )
***************
*** 67,71 ****
{
this.measurement_condition_id = new NumberKey(v);
! }
else
{
--- 68,72 ----
{
this.measurement_condition_id = new NumberKey(v);
! }
else
{
***************
*** 116,120 ****
public int getFieldStrength()
{
! return field_strength;
}
--- 117,121 ----
public int getFieldStrength()
{
! return field_strength;
}
***************
*** 123,127 ****
* Set the value of FieldStrength
*/
! public void setFieldStrength(int v )
{
--- 124,128 ----
* Set the value of FieldStrength
*/
! public void setFieldStrength(int v )
{
***************
*** 172,176 ****
! /**
* Set the value of UserId
*/
--- 173,177 ----
! /**
* Set the value of UserId
*/
***************
*** 179,183 ****
aNmrshiftdbUser = null;
!
if ( !ObjectUtils.equals(this.user_id, v) )
--- 180,184 ----
aNmrshiftdbUser = null;
!
if ( !ObjectUtils.equals(this.user_id, v) )
***************
*** 224,232 ****
! public NmrshiftdbUser getNmrshiftdbUser() throws Exception
{
! if ( aNmrshiftdbUser==null && (!ObjectUtils.equals(this.user_id, null)) )
{
! aNmrshiftdbUser = (NmrshiftdbUser) NmrshiftdbUserPeer.retrieveByPK(this.user_id);
// The following can be used instead of the line above to
// guarantee the related object contains a reference
--- 225,233 ----
! public NmrshiftdbUser getNmrshiftdbUser() throws Exception
{
! if ( aNmrshiftdbUser==null && (!ObjectUtils.equals(this.user_id, null)) )
{
! aNmrshiftdbUser = NmrshiftdbUserPeer.retrieveByPK(this.user_id);
// The following can be used instead of the line above to
// guarantee the related object contains a reference
***************
*** 235,239 ****
// As it can lead to a db query with many results that may
// never be used.
! // NmrshiftdbUser obj = NmrshiftdbUserPeer.retrieveByPK(this.user_id);
// obj.addDBMeasurementConditions(this);
}
--- 236,240 ----
// As it can lead to a db query with many results that may
// never be used.
! // NmrshiftdbUser obj = NmrshiftdbUserPeer.retrieveByPK(this.user_id);
// obj.addDBMeasurementConditions(this);
}
***************
*** 291,295 ****
}
else
! {
collDBSpectrums.add(l);
}
--- 292,296 ----
}
else
! {
collDBSpectrums.add(l);
}
***************
*** 347,351 ****
collDBSpectrums.add(tempcollDBSpectrums.get(i));
}
! tempcollDBSpectrums = null;
}
*/
--- 348,352 ----
collDBSpectrums.add(tempcollDBSpectrums.get(i));
}
! tempcollDBSpectrums = null;
}
*/
Index: BaseDBMolecule.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBMolecule.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** BaseDBMolecule.java 28 Feb 2002 15:37:05 -0000 1.1
--- BaseDBMolecule.java 1 Mar 2002 09:42:27 -0000 1.2
***************
*** 1,3 ****
! package org.openscience.nmrshiftdb.om;
--- 1,3 ----
! package org.openscience.nmrshiftdb.om;
***************
*** 73,88 ****
- // update associated DBMoleculeNmrshiftdbUser
- if (collDBMoleculeNmrshiftdbUsers != null )
- {
- for (int i=0; i<collDBMoleculeNmrshiftdbUsers.size(); i++)
- {
- ((DBMoleculeNmrshiftdbUser)collDBMoleculeNmrshiftdbUsers.get(i))
- .setMoleculeId(v);
- }
- }
-
-
-
// update associated DBAtom
if (collDBAtoms != null )
--- 73,76 ----
***************
*** 423,433 ****
}
!
! public NmrshiftdbUser getNmrshiftdbUser() throws Exception
! {
if ( aNmrshiftdbUser==null && (!ObjectUtils.equals(this.user_id, null)) )
! {
! aNmrshiftdbUser = (NmrshiftdbUser) NmrshiftdbUserPeer.retrieveByPK(this.user_id);
! // 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
--- 411,421 ----
}
!
! public NmrshiftdbUser getNmrshiftdbUser() throws Exception
! {
if ( aNmrshiftdbUser==null && (!ObjectUtils.equals(this.user_id, null)) )
! {
! aNmrshiftdbUser = (NmrshiftdbUser) NmrshiftdbUserPeer.retrieveByPK(this.user_id);
! // 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
***************
*** 734,916 ****
/**
- * Collection to store aggregation of collDBMoleculeNmrshiftdbUsers
- */
- protected Vector collDBMoleculeNmrshiftdbUsers;
- /**
- * Temporary storage of collDBMoleculeNmrshiftdbUsers to save a possible db hit in
- * the event objects are add to the collection, but the
- * complete collection is never requested.
- */
- // private Vector tempcollDBMoleculeNmrshiftdbUsers;
-
- protected void initDBMoleculeNmrshiftdbUsers()
- {
- if (collDBMoleculeNmrshiftdbUsers == null)
- collDBMoleculeNmrshiftdbUsers = new Vector();
- }
-
- /**
- * Method called to associate a DBMoleculeNmrshiftdbUser object to this object
- * through the DBMoleculeNmrshiftdbUser foreign key attribute
- *
- * @param DBMoleculeNmrshiftdbUser l
- */
- public void addDBMoleculeNmrshiftdbUser(DBMoleculeNmrshiftdbUser l) throws Exception
- {
- /*
- if (collDBMoleculeNmrshiftdbUsers == null)
- {
- if (tempcollDBMoleculeNmrshiftdbUsers == null)
- {
- tempcollDBMoleculeNmrshiftdbUsers = new Vector();
- }
- tempcollDBMoleculeNmrshiftdbUsers.add(l);
- }
- else
- {
- collDBMoleculeNmrshiftdbUsers.add(l);
- }
- */
- getDBMoleculeNmrshiftdbUsers().add(l);
- l.setDBMolecule((DBMolecule)this);
- }
-
- /**
- * The criteria used to select the current contents of collDBMoleculeNmrshiftdbUsers
- */
- private Criteria lastDBMoleculeNmrshiftdbUsersCriteria = null;
-
- /**
- * If this collection has already been initialized, returns
- * the collection. Otherwise returns the results of
- * getDBMoleculeNmrshiftdbUsers(new Criteria())
- */
- public Vector getDBMoleculeNmrshiftdbUsers() throws Exception
- {
- if (collDBMoleculeNmrshiftdbUsers == null)
- {
- collDBMoleculeNmrshiftdbUsers = getDBMoleculeNmrshiftdbUsers(new Criteria(10));
- }
- return collDBMoleculeNmrshiftdbUsers;
- }
-
- /**
- * If this collection has already been initialized with
- * an identical criteria, it returns the collection.
- * Otherwise if this DBMolecule has previously
- * been saved, it will retrieve related DBMoleculeNmrshiftdbUsers from storage.
- * If this DBMolecule is new, it will return
- * an empty collection or the current collection, the criteria
- * is ignored on a new object.
- */
- public Vector getDBMoleculeNmrshiftdbUsers(Criteria criteria) throws Exception
- {
- if (collDBMoleculeNmrshiftdbUsers == null)
- {
- if ( isNew() )
- {
- collDBMoleculeNmrshiftdbUsers = new Vector();
- }
- else
- {
- criteria.add(DBMoleculeNmrshiftdbUserPeer.MOLECULE_ID, getMoleculeId() );
- collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.doSelect(criteria);
- }
- /*
- if (tempcollDBMoleculeNmrshiftdbUsers != null)
- {
- for (int i=0; i<tempcollDBMoleculeNmrshiftdbUsers.size(); i++)
- {
- collDBMoleculeNmrshiftdbUsers.add(tempcollDBMoleculeNmrshiftdbUsers.get(i));
- }
- tempcollDBMoleculeNmrshiftdbUsers = 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(DBMoleculeNmrshiftdbUserPeer.MOLECULE_ID, getMoleculeId() );
- if ( !lastDBMoleculeNmrshiftdbUsersCriteria.equals(criteria) )
- {
- collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.doSelect(criteria);
- }
- }
- }
- lastDBMoleculeNmrshiftdbUsersCriteria = criteria;
-
- return collDBMoleculeNmrshiftdbUsers;
- }
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- /**
- * If this collection has already been initialized with
- * an identical criteria, it returns the collection.
- * Otherwise if this DBMolecule is new, it will return
- * an empty collection; or if this DBMolecule has previously
- * been saved, it will retrieve related DBMoleculeNmrshiftdbUsers from storage.
