Questions of installation of Jchem base

Dear Sir/Madam:





I have received license keys from Chemaxon. Now I am working on intallation of the Jchem 3.1.1 package.


I have read the intruction of installation of Jchem, and have several questions because I did not find answers from th forum.


My compouter is Linux RedHat 8, and I am a organic and medicinal chemist. Please give me detailed instructions ( step by step) about these questions.





1. I would like to use Oracle, shold I install it in my compouter? If it is, what kind of Oracle data base ( I mean Model and version) I should choose?


2. There are several kinds of JDBC ( please see the list bellow), please tell me which JDBC I should download ? What is the exact URL of the data base?





Oracle Database 10/g / Release 2 (10.2.0.1.0) JDBC Drivers





*JavaDoc <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/javadoc.zip>* (4,383,404 bytes)


*README <http://www.oracle.com/technology/software/tech/java/sqlj_jdbc/htdocs/readme_10201.html>*


*JDBC Thin for All Platforms*


classes12.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/classes12.jar>; (1,590,491 bytes) - for use with JDK 1.2 and JDK 1.3


classes12_g.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/classes12_g.jar>; (2,033,507 bytes) - same as classes12.jar, except that classes were compiled with "javac -g" and contain some tracing information.


classes12dms.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/classes12dms.jar>; (1,598,183 bytes) - same as classes12.jar, except that it contains additional code`to support Oracle Dynamic Monitoring Service.


classes12dms_g.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/classes12dms_g.jar>; (2,041,904 bytes) - same as classes12dms.jar except that classes were compiled with "javac -g" and contain some tracing information.


ojdbc14.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/ojdbc14.jar>; (1,536,979 bytes) - classes for use with JDK 1.4 and 1.5


ojdbc14_g.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/ojdbc14_g.jar>; (1,928,714 bytes) - same as ojdbc14.jar, except that classes were compiled with "javac -g" and contain some tracing information.


ojdbc14dms.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/ojdbc14dms.jar>; (1,544,468 bytes) - same as ojdbc14.jar, except that it contains additional code`to support Oracle Dynamic Monitoring Service.


ojdbc14dms_g.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/ojdbc14dms_g.jar>; (1,936,765 bytes) - same as ojdbc14dms.jar, except that classes were compiled with "javac -g" and contain some tracing information.


orai18n.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/orai18n.jar>; (1,551,155 bytes) - NLS classes for use with JDK 1.2, 1.3, 1.4, and 1.5. This jar file replaces the old nls_charset jar/zip files.


ons.jar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/ons.jar>; (48,492 bytes) - for use by the pure Java client-side Oracle Notification Services (ONS) deamon.


demo.tar <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/demo.tar>; (604,160 bytes) or demo.zip <http://download.oracle.com/otn/utilities_drivers/jdbc/10201/demo.zip>; (529,267 bytes) - contains sample JDBC programs.


*Note: For platform specific JDBC-OCI libraries See Instant Client <http://www.oracle.com/technology/tech/oci/instantclient/instantclient.html>*








According to Chemaxon website, there are several other JDBCs recommended ( see bellow), which one should I download?





This page provides the following downloads and specifications:


* JDBC 4.0 API


<http://java.sun.com/products/jdbc/download.html#corespec40>;


* JDBC RowSet Implementations 1.0.1 JWSDP 1.4 Co-Bundle


<http://java.sun.com/products/jdbc/download.html#rowsetcobundle1_0>;


* JDBC RowSet Implementations 1.0.1


<http://java.sun.com/products/jdbc/download.html#rowset1_0_1>;


* JDBC 3.0 API


<http://java.sun.com/products/jdbc/download.html#corespec30>;


* JDBC Optional Package for CDC/Foundation Profile API


<http://java.sun.com/products/jdbc/download.html#cdcfp>;


* JDBC 2.1 API


<http://java.sun.com/products/jdbc/download.html#corespec21>;


* JDBC 2.0 Optional Package API


<http://java.sun.com/products/jdbc/download.html#spec>;


* JDBC API Test Suite 1.3.1


<http://java.sun.com/products/jdbc/download.html#testsuite131>;


* JDBC API Test Suite 1.2.1


<http://java.sun.com/products/jdbc/download.html#testsuite121>;








Thank you very much for your kind help and your time.





Sincerely,





Xiaobing Tian

Dear Xiaobing Tian,

Quote:

1. I would like to use Oracle, shold I install it in my compouter?

JChem can also connect to an Oracle database on an other machine, so you don't necessarily have to install Oracle on your computer.

Quote:

If it is, what kind of Oracle data base ( I mean Model and version) I should choose?

You should use Oracle 9 or 10.


(JChem is not dependent on an exact Oracle version)

Quote:

2. There are several kinds of JDBC ( please see the list bellow), please tell me which JDBC I should download ? What is the exact URL of the data base?

I recommend you the JDBC driver that can be found in your Oracle installation (so you cannot have any compatibility problems):





<Oracle_home>/jdbc/lib/classes12.jar





Please include this file into your CLASSPATH environmental variable before trying to connect to the database.





Best regards,





Szilard

Hi, Szilard,





Thank you very much for your prompt respose.


There is an installed Oracle 9i in my computer (Windows XP), and I have set JCHEMHOME and CLASSPATH. Now I am tring to fill out the table 'Connecting a Database'.





