I've got a simple dataframe with three columns. One of the columns contains a database name. I first need to check if data exists, and if not, insert it. Otherwise do nothing.
Sample data frame:
clientid;region;database
135;Europe;europedb
2567;Asia;asiadb
23;America;americadb
So I created a function to apply to dataframe this way:
library(RMySQL)
check_if_exist <- function(df){
con <- dbConnect(MySQL(),
user="myuser", password="mypass",
dbname=df$database, host="myhost")
query <- paste0("select count(*) from table where client_id='", df$clientid,"' and region='", df$region ,"'")
rs <- dbSendQuery(con, query)
rs
}
Function call:
df$new_column <- lapply(df, check_if_exist)
But this doesn't work.
This is a working example of what you are asking, if I understood correctly. But I don't have your database, so we just print the query for verification, and fetch a random number as the result.
Note that by doing lapply(df,...), you are looping over the columns of the database, and not the rows as you want.
df = read.table(text="clientid;region;database
135;Europe;europedb
2567;Asia;asiadb
23;America;americadb",header=T,sep=";")
check_if_exist <- function(df){
query = paste0("select count(*) from table where client_id='", df$clientid,"' and region='", df$region ,"'")
print(query)
rs <- runif(1,0,1)
return(rs)
}
df$new_column <- sapply(split(df,seq(1,nrow(df))),check_if_exist)
Hope this helps.
Related
Using R's DBI, I need to:
run a parametrized query with different parameters (i.e. a vector of parameters);
get the results sets concatenated (i.e. rbinded as per R terminology or unioned as per SQL terminology);
and get the resulting table in the database for further manipulation.
dbBind/dbGetquery fullfils requirements 1 and 2, but I then need to write the resulting data frame to the database using dbWriteTable, which is ineficient:
library(DBI)
con <- dbConnect(RSQLite::SQLite(), ":memory:")
dbWriteTable(con, "iris", iris)
res <- dbGetQuery(con,
"select * from iris where Species = ?",
params = list(c("setosa", "versicolor")))
dbWriteTable(con, "mytable", res)
Conversely, dbExecute fulfils requirement 3, but I don't think it has the "rbind feature". Of course, this throw an error because the table would get overwritten:
dbExecute(con,
"create table mytable as select * from iris where Species = ?",
params = list(c("setosa", "versicolor")))
What is the most efficient/recommended way of doing so?
Notes:
I am not the DBA and can only access the database through R.
My example is too trivial and could be achieved in a single query. My use case really requires a parametrized query to be run multiple times with different parameters.
I have to use Oracle, but I am interested in a solution even if it don't works with Oracle.
1) Create the table with the first parameter and then insert each of the others into it.
library(RSQLite)
con <- dbConnect(SQLite())
dbWriteTable(con, "iris", iris)
parms <- c("setosa", "versicolor")
dbExecute(con, "create table mytable as
select * from iris where Species = ?",
params = parms[1])
for (p in parms[-1]) {
dbExecute(con, "insert into mytable
select * from iris where Species = ?",
params = p)
}
# check
res <- dbGetQuery(con, "select * from mytable")
str(res)
2) Alternately generate the text of an SQL statement to do it all. sqldf pulls in RSQLite and gsubfn which supplies fn$ that enables the text substitution.
library(sqldf)
con <- dbConnect(SQLite())
dbWriteTable(con, "iris", iris)
parms <- c("setosa", "versicolor")
parmString <- toString(sprintf("'%s'", parms))
fn$dbExecute(con, "create table mytable as
select * from iris where Species in ($parmString)")
# check
res <- dbGetQuery(con, "select * from mytable")
str(res)
3) A variation of (2) is to insert the appropriate number of question marks.
library(sqldf)
con <- dbConnect(SQLite())
dbWriteTable(con, "iris", iris)
params <- list("setosa", "versicolor")
quesString <- toString(rep("?", length(params)))
fn$dbExecute(con, "create table mytable as
select * from iris where Species in ($quesString)", params = params)
# check
res <- dbGetQuery(con, "select * from mytable")
str(res)
Based on #r2evans comment and #G.Grothendieck answer, instead of query/download/combine/upload, I used a parameterized query that inserts directly into a table.
First, I created the table with the appropriate columns to collect the results:
library(DBI)
con <- dbConnect(RSQLite::SQLite(), ":memory:")
create_table <-
"CREATE TABLE warpbreaks2 (
breaks real,
wool text,
tension text
)"
dbExecute(con, create_table)
Then I executed an INSERT INTO step:
dbWriteTable(con, "warpbreaks", warpbreaks)
insert_into <-
"INSERT INTO warpbreaks2
SELECT warpbreaks.breaks,
warpbreaks.wool,
warpbreaks.tension
FROM warpbreaks
WHERE tension = ?"
dbExecute(con, insert_into, params = list(c("L", "M")))
This is a dummy example for illustration purpose. It could be achieve more directly with e.g.:
direct_query <-
"CREATE TABLE warpbreaks3 AS
SELECT *
FROM warpbreaks
WHERE tension IN ('L', 'M')"
dbExecute(con, direct_query )
I have an SQL script which I need to run using R Studio. However, my SQL script has one variable that is defined in my R environment. I am using dbGetQuery; however, I do not know (and I didn't find a solution) how to pass these variables.
library(readr)
library(DBI)
library(odbc)
library(RODBC)
#create conection (fake one here)
con <- odbcConnect(...)
dt = Sys.Date()
df = dbGetQuery(.con, statement = read_file('Query.sql'))
The file 'Query.sql' makes reference to dt. How do I make the file recognize my variable dt?
