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[bioontology-support] Visualization tab

Madani,Sina AHMadani at
Fri Feb 22 05:13:56 PST 2013

I just tried IP instead of the domain name too and visualization is working


From: Erick Antezana [mailto:erick.antezana at]
Sent: Friday, February 22, 2013 3:51 AM
To: Madani,Sina
Cc: Paul R Alexander; Ray Fergerson; support at; Eric Verbeek; Riben,Michael Warren
Subject: Re: [bioontology-support] Visualization tab


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 ( and not with the alias (http://vm-ncboportal/ontologies/10013/?p=terms&conceptid=TO:0000017)

any suggestions?


On 7 February 2013 21:26, Madani,Sina <AHMadani at<mailto:AHMadani at>> 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....


[cid:image001.png at 01CE10CC.2AE50CF0]

From: Paul R Alexander [mailto:palexander at<mailto:palexander at>]
Sent: Thursday, February 07, 2013 1:35 PM
To: Madani,Sina
Cc: Eric Verbeek; Ray Fergerson; Riben,Michael Warren; support at<mailto:support at>

Subject: Re: [bioontology-support] Visualization tab

Sorry, deployui is the correct one.


On Feb 7, 2013, at 11:23 AM, "Madani,Sina" <AHMadani at<mailto:AHMadani at>> wrote:

Thank you Paul & Eric
Bpdeploy offers me these options though....


From: Paul R Alexander [mailto:palexander@<mailto:palexander@><>]
Sent: Thursday, February 07, 2013 12:58 PM
To: Eric Verbeek
Cc: Ray Fergerson; Madani,Sina; Riben,Michael Warren; support at<mailto:support at>
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.


On Feb 7, 2013, at 10:49 AM, Eric Verbeek <eric.l.verbeek at<mailto:eric.l.verbeek at>> 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.

On 07/02/2013 10:32 AM, Ray Fergerson wrote:

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?


From: bioontology-support-bounces at<mailto:bioontology-support-bounces at> [mailto:bioontology-support-bounces at] On Behalf Of Madani,Sina
Sent: Thursday, February 07, 2013 5:56 AM
To: support at<mailto:support at>
Cc: Riben,Michael Warren
Subject: [bioontology-support] Visualization tab

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?


Our local instance
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Stanford instance

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