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[bioontology-support] Visualization tab

Erick Antezana erick.antezana at gmail.com
Wed Feb 27 01:05:43 PST 2013


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 (
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)"

cheers,
Erick

On 27 February 2013 10:01, Erick Antezana <erick.antezana at gmail.com> wrote:

> Hi Eric,
>
> thanks for clarifying this "issue".
>
> cheers,
> Erick
>
>
> On 22 February 2013 18:31, Eric Verbeek <eric.l.verbeek at gmail.com> 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 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*
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *Stanford instance *
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>>
>>
>>
>
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