Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] looking for the right BioPortal version

Paul R Alexander palexander at
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.

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/ rev2735.
>>> Here's a patch (this is still relatively untested on our end):
>>> Index:
>>> ===================================================================
>>> ---    (revision 2734)
>>> +++    (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:
>>> 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:
>>>> 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
> Best,
> Vyacheslav
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list