dwctaxon
Edit and Validate Darwin Core Taxon Data

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tests/testthat/_snaps/dct_check_mapping.md

tests/testthat/_snaps/dct_check_mapping.md
In dwctaxon: Edit and Validate Darwin Core Taxon Data

check_mapping_to_self works bad_dat=1 , 2 , 3 , NA , 1 , 3 , Species foo, Species bar, Species bat, Accepted , Synonym , Synonym , bad_col=acceptedNameUsageID

Code
  (expect_error(check_mapping_to_self(bad_dat, col_select = bad_col)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical acceptedNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad acceptedNameUsageID: 3>

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

Code
  (expect_error(dct_check_mapping(bad_dat, col_select = bad_col)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical acceptedNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad acceptedNameUsageID: 3>

Code
  dct_check_mapping(bad_dat, col_select = bad_col, 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~

check_mapping_to_self works bad_dat=1 , 2 , 3 , NA , 1 , 3 , Species foo, Species bar, Species bat, Accepted , Synonym , Synonym , bad_col=parentNameUsageID

Code
  (expect_error(check_mapping_to_self(bad_dat, col_select = bad_col)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical parentNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad parentNameUsageID: 3>

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

Code
  (expect_error(dct_check_mapping(bad_dat, col_select = bad_col)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical parentNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad parentNameUsageID: 3>

Code
  dct_check_mapping(bad_dat, col_select = bad_col, 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~

check_mapping_to_self works bad_dat=1 , 2 , 3 , NA , 1 , 3 , Species foo, Species bar, Species bat, Accepted , Synonym , Synonym , bad_col=originalNameUsageID

Code
  (expect_error(check_mapping_to_self(bad_dat, col_select = bad_col)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical originalNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad originalNameUsageID: 3>

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

Code
  (expect_error(dct_check_mapping(bad_dat, col_select = bad_col)))
Output
  <assertError: check_mapping failed.
  taxonID detected with identical originalNameUsageID.
  Bad taxonID: 3
  Bad scientificName: Species bat
  Bad originalNameUsageID: 3>

Code
  dct_check_mapping(bad_dat, col_select = bad_col, 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_exists works bad_dat=1 , 2 , 3 , NA , 1 , 4 , Species foo, Species bar, Species bat, bad_col=acceptedNameUsageID

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

Code
  (expect_error(dct_check_mapping(bad_dat, col_select = bad_col)))
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
  dct_check_mapping(bad_dat, col_select = bad_col, 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~

check_mapping_exists works bad_dat=1 , 2 , 3 , NA , 1 , 4 , Species foo, Species bar, Species bat, bad_col=parentNameUsageID

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

Code
  (expect_error(dct_check_mapping(bad_dat, col_select = bad_col)))
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
  dct_check_mapping(bad_dat, col_select = bad_col, 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~

check_mapping_exists works bad_dat=1 , 2 , 3 , NA , 1 , 4 , Species foo, Species bar, Species bat, bad_col=originalNameUsageID

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

Code
  (expect_error(dct_check_mapping(bad_dat, col_select = bad_col)))
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
  dct_check_mapping(bad_dat, col_select = bad_col, 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~


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

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