Merge pull request #503 from katy-sadowski/katy__v25

Release preparation
OHDSI · Nov 4, 2023 · 2e601f2 · 2e601f2
2 parents b3a1f5e + ef4f61f
commit 2e601f2
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Showing 48 changed files with 272 additions and 137 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DataQualityDashboard
 Type: Package
 Title: Execute and View Data Quality Checks on OMOP CDM Database
-Version: 2.4.1
-Date: 2023-10-18
+Version: 2.5.0
+Date: 2023-11-04
 Authors@R: c(
   person("Katy", "Sadowski", email = "sadowski@ohdsi.org", role = c("aut", "cre")),
   person("Clair", "Blacketer", role = c("aut")),

diff --git a/R/executeDqChecks.R b/R/executeDqChecks.R
@@ -93,7 +93,7 @@ executeDqChecks <- function(connectionDetails,
   if (!str_detect(cdmVersion, regex(acceptedCdmRegex))) {
     stop("cdmVersion must contain a version of the form '5.X' where X is an integer between 2 and 4 inclusive.")
   }
-  
+
   if (sqlOnlyIncrementalInsert == TRUE && sqlOnly == FALSE) {
     stop("Set `sqlOnly` to TRUE in order to use `sqlOnlyIncrementalInsert` mode.")
   }
@@ -139,7 +139,7 @@ executeDqChecks <- function(connectionDetails,
       stop("Please populate the cdm_source table before executing data quality checks.")
     }
     if (nrow(metadata) > 1) {
-      metadata <- metadata[1,]
+      metadata <- metadata[1, ]
       warning("The cdm_source table has more than 1 row. A single row from this table has been selected to populate DQD metadata.")
     }
     metadata$dqdVersion <- as.character(packageVersion("DataQualityDashboard"))

diff --git a/R/writeDBResultsTo.R b/R/writeDBResultsTo.R
@@ -27,52 +27,51 @@
 #'
 
 writeDBResultsToJson <- function(connection,
-                                    resultsDatabaseSchema,
-                                    cdmDatabaseSchema,
-                                    writeTableName,
-                                    outputFolder,
-                                    outputFile) {
-    metadata <- DatabaseConnector::renderTranslateQuerySql(
-          connection,
-          sql = "select * from @cdmDatabaseSchema.cdm_source;",
-          snakeCaseToCamelCase = TRUE,
-          cdmDatabaseSchema = cdmDatabaseSchema
-        )
+                                 resultsDatabaseSchema,
+                                 cdmDatabaseSchema,
+                                 writeTableName,
+                                 outputFolder,
+                                 outputFile) {
+  metadata <- DatabaseConnector::renderTranslateQuerySql(
+    connection,
+    sql = "select * from @cdmDatabaseSchema.cdm_source;",
+    snakeCaseToCamelCase = TRUE,
+    cdmDatabaseSchema = cdmDatabaseSchema
+  )
 
-    checkResults <- DatabaseConnector::renderTranslateQuerySql(
-          connection,
-          sql = "select * from @resultsDatabaseSchema.@writeTableName;",
-          snakeCaseToCamelCase = TRUE,
-          resultsDatabaseSchema = resultsDatabaseSchema,
-          writeTableName = writeTableName
-        )
+  checkResults <- DatabaseConnector::renderTranslateQuerySql(
+    connection,
+    sql = "select * from @resultsDatabaseSchema.@writeTableName;",
+    snakeCaseToCamelCase = TRUE,
+    resultsDatabaseSchema = resultsDatabaseSchema,
+    writeTableName = writeTableName
+  )
 
-    # Quick patch for missing value issues related to SQL Only Implementation
-    checkResults["error"][checkResults["error"] == ''] <- NA
-    checkResults["warning"][checkResults["warning"] == ''] <- NA
-    checkResults["executionTime"][checkResults["executionTime"] == ''] <- '0 secs'
-    checkResults["queryText"][checkResults["queryText"] == ''] <- '[Generated via SQL Only]'
+  # Quick patch for missing value issues related to SQL Only Implementation
+  checkResults["error"][checkResults["error"] == ""] <- NA
+  checkResults["warning"][checkResults["warning"] == ""] <- NA
+  checkResults["executionTime"][checkResults["executionTime"] == ""] <- "0 secs"
+  checkResults["queryText"][checkResults["queryText"] == ""] <- "[Generated via SQL Only]"
 
-    overview <- .summarizeResults(
-        checkResults = checkResults
-        )
+  overview <- .summarizeResults(
+    checkResults = checkResults
+  )
 
-    # Quick patch for non-camel-case column name
-    names(checkResults)[names(checkResults) == "checkid"] <- "checkId"
+  # Quick patch for non-camel-case column name
+  names(checkResults)[names(checkResults) == "checkid"] <- "checkId"
 
-    allResults <- list(
-        startTimestamp = Sys.time(),
-        endTimestamp = Sys.time(),
-        executionTime = '0 secs',
-        CheckResults = checkResults,
-        Metadata = metadata,
-        Overview = overview
-        )
+  allResults <- list(
+    startTimestamp = Sys.time(),
+    endTimestamp = Sys.time(),
+    executionTime = "0 secs",
+    CheckResults = checkResults,
+    Metadata = metadata,
+    Overview = overview
+  )
 
-    .writeResultsToJson(
-        allResults,
-        outputFolder,
-        outputFile
-        )
-
-}
+  .writeResultsToJson(
+    allResults,
+    outputFolder,
+    outputFile
+  )
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -63,3 +63,7 @@ reference:
     desc: > 
       Function to convert the case of a results JSON file between snakecase and camelcase
     contents: convertJsonResultsFileCase
+  - title: "Write database results to a JSON file"
+    desc: > 
+      Function to write DQD results from a database table into a JSON file
+    contents: writeDBResultsToJson
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/AddNewCheck.html b/docs/articles/AddNewCheck.html
diff --git a/docs/articles/CheckStatusDefinitions.html b/docs/articles/CheckStatusDefinitions.html
diff --git a/docs/articles/CheckTypeDescriptions.html b/docs/articles/CheckTypeDescriptions.html
diff --git a/docs/articles/DataQualityDashboard.html b/docs/articles/DataQualityDashboard.html
diff --git a/docs/articles/DqdForCohorts.html b/docs/articles/DqdForCohorts.html
diff --git a/docs/articles/SqlOnly.html b/docs/articles/SqlOnly.html