How to connect to / get data from an already existing duckdb in-memory database `dplyr::tbl()` object? #445

marianschmidt · 2022-11-14T08:49:18Z

marianschmidt
Nov 14, 2022

I am currently trying to figure out how to connect to / get data from an already existing duckdb in-memory database that is an dplyr::tbl() object. Is this somehow possible?
Below is a small reprex, but the actual use case are larger-than-memory csv-files.

# Reprex How to connect to / get data from an already existing duckdb in-memory database?

library(pointblank)
#> Warning: Paket 'pointblank' wurde unter R Version 4.2.2 erstellt
library(DBI)
library(tidyverse)

write.csv(small_table, file = "s_table.csv")

#setting up a duckdb in memory access to the csv-file (actually to be used with larger than memory sized files)
duck <- dbConnect(duckdb::duckdb())
duckdb::duckdb_read_csv(conn = duck, name = "s_table", files = "s_table.csv")
tbl(duck, "s_table") %>% head()
#> # Source:   SQL [6 x 9]
#> # Database: DuckDB 0.5.1 [ga27jar@Windows 10 x64:R 4.2.1/:memory:]
#>       X date_time           date           a b         c          d e     f    
#>   <int> <chr>               <chr>      <int> <chr>     <chr>  <dbl> <lgl> <chr>
#> 1     1 2016-01-04 11:00:00 2016-01-04     2 1-bcd-345 3      3423. TRUE  high 
#> 2     2 2016-01-04 00:32:00 2016-01-04     3 5-egh-163 8     10000. TRUE  low  
#> 3     3 2016-01-05 13:32:00 2016-01-05     6 8-kdg-938 3      2343. TRUE  high 
#> 4     4 2016-01-06 17:23:00 2016-01-06     2 5-jdo-903 NA     3892. FALSE mid  
#> 5     5 2016-01-09 12:36:00 2016-01-09     8 3-ldm-038 7       284. TRUE  low  
#> 6     6 2016-01-11 06:15:00 2016-01-11     4 2-dhe-923 4      3291. TRUE  mid

#Let's try if pointblank can directly access
scan_data(tbl = tbl(duck, "s_table")) # :-( 
#> Error in `dplyr::pull()`:
#> ! Can't extract columns that don't exist.
#> ✖ Column `DATA_TYPE` doesn't exist.

#> Backtrace:
#>      ▆
#>   1. ├─pointblank::scan_data(tbl = tbl(duck, "s_table"))
#>   2. │ └─pointblank:::build_table_scan_page(...)
#>   3. │   └─sections %>% ...
#>   4. ├─base::lapply(...)
#>   5. │ └─pointblank (local) FUN(X[[i]], ...)
#>   6. │   └─pointblank:::probe_overview_stats_assemble(...)
#>   7. │     └─pointblank:::probe_overview_stats(data = data, lang = lang, locale = locale)
#>   8. │       └─pointblank:::get_tbl_information(tbl = data)
#>   9. │         └─pointblank:::get_tbl_information_dbi(tbl)
#>  10. │           └─... %>% tolower()
#>  11. ├─base::tolower(.)
#>  12. ├─dplyr::pull(., ifelse(tbl_src == "bigquery", "data_type", "DATA_TYPE"))
#>  13. ├─dplyr:::pull.data.frame(., ifelse(tbl_src == "bigquery", "data_type", "DATA_TYPE"))
#>  14. │ └─tidyselect::vars_pull(names(.data), !!enquo(var))
#>  15. │   └─tidyselect:::pull_as_location2(...)
#>  16. │     ├─tidyselect:::with_subscript_errors(...)
#>  17. │     │ └─rlang::try_fetch(...)
#>  18. │     │   └─base::withCallingHandlers(...)
#>  19. │     └─vctrs::vec_as_location2(...)
#>  20. │       ├─vctrs:::result_get(...)
#>  21. │       └─vctrs:::vec_as_location2_result(...)
#>  22. │         ├─base::tryCatch(...)
#>  23. │         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#>  24. │         │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#>  25. │         │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#>  26. │         └─vctrs::vec_as_location(i, n, names = names, arg = arg, call = call)
#>  27. └─vctrs (local) `<fn>`()
#>  28.   └─vctrs:::stop_subscript_oob(...)
#>  29.     └─vctrs:::stop_subscript(...)
#>  30.       └─rlang::abort(...)
# Should this work? According to documentation tbl can be a tbl_dbi object https://dbplyr.tidyverse.org/reference/tbl.src_dbi.html
s_table <- tbl(duck, "s_table")
class(s_table)
#> [1] "tbl_duckdb_connection" "tbl_dbi"               "tbl_sql"              
#> [4] "tbl_lazy"              "tbl"
scan_data(tbl = s_table) # :-( 
#> Error in `dplyr::pull()`:
#> ! Can't extract columns that don't exist.
#> ✖ Column `DATA_TYPE` doesn't exist.

