tests/testthat/_snaps/dct_validate.md

In dwctaxon: Edit and Validate Darwin Core Taxon Data

check_mapping_* works for dup taxid bad_dat=1 , 2 , 3 , NA , 1 , 3 , Species foo, Species bar, Species bat, Accepted , Synonym , Synonym

Code
  (expect_error(dct_validate(bad_dat)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical acceptedNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad acceptedNameUsageID: 3>

Code
  (expect_warning(dct_validate(bad_dat, on_fail = "summary")))
Output
  <simpleWarning: taxonID detected with identical acceptedNameUsageID>

Code
  dct_validate(bad_dat, on_fail = "summary", quiet = TRUE)
Output
  # A tibble: 1 x 5
    taxonID acceptedNameUsageID scientificName error                         check
    <chr>   <chr>               <chr>          <glue>                        <chr>
  1 3       3                   Species bat    taxonID detected with identi~ chec~

Code
  (expect_error(dct_validate(bad_dat)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical parentNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad parentNameUsageID: 3>

Code
  (expect_warning(dct_validate(bad_dat, on_fail = "summary")))
Output
  <simpleWarning: taxonID detected with identical parentNameUsageID>

Code
  dct_validate(bad_dat, on_fail = "summary", quiet = TRUE)
Output
  # A tibble: 1 x 5
    taxonID parentNameUsageID scientificName error                           check
    <chr>   <chr>             <chr>          <glue>                          <chr>
  1 3       3                 Species bat    taxonID detected with identica~ chec~

Code
  (expect_error(dct_validate(bad_dat)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical originalNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad originalNameUsageID: 3>

Code
  (expect_warning(dct_validate(bad_dat, on_fail = "summary")))
Output
  <simpleWarning: taxonID detected with identical originalNameUsageID>

Code
  dct_validate(bad_dat, on_fail = "summary", quiet = TRUE)
Output
  # A tibble: 1 x 5
    taxonID originalNameUsageID scientificName error                         check
    <chr>   <chr>               <chr>          <glue>                        <chr>
  1 3       3                   Species bat    taxonID detected with identi~ chec~

check_mapping_* works for missing taxid bad_dat=1 , 2 , 3 , NA , 1 , 4 , Species foo, Species bar, Species bat

Code
  (expect_error(dct_validate(bad_dat)))
Output
  <assertError: check_mapping failed.
  taxonID detected whose acceptedNameUsageID value does not map to taxonID of an existing name.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad acceptedNameUsageID: 4>

Code
  (expect_warning(dct_validate(bad_dat, on_fail = "summary")))
Output
  <simpleWarning: taxonID detected whose acceptedNameUsageID value does not map to taxonID of an existing name.>

Code
  dct_validate(bad_dat, on_fail = "summary", quiet = TRUE)
Output
  # A tibble: 1 x 5
    taxonID acceptedNameUsageID scientificName error                         check
    <chr>   <chr>               <chr>          <glue>                        <chr>
  1 3       4                   Species bat    taxonID detected whose accep~ chec~

Code
  (expect_error(dct_validate(bad_dat)))
Output
  <assertError: check_mapping failed.
  taxonID detected whose parentNameUsageID value does not map to taxonID of an existing name.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad parentNameUsageID: 4>

Code
  (expect_warning(dct_validate(bad_dat, on_fail = "summary")))
Output
  <simpleWarning: taxonID detected whose parentNameUsageID value does not map to taxonID of an existing name.>

Code
  dct_validate(bad_dat, on_fail = "summary", quiet = TRUE)
Output
  # A tibble: 1 x 5
    taxonID parentNameUsageID scientificName error                           check
    <chr>   <chr>             <chr>          <glue>                          <chr>
  1 3       4                 Species bat    taxonID detected whose parentN~ chec~

Code
  (expect_error(dct_validate(bad_dat)))
Output
  <assertError: check_mapping failed.
  taxonID detected whose originalNameUsageID value does not map to taxonID of an existing name.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad originalNameUsageID: 4>

Code
  (expect_warning(dct_validate(bad_dat, on_fail = "summary")))
Output
  <simpleWarning: taxonID detected whose originalNameUsageID value does not map to taxonID of an existing name.>

Code
  dct_validate(bad_dat, on_fail = "summary", quiet = TRUE)
Output
  # A tibble: 1 x 5
    taxonID originalNameUsageID scientificName error                         check
    <chr>   <chr>               <chr>          <glue>                        <chr>
  1 3       4                   Species bat    taxonID detected whose origi~ chec~

dwctaxon documentation built on May 29, 2024, 5:53 a.m.