library(BED)
library(jsonlite)
library(dplyr)
library(BDSTools)
source("helpers/loadMBObjects_fromTKCat.R")
## Config ----
config <- jsonlite::read_json("deploy_config.json")
config <- lapply(
config, function(x){
if(!is.character(x)){
return(x)
}else{
sub(pattern="___HOME___", replacement=Sys.getenv("HOME"), x = x)
}
}
)
config <- lapply(
config, function(x){
if(!is.character(x)){
return(x)
}else{
sub(pattern="___ROOT___", replacement=config$ROOT, x = x)
}
}
)
## Connection ----
connectToBed(
url=sprintf("localhost:%s", config$NJ_HTTP_PORT),
remember=FALSE,
useCache=TRUE,
importPath=config$BED_IMPORT
)
clearBedCache(force = TRUE, hard = TRUE)
## Add MetaBase identifiers ----
mb <- get_MDB(ap_rd_tkcat(), "MetaBase", check = FALSE)
loadMBObjects_fromTKCat(
orgOfInt = c("Homo sapiens", "Mus musculus", "Rattus norvegicus"),
tkmb = mb
)
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