#> Backtrace:
#>      ▆
#>   1. ├─pointblank::scan_data(tbl = s_table)
#>   2. │ └─pointblank:::build_table_scan_page(...)
#>   3. │   └─sections %>% ...
#>   4. ├─base::lapply(...)
#>   5. │ └─pointblank (local) FUN(X[[i]], ...)
#>   6. │   └─pointblank:::probe_overview_stats_assemble(...)
#>   7. │     └─pointblank:::probe_overview_stats(data = data, lang = lang, locale = locale)
#>   8. │       └─pointblank:::get_tbl_information(tbl = data)
#>   9. │         └─pointblank:::get_tbl_information_dbi(tbl)
#>  10. │           └─... %>% tolower()
#>  11. ├─base::tolower(.)
#>  12. ├─dplyr::pull(., ifelse(tbl_src == "bigquery", "data_type", "DATA_TYPE"))
#>  13. ├─dplyr:::pull.data.frame(., ifelse(tbl_src == "bigquery", "data_type", "DATA_TYPE"))
#>  14. │ └─tidyselect::vars_pull(names(.data), !!enquo(var))
#>  15. │   └─tidyselect:::pull_as_location2(...)
#>  16. │     ├─tidyselect:::with_subscript_errors(...)
#>  17. │     │ └─rlang::try_fetch(...)
#>  18. │     │   └─base::withCallingHandlers(...)
#>  19. │     └─vctrs::vec_as_location2(...)
#>  20. │       ├─vctrs:::result_get(...)
#>  21. │       └─vctrs:::vec_as_location2_result(...)
#>  22. │         ├─base::tryCatch(...)
#>  23. │         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#>  24. │         │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#>  25. │         │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#>  26. │         └─vctrs::vec_as_location(i, n, names = names, arg = arg, call = call)
#>  27. └─vctrs (local) `<fn>`()
#>  28.   └─vctrs:::stop_subscript_oob(...)
#>  29.     └─vctrs:::stop_subscript(...)
#>  30.       └─rlang::abort(...)

# Now trying with the db_tbl function as I have understood it
s_table <- db_tbl(
   table = tbl(duck, "s_table"),
   dbtype = "duckdb",
   dbname = ":memory:"
  )  # :-(
#> Error in h(simpleError(msg, call)): Fehler bei der Auswertung des Argumentes 'name' bei der Methodenauswahl für Funktion 'dbExistsTable': Objekt 'table_stmt' nicht gefunden

^{Created on 2022-11-14 with reprex v2.0.2}

Session info

sessioninfo::session_info()
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pachadotdev · 2022-11-16T00:13:50Z

pachadotdev
Nov 16, 2022
Collaborator

@marianschmidt I have the same issue!

@rich-iannone Hi!

First of all, sorry for not looking at the pkg in a few months

I needed to use it with duckdb and I have the same problem, here's a MWE that doesn't happen with PostgreSQL (you have access to the intendo DB)

library(pointblank)
library(dplyr)
library(duckdb)

# ERROR WITH DUCK DB IN MEMORY ----

dout <- tempdir()

readr::write_csv(mtcars, paste0(dout, "/mtcars.csv"))

con_mem <- dbConnect(duckdb(), dbdir = ":memory:", read_only = FALSE)

duckdb_read_csv(con_mem, name = "mtcars", files = paste0(dout, "/mtcars.csv"))

tbl(con_mem, "mtcars") %>% 
  head()

scan_data(tbl(con_mem, "mtcars")) # FAILS

dbDisconnect(con_mem, shutdown = T)

