Api v2

New names and organization for version 2 of the opentree api.

These changes depend on some recent db structural changes introduced by taxomachine (already merged to master) which will necessitate a db update for oti. I have pushed an updated database to devapi and re-indexed the studies there as well.

@jar398, @jimallman, would you review this?  
Ugh. I expect it's because of the way the indexing was performed initially.
pg_719 is the first study to be indexed and it probably got screwed up
somehow. It would be nice not to have to re-build the entire db. We just
need to remove the study and then I expect indexing will proceed as
planned. I will think about this...

On Wed, Sep 10, 2014 at 10:33 PM, Jim Allman <notifications@github.com>
wrote:

> In TESTS.md:
>
> > @@ -0,0 +1,65 @@
> > +Currently, there are no automated test procedures for OTI. You can however, fairly thoroughly test the performance manually. Run the following command to index the current phylesystem repo on devapi.opentreeoflife.org:
> > +
> > +```bash
> > +./index_current_repo.py http://devapi.opentreeoflife.org/oti http://devapi.opentreeoflife.org/api
>
> @chinchliff <https://github.com/chinchliff>: Oddly, I'm getting an error
> on exactly one study, *pg_719* (all the others are indexed properly):
>
> Indexing http://devapi.opentreeoflife.org/api/ study pg_719 from http://devapi.opentreeoflife.org/api/default/v1/study/pg_719.json
> Calling "http://devapi.opentreeoflife.org/oti/ext/studies/graphdb/index_studies" with data="{'urls': ['http://devapi.opentreeoflife.org/api/default/v1/study/pg_719.json']}"
>
> Indexing failed for URL "http://devapi.opentreeoflife.org/api/default/v1/study/pg_719.json", study http://devapi.opentreeoflife.org/api/default/v1/study/pg_719.json. Message = "More than one hit found for ot:studyId == 719. The database is probably corrupt."
>
> Any chance this is confused by the presence of another "719" study? But I
> don't see a *ot_719*... at least not in the GitHub repo (will check the
> API server's "local" repo next).
>
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