- */
- protected Vector getDBMoleculeNmrshiftdbUsersJoinNmrshiftdbUser(Criteria criteria)
- throws Exception
- {
- if (collDBMoleculeNmrshiftdbUsers == null)
- {
- if ( isNew() )
- {
- collDBMoleculeNmrshiftdbUsers = new Vector();
- }
- else
- {
- criteria.add(DBMoleculeNmrshiftdbUserPeer.MOLECULE_ID, getMoleculeId() );
- collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.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(DBMoleculeNmrshiftdbUserPeer.MOLECULE_ID, getMoleculeId() );
- if ( !lastDBMoleculeNmrshiftdbUsersCriteria.equals(criteria) )
- {
- collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.doSelectJoinNmrshiftdbUser(criteria);
- }
- }
- lastDBMoleculeNmrshiftdbUsersCriteria = criteria;
-
- return collDBMoleculeNmrshiftdbUsers;
- }
-
-
-
-
-
-
- /**
* Collection to store aggregation of collDBAtoms
*/
--- 722,725 ----
***************
*** 1675,1687 ****
- if (collDBMoleculeNmrshiftdbUsers != null )
- {
- for (int i=0; i<collDBMoleculeNmrshiftdbUsers.size(); i++)
- {
- ((DBMoleculeNmrshiftdbUser)collDBMoleculeNmrshiftdbUsers.get(i)).save(dbCon);
- }
- }
-
-
if (collDBAtoms != null )
{
--- 1484,1487 ----
***************
*** 1807,1817 ****
List v = copyObj.getDBSpectrums();
- for (int i=0; i<v.size(); i++)
- {
- ((Persistent)v.get(i)).setNew(true);
- }
-
-
- v = copyObj.getDBMoleculeNmrshiftdbUsers();
for (int i=0; i<v.size(); i++)
{
--- 1607,1610 ----
Index: BaseDBSpectrum.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSpectrum.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** BaseDBSpectrum.java 28 Feb 2002 15:37:05 -0000 1.1
--- BaseDBSpectrum.java 1 Mar 2002 09:42:27 -0000 1.2
***************
*** 1,3 ****
! package org.openscience.nmrshiftdb.om;
--- 1,3 ----
! package org.openscience.nmrshiftdb.om;
***************
*** 55,59 ****
/**
! * Set the value of SpectrumId
*/
public void setSpectrumId(NumberKey v ) throws Exception
--- 55,59 ----
/**
! * Set the value of SpectrumId
*/
public void setSpectrumId(NumberKey v ) throws Exception
***************
*** 439,443 ****
public NmrshiftdbUser getNmrshiftdbUser() throws Exception
{
! if ( aNmrshiftdbUser==null && (!ObjectUtils.equals(this.user_id, null)) )
{
aNmrshiftdbUser = (NmrshiftdbUser) NmrshiftdbUserPeer.retrieveByPK(this.user_id);
--- 439,443 ----
public NmrshiftdbUser getNmrshiftdbUser() throws Exception
{
! if ( aNmrshiftdbUser==null && (!ObjectUtils.equals(this.user_id, null)) )
{
aNmrshiftdbUser = (NmrshiftdbUser) NmrshiftdbUserPeer.retrieveByPK(this.user_id);
Index: BaseDBSpectrumType.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSpectrumType.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** BaseDBSpectrumType.java 28 Feb 2002 15:37:05 -0000 1.1
--- BaseDBSpectrumType.java 1 Mar 2002 09:42:27 -0000 1.2
***************
*** 332,336 ****
{
setUserId(v.getUserId());
! aNmrshiftdbUser = v;
}
--- 332,336 ----
{
setUserId(v.getUserId());
! aNmrshiftdbUser = v;
}
Index: BaseNmrshiftdbUser.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseNmrshiftdbUser.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -r1.4 -r1.5
*** BaseNmrshiftdbUser.java 28 Feb 2002 15:37:05 -0000 1.4
--- BaseNmrshiftdbUser.java 1 Mar 2002 09:42:27 -0000 1.5
***************
*** 17,21 ****
* extended all references should be to NmrshiftdbUser
*/
! public abstract class BaseNmrshiftdbUser extends org.apache.jetspeed.om.dbpsml.TurbineUser
implements Retrievable
{
--- 17,21 ----
* extended all references should be to NmrshiftdbUser
*/
! public abstract class BaseNmrshiftdbUser extends TurbineUserAdapter
implements Retrievable
{
***************
*** 679,861 ****
-
-
-
-
-
-
-
-
-
-
-
-
-
- /**
- * Collection to store aggregation of collDBMoleculeNmrshiftdbUsers
- */
- protected Vector collDBMoleculeNmrshiftdbUsers;
- /**
- * Temporary storage of collDBMoleculeNmrshiftdbUsers to save a possible db hit in
- * the event objects are add to the collection, but the
- * complete collection is never requested.
- */
- // private Vector tempcollDBMoleculeNmrshiftdbUsers;
-
- protected void initDBMoleculeNmrshiftdbUsers()
- {
- if (collDBMoleculeNmrshiftdbUsers == null)
- collDBMoleculeNmrshiftdbUsers = new Vector();
- }
-
- /**
- * Method called to associate a DBMoleculeNmrshiftdbUser object to this object
- * through the DBMoleculeNmrshiftdbUser foreign key attribute
- *
- * @param DBMoleculeNmrshiftdbUser l
- */
- public void addDBMoleculeNmrshiftdbUser(DBMoleculeNmrshiftdbUser l) throws Exception
- {
- /*
- if (collDBMoleculeNmrshiftdbUsers == null)
- {
- if (tempcollDBMoleculeNmrshiftdbUsers == null)
- {
- tempcollDBMoleculeNmrshiftdbUsers = new Vector();
- }
- tempcollDBMoleculeNmrshiftdbUsers.add(l);
- }
- else
- {
- collDBMoleculeNmrshiftdbUsers.add(l);
- }
- */
- getDBMoleculeNmrshiftdbUsers().add(l);
- l.setNmrshiftdbUser((NmrshiftdbUser)this);
- }
-
- /**
- * The criteria used to select the current contents of collDBMoleculeNmrshiftdbUsers
- */
- private Criteria lastDBMoleculeNmrshiftdbUsersCriteria = null;
-
- /**
- * If this collection has already been initialized, returns
- * the collection. Otherwise returns the results of
- * getDBMoleculeNmrshiftdbUsers(new Criteria())
- */
- public Vector getDBMoleculeNmrshiftdbUsers() throws Exception
- {
- if (collDBMoleculeNmrshiftdbUsers == null)
- {
- collDBMoleculeNmrshiftdbUsers = getDBMoleculeNmrshiftdbUsers(new Criteria(10));
- }
- return collDBMoleculeNmrshiftdbUsers;
- }
-
- /**
- * If this collection has already been initialized with
- * an identical criteria, it returns the collection.
- * Otherwise if this NmrshiftdbUser has previously
- * been saved, it will retrieve related DBMoleculeNmrshiftdbUsers from storage.
- * If this NmrshiftdbUser is new, it will return
- * an empty collection or the current collection, the criteria
- * is ignored on a new object.
- */
- public Vector getDBMoleculeNmrshiftdbUsers(Criteria criteria) throws Exception
- {
- if (collDBMoleculeNmrshiftdbUsers == null)
- {
- if ( isNew() )
- {
- collDBMoleculeNmrshiftdbUsers = new Vector();
- }
- else
- {
- criteria.add(DBMoleculeNmrshiftdbUserPeer.USER_ID, getUserId() );
- collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.doSelect(criteria);
- }
- /*
- if (tempcollDBMoleculeNmrshiftdbUsers != null)
- {
- for (int i=0; i<tempcollDBMoleculeNmrshiftdbUsers.size(); i++)
- {
- collDBMoleculeNmrshiftdbUsers.add(tempcollDBMoleculeNmrshiftdbUsers.get(i));
- }
- tempcollDBMoleculeNmrshiftdbUsers = 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(DBMoleculeNmrshiftdbUserPeer.USER_ID, getUserId() );
- if ( !lastDBMoleculeNmrshiftdbUsersCriteria.equals(criteria) )
- {
- collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.doSelect(criteria);
- }
- }
- }
- lastDBMoleculeNmrshiftdbUsersCriteria = criteria;
-
- return collDBMoleculeNmrshiftdbUsers;
- }
-
-
-
-
-
-
-
-
-
-
-
- /**
- * If this collection has already been initialized with
- * an identical criteria, it returns the collection.
- * Otherwise if this NmrshiftdbUser is new, it will return
- * an empty collection; or if this NmrshiftdbUser has previously
- * been saved, it will retrieve related DBMoleculeNmrshiftdbUsers from storage.
