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

Thomas Rodenhausen thomas.rodenhausen at gmail.com
Tue Mar 4 08:28:24 PST 2014


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
>>>> %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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