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[bioontology-support] ssl for bioportal

Paul R Alexander palexander at stanford.edu
Fri Jan 27 14:54:06 PST 2012


Jonathan,

The fix is to include the apikey parameter in the body of the request 
like you would for other parameters on an HTTP POST.

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


On 1/27/12 2:47 PM, Holt, Jonathan wrote:
> great.  is there a fix?
>
>
> 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 20, 2012, at FriJan205:26 PM, Paul R Alexander wrote:
>
>> 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
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
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