Rerunning vignette data fetches on DataBricks

OHDSI · Aug 29, 2024 · b11a54c · b11a54c
1 parent f344c5c
commit b11a54c
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Showing 6 changed files with 25 additions and 23 deletions.
diff --git a/extras/MultiAnalysesVignetteDataFetch.R b/extras/MultiAnalysesVignetteDataFetch.R
@@ -17,23 +17,24 @@
 # This code should be used to fetch the data that is used in the vignettes.
 library(CohortMethod)
 library(dplyr)
-options(andromedaTempFolder = "d:/andromedaTemp")
+options(andromedaTempFolder = "e:/andromedaTemp")
 
-folder <- "d:/temp/cohortMethodVignette2"
+folder <- "e:/temp/cohortMethodVignette2"
 # unlink(folder, recursive = TRUE)
 # dir.create(folder)
 
 # Set connection details -------------------------------------------------------
-# MDCR on RedShift
-connectionDetails <- DatabaseConnector::createConnectionDetails(
-  dbms = "redshift",
-  connectionString = keyring::key_get("redShiftConnectionStringOhdaMdcr"),
-  user = keyring::key_get("redShiftUserName"),
-  password = keyring::key_get("redShiftPassword")
+# MDCR on DataBricks
+connectionDetails <- createConnectionDetails(
+  dbms = "spark",
+  connectionString = keyring::key_get("databricksConnectionString"),
+  user = "token",
+  password = keyring::key_get("databricksToken")
 )
-cdmDatabaseSchema <- "cdm_truven_mdcr_v2540"
-cohortDatabaseSchema <- "scratch_mschuemi"
+cdmDatabaseSchema <- "merative_mdcr.cdm_merative_mdcr_v3045"
+cohortDatabaseSchema <- "scratch.scratch_mschuemi"
 cohortTable  <- "cm_vignette"
+options(sqlRenderTempEmulationSchema = "scratch.scratch_mschuemi")
 
 # Define exposure cohorts ------------------------------------------------------
 library(Capr)

diff --git a/extras/SingleStudyVignetteDataFetch.R b/extras/SingleStudyVignetteDataFetch.R
@@ -17,23 +17,24 @@
 # This code should be used to fetch the data that is used in the vignettes.
 library(CohortMethod)
 library(dplyr)
-options(andromedaTempFolder = "d:/andromedaTemp")
+options(andromedaTempFolder = "e:/andromedaTemp")
 
-folder <- "d:/temp/cohortMethodVignette"
+folder <- "e:/temp/cohortMethodVignette"
 # unlink(folder, recursive = TRUE)
 # dir.create(folder)
 
 # Set connection details -------------------------------------------------------
-# MDCR on RedShift
-connectionDetails <- DatabaseConnector::createConnectionDetails(
-  dbms = "redshift",
-  connectionString = keyring::key_get("redShiftConnectionStringOhdaMdcr"),
-  user = keyring::key_get("redShiftUserName"),
-  password = keyring::key_get("redShiftPassword")
+# MDCR on DataBricks
+connectionDetails <- createConnectionDetails(
+  dbms = "spark",
+  connectionString = keyring::key_get("databricksConnectionString"),
+  user = "token",
+  password = keyring::key_get("databricksToken")
 )
-cdmDatabaseSchema <- "cdm_truven_mdcr_v2540"
-cohortDatabaseSchema <- "scratch_mschuemi"
+cdmDatabaseSchema <- "merative_mdcr.cdm_merative_mdcr_v3045"
+cohortDatabaseSchema <- "scratch.scratch_mschuemi"
 cohortTable  <- "cm_vignette"
+options(sqlRenderTempEmulationSchema = "scratch.scratch_mschuemi")
 
 
 # Define exposure cohorts ------------------------------------------------------

diff --git a/inst/doc/MultipleAnalyses.pdf b/inst/doc/MultipleAnalyses.pdf
diff --git a/inst/doc/SingleStudies.pdf b/inst/doc/SingleStudies.pdf
diff --git a/vignettes/MultipleAnalyses.Rmd b/vignettes/MultipleAnalyses.Rmd
@@ -18,7 +18,7 @@ vignette: >
 
 ```{r, echo = FALSE, message = FALSE, warning = FALSE}
 library(CohortMethod)
-folder <- "d:/temp/cohortMethodVignette2"
+folder <- "e:/temp/cohortMethodVignette2"
 folderExists <- dir.exists(folder)
 ```
 # Introduction

diff --git a/vignettes/SingleStudies.Rmd b/vignettes/SingleStudies.Rmd
@@ -20,7 +20,7 @@ editor_options:
 ```{r, echo = FALSE, message = FALSE, warning = FALSE}
 options(width = 200)
 library(CohortMethod)
-outputFolder <- "d:/temp/cohortMethodVignette"
+outputFolder <- "e:/temp/cohortMethodVignette"
 folderExists <- dir.exists(outputFolder)
 ```
 # Introduction
@@ -446,7 +446,7 @@ if (folderExists) {
 ```{r eval=FALSE}
 plotCovariateBalanceScatterPlot(balance, showCovariateCountLabel = TRUE, showMaxLabel = TRUE)
 ```
-```{r echo=FALSE,message=FALSE,eval=TRUE,fig.width=7,fig.height=4.5}
+```{r echo=FALSE,message=FALSE,warnings=FALSE,eval=TRUE,fig.width=7,fig.height=4.5}
 if (folderExists) {
   plotCovariateBalanceScatterPlot(balance, 
                                   showCovariateCountLabel = TRUE,