- */
- protected Vector getDBMoleculeNmrshiftdbUsersJoinDBMolecule(Criteria criteria)
- throws Exception
- {
- if (collDBMoleculeNmrshiftdbUsers == null)
- {
- if ( isNew() )
- {
- collDBMoleculeNmrshiftdbUsers = new Vector();
- }
- else
- {
- criteria.add(DBMoleculeNmrshiftdbUserPeer.USER_ID, getUserId() );
- collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.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(DBMoleculeNmrshiftdbUserPeer.USER_ID, getUserId() );
- if ( !lastDBMoleculeNmrshiftdbUsersCriteria.equals(criteria) )
- {
- collDBMoleculeNmrshiftdbUsers = DBMoleculeNmrshiftdbUserPeer.doSelectJoinDBMolecule(criteria);
- }
- }
- lastDBMoleculeNmrshiftdbUsersCriteria = criteria;
-
- return collDBMoleculeNmrshiftdbUsers;
- }
-
--- 679,682 ----
Index: BaseNmrshiftdbUserPeer.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseNmrshiftdbUserPeer.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -r1.4 -r1.5
*** BaseNmrshiftdbUserPeer.java 28 Feb 2002 15:37:05 -0000 1.4
--- BaseNmrshiftdbUserPeer.java 1 Mar 2002 09:42:27 -0000 1.5
***************
*** 20,24 ****
*/
public abstract class BaseNmrshiftdbUserPeer
! extends org.apache.jetspeed.om.dbpsml.TurbineUserPeer
{
--- 20,24 ----
*/
public abstract class BaseNmrshiftdbUserPeer
! extends TurbineUserPeerAdapter
{
Index: NmrshiftdbUserPeer.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/NmrshiftdbUserPeer.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -r1.5 -r1.6
*** NmrshiftdbUserPeer.java 28 Feb 2002 13:41:29 -0000 1.5
--- NmrshiftdbUserPeer.java 1 Mar 2002 09:42:27 -0000 1.6
***************
*** 1,3 ****
! package org.openscience.nmrshiftdb.om;
// JDK classes
--- 1,3 ----
! package org.openscience.nmrshiftdb.om;
// JDK classes
***************
*** 12,28 ****
import org.apache.turbine.util.db.*;
import org.apache.turbine.util.db.map.*;
! import org.apache.turbine.util.db.pool.DBConnection;
!
! // Local classes
! import org.openscience.nmrshiftdb.om.map.*;
!
! /**
! * You should add additional methods to this class to meet the
! * application requirements. This class will only be generated as
! * long as it does not already exist in the output directory.
! */
! public class NmrshiftdbUserPeer
! extends org.openscience.nmrshiftdb.om.BaseNmrshiftdbUserPeer
! {
! }
!
--- 12,62 ----
import org.apache.turbine.util.db.*;
import org.apache.turbine.util.db.map.*;
! import org.apache.turbine.util.db.pool.DBConnection;
! import org.apache.turbine.om.ObjectKey;
! import org.apache.turbine.services.db.TurbineDB;
!
! // Local classes
! import org.openscience.nmrshiftdb.om.map.*;
!
! /**
! * You should add additional methods to this class to meet the
! * application requirements. This class will only be generated as
! * long as it does not already exist in the output directory.
! */
! public class NmrshiftdbUserPeer
! extends org.openscience.nmrshiftdb.om.BaseNmrshiftdbUserPeer
! {
! public static NmrshiftdbUser retrieveByPK(ObjectKey pk) throws Exception
! {
! DBConnection db = null;
! NmrshiftdbUser retVal = null;
! try
! {
! db = TurbineDB.getConnection(getMapBuilder().getDatabaseMap().getName());
! retVal = retrieveByPK(pk, db);
! }
! finally
! {
! if(db != null)
! {
! TurbineDB.releaseConnection(db);
! }
! }
! return(retVal);
! }
!
! public static NmrshiftdbUser retrieveByPK(ObjectKey pk, DBConnection dbcon) throws Exception
! {
! Criteria criteria = new Criteria();
! criteria.add(USER_ID, pk);
! Vector v = doSelect(criteria, dbcon);
! if(v.size() != 1)
! {
! throw new Exception("Failed to select one and only one row.");
! }
! else
! {
! return(NmrshiftdbUser)v.firstElement();
! }
! }
! }
|
|
From: Stefan K. <sk...@us...> - 2002-03-01 09:42:31
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions In directory usw-pr-cvs1:/tmp/cvs-serv15745/org/apache/jetspeed/modules/actions Modified Files: CreateNewUserAndConfirm.java Log Message: modified om files, extended some entities Index: CreateNewUserAndConfirm.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions/CreateNewUserAndConfirm.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** CreateNewUserAndConfirm.java 27 Feb 2002 13:20:54 -0000 1.1 --- CreateNewUserAndConfirm.java 1 Mar 2002 09:42:27 -0000 1.2 *************** *** 237,240 **** --- 237,241 ---- NmrshiftdbUser user = (NmrshiftdbUser) JetspeedSecurity.getUserInstance(); + //User user = JetspeedSecurity.getUserInstance(); user.setUserName( username ); |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory usw-pr-cvs1:/tmp/cvs-serv16074 Removed Files: BaseDBMoleculeNmrshiftdbUser.java BaseDBMoleculeNmrshiftdbUserPeer.java DBMoleculeNmrshiftdbUser.java DBMoleculeNmrshiftdbUserPeer.java Log Message: removed on files --- BaseDBMoleculeNmrshiftdbUser.java DELETED --- --- BaseDBMoleculeNmrshiftdbUserPeer.java DELETED --- --- DBMoleculeNmrshiftdbUser.java DELETED --- --- DBMoleculeNmrshiftdbUserPeer.java DELETED --- |
|
From: Stefan K. <sk...@us...> - 2002-02-28 15:47:38
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc
In directory usw-pr-cvs1:/tmp/cvs-serv7777
Added Files:
entrel_020228_ls_A4.gd
Log Message:
added entrel_020228_ls_A4.gd
--- NEW FILE: entrel_020228_ls_A4.gd ---
Storage
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|
|
From: Stefan K. <sh...@us...> - 2002-02-28 15:45:35
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util
In directory usw-pr-cvs1:/tmp/cvs-serv7400/src/java/org/openscience/nmrshiftdb/util
Modified Files:
SubmittingData.java
Log Message:
New version
Index: SubmittingData.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/SubmittingData.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** SubmittingData.java 27 Feb 2002 14:08:52 -0000 1.1
--- SubmittingData.java 28 Feb 2002 15:45:29 -0000 1.2
***************
*** 6,9 ****
--- 6,45 ----
String molecule="";
ArrayList signalstable=new ArrayList();
+ String solvent="";
+ int fieldStrength=0;
+ long temperature=0;
+ String chemName="";
+
+ public void setChemName(String chemName){
+ this.chemName=chemName;
+ }
+
+ public String getChemName(){
+ return(chemName);
+ }
+
+ public void setTemperature(long temperature){
+ this.temperature=temperature;
+ }
+
+ public long getTemperature(){
+ return(temperature);
+ }
+
+ public void setFieldStrength(int fieldStrength){
+ this.fieldStrength=fieldStrength;
+ }
+
+ public int getFieldStrength(){
+ return(fieldStrength);
+ }
+
+ public void setSolvent(String sol){
+ solvent=sol;
+ }
+
+ public String getSolvent(){
+ return(solvent);
+ }
public void setMolecule(String mol){
|
|
From: Stefan K. <sh...@us...> - 2002-02-28 15:45:33
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory usw-pr-cvs1:/tmp/cvs-serv7400/src/java/org/openscience/nmrshiftdb/portlets Modified Files: SubmitPortlet.java Log Message: New version Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** SubmitPortlet.java 27 Feb 2002 13:08:51 -0000 1.5 --- SubmitPortlet.java 28 Feb 2002 15:45:29 -0000 1.6 *************** *** 3,10 **** --- 3,12 ---- import org.apache.jetspeed.portal.portlets.AbstractPortlet; import org.apache.turbine.util.RunData; + import org.apache.turbine.util.db.*; import org.apache.ecs.ConcreteElement; import org.apache.ecs.StringElement; import org.apache.ecs.html.*; import org.apache.jetspeed.util.servlet.*; + import org.apache.turbine.om.*; import java.util.*; *************** *** 12,15 **** --- 14,18 ---- import org.openscience.nmrshiftdb.util.*; + import org.openscience.nmrshiftdb.om.*; import org.openscience.cdk.*; import org.openscience.cdk.io.*; *************** *** 17,20 **** --- 20,25 ---- import java.io.*; + import JSX.