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[bioontology-support] looking for the right BioPortal version

Paul R Alexander palexander at stanford.edu
Thu Sep 9 11:47:35 PDT 2010


  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 <http://bioportal.bioontology.org>
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
>
>
>
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