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Created July 22, 2014 18:45
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Working API call to update a study
curl'http://devapi.opentreeoflife.org/phylesystem/v1/study/pg_2845?author_name=Jim+Allman&author_email=jim%40ibang.com&auth_token=de4916f3b38a737c2e90310db43df17760cb252b&starting_commit_SHA=2a442e80680e8785b1001a9e72d17bf234bec9d0&commit_msg='
-X PUT
-H 'Origin: http://devtree.opentreeoflife.org'
-H 'Accept-Encoding: gzip,deflate,sdch'
-H 'Accept-Language: en-US,en;q=0.8'
-H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/35.0.1916.153 Safari/537.36'
-H 'Content-Type: application/json; charset=UTF-8'
-H 'Accept: application/json, text/javascript, */*; q=0.01'
-H 'Referer: http://devtree.opentreeoflife.org/curator/study/edit/pg_2845'
-H 'Connection: keep-alive'
--compressed
--data-binary $'{"nexml":{"^ot:messages":{"message":[]},"^ot:studyPublicationReference":"Pasquet, Eric, F. Keith Barker, Jochen Martens, Annie Tillier, Corinne Cruaud, Alice Cibois. 2014. Evolution within the nuthatches (Sittidae: Aves, Passeriformes): molecular phylogeny, biogeography, and ecological perspectives. Journal of Ornithology","^ot:candidateTreeForSynthesis":[],"^ot:focalCladeOTTTaxonName":"Sittidae","@xmlns":{"xsd":"http://www.w3.org/2001/XMLSchema#","ot":"http://purl.org/opentree-terms#","$":"http://www.nexml.org/2009","nex":"http://www.nexml.org/2009","xsi":"http://www.w3.org/2001/XMLSchema-instance"},"^ot:curatorName":["Joseph Brown","Jim Allman"],"@id":"study","@nexml2json":"1.0.0","trees":[{"@id":"trees2845","@otus":"otus2845","tree":[{"node":[{"@id":"node1153055","@root":true},{"@id":"node1153056"},{"@id":"node1153057"},{"^ot:isLeaf":true,"@otu":"otu423465","@id":"node1153058"},{"^ot:isLeaf":true,"@otu":"otu423466","@id":"node1153059"},{"^ot:isLeaf":true,"@otu":"otu423467","@id":"node1153060"},{"@id":"node1153061"},{"@id":"node1153062"},{"@id":"node1153063"},{"^ot:isLeaf":true,"@otu":"otu423468","@id":"node1153064"},{"^ot:isLeaf":true,"@otu":"otu423469","@id":"node1153065"},{"@id":"node1153066"},{"@id":"node1153067"},{"@id":"node1153068"},{"@id":"node1153069"},{"^ot:isLeaf":true,"@otu":"otu423470","@id":"node1153070"},{"^ot:isLeaf":true,"@otu":"otu423471","@id":"node1153071"},{"@id":"node1153072"},{"@id":"node1153073"},{"@id":"node1153074"},{"^ot:isLeaf":true,"@otu":"otu423472","@id":"node1153075"},{"^ot:isLeaf":true,"@otu":"otu423473","@id":"node1153076"},{"^ot:isLeaf":true,"@otu":"otu423474","@id":"node1153077"},{"^ot:isLeaf":true,"@otu":"otu423475","@id":"node1153078"},{"^ot:isLeaf":true,"@otu":"otu423476","@id":"node1153079"},{"@id":"node1153080"},{"@id":"node1153081"},{"@id":"node1153082"},{"^ot:isLeaf":true,"@otu":"otu423477","@id":"node1153083"},{"^ot:isLeaf":true,"@otu":"otu423478","@id":"node1153084"},{"^ot:isLeaf":true,"@otu":"otu423479","@id":"node1153085"},{"@id":"node1153086"},{"@id":"node1153087"},{"^ot:isLeaf":true,"@otu":"otu423480","@id":"node1153088"},{"^ot:isLeaf":true,"@otu":"otu423481","@id":"node1153089"},{"@id":"node1153090"},{"@id":"node1153091"},{"@id":"node1153092"},{"^ot:isLeaf":true,"@otu":"otu423482","@id":"node1153093"},{"^ot:isLeaf":true,"@otu":"otu423483","@id":"node1153094"},{"@id":"node1153095"},{"@id":"node1153096"},{"^ot:isLeaf":true,"@otu":"otu423484","@id":"node1153097"},{"^ot:isLeaf":true,"@otu":"otu423485","@id":"node1153098"},{"^ot:isLeaf":true,"@otu":"otu423486","@id":"node1153099"},{"^ot:isLeaf":true,"@otu":"otu423487","@id":"node1153100"},{"^ot:isLeaf":true,"@otu":"otu423488","@id":"node1153101"}],"^ot:curatedType":"Fig. 