*; + /** * Description of the Class *************** *** 35,39 **** HttpSession session= req.getSession(); SubmittingData subData = (SubmittingData)session.getAttribute("subData"); ! String messages="";//Here all sort of error messages areappended String returnValue=""; //Create new SubmittingData object in case there is none in the session, i. e. no submission currently going on --- 40,44 ---- HttpSession session= req.getSession(); SubmittingData subData = (SubmittingData)session.getAttribute("subData"); ! String messages="";//Here all sort of error messages are appended String returnValue=""; //Create new SubmittingData object in case there is none in the session, i. e. no submission currently going on *************** *** 66,74 **** else figures.value2=(new Integer(intensity.trim())).intValue(); } catch(NumberFormatException ex){ messages+="Your input included wrong characters!<br>"; } - numberSpectrum.add(figures); shift=""; addingShift=true; --- 71,79 ---- else figures.value2=(new Integer(intensity.trim())).intValue(); + numberSpectrum.add(figures); } catch(NumberFormatException ex){ messages+="Your input included wrong characters!<br>"; } shift=""; addingShift=true; *************** *** 99,111 **** returnValue=submitPage(messages, subData); } if(action!=null&&action.equals("submitSpectrumForDB")){ MDLReader mdlreader=new MDLReader(new StringReader(subData.getMolecule())); ! try{ ! Molecule mol=(Molecule)mdlreader.read(new Molecule()); } ! catch(Exception ex){ ! System.out.println(ex.getMessage()); } ! returnValue="Your spectrum has been submitted and will be reviewed shortly! Thanks for your contribution!"; } --- 104,195 ---- returnValue=submitPage(messages, subData); } + //User submitted the whole input + if(action!=null&&action.equals("submitForConfirm")){ + subData.setSolvent(req.getParameter("solvent")); + subData.setChemName(req.getParameter("chemName")); + String fieldStrengthStr=req.getParameter("fieldStrength"); + String temperatureStr=req.getParameter("temperature"); + try{ + int fieldStrength=Integer.parseInt(fieldStrengthStr); + subData.setFieldStrength(fieldStrength); + } + catch(NumberFormatException ex){ + messages+="Your field strength is not a decimal figure!"; + } + try{ + long temp=Long.parseLong(temperatureStr); + subData.setTemperature(temp); + } + catch(NumberFormatException ex){ + messages+="Your temperature is not a decimal figure!"; + } + if(messages=="")//Show confirm screen + returnValue="Here the data should be reapeated!<form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitSpectrumForDB\"><input type=\"submit\" value=\"Write to Database\"></form>"; + else//Display message and show input screen again + returnValue=submitPage(messages, subData); + } + //User submittet confirm screen if(action!=null&&action.equals("submitSpectrumForDB")){ MDLReader mdlreader=new MDLReader(new StringReader(subData.getMolecule())); ! Molecule mol; ! try{ ! mol=(Molecule)mdlreader.read(new Molecule()); ! } ! catch(Throwable ex){ ! ex.printStackTrace(); } ! //Add molecule to DB ! Criteria crit=new Criteria(); ! crit.add(MoleculePeer.SERIALIZED_MOLECULE,serializeObject(mol)); ! crit.add(MoleculePeer.DATE,(java.sql.Date)new java.util.Date()); ! NumberKey nkMol=(NumberKey)MoleculePeer.doInsert(crit); ! //Add spectrum to DB ! crit=new Criteria(); ! crit.add(SpectrumPeer.MOLECULE_ID,nkMol.getValue()); ! crit.add(SpectrumPeer.REVIEW_FLAG, 'n'); ! NumberKey nkSpectrum=(NumberKey)SpectrumPeer.doInsert(crit); ! //Add atoms to db ! Atom[] atoms=mol.getAtoms(); ! NumberKey[] nkAtom=new NumberKey[atoms.length]; ! for(int i=0; i<atoms.length;i++){ ! crit=new Criteria(); ! crit.add(AtomsPeer.SYMBOL,atoms[i].getSymbol()); ! crit.add(AtomsPeer.SERIALIZED_ATOMS,serializeObject(atoms[i])); ! crit.add(AtomsPeer.MOLECULE_ID,nkMol.getValue()); ! nkAtom[i]=(NumberKey)AtomsPeer.doInsert(crit); ! } ! //Add bonds to db ! Bond[] bonds=mol.getBonds(); ! NumberKey[] nkBond=new NumberKey[bonds.length]; ! for(int i=0; i<bonds.length;i++){ ! crit=new Criteria(); ! crit.add(BondsPeer.DEGREE,bonds[i].getOrder()); ! crit.add(BondsPeer.SERIALIZED_BONDS,serializeObject(bonds[i])); ! crit.add(BondsPeer.MOLECULE_ID,nkMol.getValue()); ! nkBond[i]=(NumberKey)BondsPeer.doInsert(crit); ! //Add bonds-atoms relationship to DB ! Atoms[] neighbourAtoms=bonds[i].getAtoms(); ! for(int k=0;k<neighbourAtoms.length;k++){ ! crit=new Criteria(); ! crit.add(BondsAtomsPeer.BONDS_ID,nkBond[i].getValue()); ! crit.add(BondsAtomsPeer.ATOMS_ID,nkAtom[mol.getAtomNumber(neighbourAtoms[k])].getValue()); ! } } ! //add signals to DB ! NumberKey[] nkSignal=new NumberKey[subData.getSignalstable().size()]; ! for(int i=0;i<subData.getSignalstable().size();i++){ ! crit=new Criteria(); ! crit.add(SignalPeer.DIMENSIONALITY,1); ! crit.add(SignalPeer.SHIFT_1,((IntTriple)subData.getSignalstable().get(i)).value1); ! crit.add(SignalPeer.SPECTRUM_ID,nkSpectrum.getValue()); ! //The serialized signal is not used at the moment //Intensity still missing ! //crit.add(SignalPeer.INTENSITY,((IntTriple)subData.getSignalstable[i]).value2); ! nkSignal[i]=(NumberKey)SignalPeer.doInsert(crit); ! crit=new Criteria(); ! crit.add(SignalAtomsPeer.SIGNAL_ID,nkSignal[i].getValue()); ! crit.add(SignalAtomsPeer.ATOMS_ID,nkAtom[((IntTriple)subData.getSignalstable().get(i)).value3].getValue()); ! NumberKey nk=(NumberKey)SignalAtomsPeer.doInsert(crit); ! } ! session.removeAttribute("subData"); returnValue="Your spectrum has been submitted and will be reviewed shortly! Thanks for your contribution!"; } *************** *** 114,117 **** --- 198,208 ---- } + private String serializeObject(Object o){ + StringWriter strWriter=new StringWriter(); + ObjOut out=new ObjOut(false,strWriter); + out.writeObject(o); + return(strWriter.toString()); + } + /** * Puts together the submit page *************** *** 191,195 **** } returnValue+="<tr><td colspan=\"3\"><input type=\"submit\" value=\"Submit assignments\"></td></tr></form>"; ! returnValue+="</table><br><form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitSpectrumForDB\"><center>Chemical name:<input type=\"text\" name=\"chemName\"></center><br><center>Measurement conditions - temperature (in <sup>0</sup>K):<input type=\"text\" name=\"temperature\"> -Field strength:<input type=\"text\" name=\"fieldStrength\"> -Solvent:<input type=\"text\" name=\"solvent\"></center><br><center><input type=\"submit\" value=\"Write to Database\"></center></form>"; return (returnValue); } --- 282,286 ---- } returnValue+="<tr><td colspan=\"3\"><input type=\"submit\" value=\"Submit assignments\"></td></tr></form>"; ! returnValue+="</table><br><form action=\"/jetspeed/portal/\" method=\"post\"><input type=\"hidden\" name=\"nmrshiftdbaction\" value=\"submitForConfirm\"><center>Chemical name:<input type=\"text\" name=\"chemName\"></center><br><center>Measurement conditions - temperature (in <sup>0</sup>K):<input type=\"text\" name=\"temperature\"> -Field strength:<input type=\"text\" name=\"fieldStrength\"> -Solvent:<input type=\"text\" name=\"solvent\"></center><br><center><input type=\"submit\" value=\"Write to Database\"></center></form>"; return (returnValue); } |
|
From: Stefan K. <sh...@us...> - 2002-02-28 15:45:33
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb
In directory usw-pr-cvs1:/tmp/cvs-serv7400
Modified Files:
build.xml
Log Message:
New version
Index: build.xml
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/build.xml,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -r1.6 -r1.7
*** build.xml 22 Feb 2002 16:11:19 -0000 1.6
--- build.xml 28 Feb 2002 15:45:29 -0000 1.7
***************
*** 21,24 ****
--- 21,27 ----
<include name="*.jar" />
</fileset>
+ <fileset dir="${src}/conf/jetspeed/WEB-INF/lib">
+ <include name="*.jar" />
+ </fileset>
</path>
***************
*** 93,96 ****
--- 96,100 ----
</target>
</project>
+
|
|
From: Stefan K. <sk...@us...> - 2002-02-28 15:38:17
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db
In directory usw-pr-cvs1:/tmp/cvs-serv4961
Modified Files:
nmrshiftdb-schema.sql
Log Message:
modified nmrshiftdb-schema.sql
