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PietrH/connection_deprecated.R

Created January 23, 2026 09:04
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Example of etn with deprecated connection argument
Raw
connection_deprecated.R
library(etn)
# Creating a connection object will result in a warning and not result in a
# connection object
my_con <- connect_to_etn()
#> Warning: `connect_to_etn()` was deprecated in etn 2.3.0.
#> ℹ You will be prompted for credentials instead.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
class(my_con)
#> [1] "NULL"
get_animals(connection = my_con)
#> Warning: The `connection` argument of `get_animals()` is deprecated as of etn v2.3.0.
#> ℹ The connection argument is no longer used. You will be prompted for
#> credentials instead.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> # A tibble: 29,170 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 5923 2004_Gudena 1208 acoustic animal
#> 2 5924 2004_Gudena 1209 acoustic animal
#> 3 5915 2004_Gudena 7416 acoustic animal
#> 4 5916 2004_Gudena 7417 acoustic animal
#> 5 5917 2004_Gudena 7418 acoustic animal
#> 6 5918 2004_Gudena 7419 acoustic animal
#> 7 5919 2004_Gudena 7420 acoustic animal
#> 8 5920 2004_Gudena 7421 acoustic animal
#> 9 5921 2004_Gudena 7422 acoustic animal
#> 10 5922 2004_Gudena 7423 acoustic animal
#> # ℹ 29,160 more rows
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>, …
# Unnamed arguments will not work, because the first one will be assumed to be
# connection
get_animals(5923,"2004_Gudena")
#> Warning: The `connection` argument of `get_animals()` is deprecated as of etn v2.3.0.
#> ℹ The connection argument is no longer used. You will be prompted for
#> credentials instead.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Error in `get_animals()`:
#> ! Can't find animal_id `2004_Gudena` in: 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 28...
#> Backtrace:
#> ▆
#> 1. ├─evaluate::evaluate(...)
#> 2. │ ├─base::withRestarts(...)
#> 3. │ │ └─base (local) withRestartList(expr, restarts)
#> 4. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#> 5. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> 6. │ │ └─base (local) withRestartList(expr, restarts[-nr])
#> 7. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
#> 8. │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> 9. │ ├─evaluate:::with_handlers(...)
#> 10. │ │ ├─base::eval(call)
#> 11. │ │ │ └─base::eval(call)
#> 12. │ │ └─base::withCallingHandlers(...)
#> 13. │ ├─base::withVisible(eval(expr, envir))
#> 14. │ └─base::eval(expr, envir)
#> 15. │ └─base::eval(expr, envir)
#> 16. │ └─etnservice::get_animals(...)
#> 17. │ └─etnservice:::check_value(...)
#> 18. │ └─assertthat::assert_that(...)
#> 19. │ └─base::stop(assertError(attr(res, "msg")))
#> 20. └─evaluate (local) `<fn>`(`<assrtErr>`)
#> 21. └─watcher$push(cnd)
#> 22. └─handler$error(value)
#>
#> ℹ This is an error forwarded via the API.
get_animals(animal_id = 5923, "2004_Gudena")
#> Warning: The `connection` argument of `get_animals()` is deprecated as of etn v2.3.0.
#> ℹ The connection argument is no longer used. You will be prompted for
#> credentials instead.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> # A tibble: 1 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 5923 2004_Gudena 1208 acoustic animal
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>,
#> # capture_temperature_change <chr>, release_date_time <dttm>, …
# Named arguments will work
get_animals(animal_id = 5923, animal_project_code = "2004_Gudena")
#> # A tibble: 1 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 5923 2004_Gudena 1208 acoustic animal
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>,
#> # capture_temperature_change <chr>, release_date_time <dttm>, …
# Running functions without arguments will work
list_acoustic_project_codes() |> length()
#> [1] 299
get_animals()
#> # A tibble: 29,170 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 5923 2004_Gudena 1208 acoustic animal
#> 2 5924 2004_Gudena 1209 acoustic animal
#> 3 5915 2004_Gudena 7416 acoustic animal
#> 4 5916 2004_Gudena 7417 acoustic animal
#> 5 5917 2004_Gudena 7418 acoustic animal
#> 6 5918 2004_Gudena 7419 acoustic animal
#> 7 5919 2004_Gudena 7420 acoustic animal
#> 8 5920 2004_Gudena 7421 acoustic animal
#> 9 5921 2004_Gudena 7422 acoustic animal
#> 10 5922 2004_Gudena 7423 acoustic animal
#> # ℹ 29,160 more rows
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>, …
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