updates and fixes

switched to readr for csv writing fixes #13 added gender concepts to concept table fixes #21 fixes #19
OHDSI · Mar 25, 2022 · e330860 · e330860
1 parent b1c2070
commit e330860
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Showing 7 changed files with 15 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: Eunomia
 Type: Package
 Title: A Standard Dataset in the OMOP Common Data Model
-Version: 1.0.1
-Date: 2020-10-21
+Version: 1.0.2
+Date: 2022-03-25
 Authors@R: c(
  person("Frank", "DeFalco", , "fdefalco@ohdsi.org", role = c("aut", "cre")),
  person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut")),
@@ -17,9 +17,10 @@ Depends:
  DatabaseConnector (>= 2.2.0)
 Imports:
  SqlRender,
- RSQLite (> 2.1.1)
+ RSQLite (> 2.1.1),
+ readr
 Suggests:
  testthat
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,6 +4,7 @@ export(createCohorts)
 export(exportToCsv)
 export(getEunomiaConnectionDetails)
 import(DatabaseConnector)
+importFrom(readr,write_csv)
 importFrom(utils,read.csv)
 importFrom(utils,untar)
 importFrom(utils,unzip)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+Eunomia 1.0.2
+=============
+
+Changes
+- switch to readr::write_csv for proper concept_id handling
+- added gender concepts to concept table
+
 Eunomia 1.0.1
 =============
 

diff --git a/R/Connection.R b/R/Connection.R
@@ -39,7 +39,6 @@ getEunomiaConnectionDetails <- function(databaseFile = tempfile(fileext = ".sqli
  file <- xzfile(system.file("sqlite", "cdm.tar.xz", package = "Eunomia"), open = "rb")
  untar(file, exdir = extractFolder)
  close(file)
- # unzip(zipfile = system.file("zip", "cdm.zip", package = "Eunomia"), exdir = extractFolder)
  file.rename(from = file.path(extractFolder, "cdm.sqlite"), to = databaseFile)
  details <- DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = databaseFile)
  return(details)

diff --git a/R/Eunomia.R b/R/Eunomia.R
@@ -19,4 +19,5 @@
 
 #' @import DatabaseConnector
 #' @importFrom utils unzip read.csv write.csv untar
+#' @importFrom readr write_csv
 NULL
diff --git a/R/Export.R b/R/Export.R
@@ -63,7 +63,7 @@ exportToCsv <- function(outputFolder = file.path(getwd(), "csv"),
  fileName <- file.path(outputFolder, sprintf("%s.csv", table))
  writeLines(sprintf("Saving table %s to file %s", table, fileName))
  data <- DatabaseConnector::renderTranslateQuerySql(conn, "SELECT * FROM @table;", table = table)
- write.csv(data, fileName, row.names = FALSE, na = "")
+ write_csv(data, fileName, na = "")
  return(NULL)
  }
  lapply(tables, saveCsv)

diff --git a/inst/sqlite/cdm.tar.xz b/inst/sqlite/cdm.tar.xz