Fix incremental export for cohort relationships (#1137)

* Modified checksum calculation in cohort relationships

* checksum test fix

* Correct use of keys to overwrite old data

* fix for tests

* removed code changes that are out of scope

R/CohortRelationship.R

@@ -73,8 +73,7 @@ runCohortRelationshipDiagnostics <-
       lower = 0,
       any.missing = FALSE,
       min.len = 1,
-      unique = TRUE,
-      add = errorMessage
+      unique = TRUE
     )
     checkmate::reportAssertions(collection = errorMessage)
 
@@ -215,18 +214,20 @@ executeCohortRelationshipDiagnostics <- function(connection,
       targetChecksum = "checksum"
     ) %>%
     dplyr::distinct()
-  combinationsOfPossibleCohortRelationships <- allCohortIds %>%
+
+  posibleCombinations <- allCohortIds %>%
     tidyr::crossing(allCohortIds %>%
       dplyr::rename(
         comparatorCohortId = "targetCohortId",
         comparatorChecksum = "targetChecksum"
       )) %>%
     dplyr::filter(.data$targetCohortId != .data$comparatorCohortId) %>%
-    dplyr::arrange(.data$targetCohortId, .data$comparatorCohortId) %>%
-    dplyr::mutate(checksum = paste0(.data$targetChecksum, .data$comparatorChecksum))
+    dplyr::arrange(.data$targetCohortId, .data$comparatorCohortId)
+
+  posibleCombinations$checksum <- paste0(posibleCombinations$targetChecksum, posibleCombinations$comparatorChecksum)
 
   subset <- subsetToRequiredCombis(
-    combis = combinationsOfPossibleCohortRelationships,
+    combis = posibleCombinations,
     task = "runCohortRelationship",
     incremental = incremental,
     recordKeepingFile = recordKeepingFile
@@ -244,17 +245,17 @@ executeCohortRelationshipDiagnostics <- function(connection,
     }
 
     if (incremental &&
-      (nrow(combinationsOfPossibleCohortRelationships) - (
+      (nrow(posibleCombinations) - (
         nrow(
-          combinationsOfPossibleCohortRelationships %>%
+          posibleCombinations %>%
             dplyr::filter(.data$targetCohortId %in% c(subset$targetCohortId))
         )
       )) > 0) {
       ParallelLogger::logInfo(
         sprintf(
           " - Skipping %s combinations in incremental mode because these were previously computed.",
-          nrow(combinationsOfPossibleCohortRelationships) - nrow(
-            combinationsOfPossibleCohortRelationships %>%
+          nrow(posibleCombinations) - nrow(
+            posibleCombinations %>%
               dplyr::filter(.data$targetCohortId %in% c(subset$targetCohortId))
           )
         )
@@ -366,7 +367,11 @@ executeCohortRelationshipDiagnostics <- function(connection,
       writeToCsv(
         data = data,
         fileName = outputFile,
-        incremental = TRUE
+        incremental = TRUE,
+        cohortId = data$cohortId,
+        comparatorCohortId = data$comparatorCohortId,
+        startDay = data$startDay,
+        endDay = data$endDay
       )
 
       recordTasksDone(