R/create_netezza_queries_v2.R

In pwatrick/pwUtilities: What the Package Does (One Line, Title Case)

#' Function to create covariates table  over DBI with javaODBC for Netezza,with option to set ancestor concept_id table name
#' Last updated: 2021-03-09

#' @param drug_concept_id A string
#' @param biomarker_concept_id A string
#' @param table_name A string
#' @param table_type A string, either c("covariates", "drugs", "biomarkers")
#' @param ancestor_table A string, eg, "antihypertensive_drugs_ancestor_tbl_20210308151236"
#' @param conn A variable
#' @export

create_netezza_queries_v2 <- function(drug_concept_id, biomarker_concept_id, table_name, table_type, ancestor_table, conn,...) {

  if (table_type == "covariates") {

    sql_query <- glue::glue("CREATE TABLE {table_name} AS
  (WITH pw_codesets AS
  (SELECT s3.codeset_id, s3.concept_id, s3.concept_name
  FROM (

  (SELECT 1 as codeset_id, s1.concept_id, s1.concept_name
    FROM (
      SELECT t1.concept_id, t1.concept_name
      FROM (SELECT * FROM v_concept WHERE domain_id = 'Drug') t1
      INNER JOIN (SELECT * FROM v_concept_ancestor WHERE ancestor_concept_id = {drug_concept_id}) t2
      ON (t1.concept_id = t2.DESCENDANT_CONCEPT_ID)
      GROUP BY t1.concept_id, t1.concept_name
      ) s1)

  UNION DISTINCT

  (SELECT 2 as codeset_id, s2.concept_id, s2.concept_name
    FROM (
      SELECT t1.concept_id, t1.concept_name
      FROM (SELECT * FROM v_concept WHERE domain_id = 'Measurement') t1
      INNER JOIN (SELECT * FROM v_concept_ancestor WHERE ancestor_concept_id = {biomarker_concept_id}) t2
      ON (t1.concept_id = t2.DESCENDANT_CONCEPT_ID)
      GROUP BY t1.concept_id, t1.concept_name
      ) s2)) s3
),

pw_index_date AS
(
  SELECT s1.person_id,
         {drug_concept_id} as drug_concept_id,
         s1.drug_exposure_start_date
  FROM (
    (SELECT s2.person_id, s2.drug_concept_id, s3.concept_name as drug_concept_name, s2.drug_exposure_start_date
      FROM (SELECT * FROM v_drug_exposure) s2
      INNER JOIN (SELECT concept_id, concept_name FROM pw_codesets WHERE codeset_id = 1) s3
      ON (s2.drug_concept_id = s3.concept_id))
  ) s1
),

pw_obsperiod AS
(
  SELECT s1.person_id,
         s1.drug_concept_id,
         min(s1.drug_exposure_start_date) as first_drug_exposure,
         max(s1.drug_exposure_start_date) as last_drug_exposure
  FROM (
    (SELECT s2.person_id, s2.drug_concept_id, s2.drug_exposure_start_date
    FROM (SELECT * FROM pw_index_date) s2
    INNER JOIN (SELECT * FROM v_visit_occurrence WHERE visit_concept_id = 9202) s3
    ON (s2.person_id = s3.person_id AND s2.drug_exposure_start_date = s3.visit_start_date))
  ) s1
  GROUP BY s1.person_id, s1.drug_concept_id
),

pw_covariates AS
(
  SELECT s1.person_id,
         s1.dob,
         s1.gender_concept_id,
         s1.race_concept_id
  FROM (
    (SELECT s2.person_id, date(s2.birth_datetime) as dob, s2.gender_concept_id, s2.race_concept_id
      FROM (SELECT * FROM v_person) s2
      INNER JOIN (SELECT * FROM pw_index_date) s3
      ON (s2.person_id = s3.person_id)
      GROUP BY s2.person_id, s2.birth_datetime, s2.gender_concept_id, s2.race_concept_id)
  ) s1
),

pw_covariates_merged AS
(
  SELECT s1.person_id, s1.dob, s1.gender_concept_id, s1.race_concept_id, s1.drug_concept_id, s1.first_drug_exposure, s1.last_drug_exposure
  FROM (
    (SELECT s2.person_id, s2.dob, s2.gender_concept_id, s2.race_concept_id, s3.drug_concept_id, s3.first_drug_exposure, s3.last_drug_exposure
    FROM (SELECT * FROM pw_covariates) s2
    INNER JOIN (SELECT * FROM pw_obsperiod) s3
    ON (s2.person_id = s3.person_id)
    GROUP BY s2.person_id, s2.dob, s2.gender_concept_id, s2.race_concept_id, s3.drug_concept_id, s3.first_drug_exposure, s3.last_drug_exposure)
  ) s1
)
SELECT * FROM pw_covariates_merged);", .con = conn)
  }

  if (table_type == "drugs") {

    sql_query <- glue::glue("
    CREATE TABLE {table_name} AS
(
WITH pw_codesets AS
(
  SELECT s3.codeset_id, s3.concept_id, s3.concept_name
  FROM (