Index: nmrshiftdb-schema.sql
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/db/nmrshiftdb-schema.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** nmrshiftdb-schema.sql 27 Feb 2002 13:30:45 -0000 1.1
--- nmrshiftdb-schema.sql 28 Feb 2002 15:38:12 -0000 1.2
***************
*** 1,18 ****
# -----------------------------------------------------------------------
! # MEASUREMENT_CONDITIONS
# -----------------------------------------------------------------------
! drop table if exists MEASUREMENT_CONDITIONS;
! CREATE TABLE MEASUREMENT_CONDITIONS
(
! MEASUREMENT_CONDITIONS_ID INTEGER NOT NULL,
TEMPERATURE FLOAT NOT NULL,
FIELD_STRENGTH INTEGER NOT NULL,
SOLVENT MEDIUMTEXT NOT NULL,
USER_ID INTEGER NOT NULL,
! PRIMARY KEY(MEASUREMENT_CONDITIONS_ID),
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
! );
# -----------------------------------------------------------------------
--- 1,18 ----
# -----------------------------------------------------------------------
! # MEASUREMENT_CONDITION
# -----------------------------------------------------------------------
! drop table if exists MEASUREMENT_CONDITION;
! CREATE TABLE MEASUREMENT_CONDITION
(
! MEASUREMENT_CONDITION_ID INTEGER NOT NULL,
TEMPERATURE FLOAT NOT NULL,
FIELD_STRENGTH INTEGER NOT NULL,
SOLVENT MEDIUMTEXT NOT NULL,
USER_ID INTEGER NOT NULL,
! PRIMARY KEY(MEASUREMENT_CONDITION_ID),
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
! );
# -----------------------------------------------------------------------
***************
*** 49,59 ****
LITERATURE MEDIUMTEXT NOT NULL,
REVIEW_FLAG MEDIUMTEXT NOT NULL,
USER_ID INTEGER NOT NULL,
! MEASUREMENT_CONDITIONS_ID INTEGER NOT NULL,
SPECTRUM_TYPE_ID INTEGER NOT NULL,
MOLECULE_ID INTEGER NOT NULL,
PRIMARY KEY(SPECTRUM_ID),
! FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID),
! FOREIGN KEY (MEASUREMENT_CONDITIONS_ID) REFERENCES MEASUREMENT_CONDITIONS (MEASUREMENT_CONDITIONS_ID),
FOREIGN KEY (SPECTRUM_TYPE_ID) REFERENCES SPECTRUM_TYPE (SPECTRUM_TYPE_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
--- 49,60 ----
LITERATURE MEDIUMTEXT NOT NULL,
REVIEW_FLAG MEDIUMTEXT NOT NULL,
+ FINGERPRINT LONGBLOB NOT NULL,
USER_ID INTEGER NOT NULL,
! MEASUREMENT_CONDITION_ID INTEGER NOT NULL,
SPECTRUM_TYPE_ID INTEGER NOT NULL,
MOLECULE_ID INTEGER NOT NULL,
PRIMARY KEY(SPECTRUM_ID),
! FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID),
! FOREIGN KEY (MEASUREMENT_CONDITION_ID) REFERENCES MEASUREMENT_CONDITION (MEASUREMENT_CONDITION_ID),
FOREIGN KEY (SPECTRUM_TYPE_ID) REFERENCES SPECTRUM_TYPE (SPECTRUM_TYPE_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
***************
*** 75,81 ****
SHIFT_5 FLOAT NOT NULL,
SERIALIZED_SIGNAL MEDIUMTEXT NOT NULL,
! SPECTRUM_TYPE_ID INTEGER NOT NULL,
PRIMARY KEY(SIGNAL_ID),
! FOREIGN KEY (SPECTRUM_TYPE_ID) REFERENCES SPECTRUM_TYPE (SPECTRUM_TYPE_ID)
);
--- 76,83 ----
SHIFT_5 FLOAT NOT NULL,
SERIALIZED_SIGNAL MEDIUMTEXT NOT NULL,
! INTENSITY FLOAT NOT NULL,
! SPECTRUM_ID INTEGER NOT NULL,
PRIMARY KEY(SIGNAL_ID),
! FOREIGN KEY (SPECTRUM_ID) REFERENCES SPECTRUM (SPECTRUM_ID)
);
***************
*** 89,93 ****
MOLECULE_ID INTEGER NOT NULL,
DATE DATETIME NOT NULL,
! STRUCTURE_FILE LONGBLOB NOT NULL,
MOLECULAR_FORMULA MEDIUMTEXT NOT NULL,
SERIALIZED_MOLECULE MEDIUMTEXT NOT NULL,
--- 91,95 ----
MOLECULE_ID INTEGER NOT NULL,
DATE DATETIME NOT NULL,
! STRUCTURE_FILE LONGBLOB NOT NULL,
MOLECULAR_FORMULA MEDIUMTEXT NOT NULL,
SERIALIZED_MOLECULE MEDIUMTEXT NOT NULL,
***************
*** 95,102 ****
NMRSHIFTDB_NUMBER MEDIUMTEXT NOT NULL,
MOLECULAR_WEIGHT FLOAT NOT NULL,
USER_ID INTEGER NOT NULL,
! PRIMARY KEY(MOLECULE_ID),
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
! );
# -----------------------------------------------------------------------
--- 97,105 ----
NMRSHIFTDB_NUMBER MEDIUMTEXT NOT NULL,
MOLECULAR_WEIGHT FLOAT NOT NULL,
+ FINGERPRINT LONGBLOB NOT NULL,
USER_ID INTEGER NOT NULL,
! PRIMARY KEY(MOLECULE_ID),
FOREIGN KEY (USER_ID) REFERENCES NMRSHIFTDB_USER (USER_ID)
! );
# -----------------------------------------------------------------------
***************
*** 114,170 ****
# -----------------------------------------------------------------------
! # ATOMS
# -----------------------------------------------------------------------
! drop table if exists ATOMS;
! CREATE TABLE ATOMS
(
! ATOMS_ID INTEGER NOT NULL,
SYMBOL MEDIUMTEXT NOT NULL,
! SERIALIZED_ATOMS MEDIUMTEXT NOT NULL,
MOLECULE_ID INTEGER NOT NULL,
! PRIMARY KEY(ATOMS_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);
# -----------------------------------------------------------------------
! # SIGNAL_ATOMS
# -----------------------------------------------------------------------
! drop table if exists SIGNAL_ATOMS;
! CREATE TABLE SIGNAL_ATOMS
(
SIGNAL_ID INTEGER NOT NULL,
! ATOMS_ID INTEGER NOT NULL,
FOREIGN KEY (SIGNAL_ID) REFERENCES SIGNAL (SIGNAL_ID),
! FOREIGN KEY (ATOMS_ID) REFERENCES ATOMS (ATOMS_ID)
);
# -----------------------------------------------------------------------
! # BONDS
# -----------------------------------------------------------------------
! drop table if exists BONDS;
! CREATE TABLE BONDS
(
! BONDS_ID INTEGER NOT NULL,
DEGREE INTEGER NOT NULL,
! SERIALIZED_BONDS MEDIUMTEXT NOT NULL,
! MOLECULE_ID INTEGER NOT NULL,
! PRIMARY KEY(BONDS_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);
# -----------------------------------------------------------------------
! # BONDS_ATOMS
# -----------------------------------------------------------------------
! drop table if exists BONDS_ATOMS;
! CREATE TABLE BONDS_ATOMS
(
! BONDS_ID INTEGER NOT NULL,
! ATOMS_ID INTEGER NOT NULL,
! FOREIGN KEY (BONDS_ID) REFERENCES BONDS (BONDS_ID),
! FOREIGN KEY (ATOMS_ID) REFERENCES ATOMS (ATOMS_ID)
);
--- 117,173 ----
# -----------------------------------------------------------------------
! # ATOM
# -----------------------------------------------------------------------
! drop table if exists ATOM;
! CREATE TABLE ATOM
(
! ATOM_ID INTEGER NOT NULL,
SYMBOL MEDIUMTEXT NOT NULL,
! SERIALIZED_ATOM MEDIUMTEXT NOT NULL,
MOLECULE_ID INTEGER NOT NULL,
! PRIMARY KEY(ATOM_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);
# -----------------------------------------------------------------------
! # SIGNAL_ATOM
# -----------------------------------------------------------------------
! drop table if exists SIGNAL_ATOM;
! CREATE TABLE SIGNAL_ATOM
(
SIGNAL_ID INTEGER NOT NULL,
! ATOM_ID INTEGER NOT NULL,
FOREIGN KEY (SIGNAL_ID) REFERENCES SIGNAL (SIGNAL_ID),
! FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
);
# -----------------------------------------------------------------------
! # BOND
# -----------------------------------------------------------------------
! drop table if exists BOND;
! CREATE TABLE BOND
(
! BOND_ID INTEGER NOT NULL,
DEGREE INTEGER NOT NULL,
! SERIALIZED_BOND MEDIUMTEXT NOT NULL,
! MOLECULE_ID INTEGER NOT NULL,
! PRIMARY KEY(BOND_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
);
# -----------------------------------------------------------------------
! # BOND_ATOM
# -----------------------------------------------------------------------
! drop table if exists BOND_ATOM;
! CREATE TABLE BOND_ATOM
(
! BOND_ID INTEGER NOT NULL,
! ATOM_ID INTEGER NOT NULL,
! FOREIGN KEY (BOND_ID) REFERENCES BOND (BOND_ID),
! FOREIGN KEY (ATOM_ID) REFERENCES ATOM (ATOM_ID)
);
***************
*** 181,185 ****
PRIMARY KEY(CHEMICAL_NAME_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
! );
# -----------------------------------------------------------------------
--- 184,188 ----
PRIMARY KEY(CHEMICAL_NAME_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
! );
# -----------------------------------------------------------------------
***************
*** 196,201 ****
PRIMARY KEY(CANONICAL_NAME_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
! );
!
