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[bioontology-support] Visualization tab

Eric Verbeek eric.l.verbeek at
Wed Feb 27 09:34:51 PST 2013

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 

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, 
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:
> Eric,
> 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)"
> cheers,
> Erick
> On 27 February 2013 10:01, Erick Antezana <erick.antezana at 
> <mailto:erick.antezana at>> wrote:
>     Hi Eric,
>     thanks for clarifying this "issue".
>     cheers,
>     Erick
>     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.
>         Cheers,
>         ~Eric
>         On 22/02/2013 1:47 AM, Erick Antezana wrote:
>>         Hi,
>>         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?
>>         cheers,
>>         Erick
>>         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.
>>             ~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
>>>             <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
>>>             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_*
>>>             *_Stanford instance _*
>>             _______________________________________________
>>             bioontology-support mailing list
>>             bioontology-support at
>>             <mailto:bioontology-support at>

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