Some json files are not valid UTF8 #56
Description
Are the json files in the Phenotype library supposed to be valid UTF-8?
If not what encoding is used?
library(PhenotypeLibrary)
listPhenotypes()$cohortId |>
getPlCohortDefinitionSet() |>
dplyr::filter(!validUTF8(json))
#> # A tibble: 5 × 4
#> cohortId cohortName json sql
#> <dbl> <chr> <chr> <chr>
#> 1 6 [P] Fever (3Pe, 30Era) "{\n\t… "CRE…
#> 2 16 [P] Exposure to SARS-Cov 2 and coronavirus (7Pe, 30Era) "{\n\t… "CRE…
#> 3 29 [W] Autoimmune condition (FP) "{\n\t… "CRE…
#> 4 64 [P] Flu-like symptoms (3P, 30Era) "{\n\t… "CRE…
#> 5 73 [W] Pregnancy (270P, 0Era) "{\n\t… "CRE…Created on 2023-06-20 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 (2022-10-31)
#> os macOS Big Sur ... 10.16
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Europe/London
#> date 2023-06-20
#> pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
#> bit 4.0.5 2022-11-15 [1] CRAN (R 4.2.0)
#> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0)
#> checkmate 2.2.0 2023-04-27 [1] CRAN (R 4.2.0)
#> cli 3.6.1 2023-03-23 [1] CRAN (R 4.2.0)
#> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
#> digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0)
#> dplyr 1.1.2 2023-04-20 [1] CRAN (R 4.2.0)
#> evaluate 0.21 2023-05-05 [1] CRAN (R 4.2.0)
#> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
#> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0)
#> fs 1.6.2 2023-04-25 [1] CRAN (R 4.2.0)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
#> hms 1.1.3 2023-03-21 [1] CRAN (R 4.2.0)
#> htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.2.0)
#> knitr 1.43 2023-05-25 [1] CRAN (R 4.2.0)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
#> PhenotypeLibrary * 3.2.0 2023-06-20 [1] local
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
#> purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
#> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.2.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
#> readr 2.1.4 2023-02-10 [1] CRAN (R 4.2.0)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0)
#> rlang 1.1.1 2023-04-28 [1] CRAN (R 4.2.0)
#> rmarkdown 2.22 2023-06-01 [1] CRAN (R 4.2.0)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
#> styler 1.10.1 2023-06-05 [1] CRAN (R 4.2.0)
#> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0)
#> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
#> tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.2.0)
#> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
#> vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.2.0)
#> vroom 1.6.3 2023-04-28 [1] CRAN (R 4.2.0)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
#> xfun 0.39 2023-04-20 [1] CRAN (R 4.2.0)
#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────