--- 199,203 ----
PRIMARY KEY(CANONICAL_NAME_ID),
FOREIGN KEY (MOLECULE_ID) REFERENCES MOLECULE (MOLECULE_ID)
! );
***************
*** 209,210 ****
--- 211,213 ----
+
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map
In directory usw-pr-cvs1:/tmp/cvs-serv4425
Added Files:
DBAtomMapBuilder.java DBBondDBAtomMapBuilder.java
DBBondMapBuilder.java DBCanonicalNameMapBuilder.java
DBChemicalNameMapBuilder.java
DBMeasurementConditionMapBuilder.java
DBMoleculeMapBuilder.java
DBMoleculeNmrshiftdbUserMapBuilder.java
DBSignalDBAtomMapBuilder.java DBSignalMapBuilder.java
DBSpectrumMapBuilder.java DBSpectrumTypeMapBuilder.java
Log Message:
added map files
--- NEW FILE: DBAtomMapBuilder.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 DBAtomMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBAtomMapBuilder";
/** item */
public static String getTable( )
{
return "ATOM";
}
/** ATOM.ATOM_ID */
public static String getDBAtom_AtomId()
{
return getTable() + ".ATOM_ID";
}
/** ATOM.SYMBOL */
public static String getDBAtom_Symbol()
{
return getTable() + ".SYMBOL";
}
/** ATOM.SERIALIZED_ATOM */
public static String getDBAtom_SerializedAtom()
{
return getTable() + ".SERIALIZED_ATOM";
}
/** ATOM.MOLECULE_ID */
public static String getDBAtom_MoleculeId()
{
return getTable() + ".MOLECULE_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBAtom_AtomId(), new Integer(0) );
tMap.addColumn ( getDBAtom_Symbol(), new String() );
tMap.addColumn ( getDBAtom_SerializedAtom(), new String() );
tMap.addForeignKey ( getDBAtom_MoleculeId(), new Integer(0) , "MOLECULE" , "MOLECULE_ID" );
}
}
--- NEW FILE: DBBondDBAtomMapBuilder.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 DBBondDBAtomMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBBondDBAtomMapBuilder";
/** item */
public static String getTable( )
{
return "BOND_ATOM";
}
/** BOND_ATOM.BOND_ID */
public static String getDBBondDBAtom_BondId()
{
return getTable() + ".BOND_ID";
}
/** BOND_ATOM.ATOM_ID */
public static String getDBBondDBAtom_AtomId()
{
return getTable() + ".ATOM_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addForeignKey ( getDBBondDBAtom_BondId(), new Integer(0) , "BOND" , "BOND_ID" );
tMap.addForeignKey ( getDBBondDBAtom_AtomId(), new Integer(0) , "ATOM" , "ATOM_ID" );
}
}
--- NEW FILE: DBBondMapBuilder.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 DBBondMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBBondMapBuilder";
/** item */
public static String getTable( )
{
return "BOND";
}
/** BOND.BOND_ID */
public static String getDBBond_BondId()
{
return getTable() + ".BOND_ID";
}
/** BOND.DEGREE */
public static String getDBBond_Degree()
{
return getTable() + ".DEGREE";
}
/** BOND.SERIALIZED_BOND */
public static String getDBBond_SerializedBond()
{
return getTable() + ".SERIALIZED_BOND";
}
/** BOND.MOLECULE_ID */
public static String getDBBond_MoleculeId()
{
return getTable() + ".MOLECULE_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBBond_BondId(), new Integer(0) );
tMap.addColumn ( getDBBond_Degree(), new Integer(0) );
tMap.addColumn ( getDBBond_SerializedBond(), new String() );
tMap.addForeignKey ( getDBBond_MoleculeId(), new Integer(0) , "MOLECULE" , "MOLECULE_ID" );
}
}
--- NEW FILE: DBCanonicalNameMapBuilder.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 DBCanonicalNameMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBCanonicalNameMapBuilder";
/** item */
public static String getTable( )
{
return "CANONICAL_NAME";
}
/** CANONICAL_NAME.CANONICAL_NAME_ID */
public static String getDBCanonicalName_CanonicalNameId()
{
return getTable() + ".CANONICAL_NAME_ID";
}
/** CANONICAL_NAME.NAME */
public static String getDBCanonicalName_Name()
{
return getTable() + ".NAME";
}
/** CANONICAL_NAME.TYPE */
public static String getDBCanonicalName_Type()
{
return getTable() + ".TYPE";
}
/** CANONICAL_NAME.MOLECULE_ID */
public static String getDBCanonicalName_MoleculeId()
{
return getTable() + ".MOLECULE_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBCanonicalName_CanonicalNameId(), new Integer(0) );
tMap.addColumn ( getDBCanonicalName_Name(), new String() );
tMap.addColumn ( getDBCanonicalName_Type(), new String() );
tMap.addForeignKey ( getDBCanonicalName_MoleculeId(), new Integer(0) , "MOLECULE" , "MOLECULE_ID" );
}
}
--- NEW FILE: DBChemicalNameMapBuilder.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 DBChemicalNameMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBChemicalNameMapBuilder";
/** item */
public static String getTable( )
{
return "CHEMICAL_NAME";
}
/** CHEMICAL_NAME.CHEMICAL_NAME_ID */
public static String getDBChemicalName_ChemicalNameId()
{
return getTable() + ".CHEMICAL_NAME_ID";
}
/** CHEMICAL_NAME.NAME */
public static String getDBChemicalName_Name()
{
return getTable() + ".NAME";
}
/** CHEMICAL_NAME.MOLECULE_ID */
public static String getDBChemicalName_MoleculeId()
{
return getTable() + ".MOLECULE_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBChemicalName_ChemicalNameId(), new Integer(0) );
tMap.addColumn ( getDBChemicalName_Name(), new String() );
tMap.addForeignKey ( getDBChemicalName_MoleculeId(), new Integer(0) , "MOLECULE" , "MOLECULE_ID" );
}
}
--- NEW FILE: DBMeasurementConditionMapBuilder.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 DBMeasurementConditionMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBMeasurementConditionMapBuilder";
/** item */
public static String getTable( )
{
return "MEASUREMENT_CONDITION";
}
/** MEASUREMENT_CONDITION.MEASUREMENT_CONDITION_ID */
public static String getDBMeasurementCondition_MeasurementConditionId()
{
return getTable() + ".MEASUREMENT_CONDITION_ID";
}
/** MEASUREMENT_CONDITION.TEMPERATURE */
public static String getDBMeasurementCondition_Temperature()
{
return getTable() + ".TEMPERATURE";
}
/** MEASUREMENT_CONDITION.FIELD_STRENGTH */
public static String getDBMeasurementCondition_FieldStrength()
{
return getTable() + ".FIELD_STRENGTH";
}
/** MEASUREMENT_CONDITION.SOLVENT */
public static String getDBMeasurementCondition_Solvent()
{
return getTable() + ".SOLVENT";
}
/** MEASUREMENT_CONDITION.USER_ID */
public static String getDBMeasurementCondition_UserId()
{
return getTable() + ".USER_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBMeasurementCondition_MeasurementConditionId(), new Integer(0) );
tMap.addColumn ( getDBMeasurementCondition_Temperature(), new Double(0) );
tMap.addColumn ( getDBMeasurementCondition_FieldStrength(), new Integer(0) );
tMap.addColumn ( getDBMeasurementCondition_Solvent(), new String() );
tMap.addForeignKey ( getDBMeasurementCondition_UserId(), new Integer(0) , "NMRSHIFTDB_USER" , "USER_ID" );
}
}
