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[bioontology-support] Can't make "DELETE /provisional_classes/:provisional_class_id" work

Paul R Alexander palexander at stanford.edu
Thu Mar 20 18:31:46 PDT 2014


Thomas,

I just confirmed that this is working. In fact, if I send your exact request I get a valid response (204) and can verify that the label gets updated when I change it. Can you try again and send the response you're getting if it fails?

Paul


----- Original Message -----
From: "Thomas Rodenhausen" <thomas.rodenhausen at gmail.com>
To: "Paul R Alexander" <palexander at stanford.edu>
Cc: "Darren L Weber PhD" <darren.weber at stanford.edu>, support at bioontology.org
Sent: Monday, March 17, 2014 9:35:33 AM
Subject: Re: [bioontology-support] Can't make "DELETE /provisional_classes/:provisional_class_id" work

Paul,,

I'm still having difficulties doing the PATCH using X-HTTP-Method-Override.
Is this supported by now and I'm doing something wrong, or is it still
pending to be deployed?

Thanks


On Tue, Mar 4, 2014 at 11:43 AM, Paul R Alexander
<palexander at stanford.edu>wrote:

> Thomas,
>
> We don't currently support the use of X-HTTP-Method-Override. You may not
> even know you are using it, some libraries like jQuery add this header
> automatically to get around web browser's lack of support for HTTP verbs
> besides GET and POST.
>
> I've implemented support for X-HTTP-Method-Override, though, and it should
> be released this week. Doing the request via a direct HTTP PATCH (outside
> of a browser using curl or via code) should currently work.
>
> Paul
>
>
> On Mar 4, 2014, at 8:28 AM, Thomas Rodenhausen <
> thomas.rodenhausen at gmail.com> wrote:
>
> Hi Darren,
> since the fix has been pushed to production:
>
>  Thanks for asking, the PATCH fix has been pushed to production.
>>
>
> Should it work already? Because it currently doesn't for me, maybe I'm
> still doing something wrong?
> Or if it shouldn't, is it reasonable to assume it will work until March
> 14th?
>
>
>> Can you provide more details on what your doing?
>>
>
> Here's are the API call details:
>
> > POST
> http://data.bioontology.org/provisional_classes/b44a7a00-6751-0131-e6d9-005056010074
> > Accept: application/json
> > Authorization: apikey token={your_token}
> > Content-Type: application/json
> > X-HTTP-Method-Override: PATCH
>
> {"label":"test123","synonym":[],"definition":[],"subclassOf":null,"creator":"
> http://data.bioontology.org/users/thomas.rodenhausen
> ","created":"2014-01-24T10:17:27-08:00","permanentId":null,"noteId":null,"ontology":[],"@id":"
> http://data.bioontology.org/provisional_classes/b44a7a00-6751-0131-e6d9-005056010074
> ","@type":"http://data.bioontology.org/metadata/ProvisionalClass"}
>
> < 500
> < Connection: close
> < Content-Length: 30
> < Content-Type: text/html;charset=utf-8
> < Date: Tue, 04 Mar 2014 16:19:13 GMT
> < Status: 500 Internal Server Error
> < X-Content-Type-Options: nosniff
> < X-Frame-Options: SAMEORIGIN
> < X-Rack-Cache: invalidate, pass
> < X-XSS-Protection: 1; mode=block
