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?  

On 9/10/14 5:01 PM, Jim Allman wrote:
>
> In TESTS.md:
>
> > +      "oti_tree_id" : "1495_tree3010"
> > +    } ],
> > +    "ot:studyId" : "1495"
> > +  } ]
> > +}
> > +```
> > +
> > +### Get a list of properties available for searching studies and trees:
> > +
> > +```bash
> > +curl -X POST http://devapi.opentreeolife.org/ext/studies/graphdb/properties
> > +```
> > +
> > +```json
> > +{
> > +  "tree_properties" : [ "ot:studyPublicationReference", "is_deprecated", "ot:focalCladeOTTTaxonName", "ot:studyLastEditor", "ot:studyModified", "ot:studyLabel", "ot:comment", "ot:studyId", "ot:dataDeposit", "ot:authorContributed", "ot:studyUploaded", "ot:studyYear", "ot:focalCladeTaxonName", "ot:tag", "ot:curatorName", "ot:studyPublication", "ot:focalCladeOTTId", "ot:focalClade" ],
>
>     maybe we don't need this property now that curators can delete trees?
>
> FWIW, the current curation app completely ignores the |is_deprecated| 
> property. Also, I don't see any reference to this in the GitHub wiki 
> <https://github.com/OpenTreeOfLife/phylesystem-api/wiki/NexSON> or 
> WikiSpaces wiki <http://opentree.wikispaces.com/NexSON> about NexSON.
>
> It's briefly mentioned in this oti issue 
> <https://github.com/OpenTreeOfLife/oti/issues/9> and it definitely 
> sounds like legacy cruft.
>
> —
>
Yes, it was a work around for studies that could not be deleted before 
phylografter supported deletion.  Agree it's legacy cruft.



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