mirai - Databases and Arrow • mirai

Database Hosting - The Basics

mirai supports the hosting of multiple database connections across processes on the local machine or a remote server. everywhere() easily sets up identical database connections in each daemon process.

The following represents a simple example, which sets up 2 local daemons, and then opens a connection to the same SQLite file database in each daemon.

file <- tempfile()
library(mirai)

daemons(2)

## [1] 2

everywhere({
  library(DBI)
  con <<- dbConnect(RSQLite::SQLite(), file)
}, file = file)

mirai() calls may then be used to write to or query the database, and may be executed on either daemon.

m <- mirai(dbWriteTable(con, "iris", iris))
call_mirai(m)$data

## [1] TRUE

m <- mirai(dbListTables(con))
call_mirai(m)$data

## [1] "iris"

m <- mirai(dbGetQuery(con, 'SELECT * FROM iris WHERE "Sepal.Length" < 4.6'))
call_mirai(m)$data

##   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1          4.4         2.9          1.4         0.2  setosa
## 2          4.3         3.0          1.1         0.1  setosa
## 3          4.4         3.0          1.3         0.2  setosa
## 4          4.5         2.3          1.3         0.3  setosa
## 5          4.4         3.2          1.3         0.2  setosa

everywhere() can be used again to cleanly tear down the databases, before resetting daemons.

everywhere(dbDisconnect(con))
daemons(0)

## [1] 0

Database Hosting - Using Arrow Database Connectivity

It is possible using the DBI interface to access and manipulate data in the Apache Arrow data format efficiently through ABDC (Arrow Database Connectivity).

The example below creates an in-memory SQLite connection using the adbcsqlite backend.

Serialization is set up with the relevant serialization and deserialization functions from the arrow package. Note that the format class is ‘nanoarrow_array_stream’ as nanoarrow is the backend for all queries made by the DBI db*Arrow() functions.

library(mirai)

daemons(1)

## [1] 1

everywhere({
  library(DBI) # `adbi` and `adbcsqlite` packages must also be installed
  con <<- dbConnect(adbi::adbi("adbcsqlite"), uri = ":memory:")
})

serialization(
  refhook = list(arrow::write_to_raw,
                 function(x) arrow::read_ipc_stream(x, as_data_frame = FALSE)),
  class = "nanoarrow_array_stream"
)

mirai() calls may then be used to write to or query the database all in the Arrow format.

m <- mirai(dbWriteTableArrow(con, "iris", iris))
call_mirai(m)$data

## [1] TRUE

m <- mirai(dbReadTableArrow(con, "iris"))
call_mirai(m)$data

## Table
## 150 rows x 5 columns
## $Sepal.Length <double>
## $Sepal.Width <double>
## $Petal.Length <double>
## $Petal.Width <double>
## $Species <string>

m <- mirai(dbGetQueryArrow(con, 'SELECT * FROM iris WHERE "Sepal.Length" < 4.6'))
call_mirai(m)$data

## Table
## 5 rows x 5 columns
## $Sepal.Length <double>
## $Sepal.Width <double>
## $Petal.Length <double>
## $Petal.Width <double>
## $Species <string>

Due to the tight integration of the mirai serialization mechanism with R’s ‘refhook’ system, we can easily return complex / nested objects containing multiple queries in the Arrow format:

m <- mirai({
  a <- dbGetQueryArrow(con, 'SELECT * FROM iris WHERE "Sepal.Length" < 4.6')
  b <- dbGetQueryArrow(con, 'SELECT * FROM iris WHERE "Sepal.Width" < 2.6')
  x <- dbGetQueryArrow(con, 'SELECT * FROM iris WHERE "Petal.Length" < 1.5')
  y <- dbGetQueryArrow(con, 'SELECT * FROM iris WHERE "Petal.Width" < 0.2')
  list(sepal = list(length = a, width = b), petal = list(length = x, width = y))
})
call_mirai(m)$data

