Retrieve marine biotoxin data from IOC-UNESCO Toxins Database

This function collects data from the IOC-UNESCO Toxins Database and returns information about toxins.

Usage

get_toxin_list(return_count = FALSE, insecure = FALSE)

Arguments

return_count: Logical. If TRUE, the function returns the count of toxins available in the database. If FALSE (default), it returns detailed toxin data.
insecure: Logical. If TRUE, the request is made without verifying the server's TLS certificate. This is a workaround for periods when the toxins.hais.ioc-unesco.org certificate has expired or is otherwise invalid. Defaults to FALSE. When FALSE and a certificate error is encountered, an interactive session will prompt before retrying without verification, while a non-interactive session aborts with instructions to set insecure = TRUE. Disabling verification removes protection against tampering and should only be used when the certificate issue is known and trusted.

Value

If return_count = TRUE, the function returns a numeric value representing the number of toxins in the database. Otherwise, it returns a tibble of toxins with detailed information.

Details

The TLS certificate for toxins.hais.ioc-unesco.org may occasionally lapse. When this happens the default (secure) request fails with a certificate error. The insecure argument provides a deliberate, opt-in escape hatch: in an interactive session the function prompts before retrying without verification, while a non-interactive session aborts and instructs the caller to set insecure = TRUE. Only disable verification when you have confirmed that the failure is caused by the known certificate issue, as it removes protection against a tampered or spoofed response.

Examples

# \donttest{
# Retrieve the full list of toxins
try(toxin_list <- get_toxin_list())
#> Error in get_toxin_list() : 
#>   Could not verify the server's TLS certificate.
#> ✖ SSL peer certificate or SSH remote key was not OK
#>   [toxins.hais.ioc-unesco.org]: SSL certificate problem: certificate has
#>   expired
#> ℹ Re-run with `insecure = TRUE` to proceed without verification.
if (exists("toxin_list")) head(toxin_list)

# Retrieve only the count of toxins
try(toxin_count <- get_toxin_list(return_count = TRUE))
#> Error in get_toxin_list(return_count = TRUE) : 
#>   Could not verify the server's TLS certificate.
#> ✖ SSL peer certificate or SSH remote key was not OK
#>   [toxins.hais.ioc-unesco.org]: SSL certificate problem: certificate has
#>   expired
#> ℹ Re-run with `insecure = TRUE` to proceed without verification.
if (exists("toxin_count")) print(toxin_count)

# If the server's TLS certificate has expired, the verification step can be
# bypassed explicitly. Only do this when the certificate issue is known and
# trusted, as it disables protection against tampering.
try(toxin_list <- get_toxin_list(insecure = TRUE))
#> Warning: TLS certificate verification disabled — this download is not protected against
#> tampering.
if (exists("toxin_list")) head(toxin_list)
#> # A tibble: 6 × 55
#>      id toxin_group recommended_name synonyms recommended_acronym acronyms
#>   <int> <chr>       <chr>            <list>   <chr>               <list>  
#> 1   624 Azaspiracid Azaspiracid-68   <NULL>   AZA-68              <NULL>  
#> 2   623 Azaspiracid Azaspiracid-67   <NULL>   AZA-67              <NULL>  
#> 3   622 Azaspiracid Azaspiracid-66   <NULL>   AZA-66              <NULL>  
#> 4   621 Azaspiracid Azaspiracid-65   <NULL>   AZA-65              <NULL>  
#> 5   620 Azaspiracid Azaspiracid-61   <NULL>   AZA-61              <NULL>  
#> 6   619 Azaspiracid Azaspiracid-60   <NULL>   AZA-60              <NULL>  
#> # ℹ 49 more variables: cas_number <chr>, alternative_cas_numbers <list>,
#> #   formula <chr>, exact_mono_isotopic_mass <dbl>, molfile <chr>,
#> #   alternative_molfiles <lgl>, smiles <chr>, alternative_smiles <list>,
#> #   inchi_key <chr>, alternative_inchi_keys <list>, inchi <chr>,
#> #   alternative_inchies <lgl>, spectra_available <lgl>, certified <lgl>,
#> #   non_certified_reference_material <lgl>, chemical_analysis_research <lgl>,
#> #   chemical_analysis_standardized <lgl>, chemical_analysis_validated <lgl>, …
# }