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OpenTreeOfLife / oti

indexing service for the OpenTreeOfLife nexson repository
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In v2 we don't seem to be able to search for trees base on include ott IDs. #29

Closed mtholder closed 10 years ago

mtholder commented 10 years ago

I think that in v1 of the api, we could use ot:ot:ottTaxonName and ot:ot:ottId as properties to find a tree that had an otu that was mapped to a particular taxon (or at least I thought that is what was using those properties did).

Now we appear to only be able to search based on focalClade. A response from:

curl -X POST -H "Content-Type":"aplication/json" -H "Accept":"application/json" http://api.opentreeoflife.org/v2/studies/properties

includes

"tree_properties" : [ "ot:studyPublicationReference", "is_deprecated", "ot:focalCladeOTTTaxonName", "ot:studyLastEditor", "ot:comment", "ot:studyModified", "ot:studyLabel", "ot:studyId", "ot:dataDeposit", "ot:studyUploaded", "ot:authorContributed", "ot:studyYear", "ot:focalCladeTaxonName", "ot:tag", "ot:studyPublication", "ot:curatorName", "ot:focalCladeOTTId", "ot:focalClade" ]

Was the dropping of indexing by taxon name intentional? or was did the previous ot:ottTaxonName just doing a search on the focal clade?

It seems useful to be able to search on included taxa names (or ottIds).

chinchliff commented 10 years ago

Thats odd. I agree, we should be able to search trees for mapped taxa. I'll take a look today.

On Wednesday, September 17, 2014, Mark T. Holder notifications@github.com wrote:

I think that in v1 of the api, we could use ot:ot:ottTaxonName and ot:ot:ottId as properties to find a tree that had an otu that was mapped to a particular taxon (or at least I thought that is what was using those properties did).

Now we appear to only be able to search based on focalClade. A response from:

curl -X POST -H "Content-Type":"aplication/json" -H "Accept":"application/json" http://api.opentreeoflife.org/v2/studies/properties

includes

"tree_properties" : [ "ot:studyPublicationReference", "is_deprecated", "ot:focalCladeOTTTaxonName", "ot:studyLastEditor", "ot:comment", "ot:studyModified", "ot:studyLabel", "ot:studyId", "ot:dataDeposit", "ot:studyUploaded", "ot:authorContributed", "ot:studyYear", "ot:focalCladeTaxonName", "ot:tag", "ot:studyPublication", "ot:curatorName", "ot:focalCladeOTTId", "ot:focalClade" ]

Was the dropping of indexing by taxon name intentional? or was did the previous ot:ottTaxonName just doing a search on the focal clade?

It seems useful to be able to search on included taxa names (or ottIds).

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/oti/issues/29.

chinchliff commented 10 years ago

The issue is that the properties service is returning the wrong list. Currently that service is returning the study properties list twice. Taxon name and id properties are available for trees. I've made an edit in https://github.com/OpenTreeOfLife/oti/pull/30, please merge and redeploy the plugin to get the correct list from the properties service.