I'm accessing a PostgreSQL database through the R library RPostgreSQL. The following line successfully reads my table into object DF:
DF <- dbReadTable(conn = con, name = c("my_schema","my_table"))
However, attempting to write back into the database with the following line throws ERROR: permission denied for schema my_schema:
dbWriteTable(conn = con, name = c("my_schema", "my_table"), value = DF)
I've discovered from the question Writing to specific schemas with RPostgreSQL that the solution is to SET search_path = my_schema, public;, but I have no idea how to run this from the R Console. I've tried lines such as dbSendQuery(conn = con, statement = "SET search_path = my_schema, public;"), and I recognize that setting permissions is not querying at all, but there's not a dbSetPermissions function in RPostgreSQL.
I'm clearly missing something fundamental since the answer to the aforementioned question satisfied the user who asked it, so I appreciate your patience.
Related
The rquery package has been out for some time now, but the documentation is still very sparse. There isn't even a tag yet in SO, this question will create it.
Maybe there is someone who can help me nevertheless.
I want to connect to a schema in my Postgres-DB via rqueryto read the data into R with all the speed it promises.
Using this code it works with all the tables in the public-schema.
library(RPostgres)
library(rquery)
con <- dbConnect(RPostgres::Postgres(),
host = #####,
dbname = #####,
user = #####,
password = ######)
df <- db_td(con, "tablename") %.>%
execute(con, .)
Now when I want to access a table in a specific schema db_td() has the argument qualifiers = which is an
optional named ordered vector of strings carrying
additional db hierarchy terms,such as schema
So I did:
db_td(db, "tablename", qualifiers = c(schema = "schema"))
But:
Error in result_create(conn#ptr, statement) : Failed to prepare
query: FEHLER: Relation »tablename« existiert nicht LINE 1: SELECT
* FROM "tablename" LIMIT 1
So the qualifiers = argument seems to be completely ignored.
My question is thus pretty basic:
How can I connect to a schema in a PostgresDB via rquery?
all my attempts to solve this "within" rquery seem to fail miserably, but you can work around it by doing something like:
dbExecute(con, "SET search_path = foo_schema, public;")
before you run db_td.
I think it's caused by rq_colnames doing:
paste0("SELECT * FROM ", quote_identifier(db, table_name),
" LIMIT 1")
and hence not doing anything with its qualifiers, at least this matches the error I get back.
maybe report a bug/issue with rquery if this isn't enough
I have created an issue on github. So far regular rquery indeed doesn't have schema ability. The development version of rquery (1.3.4) however has, as of today, basic schema ability.
To be installed via:
library(devtools)
install_github("WinVector/rquery", host = "https://api.github.com")
Here's a small instruction. Seems to have been inteded to work just as I was trying in my question.
Be careful though, rquery hasn't been fully tested in schema-mode and some things might not work.
EDIT: rquery now has full schema support.
Background:
I use dbplyr and dplyr to extract data from a database, then I use the command dbSendQuery() to build my table.
Issue:
After the table is built, if I run another command I get the following warning:
Warning messages:
1. In new_result(connection#ptr, statement): Cancelling previous query
2. In connection_release(conn#ptr) :
There is a result object still in use.
The connection will be automatically released when it is closed.
Question:
Because I don’t have a result to fetch (I am sending a command to build a table) I’m not sure how to avoid this warning. At the moment I disconnect after building a table and the error goes away. Is there anything I can do do to avoid this warning?
Currently everything works, I just have this warning. I'd just like to avoid it as I assume I should be clearing something after I've built my table.
Code sample
# establish connection
con = DBI::dbConnect(<connection stuff here>)
# connect to table and database
transactions = tbl(con,in_schema(“DATABASE_NAME”,”TABLE_NAME”))
# build query string
query_string = “SELECT * FROM some_table”
# drop current version of table
DBI::dbSendQuery(con,paste('DROP TABLE MY_DB.MY_TABLE'))
# build new version of table
DBI::dbSendQuery(con,paste('CREATE TABLE PABLE MY_DB.MY_TABLE AS (‘,query_string,’) WITH DATA'))
Even though you're not retrieving stuff with a SELECT clause, DBI still allocates a result set after every call to DBI::dbSendQuery().
Give it a try with DBI::dbClearResult() in between of DBI::dbSendQuery() calls.
DBI::dbClearResult() does:
Clear A Result Set
Frees all resources (local and remote) associated with a
result set. In some cases (e.g., very large result sets) this
can be a critical step to avoid exhausting resources
(memory, file descriptors, etc.)
The example of the man page should give a hint how the function should be called:
con <- dbConnect(RSQLite::SQLite(), ":memory:")
rs <- dbSendQuery(con, "SELECT 1")
print(dbFetch(rs))
dbClearResult(rs)
dbDisconnect(con)
Error unserializing model object in Greenplum via PL/R
I store model objects in a greenplum database (the open source version) and I've successfully been able to serialize my model objects, insert them into a table in greenplum and unserialize when needed, but using R version 3.5 installed on my machine (local). This is the R code below that runs successfully:
Code:
fromtable = 'modelObjDevelopment'
mod.id = '7919'
model_obj <-
dbGetQuery(conn,
sprintf("SELECT val from standard.%s where model_id::int = '%s';",
fromtable, mod.id))
iter_model <- postgresqlUnescapeBytea(model_obj)
lm_obj_back <- unserialize(iter_model)
summary(lm_obj_back)
Recently, I have installed PL/R on greenplum with all the necessary libraries that I generally use. I am attempting to recreate the code I use in local R (mentioned above) to run on greenplum. After much research I have been trying to run the following transformed code, which relentlessly keeps failing and giving me the same error.
