The test.sh script will run a set of basic tests against the treemachine web services. The current tests are simple and relatively brittle, and were designed using the version of the synthetic tree on the dev server on 9/24/2014, so some may fail against other versions of the tree.
IMPORTANT: these tests must be run against a neo4j server connected to a valid treemachine database. By default, the script will look for the services on the local machine at the default neo4j port (7474):
# to test against localhost:7474
./test.shYou can point this script at different servers by setting the TREEMACHINE_SERVER environment variable in your shell before running the script. This variable needs to indicate the server as well as any path components preceding 'ext/...' in the service parth. For example:
# to test devapi remotely
TREEMACHINE_SERVER=devapi.opentreeoflife.org/treemachine && export TREEMACHINE_SERVER && ./test.sh# to test locally on a machine where the treemachine neo4j instance is running on a
# nonstandard port (in this case 7480)
TREEMACHINE_SERVER=localhost:7480/db/data && export TREEMACHINE_SERVER && ./test.shCurrently, there are only minimal automated tests for treemachine and its services. You may test the services manually by querying them using cURL or other clients. Here are some cURL calls and their expected return values (for the ott 2.8draft taxonomy).
Some example ott ids to play with
- struthio_camelus = 647692
- stellula_calliope = 536234
- upupa_epops = 412129
- anas_versicolor = 30854
- gavia_immer = 1057518
Some example cURL calls follow.
Summary information about the graph
curl -X POST http://devapi.opentreeoflife.org/v2/graph/aboutShould return:
{
"graph_num_source_trees" : 481,
"graph_taxonomy_version" : "ott2.8draft5",
"graph_num_tips" : 2339516,
"graph_root_name" : "life",
"graph_root_node_id" : 1,
"graph_root_ott_id" : 805080
}Get summary information about a node in the graph
curl -X POST http://devapi.opentreeoflife.org/v2/graph/node_info -H "content-type:application/json" -d '{"node_id":3019459}'Should return:
{
"synth_sources" : [ "pg_420_522_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2926_6757_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2573_5959_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "taxonomy" ],
"in_synth_tree" : true,
"rank" : "class",
"in_graph" : true,
"name" : "Aves",
"num_tips" : 14088,
"ott_id" : 81461,
"num_synth_children" : 14088,
"tax_source" : "ncbi:8782,gbif:212,irmng:1142",
"tree_sources" : [ "pg_420_522_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2573_5959_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "taxonomy" ],
"node_id" : 3019459
}Get a source tree from the graph
curl -X POST http://devapi.opentreeoflife.org/v2/graph/source_tree -H "content-type:application/json" -d '{"tree_id":"pg_420_522_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa"}'Should return:
{
"newick" : "(((Struthio_292466:1.0E-22)Struthioniformes_857847:0.068069,((Tinamidae_292469:0.091284,((Apteryx_241840:1.0E-22)Apterygiformes_816668:0.03818,((Casuarius_589156:1.0E-22)Casuariidae_589161:0.014445,(Dromaius_283193:1.0E-22)Dromaiidae_283194:0.01843)Casuariiformes_589166:0.030882):0.00232,Tinamiformes_292467:1.0E-22,(((Eudromia_292460:0.084637,Nothoprocta_292463:0.080725):0.00491,(Crypturellus_870604:0.061151,Tinamus_402450:0.042862):0.01736)Tinamidae_292469:1.0E-22,((Eudromia_292460:0.084637,Nothoprocta_292463:0.080725):0.00491,(Crypturellus_870604:0.061151,Tinamus_402450:0.042862):0.01736,(Eudromia_292460:0.084637,Nothoprocta_292463:0.080725):0.00491,(Crypturellus_870604:0.061151,Tinamus_402450:0.042862):0.01736)Tinamidae_292469:1.0E-22)Tinamiformes_292467:1.0E-22):0.001643,(Rhea_857863:1.0E-22)Rheiformes_829553:0.08311):0.011185)Palaeognathae_81443:0.055986,(((((Opisthocomus