From 7caa0956a959bc0955a4142fbedad182d426c0a3 Mon Sep 17 00:00:00 2001
From: Jamie Gilbert <JGilber2@its.jnj.com>
Date: Wed, 29 Mar 2023 15:14:58 -0700
Subject: [PATCH] Casting of time series results for Andromeda work

---
 DESCRIPTION                                | 2 +-
 R/TimeSeries.R                             | 5 +++--
 inst/sql/sql_server/ComputeTimeSeries1.sql | 2 +-
 inst/sql/sql_server/ComputeTimeSeries2.sql | 2 +-
 inst/sql/sql_server/ComputeTimeSeries3.sql | 2 +-
 5 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index bed23311a..98800272f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,7 +63,7 @@ License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics
 BugReports: https://github.com/OHDSI/CohortDiagnostics/issues
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Encoding: UTF-8
 Language: en-US
 StagedInstall: no
diff --git a/R/TimeSeries.R b/R/TimeSeries.R
index 555539748..d4f84c5d0 100644
--- a/R/TimeSeries.R
+++ b/R/TimeSeries.R
@@ -103,7 +103,6 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL,
       return(NULL)
     }
   }
-
   ## Calendar period----
   ParallelLogger::logTrace(" - Preparing calendar table for time series computation.")
   # note calendar span is created based on all dates in observation period table,
@@ -529,7 +528,7 @@ executeTimeSeriesDiagnostics <- function(connection,
   if (runCohortTimeSeries & nrow(cohortDefinitionSet) > 0) {
     subset <- subsetToRequiredCohorts(
       cohorts = cohortDefinitionSet %>%
-        dplyr::filter(cohortId %in% instantiatedCohorts),
+        dplyr::filter(.data$cohortId %in% instantiatedCohorts),
       task = "runCohortTimeSeries",
       incremental = incremental,
       recordKeepingFile = recordKeepingFile
@@ -587,6 +586,7 @@ executeTimeSeriesDiagnostics <- function(connection,
               )
           }
         )
+        
         data <- makeDataExportable(
           x = data,
           tableName = "time_series",
@@ -648,6 +648,7 @@ executeTimeSeriesDiagnostics <- function(connection,
           )
       }
     )
+
     data <- makeDataExportable(
       x = data,
       tableName = "time_series",
diff --git a/inst/sql/sql_server/ComputeTimeSeries1.sql b/inst/sql/sql_server/ComputeTimeSeries1.sql
index 07701e6fc..f3a0c68f1 100644
--- a/inst/sql/sql_server/ComputeTimeSeries1.sql
+++ b/inst/sql/sql_server/ComputeTimeSeries1.sql
@@ -7,7 +7,7 @@
 
 SELECT cohort_definition_id cohort_id,
 	time_id,
-	{@stratify_by_gender} ? {gender,} : {CAST(NULL AS VARCHAR) gender, }
+	{@stratify_by_gender} ? { CASE WHEN gender IS NULL THEN 'NULL' ELSE gender END} : {'NULL'} gender,
 	{@stratify_by_age_group} ? {FLOOR((YEAR(period_begin) - year_of_birth) / 10) age_group,} : {CAST(NULL AS INT) age_group, }
 	COUNT_BIG(DISTINCT CONCAT(cast(subject_id AS VARCHAR(30)), '_', cast(cohort_start_date AS VARCHAR(30)))) records,
 	-- records in calendar period
diff --git a/inst/sql/sql_server/ComputeTimeSeries2.sql b/inst/sql/sql_server/ComputeTimeSeries2.sql
index ac06840cd..470d05d79 100644
--- a/inst/sql/sql_server/ComputeTimeSeries2.sql
+++ b/inst/sql/sql_server/ComputeTimeSeries2.sql
@@ -8,7 +8,7 @@
 
 SELECT cohort_definition_id cohort_id,
 	time_id,
-	{@stratify_by_gender} ? {gender,} : {CAST(NULL AS VARCHAR) gender, }
+	{@stratify_by_gender} ? {CASE WHEN gender IS NULL THEN 'NULL' ELSE gender END} : {'NULL'} gender,
 	{@stratify_by_age_group} ? {FLOOR((YEAR(period_begin) - year_of_birth) / 10) AS age_group,} : {CAST(NULL AS INT) age_group, }
 	COUNT_BIG(DISTINCT CONCAT(cast(subject_id AS VARCHAR(30)), '_', cast(observation_period_start_date AS VARCHAR(30)))) records, -- records in calendar month
 	COUNT_BIG(DISTINCT subject_id) subjects, -- unique subjects
diff --git a/inst/sql/sql_server/ComputeTimeSeries3.sql b/inst/sql/sql_server/ComputeTimeSeries3.sql
index abf33b33e..d054e0ba9 100644
--- a/inst/sql/sql_server/ComputeTimeSeries3.sql
+++ b/inst/sql/sql_server/ComputeTimeSeries3.sql
@@ -7,7 +7,7 @@
 
 SELECT -44819062 cohort_id,
 	time_id,
-	{@stratify_by_gender} ? {p.gender,} : {CAST(NULL AS VARCHAR) gender, }
+	{@stratify_by_gender} ? { CASE WHEN p.gender IS NULL THEN 'NULL' ELSE p.gender END} : {'NULL'} gender,
 	{@stratify_by_age_group} ? {FLOOR((YEAR(period_begin) - year_of_birth) / 10) AS age_group,} : {CAST(NULL AS INT) age_group, }
 	COUNT_BIG(DISTINCT CONCAT(cast(o.person_id AS VARCHAR(30)), '_', cast(observation_period_start_date AS VARCHAR(30)))) records, -- records in calendar month
 	COUNT_BIG(DISTINCT o.person_id) subjects, -- unique subjects