There are several options, but my preferred is "bound parameters".
If, for instance, your 'Query.sql' looks something like
select ...
from MyTable
where CreatedDateTime > ?
The ? is a place-holder for a binding.
Then you can do
con <- dbConnect(...) # from DBI
df = dbGetQuery(con, statement = read_file('Query.sql'), params = list(dt))
With more parameters, add more ?s and more objects to the list, as in
qry <- "select ... where a > ? and b < ?"
newdat <- dbGetQuery(con, qry, params = list(var1, var2))
If you need a SQL IN clause, it gets a little dicey, since it doesn't bind things precisely like we want.
candidate_values <- c(2020, 1997, 1996, 1901)
qry <- paste("select ... where a > ? and b in (", paste(rep("?", length(candidate_values)), collapse=","), ")")
qry
# [1] "select ... where a > ? and b in ( ?,?,?,? )"
df <- dbGetQuery(con, qry, params = c(list(avar), as.list(candidate_values)))
If I want to create a new column containing observation numbers with data frames I can,
mtcars %>% mutate(i=row_number())
But row_number() does not work with sql tables.
mydb <- dbConnect(RSQLite::SQLite(), "")
dbWriteTable(mydb, "mt", mtcars)
mt.sql=tbl(mydb, "mt")
mt.sql %>% mutate(i=row_number())
Error:
Window function row_number() is not supported by this database
Would there be any other ways around this problem?
You could work around it by using SQLite syntax like this
RSQLite::dbSendQuery(mydb, "ALTER TABLE mt ADD COLUMN i INTEGER")
RSQLite::dbSendQuery(mydb, "UPDATE mt SET (i) = ROWID")
Then you can go on using dplyr syntax like after re-assigning mt from your db connection to the mt.sql object.
mt.sql=tbl(mydb, "mt")
mt.sql %>% select(mpg, i) # e.g.
SQLite doesn't support row number function.
Did you try mtcars %>% mutate(i=row_number(desc(disp)))?
It works for me even in SQL.
This question already has answers here:
How to use a variable name in a SQL statement?
(5 answers)
Closed 9 years ago.
Im extracting some data from a table using sql select statment in R,
query <- "select * from MyTable where TimeCol='6/29/2012 21:05' ";
result <- fn$sqldf(query);
The above code gives correct results, but when the time value is saved in variable, it doesn't works
mytime <- "6/29/2012 21:05";
query <- "select * from MyTable where TimeCol = $mytime"; # OR
query <- "select * from MyTable where TimeCol = $[mytime]"; # OR
query <- "select * from MyTable where TimeCol = '$[mytime]' ";
result <- fn$sqldf(query);
None of the above three lines is working
View(result) it gives the error: invalid 'x' argument
$[] and $() are not valid syntax and the quotes that were around the time string in the first instance of query in the post are missing in the subsequent instances so a correct version would be:
library(sqldf)
mytime <- "6/29/2012 21:05"
MyTable <- data.frame(TimeCol = mytime)
query <- "select * from MyTable where TimeCol = '$mytime' "
fn$sqldf(query)
Although the answer I linked to in a comment uses a different function to query the data.frame, the principle is the same: paste the variable to the rest of your select string, ensuring quotes are included when necessary (using shQuote), then pass that character string to your sql querying function of choice.
query <- paste0("select * from MyTable where TimeCol = ", shQuote(mytime))
result <- fn$sqldf(query)
The semicolons at the ends of your lines probably aren't necessary.
As Joran mentions in a comment, sprintf could also be used (perhaps with a gain in readability in case there are many variable components in your query string):
sprintf("select * from MyTable where %s = '%s'", "TimeCol", mytime)
# [1] "select * from MyTable where TimeCol = '6/29/2012 21:05'"
I've looked at the 'Pass R variable to RODBC's sqlQuery with multiple entries? ' already but can't seem to get it to work. I'm trying to do an sqlQuery() from R on a SQL Server 2008 R2 db. I'm trying to get a sample from a large db based on row numbers. First I created a list of random numbers:
sampRowNum <- sample(seq(1,100000,1), 5000)
Then I try to use those numbers in a query using:
query1 <- sqlQuery(channel, paste("select *
FROM db where row_id in (", sampRowNum,")", sep=""))
I get just the results from the db where the row_id is equal to the first number in sampRowNum. Any suggestions?
You're not pasteing your query together correctly.
If you run the paste statement in isolation, you'll see that you get a vector of length 5000, so sqlQuery is only executing the first one of those, corresponding to the first element in samRowNum.
What you want to do is something more like this:
paste("select * FROM db where row_id in (",
paste(sampRowNum,collapse = ","),")", sep="")
Just as an added note (and since I've had to do stuff like this a lot...) constructing sql queries with an IN clause with strings is a bit more of a nuisance, since you have to tack on all the single quotes:
vec <- letters[1:5]
paste("SELECT * FROM db WHERE col IN ('",
paste(vec,collapse = "','"),"')",sep = "")
[1] "SELECT * FROM db WHERE col IN ('a','b','c','d','e')"
If you do this a lot, you'll end up writing a little function that does that pasting of character vectors for you.
As always, this kind of SQL string manipulation is Not Good if you are dealing with user inputs (e.g. in a web app), due to SQL injection attacks. In my particular situation this isn't much of a concern, but in general people will prefer parametrized queries if you don't have much control over the input values.