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[bioontology-support] Visualization tab

Erick Antezana erick.antezana at gmail.com
Fri Feb 22 01:50:54 PST 2013


Hi,

I was getting a similar error message which could be by-passed by using the
IP address of the machine... bizarre... our sys admin was not able to find
why the visualisation works perfectly with the IP address (
http://10.3.156.5/ontologies/10013/?p=terms&conceptid=TO:0000017) and not
with the alias (
http://vm-ncboportal/ontologies/10013/?p=terms&conceptid=TO:0000017)

any suggestions?

cheers,
Erick

On 7 February 2013 21:26, Madani,Sina <AHMadani at mdanderson.org> wrote:

>  ** **
>
> I am getting this error now after reverting it back to the previous build.
> ****
>
> We can wait for the new version of Appliance if it’s been fixed in the
> coming one….****
>
> ** **
>
> Thanks!****
>
> Sina****
>
> ** **
>
> ** **
>
> ****
>
> ** **
>
> *From:* Paul R Alexander [mailto:palexander at stanford.edu]
> *Sent:* Thursday, February 07, 2013 1:35 PM
> *To:* Madani,Sina
> *Cc:* Eric Verbeek; Ray Fergerson; Riben,Michael Warren;
> support at bioontology.org
>
> *Subject:* Re: [bioontology-support] Visualization tab****
>
>  ** **
>
> Sorry, deployui is the correct one.****
>
> ** **
>
> Paul****
>
> ** **
>
> ** **
>
> On Feb 7, 2013, at 11:23 AM, "Madani,Sina" <AHMadani at mdanderson.org>
> wrote:****
>
>
>
> ****
>
> Thank you Paul & Eric****
>
> Bpdeploy offers me these options though….****
>
>  ****
>
> <image001.png>****
>
>  ****
>
> *From:* Paul R Alexander [mailto:palexander at stanford.edu]
> *Sent:* Thursday, February 07, 2013 12:58 PM
> *To:* Eric Verbeek
> *Cc:* Ray Fergerson; Madani,Sina; Riben,Michael Warren;
> support at bioontology.org
> *Subject:* Re: [bioontology-support] Visualization tab****
>
>  ****
>
> The new visualization code was accidentally included in the last Appliance
> release. The code won't work because it will be connecting to the main
> BioPortal REST services, not the REST services on the local machine.****
>
>  ****
>
> If you log in to the Appliance as root and run `bpdeploy buildui` it will
> fix the problem by reverting to the older Flex visualization widgets.****
>
>  ****
>
> Paul****
>
>  ****
>
>  ****
>
> On Feb 7, 2013, at 10:49 AM, Eric Verbeek <eric.l.verbeek at gmail.com>
> wrote:****
>
>
>
>
> ****
>
> Hi Sina and Ray,
>
> The visualization is in JavaScript, and makes calls to the REST services
> from there to the public BioPortal servers. I haven't worked with the VM
> yet. Does the VM have internet access? Does the configuration for BioPortal
> in the VM have different connectivity paths or requirements to the REST
> servers than the visualization uses?
>
> Sina, could you check a JavaScript error log or developer console for
> errors? If you are using Chrome, you can access it with Ctrl-Shift-J, or
> through Chrome's menu (the one with three stacked horizontal lines, on all
> OSes). There might be some hints for me in the JS errors.
>
> ~Eric****
>
> On 07/02/2013 10:32 AM, Ray Fergerson wrote:****
>
>  Sina,****
>
>  ****
>
> Copying Eric (the visualization guy). I don’t understand this at all. I
> can confirm that difference between what you see in your VM and what we
> see. I believe that we are all pointing that the same instance of the
> visualization software though.****
>
>  ****
>
> Eric, any idea why this is happening? What would cause this visualization
> configuration item to not show up?****
>
>  ****
>
> Ray****
>
>  ****
>
> *From:* bioontology-support-bounces at lists.stanford.edu [
> mailto:bioontology-support-bounces at lists.stanford.edu<bioontology-support-bounces at lists.stanford.edu>
> ] *On Behalf Of *Madani,Sina
> *Sent:* Thursday, February 07, 2013 5:56 AM
> *To:* support at bioontology.org
> *Cc:* Riben,Michael Warren
> *Subject:* [bioontology-support] Visualization tab****
>
>  ****
>
> Hi,****
>
> We noticed that the visualization widget of our local instance is not
> working properly. Comparing to your environment, apparently the “Show
> SNOMED Clinical term” from the drop down configuration menu is missing in
> our instance’s UI.****
>
> Is there a configuration file that I can set this in order to
> operationalize the Visualization tab?****
>
>  ****
>
> Thanks!****
>
> Sina****
>
>  ****
>
>  ****
>
>  ****
>
> *Our local instance*****
>
> <Mail Attachment.jpeg>****
>
>  ****
>
>  ****
>
>  ****
>
> *Stanford instance*****
>
>  ****
>
> <Mail Attachment.png>****
>
>   ****
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support****
>
>  ****
>
> ** **
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
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