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[bioontology-support] looking for the right BioPortal version

Vyacheslav Zholudev vyacheslav.zholudev at gmail.com
Thu Sep 9 11:58:44 PDT 2010


Thanks a lot, Paul!

Vyacheslav

On Sep 9, 2010, at 8:47 PM, Paul R Alexander wrote:

> The UI tag that was released around the same time was 1021. If that doesn't work, I would try 1020. Sorry I don't have more exact information but our UI tags are not synced with the Core tags.
> 
> https://bmir-gforge.stanford.edu/svn/bioportalui/tags/1021
> 
> The UI does have tags, though we don't really use branches for anything.
> 
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 
> 
> On 9/9/10 6:48 AM, Vyacheslav Zholudev wrote:
>> 
>> I would add a bit to the Immanuel's request.
>> What bioportal UI repository revision is compatible with the tag 1017 of the bioportal core? It seems there are no tags and branches in the bioportal ui repository.
>> 
>> Thanks a lot for your help,
>> Vyacheslav
>> 
>> 
>> On Sep 9, 2010, at 3:13 PM, Immanuel Normann wrote:
>> 
>>> Paul,
>>> 
>>> According to our developer we have some problem with GUI after the
>>> upgarde from tag/1014 to tag/1017:
>>> 
>>>> upgrade of the bioportal core from tag 1014 to tag 1017 itself went
>>>> smoothly. However, the GUI doesn't work right now.
>>>> For this I need the revision of bioportal gui that is compatible with
>>>> the tag 1017 of the bioportal core.
>>> Could you please help us with this as soon as possible?! Otherwise we
>>> cannot offer our clients the GUI to our repository.
>>> 
>>> Thanks in advance,
>>> 
>>> Immanuel 
>>> 
>>> Am Mittwoch, den 08.09.2010, 18:31 -0700 schrieb Paul R Alexander:
>>>> Immanuel,
>>>> 
>>>> Sorry for not getting back to you sooner. Unfortunately the
>>>> information you're looking for covers a version of BioPortal that is
>>>> more than a year old so it was a little difficult to verify the
>>>> specifics for the metadata rollout. However, I've been able to confirm
>>>> that you should be able to run tag 1017 without upgrading to the new
>>>> metadata ontology.
>>>> 
>>>> When using SVN best practices revision numbers are separate from
>>>> releases (tags), so you won't be able to correlate them. In fact, a
>>>> particular tag could have a number of revisions added as bugs are
>>>> corrected or fine-tuning is done.
>>>> 
>>>> I looked into your report of problems with the HTTP PUT and DELETE
>>>> methods. We do support these, in fact it's exactly how the reads and
>>>> writes to our persistent store work, but it does look like the "raw"
>>>> HTTP methods weren't being detected properly. Most of our calls use
>>>> "tunneled" methods where you add a parameter to the query string to
>>>> indicate which method you're using. For example, adding "method=PUT"
>>>> when doing a POST will allow a PUT method to be detected. This is to
>>>> support clients that don't implement the HTTP methods fully (most
>>>> browsers support GET and POST only).
>>>> 
>>>> I've fixed the improper detection
>>>> in /bioportal/src/java/org/ncbo/stanford/view/rest/restlet/AbstractBaseRestlet.java rev2735.
>>>> 
>>>> Here's a patch (this is still relatively untested on our end):
>>>> Index: AbstractBaseRestlet.java
>>>> ===================================================================
>>>> --- AbstractBaseRestlet.java    (revision 2734)
>>>> +++ AbstractBaseRestlet.java    (revision 2735)
>>>> @@ -57,11 +57,9 @@
>>>>                     deleteRequest(request, response);
>>>>                 }
>>>>             }
>>>> -        } else if (request.getMethod().equals(
>>>> -                MessageUtils.getMessage("http.put"))) {
>>>> +        } else if (request.getMethod().equals(Method.PUT)) {
>>>>             putRequest(request, response);
>>>> -        } else if (request.getMethod().equals(
>>>> -                MessageUtils.getMessage("http.delete"))) {
>>>> +        } else if (request.getMethod().equals(Method.DELETE)) {
>>>>             deleteRequest(request, response);
>>>>         }
>>>>     }
>>>> 
>>>> If there's anything else I can help out with, please let me know.
>>>> We're happy to accept bug reports, you can submit them at our tracker:
>>>> https://bmir-gforge.stanford.edu/gf/project/bioportal_core/tracker/?action=TrackerItemBrowse&tracker_id=103
>>>> 
>>>> Paul R Alexander
>>>> Web / UI Developer
>>>> NCBO BioPortal
>>>> Stanford Center for Biomedical Informatics Research
>>>> 
>>>> 
>>>> On 9/8/10 4:23 AM, Immanuel Normann wrote: 
>>>>> Dear BioPortal support team,
>>>>> 
>>>>> We have installed an instance of BioPortal to store ontologies for our
>>>>> own project: http://ontologies.informatik.uni-bremen.de
>>>>> 
>>>>> Unfortunately, the BioPortal revision we have taken (revision 1875,
>>>>> path /tags/1014) turned out to be buggy. We considered to upgrade to
>>>>> BioPortal 2.5, but deferred that for three reason: 1) the content
>>>>> migration seems to be not that straightforward (according to a mail by
>>>>> Paul Alexander) and thus currently to risky for us. 2) The REST API has
>>>>> changed in BioPortal 2.5, but our partners rely on the REST API of our
>>>>> current BioPortal. 3) Our main developer, Slava, who takes care for the
>>>>> BioPortal installation figured out that some (for us fundamental) bug
>>>>> apparently hasn't been fixed in the latest version: RESTful DELETE and
>>>>> PUT does not work.
>>>>> 
>>>>> Slava says that to fix this bug is very easy and so he did it on a local
>>>>> installation. But there are some other bugs that we haven't yet
>>>>> identified. We came to the decision that the best solution for us is to
>>>>> check out the stablest BioPortal revision that is still close enough to
>>>>> our current revision (1875, /tags/1014) so that we do not need to
>>>>> migrate content and that uses still the same REST API.
>>>>> 
>>>>> Our problem is that we cannot figure out from the revision logs which
>>>>> revision satisfies our needs. Appearently, it is even unclear to figure
>>>>> out to what release a certain revision belongs.
>>>>> 
>>>>> We would be very grateful for any clarification!
>>>>> 
>>>>> Thanks in advance,
>>>>> Immanuel Normann
>>>>> 
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> bioontology-support at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>> Best,
>> Vyacheslav
>> 
>> 
>> 

Best,
Vyacheslav



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