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[bioontology-support] looking for the right BioPortal version

Vyacheslav Zholudev vyacheslav.zholudev at gmail.com
Thu Sep 9 06:48:38 PDT 2010


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






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