# ERROR WITH DUCK DB IN FILE ----

con_file <- dbConnect(duckdb(), dbdir = paste0(dout, "/mtcars.duckdb"), read_only = FALSE)

duckdb_read_csv(con_file, name = "mtcars", files = paste0(dout, "/mtcars.csv"))

tbl(con_file, "mtcars") %>% 
  head()

scan_data(tbl(con_file, "mtcars")) # FAILS

dbDisconnect(con_file, shutdown = T)

# TRY WITH POSTGRESQL ----

library(RPostgres)

con <- dbConnect(
  Postgres(),
  user = Sys.getenv("dbedu_usr"),
  password = Sys.getenv("dbedu_pwd"),
  dbname = "intendo",
  host = "databases.pacha.dev"
)

dbListTables(con)

scan_data(tbl(con, "sj_user_summary_small")) # WORKS

# ℹ Starting assembly of 'Overview' section...
# ✔ ...Finished!  (4.5 s)
# ℹ Starting assembly of 'Variables' section...
# ✔ ...Finished!  (28.3 s)
# ℹ Starting assembly of 'Missing Values' section...
# ETC ...

Packages in use

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   shiny         1.7.2       2022-07-19 [1] CRAN (R 4.2.1)
   stringi       1.7.8       2022-07-11 [1] CRAN (R 4.2.1)
   stringr       1.4.1       2022-08-20 [1] CRAN (R 4.2.1)
   systemfonts   1.0.4       2022-02-11 [1] CRAN (R 4.2.1)
   textshaping   0.3.6       2021-10-13 [1] CRAN (R 4.2.1)
   tibble        3.1.8       2022-07-22 [1] CRAN (R 4.2.1)
   tidyselect    1.2.0       2022-10-10 [1] CRAN (R 4.2.1)
   tzdb          0.3.0       2022-03-28 [1] CRAN (R 4.2.1)
   urlchecker    1.0.1       2021-11-30 [1] CRAN (R 4.2.1)
   usethis       2.1.6       2022-05-25 [1] CRAN (R 4.2.1)
   utf8          1.2.2       2021-07-24 [1] CRAN (R 4.2.1)
   vctrs         0.5.0       2022-10-22 [1] CRAN (R 4.2.1)
   vroom         1.5.7       2021-11-30 [1] CRAN (R 4.2.1)
   withr         2.5.0       2022-03-03 [1] CRAN (R 4.2.1)
   xfun          0.34        2022-10-18 [1] CRAN (R 4.2.1)
   xtable        1.8-4       2019-04-21 [1] CRAN (R 4.2.1)

 [1] /home/pacha/R/x86_64-pc-linux-gnu-library/4.2
 [2] /usr/local/lib/R/site-library
 [3] /usr/lib/R/site-library
 [4] /usr/lib/R/library

 V ── Loaded and on-disk version mismatch.

0 replies

marianschmidt · 2022-11-16T11:04:14Z

marianschmidt
Nov 16, 2022
Author

@pachadotdev Thanks for your reply. That seems to me like a real bug or documentation problem then and I would file an issue.

0 replies

marianschmidt · 2022-11-16T11:05:28Z

marianschmidt
Nov 16, 2022
Author

Ah, I already see that you opened #446 and proposed #447 for this. Thanks a lot.

1 reply

pachadotdev Nov 17, 2022
Collaborator

Ah, I already see that you opened #446 and proposed #447 for this. Thanks a lot.

hi @marianschmidt ! if you install from my PR, it works

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How to connect to / get data from an already existing duckdb in-memory database `dplyr::tbl()` object? #445

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How to connect to / get data from an already existing duckdb in-memory database dplyr::tbl() object? #445

marianschmidt Nov 14, 2022

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pachadotdev Nov 17, 2022 Collaborator

How to connect to / get data from an already existing duckdb in-memory database `dplyr::tbl()` object? #445

marianschmidt
Nov 14, 2022

Replies: 3 comments 1 reply

pachadotdev
Nov 16, 2022
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marianschmidt
Nov 16, 2022
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marianschmidt
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