violating field should be non-null

OHDSI · Dec 28, 2023 · 72b2f5b · 72b2f5b
1 parent 1d33ed5
commit 72b2f5b
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Showing 4 changed files with 18 additions and 7 deletions.
diff --git a/R/executeDqChecks.R b/R/executeDqChecks.R
@@ -260,11 +260,11 @@ executeDqChecks <- function(connectionDetails,
   }
 
   if ("plausibleDuringLife" %in% checkDescriptionsDf$checkName) {
-    ParallelLogger::logWarn("DEPRECATION WARNING - The plausibleDuringLife check has been reimplemented with the plausibleBeforeDeath check.")
+    warning("DEPRECATION WARNING - The plausibleDuringLife check has been reimplemented with the plausibleBeforeDeath check.")
   }
 
   if ("plausibleTemporalAfter" %in% checkDescriptionsDf$checkName) {
-    ParallelLogger::logWarn("DEPRECATION WARNING - The plausibleTemporalAfter check has been reimplemented with the plausibleAfterBirth and plausibleStartBeforeEnd checks.")
+    warning("DEPRECATION WARNING - The plausibleTemporalAfter check has been reimplemented with the plausibleAfterBirth and plausibleStartBeforeEnd checks.")
   }
 
   checkDescriptions <- split(checkDescriptionsDf, seq_len(nrow(checkDescriptionsDf)))

diff --git a/inst/sql/sql_server/field_plausible_after_birth.sql b/inst/sql/sql_server/field_plausible_after_birth.sql
@@ -39,7 +39,8 @@ FROM
             AND c.COHORT_DEFINITION_ID = @cohortDefinitionId
         }
         JOIN @cdmDatabaseSchema.person p ON cdmTable.person_id = p.person_id
-        WHERE CAST(cdmTable.@cdmFieldName AS DATE) < COALESCE(
+        WHERE cdmTable.@cdmFieldName IS NOT NULL AND 
+            CAST(cdmTable.@cdmFieldName AS DATE) < COALESCE(
                 p.birth_datetime, 
                 CAST(CONCAT(
                     p.year_of_birth,
@@ -64,5 +65,6 @@ FROM
     JOIN @cohortDatabaseSchema.@cohortTableName c ON cdmTable.person_id = c.subject_id
         AND c.cohort_definition_id = @cohortDefinitionId
     }
+    WHERE cdmTable.@cdmFieldName IS NOT NULL
 ) denominator
 ;
diff --git a/inst/sql/sql_server/field_plausible_before_death.sql b/inst/sql/sql_server/field_plausible_before_death.sql
@@ -1,7 +1,7 @@
 
 /*********
 PLAUSIBLE_BEFORE_DEATH
-all events occur after death (PLAUSIBLE_BEFORE_DEATH == Yes)
+Chedcks for events that occur more than 60 days after death (PLAUSIBLE_BEFORE_DEATH == Yes).
 Denominator is number of events of persons who died.
 
 Parameters used in this template:
@@ -39,7 +39,8 @@ FROM
             AND c.COHORT_DEFINITION_ID = @cohortDefinitionId
         }
         JOIN @cdmDatabaseSchema.death de ON cdmTable.person_id = de.person_id
-        WHERE cast(cdmTable.@cdmFieldName AS DATE) > DATEADD(day, 60, cast(de.death_date AS DATE))
+        WHERE cdmTable.@cdmFieldName IS NOT NULL AND 
+            CAST(cdmTable.@cdmFieldName AS DATE) > DATEADD(day, 60, de.death_date)
         /*violatedRowsEnd*/
     ) violated_rows
 ) violated_row_count,
@@ -53,5 +54,6 @@ FROM
     }
     JOIN @cdmDatabaseSchema.death
         ON death.person_id = cdmTable.person_id
+    WHERE cdmTable.@cdmFieldName IS NOT NULL
 ) denominator
 ;
diff --git a/inst/sql/sql_server/field_plausible_start_before_end.sql b/inst/sql/sql_server/field_plausible_start_before_end.sql
@@ -1,7 +1,8 @@
 
 /*********
 PLAUSIBLE_START_BEFORE_END
-all start dates are before their corresponding end dates (PLAUSIBLE_START_BEFORE_END == Yes)
+all start dates are before their corresponding end dates (PLAUSIBLE_START_BEFORE_END == Yes).
+@cdmFieldName is the start date and @plausibleStartBeforeEndFieldName is the end date.
 
 Parameters used in this template:
 schema = @schema
@@ -38,7 +39,10 @@ FROM
         JOIN @cohortDatabaseSchema.@cohortTableName c ON cdmTable.person_id = c.subject_id
             AND c.cohort_definition_id = @cohortDefinitionId
         }
-        WHERE CAST(cdmTable.@cdmFieldName AS DATE) > CAST(cdmTable.@plausibleStartBeforeEndFieldName AS DATE)
+        WHERE 
+            cdmTable.@cdmFieldName IS NOT NULL AND
+            cdmTable.@plausibleStartBeforeEndFieldName IS NOT NULL AND
+            CAST(cdmTable.@cdmFieldName AS DATE) > CAST(cdmTable.@plausibleStartBeforeEndFieldName AS DATE)
         /*violatedRowsEnd*/
     ) violated_rows
 ) violated_row_count,
@@ -50,5 +54,8 @@ FROM
     JOIN @cohortDatabaseSchema.@cohortTableName c ON cdmTable.person_id = c.subject_id
         AND c.cohort_definition_id = @cohortDefinitionId 
     }
+    WHERE 
+        cdmTable.@cdmFieldName IS NOT NULL AND
+        cdmTable.@plausibleStartBeforeEndFieldName IS NOT NULL
 ) denominator
 ;