  (SELECT 1 as codeset_id, s1.concept_id, s1.concept_name
    FROM (
      SELECT t1.concept_id, t1.concept_name
      FROM (SELECT * FROM v_concept WHERE domain_id = 'Drug') t1
      INNER JOIN (SELECT * FROM v_concept_ancestor WHERE ancestor_concept_id = {drug_concept_id}) t2
      ON (t1.concept_id = t2.DESCENDANT_CONCEPT_ID)
      GROUP BY t1.concept_id, t1.concept_name
      ) s1)

  UNION DISTINCT

  (SELECT 2 as codeset_id, s2.concept_id, s2.concept_name
    FROM (
      SELECT t1.concept_id, t1.concept_name
      FROM (SELECT * FROM v_concept WHERE domain_id = 'Measurement') t1
      INNER JOIN (SELECT * FROM v_concept_ancestor WHERE ancestor_concept_id = {biomarker_concept_id}) t2
      ON (t1.concept_id = t2.DESCENDANT_CONCEPT_ID)
      GROUP BY t1.concept_id, t1.concept_name
      ) s2)) s3
      ),
pw_index_date AS
(
  SELECT s1.person_id,
         {drug_concept_id} as drug_concept_id,
         s1.drug_exposure_start_date
  FROM (
    (SELECT s2.person_id, s2.drug_concept_id, s3.concept_name as drug_concept_name, s2.drug_exposure_start_date
      FROM (SELECT * FROM v_drug_exposure) s2
      INNER JOIN (SELECT concept_id, concept_name FROM pw_codesets WHERE codeset_id = 1) s3
      ON (s2.drug_concept_id = s3.concept_id))
      ) s1
      ),
pw_obsperiod AS
(
  SELECT s1.person_id,
         s1.drug_concept_id,
         min(s1.drug_exposure_start_date) as first_drug_exposure,
         max(s1.drug_exposure_start_date) as last_drug_exposure
  FROM (
    (SELECT s2.person_id, s2.drug_concept_id, s2.drug_exposure_start_date
    FROM (SELECT * FROM pw_index_date) s2
    INNER JOIN (SELECT * FROM v_visit_occurrence WHERE visit_concept_id = 9202) s3
    ON (s2.person_id = s3.person_id AND s2.drug_exposure_start_date = s3.visit_start_date))
  ) s1
  GROUP BY s1.person_id, s1.drug_concept_id
  ),
pw_start_end AS
(
  SELECT s1.person_id, s1.drug_concept_id, add_months(s1.first_drug_exposure, -12) as start_date, add_months(s1.first_drug_exposure, 12) as end_date
  FROM (SELECT * FROM pw_obsperiod) s1
),

pw_drugs AS
(
SELECT s1.person_id, s1.start_date, s1.end_date, s1.drug_concept_id, s1.drug_exposure_start_date
FROM (
  (SELECT s2.person_id, s2.start_date, s2.end_date, s3.drug_concept_id, s3.drug_exposure_start_date
  FROM (SELECT * FROM pw_start_end) s2
  INNER JOIN (SELECT person_id, drug_concept_id, drug_exposure_start_date
              FROM v_drug_exposure
              WHERE drug_concept_id != 0) s3
  ON (s2.person_id = s3.person_id))
) s1
WHERE s1.drug_exposure_start_date >= s1.start_date
AND s1.drug_exposure_start_date <= s1.end_date
),
pw_drugs_out AS
(
SELECT s1.person_id, s1.start_date, s1.end_date, s1.drug_concept_id, s1.drug_exposure_start_date
FROM (
  (SELECT s2.person_id, s2.start_date, s2.end_date, s2.drug_concept_id, s2.drug_exposure_start_date
  FROM (SELECT * FROM pw_drugs) s2
  INNER JOIN (SELECT * FROM v_visit_occurrence WHERE visit_concept_id = 9202) s3
  ON (s2.person_id = s3.person_id AND s2.drug_exposure_start_date = s3.visit_start_date))
) s1
GROUP BY s1.person_id, s1.start_date, s1.end_date, s1.drug_concept_id, s1.drug_exposure_start_date
),
pw_drugs_selected AS
(
SELECT s1.person_id, s1.start_date, s1.end_date, s1.drug_concept_id, s1.drug_exposure_start_date
FROM (

(SELECT s2.person_id, s2.start_date, s2.end_date, s2.drug_concept_id, s2.drug_exposure_start_date
FROM (SELECT * FROM pw_drugs_out) s2
INNER JOIN(SELECT * FROM {ancestor_table}) s3
ON (s2.drug_concept_id = s3.descendant_concept_id))

