darwin-eu / darwin-eu/CDMConnector

How to add tables to the cdm object

Open
#53 0 comments 0 reactions 1 assignee Claimed by @ablack3 View on GitHub
Dominant language
HTML
Stars
17
Forks
17
PR merge metrics
No merged PRs in 30d

Description

Here is a reprex for duckdb. It might be a bit different for snowflake but should be similar.

``` r
library(CDMConnector)
#> Warning: package 'CDMConnector' was built under R version 4.5.2
con <- DBI::dbConnect(duckdb::duckdb(), eunomiaDir())
cdm <- cdmFromCon(con, "main", "main")

DBI::dbExecute(con, "create schema new")
#> [1] 0

DBI::dbWriteTable(con, DBI::Id(schema = "new", table = "cars"), cars)

DBI::dbGetQuery(con, "select * from new.cars limit 5")
#> speed dist
#> 1 4 2
#> 2 4 10
#> 3 7 4
#> 4 7 22
#> 5 8 16

attr(cdm, "cdm_source")
#> This is a duckdb cdm source

cars_ref <- dplyr::tbl(con, "new.cars") %>%
omopgenerics::newCdmTable(src = attr(cdm, "cdm_source"), name = "cars")

cdm$cars <- cars_ref

cdm
#>
#> ── # OMOP CDM reference (duckdb) of Synthea ────────────────────────────────────
#> • omop tables: care_site, cdm_source, concept, concept_ancestor, concept_class,
#> concept_relationship, concept_synonym, condition_era, condition_occurrence,
#> cost, death, device_exposure, domain, dose_era, drug_era, drug_exposure,
#> drug_strength, fact_relationship, location, measurement, metadata, note,
#> note_nlp, observation, observation_period, payer_plan_period, person,
#> procedure_occurrence, provider, relationship, source_to_concept_map, specimen,
#> visit_detail, visit_occurrence, vocabulary
#> • cohort tables: -
#> • achilles tables: -
#> • other tables: cars

cdm$cars
#> # Source: SQL [?? x 2]
#> # Database: DuckDB 1.4.4 [root@Darwin 25.4.0:R 4.5.1//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/Rtmp98KWvY/file1245631701e8e.duckdb]
#> speed dist
#>
#> 1 4 2
#> 2 4 10
#> 3 7 4
#> 4 7 22
#> 5 8 16
#> 6 9 10
#> 7 10 18
#> 8 10 26
#> 9 10 34
#> 10 11 17
#> # ℹ more rows

cdmDisconnect(cdm)
```

Created on 2026-04-16 with [reprex v2.1.1](https://reprex.tidyverse.org)

Session info

``` r
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.5.1 (2025-06-13)
#> os macOS Tahoe 26.4
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
#> date 2026-04-16
#> pandoc 3.6.3 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#> quarto 1.8.27 @ /usr/local/bin/quarto
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.5.0 2024-05-23 [1] CRAN (R 4.5.0)
#> blob 1.3.0 2026-01-14 [1] CRAN (R 4.5.2)
#> CDMConnector * 2.5.1 2026-04-03 [1] CRAN (R 4.5.2)
#> checkmate 2.3.4 2026-02-03 [1] CRAN (R 4.5.2)
#> cli 3.6.5 2025-04-23 [1] CRAN (R 4.5.0)
#> DBI 1.3.0 2026-02-25 [1] CRAN (R 4.5.2)
#> dbplyr 2.5.2 2026-02-13 [1] CRAN (R 4.5.2)
#> digest 0.6.39 2025-11-19 [1] CRAN (R 4.5.2)
#> dplyr 1.2.0 2026-02-03 [1] CRAN (R 4.5.2)
#> duckdb 1.4.4 2026-01-28 [1] CRAN (R 4.5.2)
#> evaluate 1.0.5 2025-08-27 [1] CRAN (R 4.5.0)
#> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.5.0)
#> fs 1.6.7 2026-03-06 [1] CRAN (R 4.5.2)
#> generics 0.1.4 2025-05-09 [1] CRAN (R 4.5.0)
#> glue 1.8.0 2024-09-30 [1] CRAN (R 4.5.0)
#> htmltools 0.5.9 2025-12-04 [1] CRAN (R 4.5.2)
#> httr 1.4.8 2026-02-13 [1] CRAN (R 4.5.2)
#> jsonlite 2.0.0 2025-03-27 [1] CRAN (R 4.5.0)
#> knitr 1.51 2025-12-20 [1] CRAN (R 4.5.2)
#> lifecycle 1.0.5 2026-01-08 [1] CRAN (R 4.5.2)
#> magrittr 2.0.4 2025-09-12 [1] CRAN (R 4.5.0)
#> omopgenerics 1.3.7 2026-03-07 [1] CRAN (R 4.5.2)
#> otel 0.2.0 2025-08-29 [1] CRAN (R 4.5.0)
#> pillar 1.11.1 2025-09-17 [1] CRAN (R 4.5.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.5.0)
#> purrr 1.2.1 2026-01-09 [1] CRAN (R 4.5.2)
#> R6 2.6.1 2025-02-15 [1] CRAN (R 4.5.0)
#> reprex 2.1.1 2024-07-06 [1] CRAN (R 4.5.0)
#> rlang 1.1.7 2026-01-09 [1] CRAN (R 4.5.2)
#> rmarkdown 2.30 2025-09-28 [1] CRAN (R 4.5.0)
#> rstudioapi 0.18.0 2026-01-16 [1] CRAN (R 4.5.2)
#> sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.5.0)
#> stringi 1.8.7 2025-03-27 [1] CRAN (R 4.5.0)
#> stringr 1.6.0 2025-11-04 [1] CRAN (R 4.5.0)
#> tibble 3.3.1 2026-01-11 [1] CRAN (R 4.5.2)
#> tidyr 1.3.2 2025-12-19 [1] CRAN (R 4.5.2)
#> tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.5.0)
#> vctrs 0.7.1 2026-01-23 [1] CRAN (R 4.5.2)
#> withr 3.0.2 2024-10-28 [1] CRAN (R 4.5.0)
#> xfun 0.56 2026-01-18 [1] CRAN (R 4.5.2)
#> yaml 2.3.12 2025-12-10 [1] CRAN (R 4.5.2)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library
#> * ── Packages attached to the search path.
#>
#> ──────────────────────────────────────────────────────────────────────────────
```

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.