> <h1>Internal Server Error</h1>
>
>
> Thanks,
> Thomas
>
>
>
>
>
>
>>
>>
>>
>> On 2/26/14, 9:05 AM, Thomas Rodenhausen wrote:
>>
>> Hi Darren,
>>
>> I noticed that DELETE now works fine.
>> For PATCH I still have the originally reported problem. Is this a known
>> problem or am I maybe missing out on something?
>>
>>
>> On Mon, Jan 27, 2014 at 9:10 AM, Thomas Rodenhausen <
>> thomas.rodenhausen at gmail.com> wrote:
>>
>>> Thanks.
>>>
>>>  Just want to add the issue with PATCH below, which seems to be similar.
>>>
>>>  3 > GET
>>> http://data.bioontology.org/provisional_classes/737af2a0-6751-0131-e6d9-005056010074
>>>  3 > Accept: application/json
>>> 3 > Authorization: apikey token=...
>>>
>>>  4 < 200
>>> 4 < Age: 60
>>> 4 < Cache-Control: public, max-age=60
>>> 4 < Connection: close
>>> 4 < Content-Length: 590
>>> 4 < Content-Type: application/json;charset=utf-8
>>> 4 < Date: Mon, 27 Jan 2014 16:04:24 GMT
>>> 4 < Last-Modified: Fri, 24 Jan 2014 18:17:27 GMT
>>> 4 < Status: 200 OK
>>>  4 < Vary: User-Agent, Accept, Accept-Language, Accept-Encoding,
>>> Authorization, NCBO-Slice
>>>  4 < X-Content-Digest: 44212eef4fe92be0bcc402c637645f5e801d14a8
>>>  4 < X-Content-Type-Options: nosniff
>>> 4 < X-Rack-Cache: stale, valid, store
>>>
>>> {"label":"test2","synonym":[],"definition":[],"subclassOf":null,"creator":"
>>> http://data.bioontology.org/users/thomas.rodenhausen
>>> ","created":"2014-01-24T10:15:38-08:00","permanentId":null,"noteId":null,"ontology":[],"@id":"
>>> http://data.bioontology.org/provisional_classes/737af2a0-6751-0131-e6d9-005056010074
>>> ","@type":"http://data.bioontology.org/metadata/ProvisionalClass
>>> ","@context":{"@vocab":"http://data.bioontology.org/metadata/
>>> ","creator":{"@id":"http://data.bioontology.org/metadata/User
>>> ","@type":"@id"},"ontology":{"@id":"
>>> http://data.bioontology.org/metadata/Ontology","@type":"@id"}}}
>>>
>>>  5 > POST
>>> http://data.bioontology.org/provisional_classes/737af2a0-6751-0131-e6d9-005056010074
>>> 5 > Accept: application/json
>>> 5 > Authorization: apikey token=...
>>> 5 > Content-Type: application/json
>>> 5 > X-HTTP-Method-Override: PATCH
>>>
>>> {"label":"test3","synonym":[],"definition":[],"subclassOf":null,"creator":"
>>> http://data.bioontology.org/users/thomas.rodenhausen
>>> ","created":"2014-01-24T10:15:38-08:00","permanentId":null,"noteId":null,"ontology":[],"@id":"
>>> http://data.bioontology.org/provisional_classes/737af2a0-6751-0131-e6d9-005056010074
>>> ","@type":"http://data.bioontology.org/metadata/ProvisionalClass"}
>>>
>>>  6 < 500
>>> 6 < Connection: close
>>> 6 < Content-Length: 30
>>> 6 < Content-Type: text/html;charset=utf-8
>>> 6 < Date: Mon, 27 Jan 2014 16:04:24 GMT
>>>  6 < Status: 500 Internal Server Error
>>> 6 < X-Content-Type-Options: nosniff
>>> 6 < X-Frame-Options: SAMEORIGIN
>>> 6 < X-Rack-Cache: invalidate, pass
>>> 6 < X-XSS-Protection: 1; mode=block
>>> <h1>Internal Server Error</h1>
>>>
>>>
>>> On Thu, Jan 23, 2014 at 1:47 PM, Darren Weber <dlweber at stanford.edu>wrote:
>>>
>>>>
>>>> Hi Thomas,
>>>>