2 (topology)","@id":"tree6606","^ot:inGroupClade":"node1153061","@xsi:type":"nex:FloatTree","edge":[{"@source":"node1153055","@id":"edge1153056","@target":"node1153056"},{"@source":"node1153056","@id":"edge1153057","@target":"node1153057"},{"@source":"node1153057","@id":"edge1153058","@target":"node1153058"},{"@source":"node1153057","@id":"edge1153059","@target":"node1153059"},{"@source":"node1153056","@id":"edge1153060","@target":"node1153060"},{"@source":"node1153055","@id":"edge1153061","@target":"node1153061"},{"@source":"node1153061","@id":"edge1153062","@target":"node1153062"},{"@source":"node1153062","@id":"edge1153063","@target":"node1153063"},{"@source":"node1153063","@id":"edge1153064","@target":"node1153064"},{"@source":"node1153063","@id":"edge1153065","@target":"node1153065"},{"@source":"node1153062","@id":"edge1153066","@target":"node1153066"},{"@source":"node1153066","@id":"edge1153067","@target":"node1153067"},{"@source":"node1153067","@id":"edge1153068","@target":"node1153068"},{"@source":"node1153068","@id":"edge1153069","@target":"node1153069"},{"@source":"node1153069","@id":"edge1153070","@target":"node1153070"},{"@source":"node1153069","@id":"edge1153071","@target":"node1153071"},{"@source":"node1153068","@id":"edge1153072","@target":"node1153072"},{"@source":"node1153072","@id":"edge1153073","@target":"node1153073"},{"@source":"node1153073","@id":"edge1153074","@target":"node1153074"},{"@source":"node1153074","@id":"edge1153075","@target":"node1153075"},{"@source":"node1153074","@id":"edge1153076","@target":"node1153076"},{"@source":"node1153073","@id":"edge1153077","@target":"node1153077"},{"@source":"node1153072","@id":"edge1153078","@target":"node1153078"},{"@source":"node1153067","@id":"edge1153079","@target":"node1153079"},{"@source":"node1153066","@id":"edge1153080","@target":"node1153080"},{"@source":"node1153080","@id":"edge1153081","@target":"node1153081"},{"@source":"node1153081","@id":"edge1153082","@target":"node1153082"},{"@source":"node1153082","@id":"edge1153083","@target":"node1153083"},{"@source":"node1153082","@id":"edge1153084","@target":"node1153084"},{"@source":"node1153081","@id":"edge1153085","@target":"node1153085"},{"@source":"node1153080","@id":"edge1153086","@target":"node1153086"},{"@source":"node1153086","@id":"edge1153087","@target":"node1153087"},{"@source":"node1153087","@id":"edge1153088","@target":"node1153088"},{"@source":"node1153087","@id":"edge1153089","@target":"node1153089"},{"@source":"node1153086","@id":"edge1153090","@target":"node1153090"},{"@source":"node1153090","@id":"edge1153091","@target":"node1153091"},{"@source":"node1153091","@id":"edge1153092","@target":"node1153092"},{"@source":"node1153092","@id":"edge1153093","@target":"node1153093"},{"@source":"node1153092