Merge pull request #416 from OHDSI/cohortvalidation

Validate cohorts in functions that modify dates
OHDSI · Dec 19, 2024 · 21088e6 · 21088e6
2 parents 7502eca + 85aff2e
commit 21088e6
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Showing 9 changed files with 10 additions and 9 deletions.
diff --git a/R/collapseCohorts.R b/R/collapseCohorts.R
@@ -73,7 +73,7 @@ collapseCohorts <- function(cohort,
       dplyr::compute(name = name, temporary = FALSE)
   }
   newCohort <- newCohort |>
-    omopgenerics::newCohortTable(.softValidation = TRUE) |>
+    omopgenerics::newCohortTable(.softValidation = FALSE) |>
     omopgenerics::recordCohortAttrition(
       reason = "Collapse cohort with a gap of {gap} days.",
       cohortId = cohortId)

diff --git a/R/exitAtColumnDate.R b/R/exitAtColumnDate.R
@@ -216,7 +216,7 @@ exitAtColumnDate <- function(cohort,
   newCohort <- newCohort |>
     dplyr::relocate(dplyr::all_of(omopgenerics::cohortColumns("cohort"))) |>
     dplyr::compute(name = name, temporary = FALSE) |>
-    omopgenerics::newCohortTable(.softValidation = TRUE)
+    omopgenerics::newCohortTable(.softValidation = FALSE)
 
   cdm <- omopgenerics::dropTable(cdm, name = dplyr::starts_with(tmpPrefix))
 

diff --git a/R/exitAtDate.R b/R/exitAtDate.R
@@ -105,7 +105,7 @@ exitAtObservationEnd <- function(cohort,
 
   newCohort <- newCohort |>
     dplyr::compute(name = name, temporary = FALSE) |>
-    omopgenerics::newCohortTable(.softValidation = TRUE) |>
+    omopgenerics::newCohortTable(.softValidation = FALSE) |>
     omopgenerics::recordCohortAttrition(reason = reason, cohortId = cohortId)
 
   omopgenerics::dropTable(cdm = cdm, name = tmpTable)
@@ -186,7 +186,7 @@ exitAtDeath <- function(cohort,
     # no overlapping periods
     joinOverlap(name = name) |>
     dplyr::compute(name = name, temporary = FALSE) |>
-    omopgenerics::newCohortTable(.softValidation = TRUE) |>
+    omopgenerics::newCohortTable(.softValidation = FALSE) |>
     omopgenerics::recordCohortAttrition(reason = "Exit at death", cohortId = cohortId)
 
   useIndexes <- getOption("CohortConstructor.use_indexes")

diff --git a/R/matchCohorts.R b/R/matchCohorts.R
@@ -164,7 +164,7 @@ matchCohorts <- function(cohort,
           "match_status" = "target"
         )
       ,
-      .softValidation = TRUE
+      .softValidation = FALSE
     )
 
   # Bind both cohorts

diff --git a/R/padCohortDate.R b/R/padCohortDate.R
@@ -213,6 +213,7 @@ padCohortStart <- function(cohort,
     ) |>
     dplyr::union_all(subCohort) |>
     dplyr::compute(name = name, temporary = FALSE) |>
+    omopgenerics::newCohortTable(.softValidation = FALSE) |>
     omopgenerics::recordCohortAttrition(cohortId = cohortId, reason = reason)
 
   # drop temp table

diff --git a/R/requireDateRange.R b/R/requireDateRange.R
@@ -149,7 +149,7 @@ trimToDateRange <- function(cohort,
 
   cohort <- cohort |>
     dplyr::compute(name = name, temporary = FALSE) |>
-    omopgenerics::newCohortTable(.softValidation = TRUE)
+    omopgenerics::newCohortTable(.softValidation = FALSE)
 
   useIndexes <- getOption("CohortConstructor.use_indexes")
   if (!isFALSE(useIndexes)) {

diff --git a/R/trimDemographics.R b/R/trimDemographics.R
@@ -320,7 +320,7 @@ trimDemographics <- function(cohort,
       cohortSetRef = newSet,
       cohortAttritionRef = attrition(newCohort),
       cohortCodelistRef = newCod,
-      .softValidation = TRUE
+      .softValidation = FALSE
     )
 
   omopgenerics::dropTable(cdm = cdm, name = dplyr::starts_with(tablePrefix))

diff --git a/R/unionCohorts.R b/R/unionCohorts.R
@@ -80,7 +80,7 @@ unionCohorts <- function(cohort,
       cohortSetRef = cohSet,
       cohortAttritionRef = NULL,
       cohortCodelistRef = cohCodelist,
-      .softValidation = TRUE
+      .softValidation = FALSE
     )
 
   if (isFALSE(keepOriginalCohorts)) {

diff --git a/R/yearCohorts.R b/R/yearCohorts.R
@@ -178,7 +178,7 @@ yearCohorts <- function(cohort,
       cohortSetRef = newSet,
       cohortAttritionRef = newAttrition |> dplyr::bind_rows(),
       cohortCodelistRef = newCodelist,
-      .softValidation = TRUE
+      .softValidation = FALSE
     )
 
   omopgenerics::dropTable(cdm = cdm, name = dplyr::starts_with(tablePrefix))