_70726:1.0E-22)Opisthocomiformes_928359:0.089041,((((Gavia_803675:1.0E-22)Gaviiformes_70684:0.049699,(((((((Phalacrocorax_322277:1.0E-22)Phalacrocoracidae_969838:0.051194,(Anhinga_443638:1.0E-22)Anhingidae_443646:0.039714):0.004943,(Morus_752683:1.0E-22)Sulidae_452462:0.031659):0.017862,(Fregata_108973:1.0E-22)Fregatidae_452471:0.036293):0.005898,(((Cochlearius_154816:0.025018,Ardea_860130:0.029045)Ardeidae_609781:0.032668,(Eudocimus_689774:1.0E-22)Threskiornithidae_480157:0.053985):0.001574,((Pelecanus_316994:1.0E-22)Pelecanidae_452465:0.045666,((Balaeniceps_597797:1.0E-22)Balaenicipitidae_597796:0.033735,(Scopus_464703:1.0E-22)Scopidae_1057476:0.05511):0.001343):0.010306):0.001878):0.00116,(Ciconia_363012:1.0E-22)Ciconiidae_363013:0.043283):0.001253,((Eudyptula_388853:1.0E-22)Sphenisciformes_494366:0.044753,(((Diomedea_379419:1.0E-22)Diomedeidae_85277:0.026207,(Oceanodroma_172642:0.032772,((Pelecanoides_904488:1.0E-22)Pelecanoididae_904487:0.024161,(Puffinus_1028843:1.0E-22)Procellariidae_1028841:0.015536):0.015313):0.002986):8.24E-4,Oceanites_656590:0.045177)Procellariiformes_452461:0.004445):0.002742):0.001953):0.0014,:0.040747,Musophagiformes_539139:1.0E-22,((Corythaeola_842352:0.040341,Tauraco_539140:0.045392):1.0E-22,(Corythaeola_842352:0.040341,Tauraco_539140:0.045392,Corythaeola_842352:0.040341,Tauraco_539140:0.045392):1.0E-22)Musophagiformes_539139:1.0E-22):0.001505,((((((Aramus_915651:1.0E-22)Aramidae_915649:0.034399,(Grus_414354:1.0E-22)Gruidae_446460:0.027902):0.016386,(Psophia_915642:1.0E-22)Psophiidae_915652:0.06858):0.007701,((Himantornis_383930:0.036588,Rallus_440612:0.035633):0.045303,(Sarothrura_399793:0.098432,(Heliornis_440620:1.0E-22)Heliornithidae_440606:0.081266):0.013724):0.041851):0.020906,((((Centropus_1039514:1.0E-22)Centropidae_1040900:0.105747,Coua_787071:0.072867):0.00457,(((Coccyzus_891428:1.0E-22)Coccyzidae_1041414:0.038539,Phaenicophaeus_1041421:0.024286):0.034617,Cuculus_1041429:0.052701):0.028485):0.010289,((Geococcyx_212185:1.0E-22)Neomorphidae_173050:0.075601,(Crotophaga_1041422:1.0E-22)Crotophagidae_1041423:0.06579):0.015668)Cuculiformes_212171:0.047155):0.001564,(Choriotis_3600037:0.022179,Eupodotis_521835:0.024254)Otididae_966318:0.063626):0.002641):0.002031):0.002382,((((((:0.086987,((((Upupa_412128:1.0E-22)Upupidae_291860:0.099034,(Phoeniculus_834690:1.0E-22)Phoeniculidae_834689:0.098169)Upupiformes_815967:0.100031,((Bucorvus_991312:1.0E-22)Bucorvidae_991314:0.0305,(Tockus_1097399:1.0E-22)Bucerotidae_489457:0.067023)Bucerotiformes_341907:0.062953):0.015769,((((Galbula_484896:1.0E-22)Galbulidae_484892:0.093829,(Bucco_483803:1.0E-22)Bucconidae_483802:0.097348)Galbuliformes_484893:0.02902,(((Indicator_467838:1.0E-22)Indicatoridae_467845:0.040802,(Dryocopus_733986:1.0E-22)Picidae_1020138:0.045771):0.019814,((Capito_815707:1.0E-22)Ramphastidae_489463:0.061571,(Megalaima_291638:1.0E-22)Megalaimidae_291635:0.070621):0.028918)Piciformes_472432:0.080422):0.012788,((Merops_989088:1.0E-22)Meropidae_815968:0.113525,(((Brachypteracias_483804:1.0E-22)Brachypteraciidae_483798:0.059926,(Coracias_244695:1.0E-22)Coraciidae_244696:0.059306):0.025887,(((Alcedo_549518:1.0E-22)Alcedinidae_938411:0.120941,(Momotus_989084:1.0E-22)Momotidae_489432:0.084333):0.009393,(Todus_284297:1.0E-22)Todidae_815966:0.096383):0.014113):0.00185):0.012257):0.004011):0.006487,Trogoniformes_539130:1.0E-22,((Trogon_1065611:0.03286,Pharomachrus_989089:0.03198):1.0E-22,(Trogon_1065611:0.03286,Pharomachrus_989089:0.03198,Trogon_1065611:0.03286,Pharomachrus_989089:0.03198):1.0E-22)Trogoniformes_539130:1.0E-22):0.00136,(Leptosomus_897862:1.0E-22)Leptosomidae_897861:0.08109):0.003193,(((Tyto_1065605:0.02467,Phodilus_178684:0.021908)Tytonidae_402457:0.038841,(Strix_427905:0.019555,Athene_98071:0.04265):0.038003)Strigiformes_1028829:0.011322,(Urocolius