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out of box config for ajax 5.2.3_1
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bobthechemist

Joined: 24 Jul 2009
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Link to postPosted: Wed Aug 05, 2009 3:45 pmPost subject: out of box config for ajax 5.2.3_1 Reply with quote

Pardon the noob question.  I have tomcat up and running, with ajax in the webapps folder.  I used JChemManager to setup a mysql database with some SMILES structures imported.  When navigating to Ajax, it is clear I can connect to the database (it notices I have made several tables) however I receive an "invalid standardizer configuration" error.  The same error appears when I try to connect to the database using jchem/examples/db_search.  I have created two tables in the database, one with structures and one empty, and the error occurs regardless of which one I choose in the db_search case. 

Clearly, I have a configuration problem.  In all likelihood, it is with the database, however I am unsure how to diagnose the problem further.  Any suggestions would be helpful.

 

BoB

bobthechemist

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Link to postPosted: Wed Aug 05, 2009 3:49 pmPost subject: Stack trace from db_search Reply with quote

JChem version : 5.2.3_1
JVM : Sun Microsystems Inc. 1.6.0_14
OS : amd64 Linux 2.6.28-14-server


Stack trace:
------------


chemaxon.jchem.db.DatabaseSearchException: Invalid standardizer configuration
at chemaxon.jchem.db.JChemSearch.initTable(JChemSearch.java:2698)
at chemaxon.jchem.db.JChemSearch.init(JChemSearch.java:3444)
at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2214)
at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:2114)
at chemaxon.jchem.db.JChemSearch.access$1900(JChemSearch.java:115)
at chemaxon.jchem.db.JChemSearch$SearchThread.run(JChemSearch.java:507)
jlee

Joined: 11 Aug 2008
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Link to postPosted: Wed Aug 05, 2009 4:58 pmPost subject: Reply with quote

BoB,

Thanks for your interest in JChem Web Services!

Since the error occurs in both the AJAX client and the db_search client, the problem is probably not related to JChem Web Services. 

By the looks of the error message, we should ask if you are using a custom standardization file, most likely added when you created the tables.  If so, please attach them.

Jonathan Lee

 

bobthechemist

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Link to postPosted: Wed Aug 05, 2009 6:23 pmPost subject: Reply with quote

I don't know what a standardization file is, or where it goes, so if I created a custom one, I have done so unintentionally :-).  I interpreted the error to mean that I either needed to create a standardization file or I created the database incorrectly.

I need to use mysql as my database server.  JChemManager doesn't complain when I create a database, add a table and populate it with a few SMILES structures (with no additional data).  Is there something else I need to add to the database creation process?

Thanks for the help.

bobthechemist

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Link to postPosted: Thu Aug 06, 2009 2:28 pmPost subject: Solved? Reply with quote

For what it's worth, I've figured out how to solve the problem.   For reasons that are unclear to me, the default standardizer configuration doesn't work.  I've attached the output of  `jcman t <table>` for two tables designed the same way except one has a custom standardizer configuration (added the 2D and 3D visualization options).




 Filename: doesnt.txt    Filesize: 1.12 KB    Downloaded: 301 Time(s)
 Description:  

 Filename: works.txt    Filesize: 1.6 KB    Downloaded: 195 Time(s)
 Description:  
ebuki
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Link to postPosted: Thu Aug 06, 2009 6:09 pmPost subject: Reply with quote

BoB,

thank you for the report, we are trying to reproduce the error.

Regards, Edvard

jlee

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Link to postPosted: Fri Aug 07, 2009 3:07 pmPost subject: Reply with quote

BoB,

We have a two questions that might help us understand the problem further. 

1.  There is jchemproperties table in the mysql database.  There should be a row with prop_name column = "<Name of custom configured table>.standardizerConfig" and the prop_value_ext column containing the blob with your Standardizer configurtation you sent in your previous post. 

Please look for another row in the jchemproperties table with the prop_name of "<Name of default configured table>.standardizerConfig"

The first table you created with the default Standardizer Configuration should not have the analogous row in the jchemproperties table, but we want to confirm it does not exist. 

