Rest python examples

Update: I've printed out "detail" and I have this:-

{u'errorCode': 0, u'rootCause': u'java.lang.NoClassDefFoundError', u'errorMessage': u'Could not initialize class sun.awt.X11.XToolkit'}

 

I don't want to run anything through a display I just want the raw data (smiles etc) as everything I'm doing will be via commandline scripts, would it be possible to generate an example for this?

 

Many thanks

 

 

Hi

I've downloaded and deployed the .war file from webservices-6.1.0-b917.zip into my tomcat 7 install on linux.

I'm trying to learn how to use the web services from python using the sample db and examples in the docs before I start to try to query my own data.

I've modified the query_post.py example to run against my installation but the example is only partially working. The data being returned from Chebi is this:-

{u'cd_molweight': 286.3655, u'acc': 3, u'cd_id': 2, u'don': 2, u'logp': 3.4379631133333346}
Failed
{u'cd_molweight': 252.2647, u'acc': 3, u'cd_id': 5, u'don': 0, u'logp': 3.1798970889999993}
Failed
{u'cd_molweight': 122.1644, u'acc': 1, u'cd_id': 6, u'don': 1, u'logp': 1.7193174379999998}
Traceback (most recent call last):
  File "./query_post27.py", line 97, in <module>
    print("OK: "+detail["format"]["smiles"])
KeyError: 'format'

 

I've changed the include values in both the searchOptions and detailOptions to include "format" and "smiles", but the result is still the same - I'm just getting the property calculations how do I return the smiles?

Many thanks

Ceara

Hi Ceara,

 

    do you use Oracle JVM?

 

Gabor

 

Hi Gabor

In my environment I'm using this jdk:-

jdk1.6.0_45

Kind regards

Ceara

Hi Ceara,

 

   from "jdk1.6.0_45" string it is not clear for me whether your installation is a jdk or openjdk (openjdk is the default under linux). I will check this anyway and update you about the results.

Hi Gabor

it's a donwloaded & installed JDK not a default linux one.

Kind regards

Ceara

Hi Ceara,

   For image generation we use Graphics library of Java which needs X11 even if we do not have any GUI. We recommend to install a xvfb ("fake X11"). In parallel we investigate this issue in details.

Please, let me know whether this workaround helps or not!

 

Gabor

Hi Ceara,

 

   We cannot reproduce: on a plain Ubuntu 12.04.3 LTS server, tomcat 7.0.47 / oracle jdk 1.6.0_45. (we also removed all x11 libs by "sudo apt-get autoremove libx11-6").

 

Gabor

Can you help us to reproduce by sending us further config information by e-mail? 

Startup message of the tomcat may be valuable (JAVA_HOME), installed packages and linux version. Have you modified the query parameter payload in the example?

 

Gabor

For image generation we use Graphics library of Java which needs X11 even if we do not have any GUI. We recommend to install a xvfb ("fake X11"). In parallel we investigate this issue in details.

________________________

asad