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Description
Calling load_dictionary on the json file provided in the documentation (https://cran.r-project.org/web/packages/ricu/ricu.pdf) (page 34/35), yields this error:
! Cannot merge concept 'glu' due to malformed 'sources' entry
Backtrace:
ricu::load_dictionary(cfg_dirs = "../ricu-extensions/configs/chemistry/")
ricu:::parse_dictionary(...)
ricu:::read_dictionary(name, cfg_dirs)
ricu::get_config(...)
base::Reduce(combine_fun, res, NULL)
ricu (local) f(init, x[[i]])
ricu:::map(combine_sources, x[dups], y[dups], dups)
base::Map(f, ..., USE.NAMES = FALSE)
base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
ricu (local) ''(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]])
ricu:::stop_ricu(...)
rlang::abort(...)
Execution halted
What exactly is wrong with the concept-dict.json:
{
"glu": {
"unit": "mg/dL",
"min": 0,
"max": 1000,
"description": "glucose",
"category": "chemistry",
"sources": {
"mimic_demo": [
{
"ids": [50809, 50931],
"table": "labevents",
"sub_var": "itemid"
}
]
}
}
}
I'm using R 4.2.2, and ricu 0.6.0 (below is the entry for ricu from my renv.lock):
"ricu": { "Package": "ricu", "Version": "0.6.0", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteRepo": "ricu-package", "RemoteUsername": "prockenschaub", "RemoteRef": "monkeypatch0.6.0", "RemoteSha": "0969a52747c71ae9f47051d640caa5df2d5169a0", "Requirements": [ "R", "assertthat", "backports", "cli", "curl", "data.table", "fansi", "fst", "jsonlite", "methods", "openssl", "prt", "readr", "rlang", "stats", "tibble", "utils", "vctrs" ], "Hash": "2681cdea2f2f3446691071ea30f745b5" },