_261312:1.0E-22)Coliiformes_815970:0.148957):0.001582):0.001889,((((Pandion_509844:1.0E-22)Pandioninae_509843:0.039038,(Buteo_119211:0.026466,Gampsonyx_767825:0.047509)Accipitrinae_786440:0.006245)Accipitridae_1036185:0.009904,(Sagittarius_1036187:1.0E-22)Sagittariidae_1036188:0.048561):0.011531,(Sarcoramphus_819164:0.007934,Cathartes_317003:0.008966)Cathartidae_363021:0.028138):0.001418):0.001111,((((Falco_786441:0.042045,Daptrius_438662:0.025422):0.020204,(Micrastur_1015202:0.015684,Herpetotheres_438656:0.013273):0.017691)Falconidae_212186:0.033545,(((Acanthisitta_1085741:1.0E-22)Acanthisittidae_901940:0.104596,(((Menura_73933:1.0E-22)Menuridae_73954:0.059299,((Climacteris_531218:1.0E-22)Climacteridae_73972:0.077503,((Malurus_901831:1.0E-22)Maluridae_901832:0.083712,(((Picathartes_699624:1.0E-22)Picathartidae_176465:0.053895,((((Ploceus_370815:1.0E-22)Ploceidae_1031977:0.023436,(Vidua_507121:1.0E-22)Estrildidae_507124:0.027999):0.005305,((Fringilla_28336:1.0E-22)Fringillidae_839319:0.036294,(Passer_515158:1.0E-22)Passeridae_1011209:0.040818):0.008852)Passeroidea_176458:0.013079,(((Sylvia_463177:1.0E-22)Sylviidae_259942:0.055851,(Turdus_568571:1.0E-22)Turdidae_96286:0.063024):0.00352,(Bombycilla_613883:1.0E-22)Bombycillidae_613878:0.069549):3.93E-4):0.009812):0.006319,(Corvus_952596:1.0E-22)Corvoidea_635217:0.044225):0.009903):0.012328):0.006066):0.026149,((((Tyrannus_463185:0.042419,Mionectes_683046:0.038317):0.011208,(Pipra_872124:1.0E-22)Pipridae_881043:0.037734):0.028602,(((Grallaria_1041027:1.0E-22)Formicariidae_472037:0.058324,((Dendrocolaptes_390841:1.0E-22)Dendrocolaptidae_155232:0.055765,(Scytalopus_44860:1.0E-22)Rhinocryptidae_44868:0.055361):0.004101):0.004199,(Thamnophilus_799167:1.0E-22)Thamnophilidae_799152:0.061805):0.014647):0.013458,(((Pitta_44875:1.0E-22)Pittidae_44873:0.07916,(Smithornis_622872:1.0E-22)Eurylaimidae_622873:0.054061):0.002972,Sapayoa_29742:0.064324):0.032117):0.014098):0.011135)Passeriformes_1041547:0.05194,((Cacatua_619340:1.0E-22)Cacatuidae_512919:0.03402,:0.007079,(:1.0E-22,(((Platycercus_512910:0.031536,Chalcopsitta_276608:0.035748):0.003623,((Alisterus_682886:0.025857,Psittacula_1020126:0.02314):0.002518,Micropsitta_989086:0.035173):0.003373):0.005708,Psittacus_332937:0.044181,((Platycercus_512910:0.031536,Chalcopsitta_276608:0.035748):0.003623,((Alisterus_682886:0.025857,Psittacula_1020126:0.02314):0.002518,Micropsitta_989086:0.035173):0.003373):0.005708,Psittacus_332937:0.044181,((Platycercus_512910:0.031536,Chalcopsitta_276608:0.035748):0.003623,((Alisterus_682886:0.025857,Psittacula_1020126:0.02314):0.002518,Micropsitta_989086:0.035173):0.003373):0.005708,Psittacus_332937:0.044181):1.0E-22)Psittacidae_1020130:1.0E-22):0.080722):0.003214):0.001248,(Cariama_966327:1.0E-22)Cariamidae_966325:0.064557):0.002413):0.005212,((((Charadrius_112946:0.02814,Phegornis_214795:0.026739)Charadriidae_313123:0.014782,(Haematopus_193407:1.0E-22)Haematopodidae_675126:0.032531):0.014788,(Burhinus_261316:1.0E-22)Burhinidae_261310:0.045568):0.003951,((((Larus_887695:1.0E-22)Laridae_887693:0.032647,(Dromas_960243:1.0E-22)Dromadidae_960242:0.025419):0.015026,(Turnix_365489:1.0E-22)Turniciformes_810755:0.18873):0.00881,((((Thinocorus_628492:1.0E-22)Thinocoridae_628493:0.053497,(Pedionomus_163950:1.0E-22)Pedionomidae_163951:0.04395):0.016681,((Rostratula_5275:1.0E-22)Rostratulidae_5274:0.055239,(Jacana_332001:1.0E-22)Jacanidae_331999:0.05956):0.009395):0.01752,(Arenaria_821756:1.0E-22)Scolopacidae_887699:0.046052):0.024302):0.009831):0.01301):0.002734):0.001494,(((((Syrrhaptes_880217:0.028131,Pterocles_244698:0.030308)Pteroclidae_244699:0.070212,((Monias_582942:0.023104,Mesitornis_966321:0.023582)Mesitornithidae_966320:0.083163,((Otidiphaps_392964:0.023405,Columbina_935135:0.038143):0.002133,((Columba_938415:0.033245,Geotrygon_449653:0.032737):0.009269,Treron_873964:0.035234):0.001206)Columbiformes_363030:0.078976):0.002749):0.00144,Phaethon_330010:0.075196,((Phaethon_lepturus_855119:0.002726,Phaethon_rubricauda_509057:0.002406,Phaethon_lepturus_855119:0.002726,Phaethon_rubricauda_509057:0.002406)Phaethon_330010:1.0E-22)Phaethontidae_452467:1.0E-22):0.001028,((Phoenicopterus_443649:1.0E-22)Phoenicopteriformes_472435:0.036539,(Podiceps_329993:1.0E-22)Podicipediformes_452464:0.070732):0.019648):0.001701,((((((Eurostopodus_726315:1.0E-22)Eurostopodidae_726316:0.042431,(Caprimulgus_275134:1.0E-22)Caprimulgidae_275127:0.045907):0.033167,((Aegotheles_540029:1.0E-22)Aegothelidae_540031:0.092918,(Trochilidae_810751:0.086258,((Hemiprocne_697438:1.0E-22)Hemiprocnidae_882744:0.041301,(Streptoprocne_697413:0.026977,Aerodramus_534819:0.042417)Apodidae_609796:0.013721)Apodiformes_609798:0.037704,((Phaethornis_174369:0.039041,Colibri_804122:0.036348,Phaethornis_174369:0.039041,Colibri_804122:0.036348)Trochilidae_810751:1.0E-22)Trochiliformes_810738:1.0E-22):0.014326):0.012744):0.001994,((Batrachostomus_275129:1.0E-22)Batrachostomatidae_275130:0.038779,(Podargus_313122:1.0E-22)Podargidae_313130:0.031374):0.051052):0.002299,(Nyctibius_178253:0.040279,(Steatornis_701547:1.0E-22)Steatornithidae_701556:0.075216,((Nyctibius_grandis_178249:0.017044,Nyctibius_bracteatus_178250:0.023877,Nyctibius_grandis_178249:0.017044,Nyctibius_bracteatus_178250:0.023877)Nyctibius_178253:1.0E-22)Nyctibiidae_178243:1.0E-22):0.001377):0.003449,((Eurypyga_86682:1.0E-22)Eurypygidae_86683:0.049583,(Rhynochetos_86676:1.0E-22)Rhynochetidae_86678:0.045071):0.067821):0.002659):0.002134):0.044959,((((Crax_979429:1.0E-22)Cracidae_109893:0.090261,((Numida_684050:1.0E-22)Numididae_684043:0.044719,((Rollulus_352754:0.068711,((Gallus_153562:1.0E-22)Phasianinae_51353:0.03635,Coturnix_1098759:0.066402):0.010595)Phasianidae_728070:0.014614,(Colinus_204725:1.0E-22)Odontophoridae_594197:0.099855):0.008216):0.06343):0.013369,(Alectura_570959:0.03048,Megapodius_837567:0.029367)Megapodiidae_620981:0.069087)Galliformes_837585:0.032204,(((((Biziura_432080:0.034803,(Anas_765185:0.012596,Aythya_693334:0.011903):0.023881):0.003654,(Anser_190884:0.022753,Malacorhynchus_436831:0.04328):0.003531):0.002077,Oxyura_88395:0.040265)Anatidae_765193:0.054998,(Anseranas_714466:1.0E-22)Anseranatidae_732899:0.048445):0.008696,(Chauna_241847:1.0E-22)Anhimidae_241842:0.057828)Anseriformes_241841:0.008393):0.044868)Neognathae_241846:0.066177)Aves_81461",
"tree_id" : "pg_420_522_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa"
}Summary information about the current synthetic tree
curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/aboutShould return:
{
"root_node_id" : 132,
"study_list" : [ "pg_2827_6577_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_761_1415_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_77_5878_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_754_1392_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_330_325_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_1131_2265_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2608_6288_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2539_6294_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2645_6165_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2644_6164_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2642_6161_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2140_4483_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2626_6142_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_30_2281_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_332_333_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2832_6586_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_1866_3765_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", 