R dbGetQuery insert blob data with other text data - sql

Question

library(DBI)
library(RSQLite)
db <- dbConnect(RSQLite::SQLite(), ":memory:")
dbExecute(db , "create table if not exists drug_rank (
_id integer primary key autoincrement,
pertData_type text,
pertData_name text,
pathway_name text,
drug_name text,
drug_rank_RData blob
)"
)
I want to insert the data using a prepared statement. I have all the drug_rank_RData saved as .RData, which essentially is a list, I want to put them all in the database. How can I do so?
I tried the following but does not work:
df <- list(a =c(1, 2,3), b = c(2, 4, 6), c = c(3, 6, 9)) |> as.data.frame()
drug_rank_obj <- list(sig_drugs = df, name = "test_drug_rank_obj")
dbGetQuery(db,
"insert into drug_rank values (?, ?, ?, ?, ?, ?)",
params = list(
1,
"test type",
"test name",
"test pathway",
"test drugname",
drug_rank_obj
)
)
Thank you.

Answer 1

The only issue is that you need to serialize your data into a binary format in order to insert it into a blog. This example should work
library(DBI)
library(RSQLite)
db <- dbConnect(RSQLite::SQLite(), ":memory:")
dbExecute(db , "create table if not exists drug_rank (
_id integer primary key autoincrement,
name text,
object blob)"
)
# serialize data to binary
drug_rank_obj <- list(a =c(1, 2,3), b = c(2, 4, 6), c = c(3, 6, 9)) |>
as.data.frame() |> serialize(NULL)
# insert into data base
dbExecute(db,
"insert into drug_rank values (?, ?, ?)",
params = list(1, "my data", list(drug_rank_obj))
)
## retrieve data
rows <- dbGetQuery(db, "select * from drug_rank where _id==?",
params=list(1))
## un-serialize data into object
data <- unserialize(rows$object[[1]])
When doing an insert, use dbExecute rather than dbGetQuery