>>>> A fix for this should be available in the next release.  Thanks for
>>>> reporting the bug.
>>>>
>>>> Take care,
>>>> Darren
>>>>
>>>> PS, details of the fix are at
>>>> https://github.com/ncbo/ontologies_api/commit/0a0dddbfe7aec2db3d8c291bac5a1508351bea1c
>>>>
>>>>
>>>>
>>>> On 1/23/14, 11:07 AM, Thomas Rodenhausen wrote:
>>>>
>>>>  I had tried this before, it results in the same HTTP 500, see below.
>>>> Also note that a GET for the URI returns a 404, that's why I had tried
>>>> only the last part of the URI, which works at least for GET.
>>>>
>>>>  3 > DELETE
>>>> http://data.bioontology.org/provisional_classes/http%3A%2F%2Fdata.bioontology.org%2Fprovisional_classes%2F4e3b6790-65eb-0131-7e69-005056010073
>>>> 3 > Accept: application/json
>>>> 3 > Authorization: apikey token=...
>>>>
>>>>  4 < 500
>>>> 4 < Connection: close
>>>> 4 < Content-Length: 30
>>>> 4 < Content-Type: text/html;charset=utf-8
>>>> 4 < Date: Thu, 23 Jan 2014 19:03:36 GMT
>>>> 4 < Status: 500 Internal Server Error
>>>> 4 < X-Content-Type-Options: nosniff
>>>> 4 < X-Frame-Options: SAMEORIGIN
>>>> 4 < X-Rack-Cache: invalidate, pass
>>>> 4 < X-XSS-Protection: 1; mode=block
>>>> <h1>Internal Server Error</h1>
>>>>
>>>>  1 > GET
>>>> http://data.bioontology.org/provisional_classes/http%3A%2F%2Fdata.bioontology.org%2Fprovisional_classes%2F4e3b6790-65eb-0131-7e69-005056010073
>>>> 1 > Accept: application/json
>>>> 1 > Authorization: apikey token=...
>>>>
>>>>  2 < 404
>>>> 2 < Age: 0
>>>> 2 < Cache-Control: public, max-age=60
>>>> 2 < Connection: close
>>>> 2 < Content-Length: 140
>>>> 2 < Content-Type: application/json;charset=utf-8
>>>> 2 < Date: Thu, 23 Jan 2014 19:05:27 GMT
>>>> 2 < Last-Modified: Wed, 22 Jan 2014 23:38:27 GMT
>>>> 2 < Status: 404 Not Found
>>>> 2 < Vary: User-Agent, Accept, Accept-Language, Accept-Encoding,
>>>> Authorization, NCBO-Slice
>>>> 2 < X-Content-Digest: 2d9b8c551b17ead68f6a51e042464baab321c87a
>>>> 2 < X-Content-Type-Options: nosniff
>>>> 2 < X-Rack-Cache: miss, store
>>>> {"errors":["Provisional class
>>>> http://data.bioontology.org/provisional_classes/4e3b6790-65eb-0131-7e69-005056010073not found"],"status":404}
>>>>
>>>>
>>>>
>>>> On Thu, Jan 23, 2014 at 11:58 AM, Darren Weber <dlweber at stanford.edu>wrote:
>>>>
>>>>>
>>>>> Hi Thomas,
>>>>>
>>>>> Looking at the documentation at
>>>>> http://data.bioontology.org/documentation#ProvisionalClass
>>>>>
>>>>> There is a DELETE method available.  The URI takes the form:
>>>>>
>>>>> {service_endpoint}/{resource_id}
>>>>>
>>>>> where {resource_id} is a full URI; translating for this example we get:
>>>>>
>>>>> service_endpoint = http://data.bioontology.org/provisional_classes/
>>>>> resource_id =
>>>>> http://data.bioontology.org/provisional_classes/4e3b6790-65eb-0131-7e69-005056010073
>>>>> resource_id_encoded = http%3A%2F%2Fdata.bioontology.org<http://2fdata.bioontology.org/>
>>>>> %2Fprovisional_classes%2F4e3b6790-65eb-0131-7e69-005056010073
>>>>>
>>>>> (Encoding the resource_id can be done with various tools; for this
>>>>> example, I've used http://meyerweb.com/eric/tools/dencoder/.)
