ShinyLIMS: Core API fucntions

##tests


#for testing only - to be removed
library(testthat)
library(mongolite)
library(jsonlite)

print(getwd())

source("../lims_config.R")
source("../CreateScripts/create_metadb.R")
source("../CreateScripts/Create_dB.R")
source("../CreateScripts/drop_database.R")

creds <- readRDS("../CreateScripts/creds.RDS")


lims_database <- "lims_test"

#for testing only - to be removed


d <- drop_database(lims_database,creds)

expect_equal(d$ok,1)





lims <- lims_create(lims_database,creds,lims_types,valdoc)

test_that("created LIMS successful", {
expect_equal(lims$createdCollectionAutomatically,F)
}
)

lims_fail <- lims_create(lims_databas,creds,lims_types)

test_that("failed LIMS", {
  expect_equal(lims_fail,"Error Creating database")
   }
)


url_path = paste0("mongodb+srv://",creds$user,":",creds$pass,"@cluster0-wz8ra.mongodb.net/",lims_database)


metadb <- mongo(db=lims_database,url = url_path ,collection = "metadb",verbose = T)  

test_that("required fields work1", {

  entry <- data.frame(type="thing",count=1)
   
  expect_error(metadb$insert(entry))
  
  entry2 <- data.frame(name ="tube",table ="thingsdb",type="container",fields=paste("vol","format",sep=","),
                       fieldtype=paste("float","string",sep=","),fieldreq = paste("Y","N",sep=","),
                       bccount =as.integer(0),bcprefix="Tub",stringsAsFactors = F
                       )
  result <- metadb$insert(entry2)
  expect_equal(length(result$writeErrors) ,expected =  0)
  
})



test_that("required fields work2", {

entry3<- data.frame(name ="vial",table ="thingsdb",type="container",fields=paste("vol","format",sep=","),
                    fieldtype=paste("float","string",sep=","),fieldreq = paste("true","false",sep=","),
                    bccount =as.integer(0),bcprefix="Tub",stringsAsFactors = F
                    )

expect_error(metadb$insert(entry3))



entry4 <- data.frame(name ="vial",table ="thingsdb",type="container",fields=paste("vol","format",sep=","), 
                     fieldtype=paste("float","string",sep=","),fieldreq = paste("true","false",sep=","),
                      bccount =as.integer(0),bcprefix="Vial",stringsAsFactors = F
)

result <- metadb$insert(entry4)
expect_equal(length(result$writeErrors) ,expected =  0)


})
print("pausing")

Sys.sleep(3)

d <- drop_database(lims_database,creds)

expect_equal(d$ok,1)