","@id":"edge1153094","@target":"node1153094"},{"@source":"node1153091","@id":"edge1153095","@target":"node1153095"},{"@source":"node1153095","@id":"edge1153096","@target":"node1153096"},{"@source":"node1153096","@id":"edge1153097","@target":"node1153097"},{"@source":"node1153096","@id":"edge1153098","@target":"node1153098"},{"@source":"node1153095","@id":"edge1153099","@target":"node1153099"},{"@source":"node1153090","@id":"edge1153100","@target":"node1153100"},{"@source":"node1153061","@id":"edge1153101","@target":"node1153101"}],"^ot:specifiedRoot":"","^ot:outGroupEdge":"","^ot:branchLengthTimeUnit":"","^ot:branchLengthDescription":"","^ot:tag":[],"^ot:branchLengthMode":"","@label":"Untitled (tree6606)","^ot:unrootedTree":true}]}],"^ot:studyYear":2014,"@nexmljson":"http://purl.org/opentree/nexson","^ot:annotationEvents":{"annotation":[{"@preserve":false,"@description":"Open Tree NexSON validation","@passedChecks":true,"@wasAssociatedWithAgentId":"peyotl-validator","message":[{"data":["^ot:dataDeposit"],"@code":"MISSING_OPTIONAL_KEY","@severity":"WARNING","refersTo":{"@idref":"study","@top":"nexml"}}],"@id":"peyotl-validator-event"},{"@id":"otu-mapping-hints","@description":"Aids for mapping study OTUs to OTT taxa","@wasAssociatedWithAgentId":"opentree-curation-webapp","@dateCreated":"2014-07-22T18:41:31.574Z","@passedChecks":true,"@preserve":true,"message":[{"@severity":"INFO","@code":"OTU_MAPPING_HINTS","@humanMessageType":"NONE","data":{"searchContext":{"$":"All life"},"substitutions":{"substitution":[{"old":{"$":""},"new":{"$":""},"@valid":true,"@active":false}]}},"refersTo":{"@top":{"$":"meta"}}}]},{"@id":"supporting-files-metadata","@description":"Describes supporting data files for this study","@wasAssociatedWithAgentId":"opentree-curation-webapp","@dateCreated":"2014-07-22T18:41:31.574Z","@passedChecks":true,"@preserve":true,"message":[{"@severity":"INFO","@code":"SUPPORTING_FILE_INFO","@humanMessageType":"NONE","data":{"@movedToPermanentArchive":false,"files":{"file":[]}},"refersTo":{"@top":{"$":"meta"}}}]}]},"^ot:studyId":"2845","^ot:studyPublication":{"@href":"http://dx.doi.org/10.1007/s10336-014-1063-7"},"^ot:agents":{"agent":[{"@description":"validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life\'s phylogenetic synthesis tools","@name":"validate_ot_nexson.py","@version":"0.0.4a","@url":"https://github.com/OpenTreeOfLife/peyotl","invocation":{"otherProperty":[{"name":"pythonVersion","value":"2.7.5+"},{"name":"pythonImplementation","value":"CPython"}],"commandLine":["--embed","--agent-only"]},"@id":"peyotl-validator"},{"@id":"opentree-curation-webapp","@name":"OpenTree curation webapp","@description":"Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.","@url":"https://github.com/OpenTreeOfLife/opentree","@version":"0.0.0"}]},"@generator":"Phylografter nexml-json exporter","^ot:tag":["ingroup added;","ingroup added;","test tag"],"otus":[{"@id":"otus2845","otu":[{"@id":"otu423465","^ot:ottId":1007196,"^ot:originalLabel":"Certhia familiaris","^ot:ottTaxonName":"Certhia familiaris"},{"@id":"otu423466","^ot:ottId":293378,"^ot:originalLabel":"Troglodytes aedon","^ot:ottTaxonName":"Troglodytes