1. What are [host address], [port] and [database sid] in my case? For example, jdbc:oracle:thin:@[host address]:[port]:[database sid].





2. Should I just use my forum username and password as login name and password?





Thank you very much.





Xiaobing

Hi,

Quote:

1. What are [host address], [port] and [database sid] in my case? For example, jdbc:oracle:thin:@[host address]:[port]:[database sid].

[host address] : this is the machine where your Oracle installation runs on. If you install it on your own machine, it's "localhost", otherwise the IP address or the network name of the other machine.





[port] : the default port for TCP/IP connection in Oracle is 1521.





[database sid] : the name of the database. You specify this when you create a new database in Oracle.

Quote:

2. Should I just use my forum username and password as login name and password?

No.


A database username and password is required.


(usually a sample DB user is created during installation as SCOTT, with the password "tiger")





Best regards,





Szilard

Hi, Szilard:





Thank you so muchf for your detailed explanation. Now I realized I can not use the Oracle data base because I do not know its user name and password. Can I connect to Chemaxon's data base? If can, please tell me the host address, port, database_sid, username and password.





Thanks and I appreciate your help.





Best regards,





Xiaobing Tian

Hi,

Quote:

Thank you so muchf for your detailed explanation. Now I realized I can not use the Oracle data base because I do not know its user name and password.

You should ask your database administrator.


Alternatively you can also set up your own Oracle database.


Oracle has just made available a free version, which is suitable for small databases:


http://www.oracle.com/technology/products/database/xe/index.html





Alternatively you may also try using MySQL, which is also free:


http://www.mysql.com/ width="90%" cellspacing="0" cellpadding="3" border="0" align="center"> Quote:


Can I connect to Chemaxon's data base? If can, please tell me the host address, port, database_sid, username and password. No.


You must have an own database instance.





Best regards,





Szilard

Hi, Szilard,





I downloaded and successfully installed Oracle XE in my computer (Windows), following the link you sent to me. I have set up the JCHEMHOME and CLASSPATH (C:\oraclexe\app\oracle\product\10.2.0\server\jdbc\lib\ojdbc14.jar). Then I tried to connect Jchem to the data base. According to the installation guide of the Oracle XE, the URL is http://host:port/htmldb/, and the port number is 8080. I also created an admistration account (XIAOBING) which I though is my Oracle_sid. Then I started jcman and filled out the table of 'Connecting to a Database' as follows:





oracle.jdbc.driver.OracleDriver


jdbc:oracle:xe:@localhost:8080/htmldb/:XIAOBING


JchemProperties


system


password





It showed following error masseges:





SQL warning


SQLSate:null


Message: Invalid Oracle URL specified


Vendor: 17067





On the MS-DOS terminal, messages are:





C:\>jcman


java.sql.SQLException: Invalid Oracle URL specified


at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java


:112)


at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java


:146)


at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java


:208)


at oracle.jdbc.driver.OracleDriver.connect(OracleDriver.java:538)


at java.sql.DriverManager.getConnection(Unknown Source)


at java.sql.DriverManager.getConnection(Unknown Source)


at chemaxon.util.ConnectionHandler.setConnected(ConnectionHandler.java:2


06)


at chemaxon.util.ConnectionHandler.connect(ConnectionHandler.java:246)


at chemaxon.jchem.gui.Connector.go(Connector.java:95)


at chemaxon.jchem.gui.JChemFrame.connect(JChemFrame.java:561)


at chemaxon.jchem.JChemManager.init(JChemManager.java:89)


at chemaxon.jchem.JChemManager.main(JChemManager.java:106)





What should I do to solve these problems?





Many thanks for your advice.





Best regards,





Xiaobing

Hi,

Quote:

Then I tried to connect Jchem to the data base. According to the installation guide of the Oracle XE, the URL is http://host:port/htmldb/, and the port number is 8080.

No.


This is an http URL for database administration via a browser, and not a URL for connecting to the database.

Quote:

I also created an admistration account (XIAOBING) which I though is my Oracle_sid.

No.


The database_sid is the name of the database.





If you have installed Oracle on the local computer with the default settings, the URL should be like this:





jdbc:oracle:thin:@localhost:1521:<database_name>





Substitute <database_name> with the name of the database.





Best regards,





Szilard

Hi, Szilard,





I successfully ceated a database in Oracle9i. I set





CLASSPATH=C:\<Oracle_Home>\jdbc\lib\classes12.jar


Path=C:\<Oracle_Home>\jdbc\lib\classes12.jar





I then tried to connect Jcman to the database as follows:





oracle.jdbc.driver.OracleDriver


jdbc:oracle:thin:@localhost:1521:mydatabase


JchemProperties


sys (or system)


mydatabase password (or system password)





It resulted in error as follows:





Java.lang.ClassNotFoundException





oracle.jdbc.driver.OracleDriver





Could you kindly tell me what was wrong with the connection?





Thanks a lot.





Xiaobing

Hi,





1. Your CLASSPATH is incorrect, that's why you get the error.


It should point to a classes12.jar on your local filesystem.





2. Putting .jar files into your PATH environmental variable makes no sense, though makes no harm either.





3. You will not be able to connect as SYS to Oracle with JChemManager.


(this user requires a special connection mode)





Best regards,





Szilard