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"pg_1338_2666_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2068_6488_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2092_4335_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2156_5953_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2544_6482_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2696_6249_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2709_6290_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2842_6603_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2708_6289_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_1343_6255_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_1788_6534_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_1786_6257_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2678_6224_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_421_523_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_1366_6166_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_1761_6151_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2710_6291_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_335_360_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_338_5527_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_339_365_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_340_5532_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_343_5534_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_348_381_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_349_5539_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_353_5542_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_355_400_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_358_406_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_361_5551_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_366_5552_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_367_418_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_368_5553_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_369_5554_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_370_426_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_372_431_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_373_432_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_374_433_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_375_436_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_376_438_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_380_5560_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_382_449_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_387_5562_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_388_469_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_389_470_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_393_482_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_397_494_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_399_5565_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_400_497_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_402_5570_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_403_503_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_404_506_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_405_507_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_407_513_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_408_5571_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_411_518_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_414_519_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_415_5572_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_430_541_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_441_5575_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_444_564_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_446_565_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_447_5576_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_448_5577_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_449_570_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_450_574_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_443_562_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_463_604_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_470_615_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_471_617_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_473_623_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_474_627_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_475_5594_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_477_633_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_479_636_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_480_637_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_481_644_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_482_5595_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_483_647_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_485_651_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2542_5590_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2737_6322_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2738_6323_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2738_6324_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2554_5580_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2892_6700_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2891_6699_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2739_6601_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "ot_106_1_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2731_6428_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2715_6308_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_263_149_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2713_6309_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2753_6360_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2742_6342_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2757_6369_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2553_5579_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2556_5586_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_312_264_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_313_6681_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2484_6607_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2849_6615_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "pg_2822_6569_96e3dcc7d18b5ba7b96b888ef18fdf7c14c088fa", "taxonomy" ],
"root_taxon_name" : "cellular organisms",
"num_source_studies" : 481,
"taxonomy_version" : "ott2.8draft5",
"root_ott_id" : 93302,
"num_tips" : 2339460,
"date" : "Thu Aug 14 01:06:35 EDT 2014",
"tree_id" : "otol.draft.22"
}Get MRCA in the current synthetic tree of a bunch of nodes
curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/mrca -H "content-type:application/json" -d '{"ott_ids":[412129, 536234]}'
Should return:
{
"mrca_name" : "",
"nearest_taxon_mrca_rank" : "superorder",
"mrca_rank" : "",
"nearest_taxon_mrca_ott_id" : 241846,
"invalid_node_ids" : [ ],
"nearest_taxon_mrca_node_id" : 3019669,
"ott_ids_not_in_tree" : [ ],
"nearest_taxon_mrca_unique_name" : "",
"ott_id" : "null",
"mrca_node_id" : 3853465,
"mrca_unique_name" : "",
"nearest_taxon_mrca_name" : "Neognathae",
"node_ids_not_in_tree" : [ ],
"invalid_ott_ids" : [ ]
}From the current synthetic tree, get the complete subtree below a given node
curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/subtree -H "content-type:application/json" -d '{"ott_id":3599390}'Should return:
{
