Merge pull request #84 from darwin-eu-dev/issue72

time series

Author: ablack3

R/runTimeSeries.R

@@ -324,8 +324,8 @@ tempTableExists <- function(connection, tempTableName) {
       DatabaseConnector::renderTranslateQuerySql(
         connection = connection, 
         sql = "select top 1 * from  #@tempTableName;",
-         tempTableName = tempTableName)
-      ),
+        tempTableName = tempTableName)
+    ),
     error = function(e) {
       if (methods::is(connection, "DatabaseConnectorJdbcConnection") &&
           DatabaseConnector::dbms(connection) %in% c("postgresql", "redshift")) {
@@ -344,7 +344,7 @@ exportDataToCsv <- function(data, tableName, fileName, minCellCount = 5, databas
     minCellCount = minCellCount,
     databaseId = databaseId
   )
-  
+
   if (!is.null(enforceMinCellValueFunc) && nrow(data) > 0) {
     data <- enforceMinCellValueFunc
   }
@@ -358,7 +358,6 @@ exportDataToCsv <- function(data, tableName, fileName, minCellCount = 5, databas
   return(data)
 }
 
-
 assertCohortDefinitionSetContainsAllParents <- function(cohortDefinitionSet) {
   stopifnot(CohortGenerator::isCohortDefinitionSet(cohortDefinitionSet))
   if ("subsetParent" %in% names(cohortDefinitionSet)) {

R/utils.R

@@ -0,0 +1,41 @@
+DROP TABLE IF EXISTS #ts_cohort;
+DROP TABLE IF EXISTS #ts_cohort_first;
+DROP TABLE IF EXISTS #ts_output;
+
+--HINT DISTRIBUTE_ON_KEY(subject_id)
+SELECT *
+INTO #ts_cohort
+FROM @cohort_database_schema.@cohort_table {@cohort_ids != '' } ? {
+WHERE cohort_definition_id IN (@cohort_ids) };
+
+--HINT DISTRIBUTE_ON_KEY(subject_id)
+SELECT cohort_definition_id,
+	subject_id,
+	min(cohort_start_date) cohort_start_date,
+	min(cohort_end_date) cohort_end_date
+INTO #ts_cohort_first
+FROM #ts_cohort
+GROUP BY cohort_definition_id,
+	subject_id;
+
+
+SELECT c.*,
+	CASE
+		WHEN c.cohort_start_date = cf.cohort_start_date
+			THEN 'Y'
+		ELSE 'N'
+		END first_occurrence {@stratify_by_gender} ? {,
+	concept.concept_name gender} {@stratify_by_age_group} ? {,
+	p.year_of_birth}
+INTO #cohort_ts
+FROM #ts_cohort c
+INNER JOIN #ts_cohort_first cf
+	ON c.cohort_definition_id = cf.cohort_definition_id
+		AND c.subject_id = cf.subject_id {@stratify_by_gender | @stratify_by_age_group} ? {
+INNER JOIN @cdm_database_schema.person p
+	ON c.subject_id = p.person_id} {@stratify_by_gender} ? {
+INNER JOIN @cdm_database_schema.concept
+	ON p.gender_concept_id = concept.concept_id};
+
+DROP TABLE IF EXISTS #ts_cohort;
+DROP TABLE IF EXISTS #ts_cohort_first;

inst/sql/sql_server/ComputeTimeSeries4.sql

@@ -3,4 +3,4 @@
 #'                              of the results data model.
 #' @param databaseId            The databaseId to retrieve the results for. This is a 
 #'                              character field values from the `databaseId` field of the `database` table 
-#'                              of the results data model.
+#'                              of the results data model.