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[bioontology-support] Visualization tab

Madani,Sina AHMadani at
Thu Feb 28 06:24:50 PST 2013

Thank you Paul,

Do we need to do this change in the upcoming Bioportal appliance release (March?) as well ?


From: Paul R Alexander [mailto:palexander at]
Sent: Wednesday, February 27, 2013 5:25 PM
To: Eric Verbeek
Cc: Erick Antezana; Ray Fergerson; Madani,Sina; Riben,Michael Warren; support at
Subject: Re: [bioontology-support] Visualization tab

Sorry everyone, I didn't connect that this was an issue with the Flex-based widgets. The widgets use an ip address that we detect in the config file as it is the most reliable method for discovering the machine's location. However, because of the same origin policy in the browser, accessing the UI on a different domain/ip as the REST service will cause widgets to fail.

If you want to override this behavior, you can modify the file 'bioportal_config.rb' to hardcode the domain. On line 19, change:
$LOCAL_IP = local_ip
$LOCAL_IP = "<>"
where<> is actually the domain you are using.

The file is located in /srv/ncbo/rails/BioPortal/current/config. This change will need to be done each time you update the UI code.

I also don't really have a way to test this, so please let me know if it doesn't work.


On Feb 27, 2013, at 9:34 AM, Eric Verbeek <eric.l.verbeek at<mailto:eric.l.verbeek at>> wrote:

Hi Erick, Sina, and Paul,

I was hoping that someone else had an idea and had shared it already, as I don't have experience with the virtual appliance. Maybe I can come up with something. Sorry for this delay, Erick and Sina.

Sina, you were directed to revert to using the older Flex based visualization. That version of the visualization predates me by a little over 2 years, and I have no experience in Flex/Flash development. Paul said that the reason Sina needed to revert to the Flex visualization was to allow because the older visualization was set up to access the same data source URL as used in the virtual appliance, wheras the current version accesses the public servers for data. The current Java & JS based visualization uses different REST calls that work across different domains, whereas the Flex version uses REST calls that must resolve to the same domain that the application is served out of, if I understand this as applied to Flash.

1) Paul and Erick, so that you can use the Java/JS (rather than Flex/Flash) version of the visualization, is there a way we can think of to tell the JS ajax calls to go to the VM appliance local machine URL? What cue or tip would there be that we are running in the virtual appliance?

2) Or would it be possible to set up a redirection at a different layer so that calls to bioportla REST are redirected to the local machine? Something like seen here: . The REST URLs start like so: ""<>. There may be calls to ""<> as well, if accessing an older version. Perhaps the sysadmin could help out with this possible solution.

3) If we cannot redirect the new version of the visualization within the appliance, I'm not sure about this problem. It probably has to do wit the REST calls counting as cross-domain when access http:vm-ncboportal<http://vm-ncboportal/>, but counting as within domain for the IP based URL. Looking back, Sina emailed a screenshot with an error that mentions the crossdomain.xml. I have re-attached that here. Those are different URLs than you mention below. You could try creating/editing your crossdomain.xml file at the server with the IP specified in any error you see that matches the screenshot error. Your sysadmin should be able to help with this, and perhaps adding URLs that result in cross domain errors to the crossdomain.xml file.

Again, I apologize for not offering advice earlier. I was not sure, and didn't want to clutter the thread with bad advice. Let's keep going and try to figure out this problem.

On 27/02/2013 1:05 AM, Erick Antezana wrote:

do you have any suggestion on where to look at for the issue I mentioned on this thread (IP address: working / name: not working)?

"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)"

On 27 February 2013 10:01, Erick Antezana <erick.antezana at<mailto:erick.antezana at>> wrote:
Hi Eric,

thanks for clarifying this "issue".


On 22 February 2013 18:31, Eric Verbeek <eric.l.verbeek at<mailto:eric.l.verbeek at>> wrote:
Hi Erick,

The calls that the visualization makes are passing very sparse information; concept ids, ontology ids. Nothing large or detailed is sent out. I would suggest that you satisfy your users' concerns by looking at the relevant pieces of javascript, but it's all been generated from Java by GWT, and is not very readable.

All of the calls are for BioPortal REST services, and all are tring to fetch additional data (such as mappings, of cocnept details) from identifiers such as concept and ontology ids. I don't think there is any need for concern about data or ontology information leaking out.


On 22/02/2013 1:47 AM, Erick Antezana wrote:

does it mean that my local bioportal (appliance) is sending some data so that the visualisation could be rendered? My users are a bit paranoid with their data/ontologies. This could be an issue...if so, is there a way to close/block it without loosing functionalities?


On 7 February 2013 19:49, 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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bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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