ChemAxon Forum Archive » Storage & search: JChem Base and JChem Oracle Cartridge

Problem installing JChem 3.1.1 on Linux

User f698d0529d

12-09-2005 12:50:43

Hi





java 1.5.0_04


oracle 9.2.0.6


Red Hat Enterprise Linux ES release 3 (Taroon Update 5)


Kernel 2.4.21-32.0.1.ELsmp on an i686


tomcat 4.1.31





I am trying to install JChem version 3.1.11 on this machine, but I run into a problem when I try to run the install.sh script. This machine did not previously have jchem on it, and I just installed tomcat and java 1.5 on it this morning





I think the first time I tried to run install.sh I made some mistake, so I ran the uninstall.sh script and installed it again.





The second time I ran the script, I got this problem





Code:



Disconnected from Oracle9i Release 9.2.0.6.0 - Production


JServer Release 9.2.0.6.0 - Production


+ echo 'Create the SQL script used to register the JChem service URLs'


Create the SQL script used to register the JChem service URLs


+ /home/oracle/jdk1.5.0_04/bin/java -cp ../lib/jchem.jar chemaxon.jchem.cartridge.ChUrl register-urls jchem/jchem@ccdlive http://uksap12:8089/jchemstreams


java.lang.Exception: The following exception has been thrown by the servlet:


Exception: INCONSISTENT JCHEM VERSIONS:


JChem version in Oracle: 3.1.1, JChem version in servlet: 3.0.13


        at chemaxon.jchem.cartridge.jcservcli.JcsClientBase.checkForException(JcsClientBase.java:162)


        at chemaxon.jchem.cartridge.jcservcli.BlockingClient.callService(BlockingClient.java:179)


        at chemaxon.jchem.cartridge.jcservcli.BlockingClient.callService(BlockingClient.java:29)


        at chemaxon.jchem.cartridge.ChUrl.checkEndPoint(ChUrl.java:117)


        at chemaxon.jchem.cartridge.ChUrl.getServiceEndPoints(ChUrl.java:59)


        at chemaxon.jchem.cartridge.ChUrl.main(ChUrl.java:166)






so I made sure that I had followed all the steps on your installation page. I had forgotten to add the java optimisation parameters to the start of the tomcat server.xml file, so I added these, and ran uninstall.sh.





The third time I ran install.sh, the error changed, to the one below.





Code:



Disconnected from Oracle9i Release 9.2.0.6.0 - Production


JServer Release 9.2.0.6.0 - Production


+ echo 'Create the SQL script used to register the JChem service URLs'


Create the SQL script used to register the JChem service URLs


+ /home/oracle/jdk1.5.0_04/bin/java -cp ../lib/jchem.jar chemaxon.jchem.cartridge.ChUrl register-urls jchem/jchem@ccdlive http:/uksap22:8089/jchemstreams


java.lang.IllegalArgumentException: protocol = http host = null


        at sun.net.spi.DefaultProxySelector.select(DefaultProxySelector.java:146)


        at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:739);


        at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:669);


        at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:836);


        at chemaxon.jchem.cartridge.jcservcli.JcsClientBase.getOutputStream(JcsClientBase.java:102)


        at chemaxon.jchem.cartridge.jcservcli.BlockingClient.callService(BlockingClient.java:49)


        at chemaxon.jchem.cartridge.jcservcli.BlockingClient.callService(BlockingClient.java:29)


        at chemaxon.jchem.cartridge.ChUrl.checkEndPoint(ChUrl.java:117)


        at chemaxon.jchem.cartridge.ChUrl.getServiceEndPoints(ChUrl.java:59)


        at chemaxon.jchem.cartridge.ChUrl.main(ChUrl.java:166)


+ exit 1






Both the 2nd and 3rd time I ran install.sh, trying to run test.sh gave the following error





Code:



ERROR at line 1:


ORA-29532: Java call terminated by uncaught Java exception:


java.lang.IndexOutOfBoundsException: Index: 0, Size: 0


ORA-06512: at "JCHEM.JCHEM_CORE_PKG", line 0


ORA-06512: at "JCHEM.JCHEM_CORE_PKG", line 84






and trying to create a JChem index gave the following error





Code:



create table test_mcr(smiles varchar2 (4000));





CREATE INDEX JC_IDX_TEST ON TEST_MCR


 (SMILES)


 INDEXTYPE IS JCHEM.JC_IDXTYPE


 PARAMETERS('TABLESPACE=data_jchem');





ORA-29855: error occurred in the execution of ODCIINDEXCREATE routine


ORA-29532: Java call terminated by uncaught Java exception: java.lang.RuntimeException: ORA-00904: "JCHEM_CORE_PKG"."GET_CARTOWNER_SCHEMA": invalid identifier


ORA-06512: at "JCHEM.JCHEM_CORE_PKG", line 0


ORA-06512: at "JCHEM.JC_IDXTYPE_IM", line 17






Can you help?

ChemAxon aa7c50abf8

12-09-2005 13:27:11

Code:
JChem version in Oracle: 3.1.1, JChem version in servlet: 3.0.13






The first code block posted tells that http://uksap12:8089/jchemstreams points to version 3.0.13 of JChem Streams. Did you replace it with 3.1.1 (in Tomcat) in the meantime?

User f698d0529d

12-09-2005 15:19:36

Peter


I think I have solved the problem





There was no previous installation of JChem on this server, so to be honest I really don't know where it got the 3.0.13 version conflict. Maybe it is a "red herring" (irrelevant), since it did not happen the second time.





Also, I can start the jchemstreams web application, and when you click on check JChem version, it says 3.1.1 for both JChem and JChem streams.





I have recopied the jchemstreams.war file from the jchem directory to the tomcat webapps directory, and have just tried the installation again.





This time, it seemed to complete successfully - there was one error message output (below), but test.sh completes normally, and more importantly it is possible to create a jchem index as an end user and successfully query it.





Code:



delete from jc_idx_property where prop_name like 'jchem.service.endPoint.url.%'


            *


ERROR at line 1:


ORA-00942: table or view does not exist











Call completed.






I remembered that the other error message I was seeing





java.lang.RuntimeException: ORA-00904: "JCHEM_CORE_PKG"."GET_CARTOWNER_SCHEMA": invalid identifier





can be solved by creating local synonyms for all jchem objects. You can do this by preparing a script as follows





select 'create synonym ' || a.OBJECT_NAME || ' for jchem.' || a.OBJECT_NAME || ';' from all_objects a where lower(a.OWNER) = 'jchem' and a.OBJECT_TYPE in


('PACKAGE', 'FUNCTION', 'OPERATOR', 'TYPE', 'INDEXTYPE', 'PROCEDURE');





The necessity to create private synonyms (maybe public ones would also work - I don't know) to avoid this error I first saw in Jchem 3.1. In previous versions, there was no such problem. However, it is not important.





Thanks for your help


Mark