commit v2.3.1

NEWS.md

@@ -1,3 +1,8 @@
+# EHDEN HMB v2.3.1
+
+* Added Redshift connectivity in function `cdmFromConAllDbs`
+* Updated the `KeyringSetup.R` file to add two additional credentials: port and server 
+
 # EHDEN HMB v2.3.0
 
 * Added function `cdmFromConAllDbs` to connect to different SQL servers with ODBC drivers

analysis/private/_incidenceAnalysis.R

@@ -266,14 +266,36 @@ cdmFromConAllDbs <- function(executionSettings) {
   }
 
 
-  ## Postgre
+  ## PostgreSql
   if (executionSettings$dbms == "postgresql") {
 
     ## Connect to server
     con <- DBI::dbConnect(
       drv = RPostgres::Postgres(),
-      host = host,
-      port = 5441,
+      host = executionSettings$server,
+      port = executionSettings$port,
+      dbname = dbName,
+      user = executionSettings$user,
+      password = executionSettings$password
+    )
+
+    ## Connect to database
+    cdm <- cdm_from_con(
+      con = con,
+      cdm_schema = schemaName,
+      write_schema = writeSchemaName
+    )
+
+  }
+
+  ## Redshift
+  if (executionSettings$dbms == "redshift") {
+
+    ## Connect to server
+    con <- DBI::dbConnect(
+      drv = RPostgres::Redshift(),
+      host = executionSettings$server,
+      port = executionSettings$port,
       dbname = dbName,
       user = executionSettings$user,
       password = executionSettings$password

analysis/private/_utilities.R

@@ -168,3 +168,21 @@ zipResults <- function(database) {
                   crayon::cyan(here::here(paste0(zipName, ".zip"))),bullet = "info", bullet_col = "blue")
 
 }
+
+
+defaultCreds <- function() {
+
+  creds <- c(
+    "dbms", # the database dialect
+    "user", # the user name for the db
+    "password", # the password for the db
+    "port",
+    "server",
+    "connectionString", # the connection string to access the db
+    "cdmDatabaseSchema", # the database + schema (or just schema) hosting the cdm
+    "vocabDatabaseSchema", # the database + schema (or just schema) hosting the vocabulary, usually same as cdm
+    "workDatabaseSchema" # the database + schema (or just schema) hosting the work or scratch
+  )
+
+  return(creds)
+}

extras/KeyringSetup.R

@@ -10,7 +10,7 @@
 library(tidyverse, quietly = TRUE)
 library(Ulysses)
 library(keyring)
-
+source("analysis/private/_utilities.R")
 
 ## B. Set Parameters ------------
 
@@ -36,7 +36,7 @@ setStudyKeyring(keyringName = keyringName,
                 keyringPassword = keyringPassword)
 
 ### Set credential keys in keyring
-setMultipleCredentials(cred = defaultCredentials(),
+setMultipleCredentials(cred = defaultCreds(),
                        db = configBlock,
                        keyringName = keyringName,
                        keyringPassword = keyringPassword,