Making an iterative query to an SQL database - r

I'm trying to get to make a query from R to a MySQL database. The query iterates over a list, and therefore changes dynamically. Each query based on each element in the list will also in general result in multiple rows being extract. The database I'm using can be downloaded from here: http://www.ghtorrent.org/msr14.html
In the end of the day all the results should end up in the same output, and look like this:
pull_req_id,user,action,created_at
12359,arthurnn,opened,1380126837
12359,rafaelfranca,discussed,1380127245
12359,arthurnn,discussed,1380127676
...
The code that I have now looks like this, but it's not working:
library(DBI)
library(RMySQL)
m <- dbDriver("MySQL");
con <- dbConnect(m, user='msr14', password='msr14', host='localhost', dbname='msr14');
all_rails_projects <- dbGetQuery(con, 'SELECT * FROM projects WHERE name = "rails";')
all_rails_prs <- dbGetQuery(con, 'SELECT id FROM pull_requests WHERE base_repo_id = 78852;')
out <- nrow(all_rails_prs)
names(out) <- as.list(all_rails_prs)
df <- c('pull_req_id', 'user', 'action', 'created_at')
out <- numeric(length(df))
names(out) <- df
for (i in nrow(all_rails_prs)) {
SQL <- paste("select user, action, created_at from
(
select prh.action as action, prh.created_at as created_at, u.login as user
from pull_request_history prh, users u
where prh.pull_request_id ='", all_rails_prs[i,], "'",
" and prh.actor_id = u.id
union
select ie.action as action, ie.created_at as created_at, u.login as user
from issues i, issue_events ie, users u
where ie.issue_id = i.id
and i.pull_request_id ='", all_rails_prs[i,], "'",
" and ie.actor_id = u.id
union
select 'discussed' as action, ic.created_at as created_at, u.login as user
from issues i, issue_comments ic, users u
where ic.issue_id = i.id
and u.id = ic.user_id
and i.pull_request_id ='", all_rails_prs[i,], "'",
"union
select 'reviewed' as action, prc.created_at as created_at, u.login as user
from pull_request_comments prc, users u
where prc.user_id = u.id
and prc.pull_request_id ='", all_rails_prs[i,], "'",
") as actions
order by created_at;", sep = "")
res <- dbGetQuery(con, SQL)
out[i] <- dbFetch(res, n = -1)
}
This generates the following error message:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘dbFetch’ for signature ‘"data.frame"’
In addition: Warning message:
In mysqlExecStatement(conn, statement, ...) :
RS-DBI driver warning: (unrecognized MySQL field type 7 in column 2 imported as character)
I've tried different variants, but they all result in some kind of error, so it seems as if I'm simply not setting up the query structure the right way. Anyone has any advice?

According to the docs, dbGetQuery calls fetch by default if the query is successful.
res is already a database and you can put it into out directly without having to fetch the records.
Also, if you want to store the results in a dataframe and not a list, you might want to try:
#get the results
res<-dbGetQuery(con, SQL)
#if it's not null, add the request id and rbind it to the out dataframe
if(!is.null(res)){
out<-rbind(out,cbind(rep(all_rails_prs[i,],nrow(res)),res))
}
There might also be an error in your for syntax, you might need for (i in 1:nrow(all_rails_prs))

Related

Join a data frame (or other R object) to a table in a read-only Postgresql database?

I have read-only access to a Postgres database. I can not write to the database.
Q. Is there a way to construct and run a SQL query where I join a data frame (or other R object) to a table in a read-only Postgres database?
This is for accessing data from WRDS, https://wrds-www.wharton.upenn.edu/
Here's an attempt at pseudocode
#establish a connection to a database
con <- dbConnect( Postgres(),
host = 'host.org',
port = 1234,
dbname = 'db_name',
sslmode = 'require',
user = 'username', password = 'password')
#create an R dataframe (or other object)
df <- data.frame( customer_id = c('a123', 'a-345', 'b0') )
#write a sql query we will run
sql_query <- "
SELECT t.customer_id, t.* FROM df t
LEFT JOIN table_name df
on t.customer_id = df.customer_id
"
my_query_results <- dbSendQuery(con, sql_query)
temp <- dbFetch(res, n = 1)
dbClearResult(res)
my_query_results
Note and edit: The example query I provided is intentionally super simple for example purposes.
In my actual queries, there might be 3 or more columns I want to join on, and millions of rows I want to join on.
Use the copy_inline function from the dbplyr package, which was added following an issue filed on this topic. See also the question here.
An example of its use is found here.
If your join is on a single condition, it can be rewritten using an in clause:
In SQL:
SELECT customer_id
FROM table_name
WHERE customer_id in ('a123', 'a-345', 'b0')
Programmatically from R:
sql_query = sprintf(
"SELECT customer_id
FROM table_name
WHERE customer_id in (%s)",
paste(sQuote(df$customer_id, q = FALSE), collapse = ", ")
)

