diff --git a/R/mockDatasets.R b/R/mockDatasets.R index d7ae840..a698b73 100644 --- a/R/mockDatasets.R +++ b/R/mockDatasets.R @@ -23,6 +23,13 @@ mockCdmFromDataset <- function(datasetName = "GiBleed", cn <- omock::mockDatasets$cdm_name[omock::mockDatasets$dataset_name == datasetName] cv <- omock::mockDatasets$cdm_version[omock::mockDatasets$dataset_name == datasetName] + + + + if (datasetName == "GiBleed") { + cli::cli_inform(c(i = "Loading bundled {.pkg {datasetName}} tables from package data.")) + tables <- gibleed + } else { # make dataset available datasetPath <- datasetAvailable(datasetName) @@ -41,6 +48,8 @@ mockCdmFromDataset <- function(datasetName = "GiBleed", # delete csv files unlink(x = tmpFolder, recursive = TRUE) + } + # add drug strength cli::cli_inform(c(i = "Adding {.pkg drug_strength} table.")) if (datasetName == "GiBleed") { @@ -549,3 +558,4 @@ attemptDownload <- function(url, destfile, datasetName, out } + diff --git a/R/sysdata.rda b/R/sysdata.rda index 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a/data-raw/GiBleed_5.3/GiBleed/visit_occurrence.parquet b/data-raw/GiBleed_5.3/GiBleed/visit_occurrence.parquet new file mode 100644 index 0000000..a0b9b5c Binary files /dev/null and b/data-raw/GiBleed_5.3/GiBleed/visit_occurrence.parquet differ diff --git a/data-raw/GiBleed_5.3/GiBleed/vocabulary.parquet b/data-raw/GiBleed_5.3/GiBleed/vocabulary.parquet new file mode 100644 index 0000000..516fd6d Binary files /dev/null and b/data-raw/GiBleed_5.3/GiBleed/vocabulary.parquet differ diff --git a/data-raw/internalData.R b/data-raw/internalData.R index 1628938..5a1617f 100644 --- a/data-raw/internalData.R +++ b/data-raw/internalData.R @@ -1,6 +1,7 @@ library(dplyr) library(here) library(readr) +library(arrow) # add the default mock vocabulary data mockDrugStrength <- readr::read_csv( @@ -150,6 +151,10 @@ namesTable <- dplyr::tribble( NA ) +#read in giBleed +gibleed <- readTables(here::here("data-raw","GiBleed_5.3","GiBleed"), "5.3") + + usethis::use_data( mockDrugStrength, mockConcept, @@ -167,8 +172,10 @@ usethis::use_data( eunomiaConceptSynonym, namesTable, cdmTable, + gibleed, internal = TRUE, - overwrite = TRUE + overwrite = TRUE, + compress = "xz" ) mockDatasets <- dplyr::tribble( @@ -240,3 +247,5 @@ mockDatasets <- mockDatasets |> dplyr::left_join(x, by = "dataset_name") usethis::use_data(mockDatasets, overwrite = TRUE) + +