"newick" : "((((((((Leucopeza_semperi_ott636990)Leucopeza_ott636993,(Oporornis_agilis_ott659603)Oporornis_ott119886),(Geothlypis_chiriquensis_ott3597227,(((Geothlypis_semiflava_ott636992,Geothlypis_speciosa_ott85253),(((Geothlypis_flavovelata_ott63583,Geothlypis_trichas_ott998127,Geothlypis_nelsoni_ott63582),Geothlypis_rostrata_ott375821),Geothlypis_beldingi_ott63581)),Geothlypis_formosa_ott3597225),Geothlypis_auricularis_ott3597223,((Geothlypis_aequinoctialis_ott669575,Geothlypis_poliocephala_ott63586),(Geothlypis_philadelphia_ott3597222,Geothlypis_tolmiei_ott3597226)),Geothlypis_velata_ott3597224)Geothlypis_ott998126),((((Vermivora_celata_lutescens_ott669574)Oreothlypis_celata_ott88835,(Oreothlypis_crissalis_ott85251,((Oreothlypis_virginiae_ott759416,(Oreothlypis_ruficapilla_ridgwayi_ott900162,Oreothlypis_ruficapilla_ruficapilla_ott1001290)Oreothlypis_ruficapilla_ott392341),Oreothlypis_luciae_ott711624))),Oreothlypis_peregrina_ott430151),(Oreothlypis_superciliosa_ott430147,Oreothlypis_gutturalis_ott956238))Oreothlypis_ott4947615),((((Myiothlypis_bivittatus_ott3599828,((Myiothlypis_cinereicollis_ott3599528,Myiothlypis_conspicillatus_ott3599392),(Myiothlypis_coronatus_ott3599881,Myiothlypis_fraseri_ott3599779))),(Myiothlypis_luteoviridis_ott3599766,(((Myiothlypis_nigrocristatus_ott3599882,Myiothlypis_signatus_ott3599512),(Myiothlypis_fulvicauda_ott3599607,Myiothlypis_rivularis_ott3599526)),((Myiothlypis_leucoblepharus_ott3599810,Myiothlypis_flaveolus_ott3599765),Myiothlypis_leucophrys_ott3599780))),Myiothlypis_griseiceps_ott3599568)Myiothlypis_ott3599393,(((((((Myioborus_torquatus_ott992006,(Myioborus_pariae_ott992008,(Myioborus_albifacies_ott659607,(Myioborus_cardonai_ott992007,Myioborus_castaneocapilla_ott3597186)))),((Myioborus_albifrons_ott85245,(Myioborus_ornatus_ott449735,Myioborus_melanocephalus_ott315419)),Myioborus_flavivertex_ott992009)),Myioborus_brunniceps_ott859999),Myioborus_miniatus_ott859998),Myioborus_pictus_ott285205,Myioborus_castaneocapillus_ott315418)Myioborus_ott886174,(((Cardellina_rubrifrons_ott1061912,(Cardellina_versicolor_ott3597184,Cardellina_rubra_ott3597183)),Cardellina_pusilla_ott3597185),Cardellina_canadensis_ott3597182)Cardellina_ott5266838),(Basileuterus_conspicillatus_ott384904,Basileuterus_chrysogaster_ott384910,Basileuterus_basilicus_ott405179,Basileuterus_leucophrys_ott317448,Basileuterus_fulvicauda_ott357657,Basileuterus_signatus_ott1034068,Basileuterus_rivularis_ott817143,Basileuterus_nigrocristatus_ott5620,(Basileuterus_luteoviridis_euophrys_ott578348,Basileuterus_luteoviridis_luteoviridis_ott5626,Basileuterus_luteoviridis_striaticeps_ott5625)Basileuterus_luteoviridis_ott1034069,Basileuterus_culicivorus_x_Basileuterus_hypoleucus_ott4947614,Basileuterus_bivittatus_ott994339,Basileuterus_ignotus_ott3597219,Basileuterus_flaveolus_ott865397,Basileuterus_griseiceps_ott3597218,Basileuterus_lachrymosus_ott3597220,(((Basileuterus_rufifrons_mesocrysus_ott1034067)Basileuterus_rufifrons_ott1034070,(Basileuterus_melanogenys_ott384916,Basileuterus_belli_ott410568)),(((Basileuterus_tristriatus_auricularis_ott1034074)Basileuterus_tristriatus_ott117643,Basileuterus_trifasciatus_ott384908),((Basileuterus_culicivorus_austerus_ott508026,Basileuterus_culicivorus_auricapilla_ott813148,Basileuterus_culicivorus_flavescens_ott289268,Basileuterus_culicivorus_culicivorus_ott289274,Basileuterus_culicivorus_azarae_ott289272)Basileuterus_culicivorus_ott508027,Basileuterus_hypoleucus_ott384914))),Basileuterus_chlorophrys_ott301266,(Basileuterus_coronatus_regulis_ott508024)Basileuterus_coronatus_ott508025,Basileuterus_leucoblepharus_ott292918,(Basileuterus_cinereicollis_pallidulus_ott508022)Basileuterus_cinereicollis_ott508023,Basileuterus_fraseri_ott384906)Basileuterus_ott758213)),((Catharopeza_bishopi_ott335225)Catharopeza_ott335224,(Setophaga_flavescens_ott3597198,(Setophaga_citrina_ott3597211,(((Setophaga_kirtlandii_ott3597203,((Setophaga_cerulea_ott3597212,(Setophaga_pitiayumi_ott3597201