From 8dfeb4f0284d64273f8610cbaeae19557f750e4d Mon Sep 17 00:00:00 2001 From: John Waller Date: Thu, 4 Jan 2024 13:45:02 +0100 Subject: [PATCH] fixing tests --- tests/fixtures/name_backbone.yml | 8 ++-- tests/fixtures/name_backbone_verbose_true.yml | 39 ++++++++++--------- tests/testthat/test-name_backbone.r | 8 ++-- 3 files changed, 27 insertions(+), 28 deletions(-) diff --git a/tests/fixtures/name_backbone.yml b/tests/fixtures/name_backbone.yml index a493a21d..fd2cfae0 100644 --- a/tests/fixtures/name_backbone.yml +++ b/tests/fixtures/name_backbone.yml @@ -22,7 +22,7 @@ http_interactions: string: '{"usageKey":9206251,"scientificName":"Helianthus annuus L.","canonicalName":"Helianthus annuus","rank":"SPECIES","status":"ACCEPTED","confidence":99,"matchType":"EXACT","kingdom":"Plantae","phylum":"Tracheophyta","order":"Asterales","family":"Asteraceae","genus":"Helianthus","species":"Helianthus annuus","kingdomKey":6,"phylumKey":7707728,"classKey":220,"orderKey":414,"familyKey":3065,"genusKey":3119134,"speciesKey":9206251,"synonym":false,"class":"Magnoliopsida"}' - recorded_at: 2023-08-29 13:20:12 GMT + recorded_at: 2024-01-04 12:44:07 GMT recorded_with: vcr/1.2.0, webmockr/0.9.0 - request: method: get @@ -46,10 +46,10 @@ http_interactions: file: no string: '{"usageKey":9206251,"scientificName":"Helianthus annuus L.","canonicalName":"Helianthus annuus","rank":"SPECIES","status":"ACCEPTED","confidence":99,"note":"Similarity: - name=110; authorship=0; classification=-2; rank=6; status=1; nextMatch=5","matchType":"EXACT","alternatives":[{"usageKey":4252034,"acceptedUsageKey":4250528,"scientificName":"Helianthus + name=110; authorship=0; classification=-2; rank=6; status=1; score=115; nextMatch=5","matchType":"EXACT","alternatives":[{"usageKey":4252034,"acceptedUsageKey":4250528,"scientificName":"Helianthus canus (Britton) Wooton & Standl.","canonicalName":"Helianthus canus","rank":"SPECIES","status":"SYNONYM","confidence":9,"note":"Similarity: - name=5; authorship=0; classification=-2; rank=6; status=0","matchType":"FUZZY","kingdom":"Plantae","phylum":"Tracheophyta","order":"Asterales","family":"Asteraceae","genus":"Helianthus","species":"Helianthus + name=5; authorship=0; classification=-2; rank=6; status=0; score=9","matchType":"FUZZY","kingdom":"Plantae","phylum":"Tracheophyta","order":"Asterales","family":"Asteraceae","genus":"Helianthus","species":"Helianthus petiolaris","kingdomKey":6,"phylumKey":7707728,"classKey":220,"orderKey":414,"familyKey":3065,"genusKey":3119134,"speciesKey":3119225,"synonym":true,"class":"Magnoliopsida"}],"kingdom":"Plantae","phylum":"Tracheophyta","order":"Asterales","family":"Asteraceae","genus":"Helianthus","species":"Helianthus annuus","kingdomKey":6,"phylumKey":7707728,"classKey":220,"orderKey":414,"familyKey":3065,"genusKey":3119134,"speciesKey":9206251,"synonym":false,"class":"Magnoliopsida"}' - recorded_at: 2023-08-29 13:20:12 GMT + recorded_at: 2024-01-04 12:44:07 GMT recorded_with: vcr/1.2.0, webmockr/0.9.0 diff --git a/tests/fixtures/name_backbone_verbose_true.yml b/tests/fixtures/name_backbone_verbose_true.yml index e919bad7..ab912b2c 100644 --- a/tests/fixtures/name_backbone_verbose_true.yml +++ b/tests/fixtures/name_backbone_verbose_true.yml @@ -1,7 +1,7 @@ http_interactions: - request: method: get - uri: https://api.gbif.org/v1/species/match?name=Calopteryx&rank=species&strict=false&verbose=FALSE&limit=100 + uri: https://api.gbif.org/v1/species/match?name=Calopteryx&rank=GENUS&strict=false&verbose=FALSE&limit=100 body: encoding: '' string: '' @@ -19,12 +19,12 @@ http_interactions: body: encoding: '' file: no - string: '{"usageKey":1427007,"scientificName":"Calopteryx Leach, 1815","canonicalName":"Calopteryx","rank":"GENUS","status":"ACCEPTED","confidence":92,"matchType":"HIGHERRANK","kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","family":"Calopterygidae","genus":"Calopteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"familyKey":4211,"genusKey":1427007,"synonym":false,"class":"Insecta"}' - recorded_at: 2023-08-29 13:20:12 GMT + string: '{"confidence":100,"note":"Multiple equal matches for Calopteryx","matchType":"NONE","synonym":false}' + recorded_at: 2024-01-04 12:44:08 GMT recorded_with: vcr/1.2.0, webmockr/0.9.0 - request: method: get - uri: