generating structure images

Hello,


I have been looking at the JSP file in the JChem/Marvinbeans package to generate a structural image instead of a regular web applet. Under marvinbeans/examples/image-generation, there are a couple of examples with a SMILES string and format as input parameters into a form and the image is supposed to be displayed in the generate_image.jsp file. For some reasons, on my web server , though the SMILES string and format are being passed fine into the JSP file, the file does not display anything. The HTML source code on the page is empty.


In the generate_image.jsp file, up until the format conversion, everything seems to be working fine. After mol.toBinFormat(format) there is no output being registered in the OutputStream.


Any hints on why this might be happening?


Thanks!

Probably, your server can not open a graphical display to generate image in Java.


You should add the headless parameter to Java VM.


Please see the linking topic.


http://www.chemaxon.com/forum/ftopic73.html

Hi Tamas,


I did run the classpath command, but nothing seems to have changed

Code:

java -classpath /path/to/Tomcat/WEB-INF/lib/MarvinBeans.jar -Djava.awt.headless=true

When I run it though, the system just refers to me for the correct usage:


Usage: java [-options] class [args...]


(to execute a class)


or java [-options] -jar jarfile [args...]


(to execute a jar file)





where options include:


-server ...................





When I run it with chemaxon.formats.MolConverter, it just prints out the MolConverter options.

Because you have missed the class to execute from the command line.


You should type this (in one line):

Code:

java -classpath /path/to/Tomcat/WEB-INF/lib/MarvinBeans.jar -Djava.awt.headless=true chemaxon.formats.MolConverter jpeg mystructure.mol

Check also if all files from the marvinbeans/lib are copied in the .../WEB-INF/lib directory. (MarvinBeans.jar uses a couple of external jars and resources, like batik-core.jar for SVG export.)

I do have the other .jar files in the Tomcat web directory. I am not sure, I understand the rationale behind specifying mystructure.mol in the command line. I am looking to provide a SMILES string and a format type from the database and generate an image on my webpage based on that, by giving those paramaters to generate_image.jsp. I tried runnig the command line without specifying any structure and it looks like the MolConvert app is looking for a filename. SO I specified the caffeine.smi in the image-generation example folder. But it still fails to render the image on the webpage

Yes, my example was not exact.


So:

Code:

java -classpath /path/to/Tomcat/WEB-INF/lib/MarvinBeans.jar -Djava.awt.headless=true chemaxon.formats.MolConverter jpeg mystructure.mol -o mystructure.jpeg

It is not clear for me how you would like convert mols to images.


If you would like to do it from command line, see the above example. (It converts only one structure.)


If you would like to call it from API (in a JSP), you should use the chemaxon.formats.MolConverter API or the chemaxon.struc.Molecule.toBinFormat(String) method and set headless parameter in Tomcat Java's. Consult with Tomcat manual howto pass parameter to its Java VM.

I am wanting to do the latter(use web APIs). That's why I gave you the generate_image.jsp example from your website. In the source code(generate_image.jsp), you do include the relevant APIs, but without having any setting for JVM, the example seems to work fine on your web server. I am not certain on what should I include in the $TOMCAT_OPTS value to make this work. Can you let me know what options you changed on your tomcat server to make it work for you

Hi,





As far as I know you should use CATALINA_OPTS, not TOMCAT_OPTS (though this may depend on the Tomcat version)





We also have a short guide for Tomcat, although it may not cover the latest versions :


http://www.chemaxon.com/jchem/doc/admin/tomcat.html


I suggest contacting the Tomcat documentation for more details.





By looking at the command-line example of Tamas above it seems obvious that the required setting is

Code:

-Djava.awt.headless=true

Best regards,





Szilard

I exported the $CATALINA_OPTS = -Djava.awt.headless=true


variable and restarted the server. Nothing seems to have changed. I also tried using System.setProperty("java.awt.headless", "true") and still no image is being generated. Clearly, I am missing something simple that is giving me this trouble.


I'd appreciate if you can help me with some troubleshooting measures


Thanks!

Which format do you use in in Molecule.toBinFormat(String)? Are you sure that mol.toBinFormat returns with an empty byte array?

I am using the JPEG (jpeg:w200,h200,#ffffff) format. I do not really know whether the byte[] array is null, since the screen does not output anything at all after the mol.toBinFormat() line.

I suggest to check firstly the returning value of the toBinFormat method. Probably, you can write the output array size into the output html to check its state. Or try to save output into a file and check whether it is a valid image.


If yes, the problem may be in the jsp generated output streams' header.