Error occur during Gene Signature creation

[Jack Ow]

Dear Support team,

  I've downloaded the transmart 1.2.4 ova and installed them onto my VM. At the moment, I'm not able to go past the step 2 of New Gene Signature creation. It shows "An error has occurred" when I pressed Next button in the wizard. There is an error in the transmart.log. However, the transmart in BT do not have this problem. Kindly please help.

 

03-02-2016 16:22:06,356 ERROR GrailsExceptionResolver - NullPointerException occurred when processing request: [POST] /transmart/geneSignature/index

Cannot get property 'id' on null object. Stacktrace follows:

org.codehaus.groovy.grails.web.pages.exceptions.GroovyPagesException: Error processing GroovyPageView: Error executing tag <g:form>: Error executing tag <g:select>: Cannot get property 'id' on null object

        at grails.plugin.springsecurity.web.filter.GrailsAnonymousAuthenticationFilter.doFilter(GrailsAnonymousAuthenticationFilter.java:53)

        at grails.plugin.springsecurity.web.authentication.RequestHolderAuthenticationFilter.doFilter(RequestHolderAuthenticationFilter.java:49)

        at grails.plugin.springsecurity.web.authentication.logout.MutableLogoutFilter.doFilter(MutableLogoutFilter.java:82)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

        at java.lang.Thread.run(Thread.java:745)

Caused by: org.codehaus.groovy.grails.web.taglib.exceptions.GrailsTagException: Error executing tag <g:form>: Error executing tag <g:select>: Cannot get property 'id' on null object

        at gsp_transmart_geneSignaturewizard3_gsp$_run_closure2.doCall(gsp_transmart_geneSignaturewizard3_gsp.groovy:183)

        at gsp_transmart_geneSignaturewizard3_gsp.run(gsp_transmart_geneSignaturewizard3_gsp.groovy:186)

        ... 6 more

Caused by: org.codehaus.groovy.grails.web.taglib.exceptions.GrailsTagException: Error executing tag <g:select>: Cannot get property 'id' on null object

        at gsp_transmart_geneSignaturewizard3_gsp$_run_closure2_closure6.doCall(gsp_transmart_geneSignaturewizard3_gsp.groovy:88)

        ... 8 more

Caused by: java.lang.NullPointerException: Cannot get property 'id' on null object

        ... 9 more

Thanks & Regards,
Jack

[keith....@transmartfoundation.org]

Hi Jack, we found a bug in this function during testing of v1.2.5 (due for release at end of Mar) but I don't think it is the same one.  We'll have a look and see if they're related.

[Janneke van der Ploeg]

Hello Jack, 

Just to be sure, there are some fields that are mandatory in the gene signature wizard. 

Can I ask you, what did you use as input in the different screens?

Best, 

Janneke Schoots

www.thehyve.nl
email jan...@thehyve.nl
office +31(0)30 700 9713 
us cell +1 617 869 9256
skype jannekevdp

the hyve

On Wednesday, February 3, 2016 at 10:14:55 AM UTC+1, Jack Ow wrote:

[Jack Ow]

Hi Janneka,

  I've used "Homo Sapiens" in Species and "Other - Other [Other]" in Technology. I have the print screen of the steps and selections in attached a word document "BugError.docx".

Best,
Jack

[Celia Alvarez]

Hello Jack,

Could the format of your file be that error?

You can see it in http://75.124.74.64/transmart/help/adminHelp/default.htm?turl=Documents%2Fgenesignaturesandgenelists.htm

Regards,

Celia

[Jack Ow]

Hi Celia,
 
  No, I did not manage to get to that page. The error occur at page 2 of the New Gene signature list wizard .

Regards,
Jack

[Celia Alvarez]

Hello,

I am working with tranSMART v1.2.rev 2. I have made your example and I haven't obtained that error. Sorry.

Regards,

Celia