From f18602a957f949847048a2b611ebc1b75ea78bf0 Mon Sep 17 00:00:00 2001
From: Jamie Gilbert <JGilber2@its.jnj.com>
Date: Thu, 4 Jan 2024 08:26:30 -0800
Subject: [PATCH] Mock cohort set function

---
 R/CohortDefinitionSet.R           | 43 +++++++++++++++++++++++++++++++
 man/getMockCohortDefinitionSet.Rd | 16 ++++++++++++
 2 files changed, 59 insertions(+)
 create mode 100644 R/CohortDefinitionSet.R
 create mode 100644 man/getMockCohortDefinitionSet.Rd

diff --git a/R/CohortDefinitionSet.R b/R/CohortDefinitionSet.R
new file mode 100644
index 0000000..7833870
--- /dev/null
+++ b/R/CohortDefinitionSet.R
@@ -0,0 +1,43 @@
+.decodeBase64 <- function(x) {
+  rawToChar(base64enc::base64decode(x))
+}
+
+#' Get Mock Cohort definition set for subset of reward cohorts.
+#' @description
+#' Useful in other analysis steps with ohdsi packages
+#'
+#' @export
+#' @param rewardConfig      Reward configuration
+#' @param cohortIds         Cohort Identifiers
+getMockCohortDefinitionSet <- function(rewardConfig, cohortIds) {
+  connection <- DatabaseConnector::connect(rewardConfig$connectionDetails)
+  on.exit(DatabaseConnector::disconnect(connection))
+
+  sql <- "
+  SELECT
+    cd.cohort_definition_id as cohort_id,
+    cd.cohort_definition_name as cohort_name,
+    COALESCE(ar.sql_definition, '') as sql,
+    COALESCE(ar.definition, '') as json,
+    CASE WHEN ar.definition IS NULL THEN 0 ELSE 1 END as has_json
+  FROM @schema.@cohort_definition cd
+  LEFT JOIN @schema.@atlas_cohort_reference ar ON cd.cohort_definition_id = ar.cohort_definition_id
+  WHERE cd.cohort_definition_id IN (@cohort_ids)
+  "
+
+  res <- DatabaseConnector::renderTranslateQuerySql(connection,
+                                                    sql,
+                                                    cohort_ids = cohortIds,
+                                                    schema = rewardConfig$resultsSchema,
+                                                    atlas_cohort_reference = rewardConfig$referenceTables$atlasCohortReference,
+                                                    cohort_definition = rewardConfig$referenceTables$cohortDefinition,
+                                                    snakeCaseToCamelCase = TRUE)
+
+
+  res <- res %>%
+    dplyr::mutate(json = ifelse(.data$hasJson == 1, .decodeBase64(.data$json), "{}")) %>%
+    dplyr::mutate(sql = ifelse(.data$hasJson == 1, .decodeBase64(.data$sql), "")) %>%
+    dplyr::select(-"hasJson")
+
+  return(res)
+}
\ No newline at end of file
diff --git a/man/getMockCohortDefinitionSet.Rd b/man/getMockCohortDefinitionSet.Rd
new file mode 100644
index 0000000..024ec53
--- /dev/null
+++ b/man/getMockCohortDefinitionSet.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CohortDefinitionSet.R
+\name{getMockCohortDefinitionSet}
+\alias{getMockCohortDefinitionSet}
+\title{Get Mock Cohort definition set for subset of reward cohorts.}
+\usage{
+getMockCohortDefinitionSet(rewardConfig, cohortIds)
+}
+\arguments{
+\item{rewardConfig}{Reward configuration}
+
+\item{cohortIds}{Cohort Identifiers}
+}
+\description{
+Useful in other analysis steps with ohdsi packages
+}