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[bioontology-support] ssl for bioportal

Paul R Alexander palexander at stanford.edu
Fri Jan 20 15:26:16 PST 2012


Jonathan,

I just tested with an instance of the Virtual Appliance and calling the 
/obs/annotate URL with the apikey parameter in the body should work 
fine. Including it in the URL as a query string parameter results in the 
same error you included below.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 1/20/12 11:54 AM, Holt, Jonathan wrote:
> Trish,
>
>
> I managed to get my VM image up and running using my own SSL.
> My issue really was with configuring VMware to do NAT and to handle 
> the SSL properly thru my apache server.
>
>
> Most services are working, except:
>
>
> my rest service for annotation using my local APIKEY says:
>
> <errorStatus>
> <accessedResource>/obs/annotator</accessedResource>
> <accessDate>2012-01-20 11:20:26.902 PST</accessDate>
> <shortMessage>Forbidden</shortMessage>
> <longMessage>The API key you supplied is invalid. Please visit 
> http://rails-ui.example.org/account to get your API key.</longMessage>
> <errorCode>403</errorCode>
> </errorStatus>
>
>
> at first I used the admin api key, then tried creating a new one. 
> (these are both created locally on my image)
>
>
> I've also restarted the ncbo services and rebooted my image.
>
> Pointing the same script at your rest service hosted at stanford and 
> using the apikey for your server works fine.
>
> my other rest services work fine locally, autocompletion, for instance.
>
>
> Is there some other configuration I need to perform to get the 
> annotation rest service up and running with a locally generated apikey?
>
> I also tried populating the ontology to the annotation service but 
> again it gives the same error above.
>
>
> I haven't been able to find any information on the wiki.
>
>
> Thanks,
>
> Jonathan
>
>
>
>
> .................................
> Jonathan Holt, DO
>
> National Library of Medicine Post-Doctoral Fellow
> Department of Biomedical Informatics
> Vanderbilt University Medical Center
> 2209 Garland Avenue, 400 Eskind Library
> Nashville, TN  37232-8340
> P 650-450-8102
> F 615-936-1427
>
> jonathan.holt at vanderbilt.edu <mailto:jonathan.holt at vanderbilt.edu>
> http://dbmi.mc.vanderbilt.edu/people/holt.html
>
>
>
> On Jan 18, 2012, at 3:43 PM, Trish Whetzel wrote:
>
>> Thanks, I've added that back into the tracker.
>>
>> Trish
>>
>>
>> On Jan 18, 2012, at 1:09 PM, Holt, Jonathan wrote:
>>
>>> since my site is secure with SSL, and the bioportal rest service is 
>>> not the user get a warning (see attached).
>>>
>>> Since I am asking then to put in PHI, I am worried that my users 
>>> will freak out, affecting my adoption and hence my study.
>>>
>>> <Screen Shot 2012-01-18 at 10.32.57 AM.png>
>>>
>>>
>>>
>>> The VM image is great, I was able to convert it to a VMX and got it 
>>> up and running pretty quickly.
>>> Configuring it challenging and time consuming.
>>>
>>>
>>> Thanks,
>>>
>>>
>>> jonathan
>>>
>>>
>>>
>>> .................................
>>> Jonathan Holt, DO
>>>
>>> National Library of Medicine Post-Doctoral Fellow
>>> Department of Biomedical Informatics
>>> Vanderbilt University Medical Center
>>> 2209 Garland Avenue, 400 Eskind Library
>>> Nashville, TN  37232-8340
>>> P 650-450-8102
>>> F 615-936-1427
>>>
>>> jonathan.holt at vanderbilt.edu <mailto:jonathan.holt at vanderbilt.edu>
>>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>>
>>>
>>>
>>> On Jan 18, 2012, at 10:21 AM, Trish Whetzel wrote:
>>>
>>>> Hi Jonathan,
>>>>
>>>> After sending the VM Appliance link, I did not pursue this since it 
>>>> seemed to no longer be an issue. Can you tell me what actions are 
>>>> resulting in warnings of insecure content? I'll re-activate the bug 
>>>> report and add this information.
>>>>
>>>> Also, can you tell me a bit more about why the VM is not working 
>>>> well enough for the tasks you are working on?
>>>>
>>>> Thank you,
>>>> Trish
>>>>
>>>>
>>>> On Jan 17, 2012, at 3:20 PM, Holt, Jonathan wrote:
>>>>
>>>>> Trish,
>>>>>
>>>>> any word on updating the SSL for the bioportal rest service?
>>>>>
>>>>> I would even consider paying for it as I know that Stanford is 
>>>>> hard up for cash these days.
>>>>>
>>>>> I got the virtual image running, but it isn't working as well as I 
>>>>> would have liked.
>>>>>
>>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> jonathan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> .................................
>>>>> Jonathan Holt, DO
>>>>>
>>>>> National Library of Medicine Post-Doctoral Fellow
>>>>> Department of Biomedical Informatics
>>>>> Vanderbilt University Medical Center
>>>>> 2209 Garland Avenue, 400 Eskind Library
>>>>> Nashville, TN  37232-8340
>>>>> P 650-450-8102
>>>>> F 615-936-1427
>>>>>
>>>>> jonathan.holt at vanderbilt.edu <mailto:jonathan.holt at vanderbilt.edu>
>>>>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> http://www.bioontology.org <http://www.bioontology.org/>
>>
>> Now on Twitter: http://twitter.com/#!/bioontology 
>> <http://twitter.com/#%21/bioontology>
>> and "Like" us on Facebook: 
>> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>>
>
>
>
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