aedon"},{"@id":"otu423467","^ot:ottId":565813,"^ot:originalLabel":"Sturnus vulgaris","^ot:ottTaxonName":"Sturnus vulgaris"},{"@id":"otu423468","^ot:ottId":82247,"^ot:originalLabel":"Sitta carolinensis","^ot:ottTaxonName":"Sitta carolinensis"},{"@id":"otu423469","^ot:ottId":3599053,"^ot:originalLabel":"Sitta magna","^ot:ottTaxonName":"Sitta magna"},{"@id":"otu423470","^ot:ottId":1076201,"^ot:originalLabel":"Sitta tephronota","^ot:ottTaxonName":"Sitta tephronota"},{"@id":"otu423471","^ot:ottId":1076198,"^ot:originalLabel":"Sitta neumayer","^ot:ottTaxonName":"Sitta neumayer"},{"@id":"otu423472","^ot:ottId":3599051,"^ot:originalLabel":"Sitta cashmirensis","^ot:ottTaxonName":"Sitta cashmirensis"},{"@id":"otu423473","^ot:ottId":3599047,"^ot:originalLabel":"Sitta nagaensis","^ot:ottTaxonName":"Sitta nagaensis"},{"@id":"otu423474","^ot:ottId":82242,"^ot:originalLabel":"Sitta europaea","^ot:ottTaxonName":"Sitta europaea"},{"@id":"otu423475","^ot:ottId":82248,"^ot:originalLabel":"Sitta himalayensis","^ot:ottTaxonName":"Sitta himalayensis"},{"@id":"otu423476","^ot:ottId":3599052,"^ot:originalLabel":"Sitta formosa","^ot:ottTaxonName":"Sitta formosa"},{"@id":"otu423477","^ot:ottId":82249,"^ot:originalLabel":"Sitta frontalis","^ot:ottTaxonName":"Sitta frontalis"},{"@id":"otu423478","^ot:ottId":3599050,"^ot:originalLabel":"Sitta oenochlamys","^ot:ottTaxonName":"Sitta oenochlamys"},{"@id":"otu423479","^ot:ottId":3599044,"^ot:originalLabel":"Sitta azurea","^ot:ottTaxonName":"Sitta azurea"},{"@id":"otu423480","^ot:ottId":377450,"^ot:originalLabel":"Sitta pusilla","^ot:ottTaxonName":"Sitta pusilla"},{"@id":"otu423481","^ot:ottId":82240,"^ot:originalLabel":"Sitta pygmaea","^ot:ottTaxonName":"Sitta pygmaea"},{"@id":"otu423482","^ot:ottId":82236,"^ot:originalLabel":"Sitta ledanti","^ot:ottTaxonName":"Sitta ledanti"},{"@id":"otu423483","^ot:ottId":82237,"^ot:originalLabel":"Sitta krueperi","^ot:ottTaxonName":"Sitta krueperi"},{"@id":"otu423484","^ot:ottId":82233,"^ot:originalLabel":"Sitta whiteheadi","^ot:ottTaxonName":"Sitta whiteheadi"},{"@id":"otu423485","^ot:ottId":82239,"^ot:originalLabel":"Sitta villosa","^ot:ottTaxonName":"Sitta villosa"},{"@id":"otu423486","^ot:ottId":603923,"^ot:originalLabel":"Sitta canadensis","^ot:ottTaxonName":"Sitta canadensis"},{"@id":"otu423487","^ot:ottId":3599045,"^ot:originalLabel":"Sitta yunnanensis","^ot:ottTaxonName":"Sitta yunnanensis"},{"@id":"otu423488","^ot:ottId":3599041,"^ot:originalLabel":"Sitta przewalskii","^ot:ottTaxonName":"Sitta przewalskii"}]}],"^ot:focalClade":603925,"@version":"0.9","^ot:notIntendedForSynthesis":false,"^ot:comment":"","^ot:dataDeposit":{"@href":""}}}'
@jimallman
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Suggested update call (please change author info and commit SHA in query-string):

curl 'http://api.opentreeoflife.org/phylesystem/v1/study/ot_99?author_name=Jim+Allman&author_email=jim%40ibang.com&auth_token=de4916f3b38a737c2e90310db43df17760cb252b&starting_commit_SHA=2a442e80680e8785b1001a9e72d17bf234bec9d0&commit_msg=' \ 
-X PUT \ 
-H 'Content-Type: application/json; charset=UTF-8' \
 --compressed \
 --data-binary @ot_99.json

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