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[bioontology-support] looking for the right BioPortal version

Paul R Alexander palexander at stanford.edu
Wed Sep 8 18:31:17 PDT 2010


  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 <http://bioportal.bioontology.org>
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
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