Problems with 5.2.3.1

User f52820d97e

16-07-2009 08:33:54

Hi,


I tried it (5.2.3_1), either out of the box or integrated into my version of tomcat, and it seems that marvin is not fired up and I don't see any tables into the drop-down menu.


I changed the config.xml file exactly as before, and I don't see any error in the logs...


Cheers,


Nicolas

User c1ce6b3d19

16-07-2009 08:41:40

Nicolas,


Did you have a chance to try the 5.2.3 release?  Is this only a problem with the 5.2.3.1 release?


I believe there was no specific changes to Web Services in the codebase for the 5.2.3.1 release, but perhaps there was an incompatibility with some recent changes. 


 


Jon

User f52820d97e

16-07-2009 08:57:14

Hi Jon,


I just tried the 5.2.3 release, and I have the same problem... and none of the buttons (query, about...) work, either! I can only use the drop down menus, with no effect ;-)


Nicolas

ChemAxon e274e1bada

16-07-2009 14:00:37

Hi Nicolas,


it seems your Ajax example cannot connect to the Web Services Server.


Please check if:
- Tomcat is running or restarted (if it was necessary),
- tomcat port settings are correct,
- you are using the right config.xml in the ajax directory, and every settings and pathes are correct.


Edvard

User f52820d97e

16-07-2009 14:27:48

Hi Edvard,


I tried with the 5.2.2 and the 5.2.3 out-of-the-box distribs with the windows startup.bat script, the only thing I changed are the 2 lines <driver> and <url> in config.xml


5.2.2 works, 5.2.3 doesn't...


Nicolas

ChemAxon e274e1bada

20-07-2009 08:12:47

Nicolas,


I tried to reproduce the failure in various environments but I could not that.
Can you confirm if the Tomcat can be running with the scripts when you try the out-of-box case?


Cheers, Edvard

User f52820d97e

20-07-2009 12:25:23

Hi Edvard,


After a lot of trials, I figured the problem: the old mysql database did not communicate with the webservices anymore, even if jcman worked, with regeneration. I don't know what went wrong, but when I created a new database with a new structure table, the interface worked.


Two points:


- The export function still does not work, I have a "line too short in atom block" in mview;


- The insert button in the left panel, as well as the edit/remove in the structure cell, disappeared, is this on purpose because they did not work with the chemical terms?


Thanks


Nicolas

User f52820d97e

20-07-2009 13:26:36

I figured out why the tables disappeared: it is when I create new columns based on chemical terms! specifically in logical forms: if I create a integer column "druglike" with this condition for example:


(mass() <= 500) && (logp() <= 5) && (donorCount() <= 5) && (acceptorCount() <= 10) && (rotatableBondCount() <= 10) && (PSA() <= 140)


A regular column like logp works, though...

ChemAxon e274e1bada

20-07-2009 14:52:20

Thank you Nicolas, we are investigating the problem.


Edvard

ChemAxon ebbce65bcf

21-07-2009 09:45:03

Nicolas,


Edit/Remove buttons can be shown if you modify the config.xml's <spreadsheet> section. Insert a writable="true" attribute into the table tag where you want to allow editing. Anyway, there can be problems about inserting special characters but probably this issue will be solved in the next minor version.


Cheers,


Roland

ChemAxon ebbce65bcf

21-07-2009 10:43:44

Regarding the Export problem could you send us the original structure in some form which you failed to export (e.g. the 5th or 199th of your export.sdf) ?

User f52820d97e

21-07-2009 12:28:11










roland wrote:

Edit/Remove buttons can be shown if you modify the config.xml's <spreadsheet> section. Insert a writable="true" attribute into the table tag where you want to allow editing. Anyway, there can be problems about inserting special characters but probably this issue will be solved in the next minor version.



Great, thanks, I reproduced the default line with the name of my table instead of "default" and writable="true". I played around with the fields to display, too, I understand it all now...

User f52820d97e

21-07-2009 13:25:44










roland wrote:

Regarding the Export problem could you send us the original structure in some form which you failed to export (e.g. the 5th or 199th of your export.sdf) ?



Here are two exports of the 5 first molecules in a NCI database, one with the ajax interface, the orther with jcman. There is one screwed-up line at molecule 4...

ChemAxon ebbce65bcf

22-07-2009 12:57:54

Hi,


I imported your correct sdfile once using jcman and once using the Ajax example. The Ajax export results were correct in both cases.  To be honest I don't know why those additional wrong characters fill your exported file. Which DBMS do you use? In which format are your structures stored in your DB originally? Do you always update your aar file when you update the Ajax example? (You should.) Only 3D structures fail during export? Or if you could discover some pattern among the failed molecules which I cannot see, please tell me. :)


Cheers,


Roland

User f52820d97e

22-07-2009 13:28:02










roland wrote:

I imported your correct sdfile once using jcman and once using the Ajax example. The Ajax export results were correct in both cases.  To be honest I don't know why those additional wrong characters fill your exported file. Which DBMS do you use? In which format are your structures stored in your DB originally? Do you always update your aar file when you update the Ajax example? (You should.) Only 3D structures fail during export? Or if you could discover some pattern among the failed molecules which I cannot see, please tell me. :)



Hi Roland,


I tried several times, each time I have a weird 4-letter/digit string at the beginning of the file.