https://api.gbif.org/v1/species/match?name=Calopteryx&rank=species&strict=false&verbose=TRUE&limit=100 + uri: https://api.gbif.org/v1/species/match?name=Calopteryx&rank=GENUS&strict=false&verbose=TRUE&limit=100 body: encoding: '' string: '' @@ -42,19 +42,20 @@ http_interactions: body: encoding: '' file: no - string: '{"usageKey":1427007,"scientificName":"Calopteryx Leach, 1815","canonicalName":"Calopteryx","rank":"GENUS","status":"ACCEPTED","confidence":92,"note":"Similarity: - name=100; classification=-2; rank=0; status=1; nextMatch=0","matchType":"HIGHERRANK","alternatives":[{"usageKey":3234109,"acceptedUsageKey":7763613,"scientificName":"Calopteryx - A.C.Sm.","canonicalName":"Calopteryx","rank":"GENUS","status":"SYNONYM","confidence":68,"note":"Similarity: - name=100; authorship=0; classification=-2; rank=-30; status=0","matchType":"EXACT","kingdom":"Plantae","phylum":"Tracheophyta","order":"Ericales","family":"Ericaceae","genus":"Thibaudia","kingdomKey":6,"phylumKey":7707728,"classKey":220,"orderKey":1353,"familyKey":2505,"genusKey":7763613,"synonym":true,"class":"Magnoliopsida"},{"usageKey":8954339,"scientificName":"Calopteryx - Vander Linden, 1825","canonicalName":"Calopteryx","rank":"GENUS","status":"DOUBTFUL","confidence":63,"note":"Similarity: - name=100; authorship=0; classification=-2; rank=-30; status=-5","matchType":"EXACT","kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","family":"Calopterygidae","genus":"Calopteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"familyKey":4211,"genusKey":8954339,"synonym":false,"class":"Insecta"},{"usageKey":7236014,"scientificName":"Calopteryx - de Charpentier, 1839","canonicalName":"Calopteryx","rank":"GENUS","status":"DOUBTFUL","confidence":63,"note":"Similarity: - name=100; authorship=0; classification=-2; rank=-30; status=-5","matchType":"EXACT","kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","genus":"Calopteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"genusKey":7236014,"synonym":false,"class":"Insecta"},{"usageKey":3258025,"acceptedUsageKey":4405042,"scientificName":"Colopteryx - O.Hofmann, 1898","canonicalName":"Colopteryx","rank":"GENUS","status":"SYNONYM","confidence":43,"note":"Similarity: - name=75; authorship=0; classification=-2; rank=-30; status=0","matchType":"FUZZY","kingdom":"Animalia","phylum":"Arthropoda","order":"Lepidoptera","family":"Gelechiidae","genus":"Catatinagma","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":797,"familyKey":3553,"genusKey":4405042,"synonym":true,"class":"Insecta"},{"usageKey":4798148,"scientificName":"Calepteryx - Leach, 1815","canonicalName":"Calepteryx","rank":"GENUS","status":"DOUBTFUL","confidence":38,"note":"Similarity: - name=75; authorship=0; classification=-2; rank=-30; status=-5","matchType":"FUZZY","kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","family":"Calopterygidae","genus":"Calepteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"familyKey":4211,"genusKey":4798148,"synonym":false,"class":"Insecta"},{"usageKey":3241589,"scientificName":"Colopteryx - Ridgway, 1888","canonicalName":"Colopteryx","rank":"GENUS","status":"DOUBTFUL","confidence":38,"note":"Similarity: - name=75; authorship=0; classification=-2; rank=-30; status=-5","matchType":"FUZZY","kingdom":"Animalia","phylum":"Chordata","order":"Passeriformes","family":"Tyrannidae","genus":"Colopteryx","kingdomKey":1,"phylumKey":44,"classKey":212,"orderKey":729,"familyKey":5291,"genusKey":3241589,"synonym":false,"class":"Aves"}],"kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","family":"Calopterygidae","genus":"Calopteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"familyKey":4211,"genusKey":1427007,"synonym":false,"class":"Insecta"}' - recorded_at: 2023-08-29 13:20:13 GMT + string: '{"confidence":100,"note":"Multiple equal matches for Calopteryx","matchType":"NONE","alternatives":[{"usageKey":1427007,"scientificName":"Calopteryx + Leach, 1815","canonicalName":"Calopteryx","rank":"GENUS","status":"ACCEPTED","confidence":105,"note":"Similarity: + name=100; authorship=0; classification=-2; rank=6; status=1; score=105","matchType":"EXACT","kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","family":"Calopterygidae","genus":"Calopteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"familyKey":4211,"genusKey":1427007,"synonym":false,"class":"Insecta"},{"usageKey":3234109,"acceptedUsageKey":7763613,"scientificName":"Calopteryx + A.C.Sm.","canonicalName":"Calopteryx","rank":"GENUS","status":"SYNONYM","confidence":104,"note":"Similarity: + name=100; authorship=0; classification=-2; rank=6; status=0; score=104","matchType":"EXACT","kingdom":"Plantae","phylum":"Tracheophyta","order":"Ericales","family":"Ericaceae","genus":"Thibaudia","kingdomKey":6,"phylumKey":7707728,"classKey":220,"orderKey":1353,"familyKey":2505,"genusKey":7763613,"synonym":true,"class":"Magnoliopsida"},{"usageKey":8954339,"scientificName":"Calopteryx + Vander Linden, 1825","canonicalName":"Calopteryx","rank":"GENUS","status":"DOUBTFUL","confidence":99,"note":"Similarity: + name=100; authorship=0; classification=-2; rank=6; status=-5; score=99","matchType":"EXACT","kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","family":"Calopterygidae","genus":"Calopteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"familyKey":4211,"genusKey":8954339,"synonym":false,"class":"Insecta"},{"usageKey":7236014,"scientificName":"Calopteryx + de Charpentier, 1839","canonicalName":"Calopteryx","rank":"GENUS","status":"DOUBTFUL","confidence":99,"note":"Similarity: + name=100; authorship=0; classification=-2; rank=6; status=-5; score=99","matchType":"EXACT","kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","genus":"Calopteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"genusKey":7236014,"synonym":false,"class":"Insecta"},{"usageKey":3258025,"acceptedUsageKey":4405042,"scientificName":"Colopteryx + O.Hofmann, 1898","canonicalName":"Colopteryx","rank":"GENUS","status":"SYNONYM","confidence":79,"note":"Similarity: + name=75; authorship=0; classification=-2; rank=6; status=0; score=79","matchType":"FUZZY","kingdom":"Animalia","phylum":"Arthropoda","order":"Lepidoptera","family":"Gelechiidae","genus":"Catatinagma","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":797,"familyKey":3553,"genusKey":4405042,"synonym":true,"class":"Insecta"},{"usageKey":4798148,"scientificName":"Calepteryx + Leach, 1815","canonicalName":"Calepteryx","rank":"GENUS","status":"DOUBTFUL","confidence":74,"note":"Similarity: + name=75; authorship=0; classification=-2; rank=6; status=-5; score=74","matchType":"FUZZY","kingdom":"Animalia","phylum":"Arthropoda","order":"Odonata","family":"Calopterygidae","genus":"Calepteryx","kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":789,"familyKey":4211,"genusKey":4798148,"synonym":false,"class":"Insecta"},{"usageKey":3241589,"scientificName":"Colopteryx + Ridgway, 1888","canonicalName":"Colopteryx","rank":"GENUS","status":"DOUBTFUL","confidence":74,"note":"Similarity: + name=75; authorship=0; classification=-2; rank=6; status=-5; score=74","matchType":"FUZZY","kingdom":"Animalia","phylum":"Chordata","order":"Passeriformes","family":"Tyrannidae","genus":"Colopteryx","kingdomKey":1,"phylumKey":44,"classKey":212,"orderKey":729,"familyKey":5291,"genusKey":3241589,"synonym":false,"class":"Aves"}],"synonym":false}' + recorded_at: 2024-01-04 12:44:08 GMT recorded_with: vcr/1.2.0, webmockr/0.9.0 diff --git a/tests/testthat/test-name_backbone.r b/tests/testthat/test-name_backbone.r index 7c169497..ea6db9ee 100644 --- a/tests/testthat/test-name_backbone.r +++ b/tests/testthat/test-name_backbone.r @@ -32,17 +32,15 @@ test_that("Throws error because a name is required in the function call", { test_that("name_backbone verbose=TRUE", { vcr::use_cassette("name_backbone_verbose_true", { - tt <- name_backbone(name = "Calopteryx", rank = 'species') - vv <- name_backbone(name = "Calopteryx", rank = 'species',verbose=TRUE) + tt <- name_backbone(name = "Calopteryx",rank="GENUS") + vv <- name_backbone(name = "Calopteryx",rank="GENUS",verbose=TRUE) }) expect_is(vv, "tbl") expect_is(vv, "tbl_df") expect_is(vv, "data.frame") expect_equal(vv$verbatim_name[1], "Calopteryx") - expect_equal(vv$verbatim_rank[1], "species") + expect_equal(vv$verbatim_rank[1], "GENUS") expect_true(all(vv$verbatim_name == "Calopteryx")) expect_true(rev(names(vv))[1] =="verbatim_rank") expect_true(nrow(vv) > nrow(tt)) - expect_true(tt$status == "ACCEPTED") - expect_true(all(vv$status %in% c("ACCEPTED","DOUBTFUL","SYNONYM"))) })