## $sepal
## $sepal$length
## Table
## 5 rows x 5 columns
## $Sepal.Length <double>
## $Sepal.Width <double>
## $Petal.Length <double>
## $Petal.Width <double>
## $Species <string>
## 
## $sepal$width
## Table
## 19 rows x 5 columns
## $Sepal.Length <double>
## $Sepal.Width <double>
## $Petal.Length <double>
## $Petal.Width <double>
## $Species <string>
## 
## 
## $petal
## $petal$length
## Table
## 24 rows x 5 columns
## $Sepal.Length <double>
## $Sepal.Width <double>
## $Petal.Length <double>
## $Petal.Width <double>
## $Species <string>
## 
## $petal$width
## Table
## 5 rows x 5 columns
## $Sepal.Length <double>
## $Sepal.Width <double>
## $Petal.Length <double>
## $Petal.Width <double>
## $Species <string>

As before, everywhere() can be used again to cleanly tear down the databases, before resetting daemons.

everywhere(dbDisconnect(con))
daemons(0)

## [1] 0

Shiny / mirai / DBI / ADBC Integrated Example

The following is an example of how database connections hosted in mirai daemons may be used to power a Shiny app.

The one-time serialization() setup ensures seamless transport of Apache Arrow data, and occurs in the global environment outside of server().

A new database connection is created in a new daemon process for every new Shiny session. The resources are freed when a sesssion ends. This logic is all defined within server(). A unique ID is used to identify each session, and is specified as the ‘compute profile’ for daemons.

Non-dispatcher daemons are created as scheduling is not required (all queries expected to take roughly the same time, and in this case each session uses only one daemon anyway).

Shiny ExtendedTask is then used to perform each query via a mirai() call, using the session-specific compute profile.

library(mirai)
library(secretbase)
library(shiny)
library(bslib)

# write 'iris' dataset to temp database file (for this demonstration)
file <- tempfile()
con <- DBI::dbConnect(adbi::adbi("adbcsqlite"), uri = file)
DBI::dbWriteTableArrow(con, "iris", iris)
DBI::dbDisconnect(con)

# common input parameters
slmin <- min(iris$Sepal.Length)
slmax <- max(iris$Sepal.Length)

ui <- page_fluid(
  p("The time is ", textOutput("current_time", inline = TRUE)),
  hr(),
  h3("Shiny / mirai / DBI / ADBC demonstration"),
  p("New daemon-hosted database connection is created for every Shiny session"),
  sliderInput(
    "sl", "Query iris dataset based on Sepal Length", min = slmin, max = slmax,
    value = c(slmin, slmax), width = "75%"
  ),
  input_task_button("btn", "Return query"),
  tableOutput("table")
)

# uses Shiny ExtendedTask with mirai
server <- function(input, output, session) {

  # create unique session id by hashing current time with a random key
  id <- secretbase::siphash13(Sys.time(), key = nanonext::random(4L))

  # create new daemon for each session (set dispatcher = FALSE)
  daemons(1L, dispatcher = FALSE, .compute = id)

  # tear down daemon when session ends
  session$onEnded(function() daemons(0L, .compute = id))

  # everywhere() loads DBI and creates ADBC connection in each daemon
  everywhere(
    {
      library(DBI) # `adbi` and `adbcsqlite` packages must also be installed
      con <<- dbConnect(adbi::adbi("adbcsqlite"), uri = file)
    },
    file = file,
    .compute = id
  )

  output$current_time <- renderText({
    invalidateLater(1000)
    format(Sys.time(), "%H:%M:%S %p")
  })

  task <- ExtendedTask$new(
    function(...) mirai(
      dbGetQueryArrow(
        con,
        sprintf(
          "SELECT * FROM iris WHERE \"Sepal.Length\" BETWEEN %.2f AND %.2f",
          sl[1L],
          sl[2L]
        )
      ),
      ...,
      .compute = id
    )
  ) |> bind_task_button("btn")

  observeEvent(input$btn, task$invoke(sl = input$sl))

  output$table <- renderTable(task$result())

}

# serialization() specifies the native Arrow serialization functions
serialization(
  refhook = list(arrow::write_to_raw,
                 function(x) arrow::read_ipc_stream(x, as_data_frame = FALSE)),
  class = "nanoarrow_array_stream"
)

# run Shiny app
shinyApp(ui = ui, server = server)

# deletes temp database file (for this demonstration)
unlink(file)