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Remove all CTEs from generateCohortSql.
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Fixes #172.
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@chrisknoll
chrisknoll committed Sep 27, 2022
1 parent 665a097 commit a87a63c
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Showing 2 changed files with 55 additions and 70 deletions.
5 changes: 2 additions & 3 deletions src/main/java/org/ohdsi/circe/cohortdefinition/CohortExpressionQueryBuilder.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,6 @@ public class CohortExpressionQueryBuilder implements IGetCriteriaSqlDispatcher,
private final static String ADDITIONAL_CRITERIA_LEFT_TEMPLATE = StringUtils.replace(ResourceHelper.GetResourceAsString("/resources/cohortdefinition/sql/additionalCriteriaExclude.sql"), "@windowedCriteria", WINDOWED_CRITERIA_TEMPLATE);
private final static String GROUP_QUERY_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortdefinition/sql/groupQuery.sql");

private final static String PRIMARY_CRITERIA_EVENTS_TABLE = "primary_events";
private final static String INCLUSION_RULE_QUERY_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortdefinition/sql/inclusionrule.sql");
private final static String INCLUSION_RULE_TEMP_TABLE_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortdefinition/sql/inclusionRuleTempTable.sql");
private final static String CENSORING_QUERY_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortdefinition/sql/censoringInsert.sql");
Expand Down Expand Up @@ -275,7 +274,7 @@ public String buildExpressionQuery(CohortExpression expression, BuildExpressionQ
String additionalCriteriaQuery = "";
if (expression.additionalCriteria != null && !expression.additionalCriteria.isEmpty()) {
CriteriaGroup acGroup = expression.additionalCriteria;
String acGroupQuery = this.getCriteriaGroupQuery(acGroup, PRIMARY_CRITERIA_EVENTS_TABLE);//acGroup.accept(this);
String acGroupQuery = this.getCriteriaGroupQuery(acGroup, String.format("(%s)", primaryEventsQuery));//acGroup.accept(this);
acGroupQuery = StringUtils.replace(acGroupQuery, "@indexId", "" + 0);
additionalCriteriaQuery = "\nJOIN (\n" + acGroupQuery + ") AC on AC.person_id = pe.person_id and AC.event_id = pe.event_id\n";
}
Expand Down Expand Up @@ -386,7 +385,7 @@ public String buildExpressionQuery(CohortExpression expression, BuildExpressionQ
resultSql = StringUtils.replace(resultSql, "@generateStats", options.generateStats ? "1" : "0");

if (options.cohortIdFieldName != null) {
resultSql = StringUtils.replaceAll(resultSql, "@cohort_id_field_name", options.cohortIdFieldName.toString());
resultSql = StringUtils.replaceAll(resultSql, "@cohort_id_field_name", options.cohortIdFieldName);
} else {
resultSql = StringUtils.replaceAll(resultSql, "@cohort_id_field_name", DEFAULT_COHORT_ID_FIELD_NAME);
}
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120 changes: 53 additions & 67 deletions src/main/resources/resources/cohortdefinition/sql/generateCohort.sql
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Original file line number Diff line number Diff line change
@@ -1,15 +1,11 @@
@codesetQuery

with primary_events (event_id, person_id, start_date, end_date, op_start_date, op_end_date, visit_occurrence_id) as
(
@primaryEventsQuery
)
SELECT event_id, person_id, start_date, end_date, op_start_date, op_end_date, visit_occurrence_id
INTO #qualified_events
FROM
(
select pe.event_id, pe.person_id, pe.start_date, pe.end_date, pe.op_start_date, pe.op_end_date, row_number() over (partition by pe.person_id order by pe.start_date @QualifiedEventSort) as ordinal, cast(pe.visit_occurrence_id as bigint) as visit_occurrence_id
FROM primary_events pe
FROM (@primaryEventsQuery) pe
@additionalCriteriaQuery
) QE
@QualifiedLimitFilter
Expand All @@ -19,8 +15,9 @@ FROM