I use MySQL 5.0.51, Tomcat 6.0.20 / Apache 2.2.11 on a Linux CentOS 4.7 server.


I tried firefox on the server, firefox and iexplore on a windowsXP client, each time I have this extra string and it is messed up inside the file every time on the client, not on the server.


It does not matter if the structures are 2D or 3D, and I import SD files to begin with, with jcman.


I always wipe clean the install, so the aar files are the new ones...


Cheers,


Nicolas


 


 

ChemAxon ebbce65bcf

22-07-2009 13:49:47

I have almost the same test environment, except the Linux part (which is a big difference :)). We are trying to find the bug... But one thing is worth to try, if the regular expression is buggy in jsp/export.jsp. Please insert an


out.print(soapResponse.toString());


before the line (near 106):


// Filter response to get export result


and comment out the rest of the lines which follow this using /* ... */. And send me the browser output, please.


Thanks,


Roland

User f52820d97e

19-10-2009 15:24:24

Hi Roland,


Back to you (a bit late) - I tried with the new version, same error. Attached are the 2 files


- sdf from regular export.jsp


- txt from the out.print(soapResponse.toString()); command


Cheers


Nicolas

User c1ce6b3d19

22-10-2009 15:02:51

Just to confirm,


It looks like there is "1ff8" as the first line.


Then there is an "8d52" interspersed in the bond block on the fourth molecule (named "NSC 4").


They look like hexadecimal bytes or something. 


 


It is possible there are some driver incompatability issues with mysql that we would like to rule out. 


 


I know you use a slightly different configuration than what is released, so I will discuss the location as it is in the normal deployment. 


There should be a jar file in the axis directory.


<JChemWebServices_dir>\tomcat\webapps\axis2\WEB-INF\lib\mysql-connector-java-5.1.6-bin.jar


Please make sure there are no mysql jars in the tomcat lib.


<JChemWebServices_dir>\tomcat\lib


 


Since your mysql version is older, 5.0.51, you could replace the original jar (perhaps change the extension to ".jar.removed") with a 5.0 mysql version. The latest 5.0 version can be downloaded here:


http://dev.mysql.com/downloads/connector/j/5.0.html


The jar file is inside the downloaded zip or tar.gz file. 


 


Jon


 

User f52820d97e

28-10-2009 13:43:00

Hi Jon,


Sorry for my late reply, I just got around to it.


I tried with the 5.0.8 connector like you said (btw, I had already the 5.1.6 connector in my classpath and it is working fine with jcman for ex.) and I have strictly the same error...


Cheers,


Nicolas


 

ChemAxon ebbce65bcf

05-11-2009 15:00:00

Hi Nicolas,


Sorry, we couldn't reproduce your bug. Soon we will create you a special package containing some more debug messages to find out what exactly causes the problem on your machine. Maybe I will also give you a simple JS client for export testing. Thank you for your patience.


Cheers,


Roland


 

User f52820d97e

05-11-2009 16:38:09

Hi Roland,


Sorry you cannot reproduce it... I'll wait, thanks!


Nicolas

User c1ce6b3d19

19-11-2009 17:22:51

Nico,


I have attached an 5.2.6-versioned aar file that includes some export debugging statements that might help us understand the export issues you are having.


 


I have placed the files at


http://www.chemaxon.com/shared/jlee/saettel/JChemWebServices.aar


 


The tomcat logs will have three new messages, discussing the Canonical Charset Name, Default Charset Name, and the molecules results. Please send me these for one of your problem structures.


Thanks,


Jon

User f52820d97e

23-11-2009 15:15:11

Allright, here are part in the catalina.out log file after a simple search and export, and the export SD File (with the problem)


Cheers,


Nicolas

User c1ce6b3d19

23-11-2009 17:02:33

Nicholas,


 


From examine the logs, the web service classes are sending out the correct molecules, but it seems that the message is getting garbled somewhere in between. 


I did some googling for "1ff8" and found this posting. 


http://lists.samba.org/archive/jcifs/2006-May/006139.html


 


After our research here, I am leaning toward a problem with the web server/servlet container you are using as being the problem.


The last thing I can recommend is to try it in the normal environment and see if the export works.


Jon

User c1ce6b3d19

23-11-2009 17:19:58

Here is another related issue from the sun forums


http://forums.sun.com/thread.jspa?threadID=398920

ChemAxon ebbce65bcf

26-01-2010 12:02:14

Nicolas,


At last I think we could reproduce the problem. The server returns "Transfer-encoding: chunked" HTTP response which should be handled in the jsp files. The easiest way to solve the issue to use HTTP 1.0 instead of HTTP 1.1, which does not support chunked mode. To do this you have to modify your img.jsp and export.jsp files in the line which defines the version of the HTTP protocol.


// Build HTTP request
StringBuffer reqStr = new StringBuffer();
reqStr.append("POST ")...    *** THIS LINE!!! ***


Change HTTP/1.1 to HTTP/1.0 there.


It works for us, so I hope it will help you, as well.


Sorry for this late answer, we haven't met this problem until this time.


Cheers,


Roland

User f52820d97e

26-01-2010 12:53:45

Oh great, I read a few articles and figured it was about the chunk mode, but I didn't know the fix... Thanks a lot, I can use the connector again!


Cheers,


Nicolas