Save phenotypic data to Breedbase

Uploads trait values of plots that are already in Breedbase (for example saved with save_breedbase()) through BrAPI. Give the plot name and the trait name with each value; the plots and traits are looked up in Breedbase first, and every problem is listed before anything is written.

Usage

save_breedbase_phenotypes(
  data,
  con = NULL,
  plot = "plot_name",
  traits = NULL,
  trait = NULL,
  value = NULL,
  timestamp = NULL,
  dry_run = FALSE,
  confirm = interactive(),
  refresh = TRUE
)

Arguments

data

A data frame with the plot names and the values.

con

A connection from breedbase_login(); NULL with dry_run = TRUE returns the observations without checking them.

plot

Name of the column with the plot names.

traits

For wide data: the trait columns. By default every column except plot, timestamp and the design columns of phenotype_template() (trial_name, accession, plot_number, block, rep, row, col, is_check).

trait, value

For long data: the names of the trait and value columns.

timestamp

Optional name of a column with the date and time of each measurement (e.g. "2026-08-15 10:30:00"). Breedbase uses it to tell repeated measurements apart.

dry_run

Logical. Check everything but write nothing.

confirm

Logical. Ask before writing (default in interactive sessions).

refresh

Logical. After saving, refresh the phenotype cache of Breedbase so the values show on the trial pages (see breedbase_refresh()).

Value

Invisibly, a tibble with one row per trait: trait, observation_variable_db_id, values_sent and values_found (read back from Breedbase after saving).

Details

The data can be wide, one row per plot and one column per trait (as made by phenotype_template()):

plot_name	fresh root yield	dry matter content percentage
AYT_2026_Ibadan_G31_1_1	25.4	31.2

or long, one row per value, with trait and value columns (trait = "trait", value = "value").

Trait names are the Breedbase names, with or without the ontology id: "fresh root yield" or "fresh root yield|CO_334:0000013" (the column names of a Breedbase phenotype download). Empty values (NA or "") are skipped. Values are checked by Breedbase against the trait (e.g. numbers within the allowed range).

Slow servers

Accessions are searched 25 names at a time, because Breedbase looks up the pedigree of each one. If the server times out (HTTP 504, 502, 503 or 429), the batch is split in half and tried again, so a busy server is slower but still works. A line is printed after each batch with the names done and the time. Accessions found are remembered until R is restarted, so save_breedbase() after breedbase_check() does not search them again.

When creating the folder, the trial or its plots times out, the save does not stop: the server may still finish the job, so it checks for the result every 20 seconds for 3 minutes, and tries once more if it is not there (Breedbase refuses names that already exist, so this cannot make duplicates). If a save is cut off anyway, run save_breedbase() again: an existing folder is used, and a trial left without plots gets its plots. Settings: options(breedtools.write_wait = 30, breedtools.write_checks = 10). Settings: options(breedtools.germplasm_batch = 10) for smaller batches, options(breedtools.breedbase_timeout = 600) to wait longer (seconds) for each answer.

Examples

rc <- augmented_row_column_design(paste0("G", 1:108), paste0("C", 1:4),
                                  12, 12, 4, 4, n_candidates = 5, seed = 1)
sheet <- phenotype_template(rc, "AYT_2026_Ibadan", traits = "fresh root yield")
sheet$`fresh root yield` <- round(rnorm(nrow(sheet), 25, 4), 1)

# What would be sent (no connection needed):
obs <- save_breedbase_phenotypes(sheet, dry_run = TRUE)
#> Dry run without a connection: returning the observations that would be sent.
head(obs)
#> # A tibble: 6 × 4
#>   plot_name               trait            value timestamp
#>   <chr>                   <chr>            <chr> <chr>    
#> 1 AYT_2026_Ibadan_G51_1_1 fresh root yield 21.9  NA       
#> 2 AYT_2026_Ibadan_G64_1_1 fresh root yield 17.4  NA       
#> 3 AYT_2026_Ibadan_G97_1_1 fresh root yield 33.6  NA       
#> 4 AYT_2026_Ibadan_C3_1_1  fresh root yield 24.9  NA       
#> 5 AYT_2026_Ibadan_G8_2_1  fresh root yield 23.8  NA       
#> 6 AYT_2026_Ibadan_C2_2_2  fresh root yield 22.4  NA       

if (FALSE) { # \dontrun{
con <- breedbase_login("https://cassavabase.org", "jdoe")
save_breedbase_phenotypes(sheet, con, dry_run = TRUE)   # check first
save_breedbase_phenotypes(sheet, con)

# Long data: one row per value
long <- data.frame(plot_name = sheet$plot_name, trait = "fresh root yield",
                   value = sheet$`fresh root yield`)
save_breedbase_phenotypes(long, con, trait = "trait", value = "value")
} # }