>>>>>
>>>>> So, the full URI for the DELETE looks like this:
>>>>>
>>>>>
>>>>> http://data.bioontology.org/provisional_classes/http%3A%2F%2Fdata.bioontology.org%2Fprovisional_classes%2F4e3b6790-65eb-0131-7e69-005056010073
>>>>>
>>>>> Hope that helps,
>>>>>
>>>>> Darren
>>>>>
>>>>>
>>>>>
>>>>> On 1/23/14, 8:49 AM, Thomas Rodenhausen wrote:
>>>>>
>>>>>   Hi,
>>>>>
>>>>>  see below I can't make this work, although a GET on the same URI
>>>>> does. Can you tell me what I am doing wrong?
>>>>>
>>>>>  Also tried
>>>>> - paths including the colon
>>>>> - the full blown id string e.g.
>>>>> http://data.bioontology.org/provisional_classes/4e3b6790-65eb-0131-7e69-005056010073
>>>>> - apikey as query string instead of authorization header
>>>>>
>>>>>  Thank you
>>>>>
>>>>>
>>>>>  1 > GET
>>>>> http://data.bioontology.org/provisional_classes/4e3b6790-65eb-0131-7e69-005056010073
>>>>> 1 > Accept: application/json
>>>>> 1 > Authorization: apikey token=...
>>>>>
>>>>>  2 < 200
>>>>> 2 < Age: 60
>>>>> 2 < Cache-Control: public, max-age=60
>>>>> 2 < Connection: close
>>>>> 2 < Content-Length: 589
>>>>> 2 < Content-Type: application/json;charset=utf-8
>>>>> 2 < Date: Thu, 23 Jan 2014 16:18:58 GMT
>>>>> 2 < Last-Modified: Wed, 22 Jan 2014 23:38:27 GMT
>>>>> 2 < Status: 200 OK
>>>>> 2 < Vary: User-Agent, Accept, Accept-Language, Accept-Encoding,
>>>>> Authorization, NCBO-Slice
>>>>> 2 < X-Content-Digest: 07c5d1cec4fc52329ff7371eebe8e07cfa25931b
>>>>> 2 < X-Content-Type-Options: nosniff
>>>>> 2 < X-Rack-Cache: stale, valid, store
>>>>>
>>>>> {"label":"test","synonym":[],"definition":[],"subclassOf":null,"creator":"
>>>>> http://data.bioontology.org/users/thomas.rodenhausen
>>>>> ","created":"2014-01-22T15:31:56-08:00","permanentId":null,"noteId":null,"ontology":[],"@id":"
>>>>> http://data.bioontology.org/provisional_classes/4e3b6790-65eb-0131-7e69-005056010073
>>>>> ","@type":"http://data.bioontology.org/metadata/ProvisionalClass
>>>>> ","@context":{"@vocab":"http://data.bioontology.org/metadata/
>>>>> ","creator":{"@id":"http://data.bioontology.org/metadata/User
>>>>> ","@type":"@id"},"ontology":{"@id":"
>>>>> http://data.bioontology.org/metadata/Ontology","@type":"@id"}}}
>>>>>
>>>>>  3 > DELETE
>>>>> http://data.bioontology.org/provisional_classes/4e3b6790-65eb-0131-7e69-005056010073
>>>>> 3 > Accept: application/json
>>>>> 3 > Authorization: apikey token=...
>>>>>
>>>>>  4 < 500
>>>>> 4 < Connection: close
>>>>> 4 < Content-Length: 30
>>>>> 4 < Content-Type: text/html;charset=utf-8
>>>>> 4 < Date: Thu, 23 Jan 2014 16:20:35 GMT
>>>>> 4 < Status: 500 Internal Server Error
>>>>> 4 < X-Content-Type-Options: nosniff
>>>>> 4 < X-Frame-Options: SAMEORIGIN
>>>>> 4 < X-Rack-Cache: invalidate, pass
>>>>> 4 < X-XSS-Protection: 1; mode=block
>>>>> <h1>Internal Server Error</h1>
>>>>>
>>>>>
>>>>>   _______________________________________________
>>>>> bioontology-support mailing listbioontology-support at lists.stanford.eduhttps://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
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