Merge pull request #286 from OHDSI/issue_284

updated functions from CDMConnector

R/mockOmopSketch.R

@@ -53,7 +53,7 @@ mockOmopSketch <- function(con = NULL,
 
 
   # WHEN WE SUPORT LOCAL CDMs WE WILL HAVE TO ACCOUNT FOR THAT HERE
-  cdm <- CDMConnector::copy_cdm_to(con = con, cdm = cdm, schema = writeSchema)
+  cdm <- CDMConnector::copyCdmTo(con = con, cdm = cdm, schema = writeSchema)
 
   return(cdm)
 }

README.Rmd

@@ -41,7 +41,7 @@ library(duckdb)
 library(CDMConnector)
 library(dplyr, warn.conflicts = FALSE)
 library(OmopSketch)
-con <- dbConnect(duckdb(), eunomia_dir())
+con <- dbConnect(duckdb(), eunomiaDir())
 cdm <- cdmFromCon(con = con, cdmSchema = "main", writeSchema = "main")
 cdm
 ```

README.md

@@ -39,14 +39,15 @@ library(duckdb)
 library(CDMConnector)
 library(dplyr, warn.conflicts = FALSE)
 library(OmopSketch)
-con <- dbConnect(duckdb(), eunomia_dir())
+con <- dbConnect(duckdb(), eunomiaDir())
 cdm <- cdmFromCon(con = con, cdmSchema = "main", writeSchema = "main")
 #> Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
 #>  target signature 'duckdb_connection#Id'.
 #>  "duckdb_connection#ANY" would also be valid
+#> ! cdm name not specified and could not be inferred from the cdm source table
 cdm
 #> 
-#> ── # OMOP CDM reference (duckdb) of Synthea synthetic health database ──────────
+#> ── # OMOP CDM reference (duckdb) of An OMOP CDM database ───────────────────────
 #> • omop tables: person, observation_period, visit_occurrence, visit_detail,
 #> condition_occurrence, drug_exposure, procedure_occurrence, device_exposure,
 #> measurement, observation, death, note, note_nlp, specimen, fact_relationship,

tests/testthat/setup.R

@@ -20,7 +20,7 @@ schema <- function(type = Sys.getenv("DB_TO_TEST", "duckdb")) {
 cdmEunomia <- function() {
   con <- connection()
   schema <- schema()
-  conDuck <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
+  conDuck <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomiaDir())
   cdmDuck <- CDMConnector::cdmFromCon(
     con = conDuck, cdmSchema = "main", writeSchema = "main"
   )

tests/testthat/test-summariseRecordCount.R

@@ -293,7 +293,7 @@ test_that("dateRnge argument works", {
 
   PatientProfiles::mockDisconnect(cdm = cdm)
 
-  db <- DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir())
+  db <- DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomiaDir())
   cdm <- CDMConnector::cdmFromCon(con = db, cdmSchema = "main",writeSchema = "main")
 
 

vignettes/B-summarise_concept_set_counts.Rmd

@@ -42,7 +42,7 @@ library(OmopSketch)
 library(CodelistGenerator)
 
 # Connect to Eunomia database
-con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
+con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomiaDir())
 cdm <- CDMConnector::cdmFromCon(
   con = con, cdmSchema = "main", writeSchema = "main"
 )