,Setophaga_americana_ott3597189)),Setophaga_tigrina_ott3597199)),(((((Setophaga_discolor_ott3597197,(Setophaga_vitellina_vitellina_ott478049,Setophaga_vitellina_crawfordi_ott478050)Setophaga_vitellina_ott3597196),(((Setophaga_graciae_ott455853,Setophaga_nigrescens_ott3597216),((Setophaga_townsendi_ott3597215,Setophaga_occidentalis_ott3597213),(Setophaga_virens_ott3597195,Setophaga_chrysoparia_ott3597192))),((Setophaga_subita_ott3597204,Setophaga_delicata_ott3597206),Setophaga_adelaidae_ott3597207))),(Setophaga_palmarum_ott3597202,((Setophaga_dominica_ott3597194,(Setophaga_coronata_coronata_ott349904,Setophaga_coronata_goldmani_ott870777,Setophaga_coronata_nigrifrons_ott870775,Setophaga_coronata_auduboni_ott870781)Setophaga_coronata_ott3597200),(Setophaga_pinus_ott3597210,Setophaga_pityophila_ott3597214)))),Setophaga_caerulescens_ott3597187),((((Setophaga_striata_ott60236,Setophaga_pensylvanica_ott3597208),(Setophaga_petechia_ruficapilla_ott22843,Setophaga_petechia_aurifrons_ott862432,Setophaga_petechia_melanoptera_ott22846,Setophaga_petechia_aureola_ott790184,Setophaga_petechia_albicollis_ott22840,Setophaga_petechia_cruciana_ott22834,Setophaga_petechia_peruviana_ott22849,Setophaga_petechia_eoa_ott22856,Setophaga_petechia_bartholemica_ott22837,Setophaga_petechia_xanthotera_ott328787,Setophaga_petechia_babad_ott328784,Setophaga_petechia_gundlachi_ott22853,Setophaga_petechia_rhizophorae_ott328778,Setophaga_petechia_aestiva_ott612073,Setophaga_petechia_cienagae_ott328790,Setophaga_petechia_petechia_ott612062,Setophaga_petechia_castaneiceps_ott872016,Setophaga_petechia_aequatorialis_ott853391,Setophaga_petechia_chrysendeta_ott328781,Setophaga_petechia_erithachorides_ott612070,Setophaga_petechia_paraguanae_ott328794)Setophaga_petechia_ott612066),(Setophaga_castanea_ott3597188,Setophaga_fusca_ott3597193)),Setophaga_magnolia_ott3597209))),Setophaga_ruticilla_ott285200)),((Setophaga_angelae_ott3597191,Setophaga_pharetra_ott3597190),Setophaga_plumbea_ott3597205))Setophaga_ott285198))),((((Mniotilta_varia_ott757859)Mniotilta_ott309802,((Limnothlypis_swainsonii_ott1024615)Limnothlypis_ott1024616,(Protonotaria_citrea_ott285212)Protonotaria_ott285204)),((Vermivora_pinus_ott85247,Vermivora_chrysoptera_ott85249),Vermivora_bachmanii_ott237566,Vermivora_cyanoptera_ott3597221)Vermivora_ott150638),(Seiurus_novaeboracensis_ott4132022,Seiurus_motacilla_ott4132023))),(Helmitheros_vermivorum_ott860003)Helmitheros_ott886630),(Teretistris_fornsi_ott3597217,Teretistris_fernandinae_ott449562)Teretistris_ott808916,Seiurus_aurocapilla_ott285207,(Dendroica_subita_ott3597234,Dendroica_aestiva_ott3597233,Dendroica_delicata_ott3597229,Dendroica_flavescens_ott3597236)Dendroica_ott666104,(Chloris_spinoides_ott4947620,Chloris_sinica_ott4947618,Chloris_monguilloti_ott4947617,Chloris_ambigua_ott4947619)Chloris_ott4947616,Setophaga_petechia_x_Geothlypis_trichas_ott4947613,(Icteria_virens_ott998133)Icteria_ott998132,(Zeledonia_coronata_ott449580)Zeledonia_ott449581,(Xenoligea_montana_ott808917)Xenoligea_ott808918,(Microligea_palustris_ott309808)Microligea_ott757867,(Granatellus_pelzelni_ott335232,Granatellus_venustus_ott972935,Granatellus_sallaei_ott972938)Granatellus_ott335231)Parulidae_ott3599390;",
"tree_id" : "otol.draft.22"
}Get the induced subtree = synthetic tree with just specified terminal nodes
curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/induced_subtree -H "content-type:application/json" -d '{"ott_ids":[292466, 501678, 267845, 666104, 316878, 102710, 176458]}'Should return:
{
"invalid_node_ids" : [ ],
"subtree" : "((((Dendroica_ott666104,Cinclus_ott267845),Stellula_ott501678),(Clangula_ott316878,Perdix_ott102710))Neognathae_ott241846,Struthio_ott292466)Aves_ott81461;",
"ott_ids_not_in_tree" : [ 176458 ],
"node_ids_not_in_tree" : [ ],
"invalid_ott_ids" : [ ]
}