Insert R list into RPostgreSQL query

I'm running a postgreSQL query based on an automated list of ID's stored in an R list. I'm trying to determine how to include that R list in my query so I don't have to hard-code the ID's each time I run my query.
For example, I have a script that produces the list
id <- c("001","002","003")
and my query looks something like this:
SELECT *
FROM my_query
WHERE my_query.id_col IN ('001', '002', '003')
which I run using Rpostgres:
library(Rpostgres)
snappConnection <- DBI::dbConnect(RPostgres::Postgres(),
host = "host",
dbname = "dbname",
user = "user",
password = "pword",
port = 0000)
core.data <- dbGetQuery(conn = snappConnection,statement = SELECT * FROM my_query WHERE my_query.id_col IN ('001', '002', '003'))
Is there a way to reference my "id" list from R in my query so that when "id" updates to new values, the query also updates to those new values?
glue_sql from glue package should work:
query <- glue::glue_sql("
SELECT *
FROM my_query
WHERE my_query.id_col IN ({id*})
", .con = snappConnection)
core.data <- dbGetQuery(conn = snappConnection, statement = query)
#dave-edison's answer solved my problem. Concurrent to trying his, I got this to work.
I saved the query below as "my_query.sql"
SELECT *
FROM my_query
WHERE my_query.id_col IN ('string_to_replace')
then created a string and used gsub on the string.
library(tidyverse)
temp.script <- read_file("my_query.sql")
core.data.script <- gsub('string_to_replace',paste0(id,collapse = "', '"),temp.script)
From there I just ran my RPostgres script like above.

R, ClickHouse: Expected: FixedString(34). Got: UInt64: While processing

I am trying to query data from ClickHouse database from R with subset.
Here is the example
library(data.table)
library(RClickhouse)
library(DBI)
subset <- paste(traffic[,unique(IDs)][1:30], collapse = ',')
conClickHouse <- DBI::dbConnect('here is the connection')
DataX <- dbgetdbGetQuery(conClickHouse, paste0("select * from database
and IDs in (", subset ,") ", sep = "") )
As a result I get error:
DB::Exception: Type mismatch in IN or VALUES section. Expected: FixedString(34).
Got: UInt64: While processing (IDs IN ....
Any help is appreciated
Thanks to the comment of #DennyCrane,
"select * from database where toFixedString(IDs,34) in
(toFixedString(ID1, 34), toFixedString(ID2,34 ))"
This query subset properly
https://clickhouse.tech/docs/en/sql-reference/functions/#strong-typing
Strong Typing
In contrast to standard SQL, ClickHouse has strong typing. In other words, it doesn’t make implicit conversions between types. Each function works for a specific set of types. This means that sometimes you need to use type conversion functions.
https://clickhouse.tech/docs/en/sql-reference/functions/type-conversion-functions/#tofixedstrings-n
select * from (select 'x' B ) where B in (select toFixedString('x',1))
DB::Exception: Types of column 1 in section IN don't match: String on the left, FixedString(1) on the right.
use casting toString or toFixedString
select * from (select 'x' B ) where toFixedString(B,1) in (select toFixedString('x',1))

Programmatically building SQL Query R/Shiny/RODBC

I'm building a SQL Query statement using inputDateRange() in R/Shiny. My issue is in handling various strings to include the dates into the WHERE condition of the SQL:
Here is my code:
t.query <- paste0("Select [sensor_name], [temperature] from [dbo].
[temperature_sensor] where network_id = '24162' and date > "
, sQuote(format(input$my.dateRange[1], format="%d-%m-%Y"))
, " and date < "
, sQuote(format(input$my.dateRange[2], format="%d-%m-%Y"))
)
Now the statement closes with a single quote and I receive the error below:
42000 102 [Microsoft][ODBC Driver 13 for SQL Server][SQL
Server]Incorrect syntax near '‘'. [RODBC] ERROR: Could not
SQLExecDirect 'Select [sensor_name], [temperature] from
[dbo].[temperature_sensor] where network_id = '24162' and date >
‘18-09-2017’ and date < ‘22-09-2017’'
I need to close the string with " as I started it in "select ...., I tried to explicitly add """ or dQuote("") to concatenate " but I'm still encountering an error.
Any advice is highly appreciated?
I'd recommend using RODBCext, which will allow you to parameterize your query as
library(RODBCext)
channel <- odbcConnect(...) # make your connection object here
Data <-
sqlExecute(channel = channel,
query = "Select [sensor_name], [temperature]
from [dbo].[temperature_sensor]
where network_id = ? and date between ? and ?",
data = list('24162',
format(input$my.dateRange[1],
format = "%Y-%m-%d"),
format(input$my.dateRange[2],
format = "%Y-%m-%d")),
fetch = TRUE,
stringsAsFactors = FALSE)
This approach has a lot of advantages, including removing the frustration of matching quotes (which you shouldn't do because of the next reason), and protecting your data against SQL injection.

Using variable in "IN" function of SQL query in R

I am having a variable x which contains 20000 IDs. I want to write a sql query like,
select * from tablename where ID in x;
I am trying to implement this in R where I can get the values only for IDs in x variable. The following is my try,
dbSendQuery(mydb, "select * from tablename where ID in ('$x') ")
I am not getting any error while trying this. But it is returning 0 values.
Next tried using
sprintf("select * from tablename where ID in %s",x)
But this is creating 20000 individual queries which could prove costly in DB.
Can anybody suggest me a way to write a command, which would loop through IDs in x and save to a Dataframe in R in a single query?
You need to have the codes in the actual string. Here is how I would do it with gsub
x <- LETTERS[1:3]
sql <- "select * from tablename where ID in X_ID_CODES "
x_codes <- paste0("('", paste(x, collapse="','"), "')")
sql <- gsub("X_ID_CODES", x_codes, sql)
# see new output
cat(sql)
select * from tablename where ID in ('A','B','C')
# then submit the query
#dbSendQuery(mydb, sql)
How about pasting it:
dbSendQuery(mydb, paste("select * from tablename where ID in (", paste(x, collapse = ","), ")"))

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