--- NEW FILE: DBMoleculeMapBuilder.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 DBMoleculeMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBMoleculeMapBuilder";
/** item */
public static String getTable( )
{
return "MOLECULE";
}
/** MOLECULE.MOLECULE_ID */
public static String getDBMolecule_MoleculeId()
{
return getTable() + ".MOLECULE_ID";
}
/** MOLECULE.DATE */
public static String getDBMolecule_Date()
{
return getTable() + ".DATE";
}
/** MOLECULE.STRUCTURE_FILE */
public static String getDBMolecule_StructureFile()
{
return getTable() + ".STRUCTURE_FILE";
}
/** MOLECULE.MOLECULAR_FORMULA */
public static String getDBMolecule_MolecularFormula()
{
return getTable() + ".MOLECULAR_FORMULA";
}
/** MOLECULE.SERIALIZED_MOLECULE */
public static String getDBMolecule_SerializedMolecule()
{
return getTable() + ".SERIALIZED_MOLECULE";
}
/** MOLECULE.CAS_NUMBER */
public static String getDBMolecule_CasNumber()
{
return getTable() + ".CAS_NUMBER";
}
/** MOLECULE.NMRSHIFTDB_NUMBER */
public static String getDBMolecule_NmrshiftdbNumber()
{
return getTable() + ".NMRSHIFTDB_NUMBER";
}
/** MOLECULE.MOLECULAR_WEIGHT */
public static String getDBMolecule_MolecularWeight()
{
return getTable() + ".MOLECULAR_WEIGHT";
}
/** MOLECULE.FINGERPRINT */
public static String getDBMolecule_Fingerprint()
{
return getTable() + ".FINGERPRINT";
}
/** MOLECULE.USER_ID */
public static String getDBMolecule_UserId()
{
return getTable() + ".USER_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBMolecule_MoleculeId(), new Integer(0) );
tMap.addColumn ( getDBMolecule_Date(), new Date() );
tMap.addColumn ( getDBMolecule_StructureFile(), new Object() );
tMap.addColumn ( getDBMolecule_MolecularFormula(), new String() );
tMap.addColumn ( getDBMolecule_SerializedMolecule(), new String() );
tMap.addColumn ( getDBMolecule_CasNumber(), new String() );
tMap.addColumn ( getDBMolecule_NmrshiftdbNumber(), new String() );
tMap.addColumn ( getDBMolecule_MolecularWeight(), new Double(0) );
tMap.addColumn ( getDBMolecule_Fingerprint(), new Object() );
tMap.addForeignKey ( getDBMolecule_UserId(), new Integer(0) , "NMRSHIFTDB_USER" , "USER_ID" );
}
}
--- NEW FILE: DBMoleculeNmrshiftdbUserMapBuilder.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 DBMoleculeNmrshiftdbUserMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBMoleculeNmrshiftdbUserMapBuilder";
/** item */
public static String getTable( )
{
return "MOLECULE_NMRSHIFTDB_USER";
}
/** MOLECULE_NMRSHIFTDB_USER.MOLECULE_ID */
public static String getDBMoleculeNmrshiftdbUser_MoleculeId()
{
return getTable() + ".MOLECULE_ID";
}
/** MOLECULE_NMRSHIFTDB_USER.USER_ID */
public static String getDBMoleculeNmrshiftdbUser_UserId()
{
return getTable() + ".USER_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addForeignKey ( getDBMoleculeNmrshiftdbUser_MoleculeId(), new Integer(0) , "MOLECULE" , "MOLECULE_ID" );
tMap.addForeignKey ( getDBMoleculeNmrshiftdbUser_UserId(), new Integer(0) , "NMRSHIFTDB_USER" , "USER_ID" );
}
}
--- NEW FILE: DBSignalDBAtomMapBuilder.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 DBSignalDBAtomMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBSignalDBAtomMapBuilder";
/** item */
public static String getTable( )
{
return "SIGNAL_ATOM";
}
/** SIGNAL_ATOM.SIGNAL_ID */
public static String getDBSignalDBAtom_SignalId()
{
return getTable() + ".SIGNAL_ID";
}
/** SIGNAL_ATOM.ATOM_ID */
public static String getDBSignalDBAtom_AtomId()
{
return getTable() + ".ATOM_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addForeignKey ( getDBSignalDBAtom_SignalId(), new Integer(0) , "SIGNAL" , "SIGNAL_ID" );
tMap.addForeignKey ( getDBSignalDBAtom_AtomId(), new Integer(0) , "ATOM" , "ATOM_ID" );
}
}
--- NEW FILE: DBSignalMapBuilder.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 DBSignalMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBSignalMapBuilder";
/** item */
public static String getTable( )
{
return "SIGNAL";
}
/** SIGNAL.SIGNAL_ID */
public static String getDBSignal_SignalId()
{
return getTable() + ".SIGNAL_ID";
}
/** SIGNAL.DIMENSIONALITY */
public static String getDBSignal_Dimensionality()
{
return getTable() + ".DIMENSIONALITY";
}
/** SIGNAL.SHIFT_1 */
public static String getDBSignal_Shift1()
{
return getTable() + ".SHIFT_1";
}
/** SIGNAL.SHIFT_2 */
public static String getDBSignal_Shift2()
{
return getTable() + ".SHIFT_2";
}
/** SIGNAL.SHIFT_3 */
public static String getDBSignal_Shift3()
{
return getTable() + ".SHIFT_3";
}
/** SIGNAL.SHIFT_4 */
public static String getDBSignal_Shift4()
{
return getTable() + ".SHIFT_4";
}
/** SIGNAL.SHIFT_5 */
public static String getDBSignal_Shift5()
{
return getTable() + ".SHIFT_5";
}
/** SIGNAL.SERIALIZED_SIGNAL */
public static String getDBSignal_SerializedSignal()
{
return getTable() + ".SERIALIZED_SIGNAL";
}
/** SIGNAL.INTENSITY */
public static String getDBSignal_Intensity()
{
return getTable() + ".INTENSITY";
}
/** SIGNAL.SPECTRUM_ID */
public static String getDBSignal_SpectrumId()
{
return getTable() + ".SPECTRUM_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBSignal_SignalId(), new Integer(0) );
tMap.addColumn ( getDBSignal_Dimensionality(), new Integer(0) );
tMap.addColumn ( getDBSignal_Shift1(), new Double(0) );
tMap.addColumn ( getDBSignal_Shift2(), new Double(0) );
tMap.addColumn ( getDBSignal_Shift3(), new Double(0) );
tMap.addColumn ( getDBSignal_Shift4(), new Double(0) );
tMap.addColumn ( getDBSignal_Shift5(), new Double(0) );
tMap.addColumn ( getDBSignal_SerializedSignal(), new String() );
tMap.addColumn ( getDBSignal_Intensity(), new Double(0) );
tMap.addForeignKey ( getDBSignal_SpectrumId(), new Integer(0) , "SPECTRUM" , "SPECTRUM_ID" );
}
}
--- NEW FILE: DBSpectrumMapBuilder.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 DBSpectrumMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBSpectrumMapBuilder";
/** item */
public static String getTable( )
{
return "SPECTRUM";
}
/** SPECTRUM.SPECTRUM_ID */
public static String getDBSpectrum_SpectrumId()
{
return getTable() + ".SPECTRUM_ID";
}
/** SPECTRUM.DATE */
public static String getDBSpectrum_Date()
{
return getTable() + ".DATE";
}
/** SPECTRUM.SPECFILE */
public static String getDBSpectrum_Specfile()
{
return getTable() + ".SPECFILE";
}
/** SPECTRUM.SERIALIZED_SPECTRUM */
public static String getDBSpectrum_SerializedSpectrum()
{
return getTable() + ".SERIALIZED_SPECTRUM";
}
/** SPECTRUM.LITERATURE */
public static String getDBSpectrum_Literature()
{
return getTable() + ".LITERATURE";
}
/** SPECTRUM.REVIEW_FLAG */
public static String getDBSpectrum_ReviewFlag()
{
return getTable() + ".REVIEW_FLAG";
}
/** SPECTRUM.FINGERPRINT */
public static String getDBSpectrum_Fingerprint()
{
return getTable() + ".FINGERPRINT";
}
/** SPECTRUM.USER_ID */
public static String getDBSpectrum_UserId()
{