Code:
DROP FUNCTION IF EXISTS mdl_load(val bytea);
CREATE FUNCTION mdl_load(val bytea)
RETURNS text AS
$$
require("RPostgreSQL")
iter_model<-postgresqlUnescapeBytea(val)
model<-unserialize(iter_model)
return(length(val))
$$
LANGUAGE 'plr';
select length(val::bytea) as len, mdl_load(val) as t
from modelObjDevelopment
where model_id::int = 7919
At this point I don't care what I return, I just want the unserialize function to work.
Error:
[22000] ERROR: R interpreter expression evaluation error Detail: Error in unserialize(iter_model) : unknown input format Where: In PL/R function mdl_load
Hope someone had a similar issue and might have a clue for me. It seems that the bytea object changes size after being passed into Pl/R. I am new to this method and hope someone can help.
$$
require(RPostgreSQL)
## load the PostgresSQL driver
drv <- dbDriver("PostgreSQL")
## connect to the default db
con <- dbConnect(drv, dbname = 'XXX')
rows<-dbGetQuery(con, 'SELECT encode(val::bytea,'escape') from standard.modelObjDevelopment where model_id::int=1234')
iter_model<-postgresqlUnescapeBytea(rows[[model_obj_column]])
model<-unserialize(iter_model)
$$
We solved this problem together. For future people coming to this site, get and unserialize model object inside R code is the way to go.
I am trying to transfer data from the Thingspeak API into a postgres database. The API limits each request to 8000 observations, but I need to pull millions! I'm using R to iteratively pull from the API, do a bunch of wrangling, and then submit the results as a data.frame to my table within the db.
The current way I am doing this relies on the dbWriteTable() function from the RPostgres package. However, this method does not account for existing observations in the db. I have to manually DELETE FROM table_name before running the script or I'll end up writing duplicate observations each time I try to update the db. I'm still wasting time re-writing observations that I deleted, and the script takes ~2 days to complete because of this.
I would prefer a script that incorporates the functionality of postgres-9.5' ON CONLFICT DO NOTHING clause, so I don't have to waste time re-uploading observations that are already within the db. I've found the st_write() and st-read() functions from the sf packages to be useful for running SQL queries directly from R, but have hit a roadblock. Currently, I'm stuck trying to upload the 8000 observations within each df from R to my db. I am getting the following error:
Connecting to database:
# db, host, port, pw, and user are all objects in my R environment
con <- dbConnect(drv = RPostgres::Postgres()
,dbname = db
,host = host
,port = port
,password = pw
,user = user)
Current approach using RPostgres:
dbWriteTable(con
,"table_name"
,df
,append = TRUE
,row.names = FALSE)
New approach using sf:
st_write(conn = conn
,obj = df
,table = 'table_name'
,query = "INSERT INTO table_name ON CONFLICT DO NOTHING;"
,drop_table = FALSE
,try_drop = FALSE
,debug = TRUE)
Error message:
Error in UseMethod("st_write") :
no applicable method for 'st_write' applied to an object of class "c('tbl_df', 'tbl', 'data.frame')"
Edit:
Converting to strictly a dataframe, i.e. df <- as.data.frame(df) or attributes(df)$class <- "data.frame", resulted in a similar error message, only without the tbl_df or tbl classes.
Most recent approach with sf:
I'm making some progress with using st_write() by changing to the following:
# convert geom from WKT to feature class
df$geom <- st_as_sfc(df$geom)
# convert from data.frame to sf class
df <- st_as_sf(df)
# write sf object to db
st_write(dsn = con # changed from drv to dsn argument
,geom_name = "geom"
,table = "table_name"
,query = "INSERT INTO table_name ON CONFLICT DO NOTHING;"
,drop_table = FALSE
,try_drop = FALSE
,debug = TRUE
)
New Error:
Error in result_create(conn#ptr, statement) :
Failed to fetch row: ERROR: type "geometry" does not exist at character 345
I'm pretty sure that this is because I have not yet installed the PostGIS extension within my PostgreSQL database. If anyone could confirm I'd appreciate it! Installing PostGIS a pretty lengthy process, so I won't be able to provide an update for a few days. I'm hoping I've solved the problem with the st_write() function though!
Debugging the R script I have come across a strange error: “Error in debug(fun, text, condition) : argument must be a closure”.
PC features: Win7/64 bit, Oracle client 12 (both 32 and 64bit), R (64bit)
Earlier the script has been debugged well without errors. I have looked for a clue in the Inet but have found no clear explanation what the mistake is and how to remove it.
Running the script as a plain script but not a function produces no errors.
I would be very grateful for your ideas
The source script (connection to oracle DB and executing a simple query)as follows (conects to Oracle DB and execute the query:
download1<-function(){
if (require("dplyr")){
#install.packages("dplyr")
}
if (require("RODBC")){
#install.packages("RODBC")
}
library(RODBC)
library(dplyr)
# to establish connection with DB or schema
con <- odbcConnect("DB", uid="ANALYTICS", pwd="122334fgcx", rows_at_time = 500,believeNRows=FALSE)
# Check that connection is working (Optional)
odbcGetInfo(con)
# Query the database and put the results into the data frame "dataframe"
ptm <- proc.time()
x<-sqlQuery(con, "select * from my_table")
proc.time()-ptm
# to extract all field names to the separate vector
#field_names<-sqlQuery(con,"SELECT column_name FROM all_tab_cols WHERE table_name = 'MY_TABLE'")
close(con)
}
debug(download1(),text = "", condition = NULL)
Use
debug(download1)
download1()