@inclusionCohortInserts

with cteIncludedEvents(event_id, person_id, start_date, end_date, op_start_date, op_end_date, ordinal) as
(
select event_id, person_id, start_date, end_date, op_start_date, op_end_date
into #included_events
FROM (
SELECT event_id, person_id, start_date, end_date, op_start_date, op_end_date, row_number() over (partition by person_id order by start_date @IncludedEventSort) as ordinal
from
(
Expand All @@ -33,83 +30,72 @@ with cteIncludedEvents(event_id, person_id, start_date, end_date, op_start_date,
-- the matching group with all bits set ( POWER(2,# of inclusion rules) - 1 = inclusion_rule_mask
WHERE (MG.inclusion_rule_mask = POWER(cast(2 as bigint),@ruleTotal)-1)
}
)
select event_id, person_id, start_date, end_date, op_start_date, op_end_date
into #included_events
FROM cteIncludedEvents Results
) Results
@ResultLimitFilter
;

@strategy_ends_temp_tables

-- generate cohort periods into #final_cohort
with cohort_ends (event_id, person_id, end_date) as
(
-- cohort exit dates
@cohort_end_unions
),
first_ends (person_id, start_date, end_date) as
(
select person_id, start_date, end_date
INTO #cohort_rows
from ( -- first_ends
select F.person_id, F.start_date, F.end_date
FROM (
select I.event_id, I.person_id, I.start_date, E.end_date, row_number() over (partition by I.person_id, I.event_id order by E.end_date) as ordinal
select I.event_id, I.person_id, I.start_date, CE.end_date, row_number() over (partition by I.person_id, I.event_id order by CE.end_date) as ordinal
from #included_events I
join cohort_ends E on I.event_id = E.event_id and I.person_id = E.person_id and E.end_date >= I.start_date
join ( -- cohort_ends
-- cohort exit dates
@cohort_end_unions
) CE on I.event_id = CE.event_id and I.person_id = CE.person_id and CE.end_date >= I.start_date
) F
WHERE F.ordinal = 1
)
select person_id, start_date, end_date
INTO #cohort_rows
from first_ends;
) FE;

with cteEndDates (person_id, end_date) AS -- the magic
(
SELECT
person_id
, DATEADD(day,-1 * @eraconstructorpad, event_date) as end_date
FROM
(
SELECT
person_id
, event_date
, event_type
, MAX(start_ordinal) OVER (PARTITION BY person_id ORDER BY event_date, event_type, start_ordinal ROWS UNBOUNDED PRECEDING) AS start_ordinal
, ROW_NUMBER() OVER (PARTITION BY person_id ORDER BY event_date, event_type, start_ordinal) AS overall_ord
FROM
(
SELECT
person_id
, start_date AS event_date
, -1 AS event_type
, ROW_NUMBER() OVER (PARTITION BY person_id ORDER BY start_date) AS start_ordinal
FROM #cohort_rows

UNION ALL


SELECT
person_id
, DATEADD(day,@eraconstructorpad,end_date) as end_date
, 1 AS event_type
, NULL
FROM #cohort_rows
) RAWDATA
) e
WHERE (2 * e.start_ordinal) - e.overall_ord = 0
),
cteEnds (person_id, start_date, end_date) AS
(
select person_id, min(start_date) as start_date, end_date
into #final_cohort
from ( --cteEnds
SELECT
c.person_id
, c.start_date
, MIN(e.end_date) AS end_date
, MIN(ed.end_date) AS end_date
FROM #cohort_rows c
JOIN cteEndDates e ON c.person_id = e.person_id AND e.end_date >= c.start_date
JOIN ( -- cteEndDates
SELECT
person_id
, DATEADD(day,-1 * @eraconstructorpad, event_date) as end_date
FROM
(
SELECT
person_id
, event_date
, event_type
, MAX(start_ordinal) OVER (PARTITION BY person_id ORDER BY event_date, event_type, start_ordinal ROWS UNBOUNDED PRECEDING) AS start_ordinal
, ROW_NUMBER() OVER (PARTITION BY person_id ORDER BY event_date, event_type, start_ordinal) AS overall_ord
FROM
(
SELECT
person_id
, start_date AS event_date
, -1 AS event_type
, ROW_NUMBER() OVER (PARTITION BY person_id ORDER BY start_date) AS start_ordinal
FROM #cohort_rows

UNION ALL


SELECT
person_id
, DATEADD(day,@eraconstructorpad,end_date) as end_date
, 1 AS event_type
, NULL
FROM #cohort_rows
) RAWDATA
) e
WHERE (2 * e.start_ordinal) - e.overall_ord = 0
) ed ON c.person_id = ed.person_id AND ed.end_date >= c.start_date
GROUP BY c.person_id, c.start_date
)
select person_id, min(start_date) as start_date, end_date
into #final_cohort
from cteEnds
) e
group by person_id, end_date
;

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