return getTable() + ".USER_ID";
}
/** SPECTRUM.MEASUREMENT_CONDITION_ID */
public static String getDBSpectrum_MeasurementConditionId()
{
return getTable() + ".MEASUREMENT_CONDITION_ID";
}
/** SPECTRUM.SPECTRUM_TYPE_ID */
public static String getDBSpectrum_SpectrumTypeId()
{
return getTable() + ".SPECTRUM_TYPE_ID";
}
/** SPECTRUM.MOLECULE_ID */
public static String getDBSpectrum_MoleculeId()
{
return getTable() + ".MOLECULE_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBSpectrum_SpectrumId(), new Integer(0) );
tMap.addColumn ( getDBSpectrum_Date(), new Date() );
tMap.addColumn ( getDBSpectrum_Specfile(), new Object() );
tMap.addColumn ( getDBSpectrum_SerializedSpectrum(), new String() );
tMap.addColumn ( getDBSpectrum_Literature(), new String() );
tMap.addColumn ( getDBSpectrum_ReviewFlag(), new String() );
tMap.addColumn ( getDBSpectrum_Fingerprint(), new Object() );
tMap.addForeignKey ( getDBSpectrum_UserId(), new Integer(0) , "NMRSHIFTDB_USER" , "USER_ID" );
tMap.addForeignKey ( getDBSpectrum_MeasurementConditionId(), new Integer(0) , "MEASUREMENT_CONDITION" , "MEASUREMENT_CONDITION_ID" );
tMap.addForeignKey ( getDBSpectrum_SpectrumTypeId(), new Integer(0) , "SPECTRUM_TYPE" , "SPECTRUM_TYPE_ID" );
tMap.addForeignKey ( getDBSpectrum_MoleculeId(), new Integer(0) , "MOLECULE" , "MOLECULE_ID" );
}
}
--- NEW FILE: DBSpectrumTypeMapBuilder.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 DBSpectrumTypeMapBuilder implements MapBuilder
{
/** the name of this class */
public static final String CLASS_NAME = "org.openscience.nmrshiftdb.om.map.DBSpectrumTypeMapBuilder";
/** item */
public static String getTable( )
{
return "SPECTRUM_TYPE";
}
/** SPECTRUM_TYPE.SPECTRUM_TYPE_ID */
public static String getDBSpectrumType_SpectrumTypeId()
{
return getTable() + ".SPECTRUM_TYPE_ID";
}
/** SPECTRUM_TYPE.DIMENSIONALITY */
public static String getDBSpectrumType_Dimensionality()
{
return getTable() + ".DIMENSIONALITY";
}
/** SPECTRUM_TYPE.NAME */
public static String getDBSpectrumType_Name()
{
return getTable() + ".NAME";
}
/** SPECTRUM_TYPE.ISOTOPE_1 */
public static String getDBSpectrumType_Isotope1()
{
return getTable() + ".ISOTOPE_1";
}
/** SPECTRUM_TYPE.ISOTOPE_2 */
public static String getDBSpectrumType_Isotope2()
{
return getTable() + ".ISOTOPE_2";
}
/** SPECTRUM_TYPE.ISOTOPE_3 */
public static String getDBSpectrumType_Isotope3()
{
return getTable() + ".ISOTOPE_3";
}
/** SPECTRUM_TYPE.ISOTOPE_4 */
public static String getDBSpectrumType_Isotope4()
{
return getTable() + ".ISOTOPE_4";
}
/** SPECTRUM_TYPE.ISOTOPE_5 */
public static String getDBSpectrumType_Isotope5()
{
return getTable() + ".ISOTOPE_5";
}
/** SPECTRUM_TYPE.USER_ID */
public static String getDBSpectrumType_UserId()
{
return getTable() + ".USER_ID";
}
/** 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("nmrshiftdb");
dbMap.addTable(getTable());
TableMap tMap = dbMap.getTable(getTable());
tMap.setPrimaryKeyMethod("none");
tMap.addPrimaryKey ( getDBSpectrumType_SpectrumTypeId(), new Integer(0) );
tMap.addColumn ( getDBSpectrumType_Dimensionality(), new Integer(0) );
tMap.addColumn ( getDBSpectrumType_Name(), new String() );
tMap.addColumn ( getDBSpectrumType_Isotope1(), new String() );
tMap.addColumn ( getDBSpectrumType_Isotope2(), new String() );
tMap.addColumn ( getDBSpectrumType_Isotope3(), new String() );
tMap.addColumn ( getDBSpectrumType_Isotope4(), new String() );
tMap.addColumn ( getDBSpectrumType_Isotope5(), new String() );
tMap.addForeignKey ( getDBSpectrumType_UserId(), new Integer(0) , "NMRSHIFTDB_USER" , "USER_ID" );
}
}
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map In directory usw-pr-cvs1:/tmp/cvs-serv22889 Removed Files: AtomsMapBuilder.java BondsAtomsMapBuilder.java BondsMapBuilder.java CanonicalNameMapBuilder.java ChemicalNameMapBuilder.java MeasurementConditionsMapBuilder.java MoleculeMapBuilder.java MoleculeNmrshiftdbUserMapBuilder.java SignalAtomsMapBuilder.java SignalMapBuilder.java SpectrumMapBuilder.java SpectrumTypeMapBuilder.java Log Message: removed map files --- AtomsMapBuilder.java DELETED --- --- BondsAtomsMapBuilder.java DELETED --- --- BondsMapBuilder.java DELETED --- --- CanonicalNameMapBuilder.java DELETED --- --- ChemicalNameMapBuilder.java DELETED --- --- MeasurementConditionsMapBuilder.java DELETED --- --- MoleculeMapBuilder.java DELETED --- --- MoleculeNmrshiftdbUserMapBuilder.java DELETED --- --- SignalAtomsMapBuilder.java DELETED --- --- SignalMapBuilder.java DELETED --- --- SpectrumMapBuilder.java DELETED --- --- SpectrumTypeMapBuilder.java DELETED --- |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory usw-pr-cvs1:/tmp/cvs-serv21755
Modified Files:
BaseNmrshiftdbUser.java BaseNmrshiftdbUserPeer.java
Removed Files:
Atoms.java BaseSignalAtoms.java BaseSignalAtomsPeer.java
Log Message:
removed om files
Index: BaseNmrshiftdbUser.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseNmrshiftdbUser.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** BaseNmrshiftdbUser.java 28 Feb 2002 13:41:29 -0000 1.2
--- BaseNmrshiftdbUser.java 28 Feb 2002 14:49:49 -0000 1.3
***************
*** 1,3 ****
! package org.openscience.nmrshiftdb.om;
--- 1,3 ----
! package org.openscience.nmrshiftdb.om;
***************
*** 17,21 ****
* extended all references should be to NmrshiftdbUser
*/
! public abstract class BaseNmrshiftdbUser extends org.apache.jetspeed.om.dbpsml.TurbineUser
implements Retrievable
{
--- 17,21 ----
* extended all references should be to NmrshiftdbUser
*/
! public abstract class BaseNmrshiftdbUser extends TurbineUser
implements Retrievable
{
Index: BaseNmrshiftdbUserPeer.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseNmrshiftdbUserPeer.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** BaseNmrshiftdbUserPeer.java 28 Feb 2002 13:41:29 -0000 1.2
--- BaseNmrshiftdbUserPeer.java 28 Feb 2002 14:49:49 -0000 1.3
***************
*** 1,3 ****
! package org.openscience.nmrshiftdb.om;
import java.util.*;
--- 1,3 ----
! package org.openscience.nmrshiftdb.om;
import java.util.*;
***************
*** 20,24 ****
*/
public abstract class BaseNmrshiftdbUserPeer
! extends org.apache.jetspeed.om.dbpsml.TurbineUserPeer
{
--- 20,24 ----
*/
public abstract class BaseNmrshiftdbUserPeer
! extends TurbineUserPeer
{
--- Atoms.java DELETED ---
--- BaseSignalAtoms.java DELETED ---
--- BaseSignalAtomsPeer.java DELETED ---
|
|
From: Stefan K. <sk...@us...> - 2002-02-28 13:59:43
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory usw-pr-cvs1:/tmp/cvs-serv8135 Removed Files: AtomsPeer.java BaseBondsAtoms.java BaseMeasurementConditions.java Log Message: removed om files --- AtomsPeer.java DELETED --- --- BaseBondsAtoms.java DELETED --- --- BaseMeasurementConditions.java DELETED --- |
