sql for alternative temporal data

initial code for revised temporal data

inst/sql/sql_server/DomainConceptTemporal.sql

@@ -0,0 +1,90 @@
+-- Feature construction
+SELECT 
+CAST(@domain_concept_id AS BIGINT) * 1000 + @analysis_id AS covariate_id,
+   time_id,
+   duration, -- does aggregation make sense for this?
+{@aggregated} ? { 
+  cohort_definition_id,
+  COUNT(*) AS sum_value
+} : {
+  row_id,
+  1 AS covariate_value 
+}
+INTO @covariate_table
+FROM (
+  SELECT DISTINCT @domain_concept_id,
+    FLOOR(DATEDIFF(@time_part, @cdm_database_schema.@domain_table.@domain_start_date, cohort.cohort_start_date)*1.0/@time_interval ) as time_id,
+    {@aggregated} ? {	
+    max(
+    }
+
+    CASE WHEN @cdm_database_schema.@domain_table.@domain_end_date <= cohort.cohort_start_date 
+    THEN
+     DATEDIFF(@time_part, @cdm_database_schema.@domain_table.@domain_start_date, @cdm_database_schema.@domain_table.@domain_end_date)*1.0/@time_interval
+     ELSE 
+     DATEDIFF(@time_part, @cdm_database_schema.@domain_table.@domain_start_date, cohort.cohort_start_date)*1.0/@time_interval
+     END
+    {@aggregated} ? {	
+    )
+    }
+   as duration,
+  {@aggregated} ? {
+    cohort_definition_id,
+    cohort.subject_id,
+    cohort.cohort_start_date
+  } : {
+    cohort.@row_id_field AS row_id
+  }
+  FROM @cohort_table cohort
+  INNER JOIN @cdm_database_schema.@domain_table
+  ON cohort.subject_id = @domain_table.person_id
+
+    WHERE @domain_start_date <= DATEADD(DAY, @end_day, cohort.cohort_start_date)
+    AND @domain_concept_id != 0
+
+  {@sub_type == 'inpatient'} ? {	AND condition_type_concept_id IN (38000183, 38000184, 38000199, 38000200)}
+  {@excluded_concept_table != ''} ? {		AND @domain_concept_id NOT IN (SELECT id FROM @excluded_concept_table)}
+  {@included_concept_table != ''} ? {		AND @domain_concept_id IN (SELECT id FROM @included_concept_table)}
+  {@included_cov_table != ''} ? {		AND CAST(@domain_concept_id AS BIGINT) * 1000 + @analysis_id IN (SELECT id FROM @included_cov_table)}
+  {@cohort_definition_id != -1} ? {		AND cohort.cohort_definition_id IN (@cohort_definition_id)}
+) by_row_id
+{@aggregated} ? {		
+  GROUP BY 
+  cohort_definition_id,
+  @domain_concept_id,
+  time_id
+} 
+;
+
+-- Reference construction
+INSERT INTO #cov_ref (
+covariate_id,
+covariate_name,
+analysis_id,
+concept_id
+)
+SELECT covariate_id,
+
+CAST(CONCAT('@domain_table: ', CASE WHEN concept_name IS NULL THEN 'Unknown concept' ELSE concept_name END {@sub_type == 'inpatient'} ? {, ' (inpatient)'}) AS VARCHAR(512)) AS covariate_name,
+
+@analysis_id AS analysis_id,
+CAST((covariate_id - @analysis_id) / 1000 AS INT) AS concept_id
+FROM (
+  SELECT DISTINCT covariate_id
+  FROM @covariate_table
+) t1
+LEFT JOIN @cdm_database_schema.concept
+ON concept_id = CAST((covariate_id - @analysis_id) / 1000 AS INT);
+
+INSERT INTO #analysis_ref (
+analysis_id,
+analysis_name,
+domain_id,
+is_binary,
+missing_means_zero
+)
+SELECT @analysis_id AS analysis_id,
+CAST('@analysis_name' AS VARCHAR(512)) AS analysis_name,
+CAST('@domain_id' AS VARCHAR(20)) AS domain_id,
+CAST('Y' AS VARCHAR(1)) AS is_binary,
+CAST(NULL AS VARCHAR(1)) AS missing_means_zero;