 

2. The full stack trace of the error can be of more use.  If you were using tomcat, the error should exist in the catalina.out log file.  Can you please attach it here.

Thanks,

Jonathan Lee

bobthechemist

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Link to postPosted: Fri Aug 07, 2009 10:02 pmPost subject: Reply with quote

Hi,

Thanks for looking in to the error.  Unfortunately (or foruntately) it seems that I can no longer reproduce the error.  I'm not sure what I've done - before getting your reponse, I deleted the non-functioning table and continued to build my database.  After your request, I recreated a table with the default standardizer, and the table doesn't give me the error as the earlier one did.

If I encounter the error again, I'll be sure to collect as much troubleshooting information as possible, but as of now, I can't reproduce it.

Thanks.

BoB

lducuny

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Link to postPosted: Mon May 24, 2010 10:54 pmPost subject: AJAX Example - Invalid standizer configuration Reply with quote

I want to try webapps folder.  I used JChemManager to create a structure table in mysql database with the default setting. When navigating to Ajax, I receive an "invalid standardizer configuration" error.

I saw there were already people reported this problem. Unfortunately, I do not know how they solved the probelm.

I checked the catalina.out log file. It says the problem was Caused by: chemaxon.jchem.db.DatabaseSearchException: Invalid standardizer configuration.


I do not know what I did was wrong with the creation of database.

Thanks,

Lei


roland
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Link to postPosted: Tue May 25, 2010 9:18 amPost subject: Reply with quote

Hi,

Which WS version do you use? Could you send us the entire stack trace or is it the same that bobthechemist posted? Could you check your corresponding standardizer configuration in the jchemproperties table and tell us? Thank you.

Regards,

Roland

lducuny

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Link to postPosted: Tue May 25, 2010 7:59 pmPost subject: Reply with quote

roland wrote:

Hi,

Which WS version do you use? Could you send us the entire stack trace or is it the same that bobthechemist posted? Could you check your corresponding standardizer configuration in the jchemproperties table and tell us? Thank you.

Regards,

Roland

Hello Roland,

Thank you for your email! I fixed the problem, after I deleted the
./chemaxon license directory and reinstalled it. It seems once the
./chemaxon directory saved some wrong information, there would be no way
to fix it, until you totally delete that directory.

with the best regards,

Lei
simy202

Joined: 07 Jan 2011
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Link to postPosted: Fri Jan 07, 2011 3:25 amPost subject: Reply with quote

lducuny wrote :
roland wrote:

Hi,

Which WS version do you use? Could you send us the entire stack trace or is it the same that bobthechemist posted? Could you check your corresponding standardizer configuration in the jchemproperties table and tell us? Thank you.

Regards,

Roland

Hello Roland,

Thank you for your email! I fixed the problem, after I deleted the
./chemaxon license directory and reinstalled it. It seems once the
./chemaxon directory saved some wrong information, there would be no way
to fix it, until you totally delete that directory.

with the best regards,

Lei

Is there a tool for PHP which can generate code for consuming a web service based on its WSDL? Something comparable to clicking "Add Web Reference" in Visual Studio or the Eclypse plugin which does the same thing for Java.  How to solve this PHP web service problem?

roland
ChemAxon personnel
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Link to postPosted: Fri Jan 07, 2011 1:10 pmPost subject: Reply with quote

Hi,

I found this article on the Internet:

http://www.mehtanirav.com/2009/01/28/wsdl-to-php-generate-php-code-from-a-wsdl-file

I just tried out WSDLInterpreter. It generated some class but unfortunately it did not make my life easier, when I attempted to use a WS of ours. Another idea I have that you mentioned you found the functionality you need inside Eclipse. The Eclipse team also developed an IDE for PHP (called PDT), so I can imagine you will find the wsdl-to-code transformation there (or a plugin).

http://www.eclipse.org/pdt/

I hope I could help.

Regards,

Roland

 

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