UNION DISTINCT

(SELECT s4.person_id, s4.start_date, s4.end_date, s4.drug_concept_id, s4.drug_exposure_start_date
FROM (SELECT * FROM pw_drugs_out) s4
INNER JOIN (SELECT concept_id, concept_name FROM pw_codesets WHERE codeset_id = 1) s5
ON (s4.drug_concept_id = s5.concept_id))
) s1
)
SELECT po.person_id,
       po.start_date,
       po.end_date,
       po.drug_exposure_start_date,
       po.drug_concept_id
 FROM (SELECT * FROM pw_drugs_selected) po
group by po.person_id, po.start_date, po.end_date, po.drug_exposure_start_date, po.drug_concept_id);", .con = conn)
  }

  if (table_type == "biomarkers") {

    sql_query <- glue::glue("
    CREATE TABLE {table_name} AS
(WITH pw_codesets AS
(
  SELECT s3.codeset_id, s3.concept_id, s3.concept_name
  FROM (

  (SELECT 1 as codeset_id, s1.concept_id, s1.concept_name
    FROM (
      SELECT t1.concept_id, t1.concept_name
      FROM (SELECT * FROM v_concept WHERE domain_id = 'Drug') t1
      INNER JOIN (SELECT * FROM v_concept_ancestor WHERE ancestor_concept_id = {drug_concept_id}) t2
      ON (t1.concept_id = t2.DESCENDANT_CONCEPT_ID)
      GROUP BY t1.concept_id, t1.concept_name
      ) s1)

  UNION DISTINCT

  (SELECT 2 as codeset_id, s2.concept_id, s2.concept_name
    FROM (
      SELECT t1.concept_id, t1.concept_name
      FROM (SELECT * FROM v_concept WHERE domain_id = 'Measurement') t1
      INNER JOIN (SELECT * FROM v_concept_ancestor WHERE ancestor_concept_id = {biomarker_concept_id}) t2
      ON (t1.concept_id = t2.DESCENDANT_CONCEPT_ID)
      GROUP BY t1.concept_id, t1.concept_name
      ) s2)) s3
      ),
pw_index_date AS
(
  SELECT s1.person_id,
         {drug_concept_id} as drug_concept_id,
         s1.drug_exposure_start_date
  FROM (
    (SELECT s2.person_id, s2.drug_concept_id, s3.concept_name as drug_concept_name, s2.drug_exposure_start_date
      FROM (SELECT * FROM v_drug_exposure) s2
      INNER JOIN (SELECT concept_id, concept_name FROM pw_codesets WHERE codeset_id = 1) s3
      ON (s2.drug_concept_id = s3.concept_id))
      ) s1
      ),
pw_obsperiod AS
(
  SELECT s1.person_id,
         s1.drug_concept_id,
         min(s1.drug_exposure_start_date) as first_drug_exposure,
         max(s1.drug_exposure_start_date) as last_drug_exposure
  FROM (
    (SELECT s2.person_id, s2.drug_concept_id, s2.drug_exposure_start_date
    FROM (SELECT * FROM pw_index_date) s2
    INNER JOIN (SELECT * FROM v_visit_occurrence WHERE visit_concept_id = 9202) s3
    ON (s2.person_id = s3.person_id AND s2.drug_exposure_start_date = s3.visit_start_date))
  ) s1
  GROUP BY s1.person_id, s1.drug_concept_id
  ),
pw_start_end AS
(
  SELECT s1.person_id, s1.drug_concept_id, add_months(s1.first_drug_exposure, -12) as start_date, add_months(s1.first_drug_exposure, 12) as end_date
  FROM (SELECT * FROM pw_obsperiod) s1
),

pw_biomarker AS
(
  SELECT s1.person_id, s1.measurement_concept_id, s2.concept_name, s1.measurement_date, s1.value_as_number
  FROM (SELECT person_id, measurement_concept_id, measurement_date, value_as_number FROM v_measurement) s1
  INNER JOIN (SELECT * FROM pw_codesets WHERE codeset_id = 2) s2
  ON (s1.measurement_concept_id = s2.concept_id)
),

pw_biomarker_obs AS
(
  SELECT s1.person_id, s1.start_date, s1.measurement_date, s1.end_date, s1.measurement_concept_id, s1.value_as_number
  FROM (
    (SELECT s2.person_id, s2.start_date,  s3.measurement_date, s2.end_date, s3.measurement_concept_id, s3.value_as_number
    FROM (SELECT * FROM pw_start_end) s2
    INNER JOIN (SELECT person_id, measurement_concept_id, measurement_date, value_as_number
                FROM pw_biomarker
                WHERE value_as_number > 0
                AND value_as_number <= 250) s3
    ON (s2.person_id = s3.person_id))
  ) s1
  WHERE s1.measurement_date >= s1.start_date
  AND s1.measurement_date <= s1.end_date
),

pw_biomarker_out AS
(
  SELECT s1.person_id, s1.start_date, s1.measurement_date, s1.end_date, s1.measurement_concept_id, s1.value_as_number
  FROM (
    SELECT s2.person_id, s2.start_date, s2.measurement_date, s2.end_date, s2.measurement_concept_id, s2.value_as_number
    FROM (SELECT * FROM pw_biomarker_obs) s2
    INNER JOIN (SELECT * FROM v_visit_occurrence WHERE visit_concept_id = 9202) s3
    ON (s2.person_id = s3.person_id AND s2.measurement_date = s3.visit_start_date)
   ) s1
)
SELECT * FROM pw_biomarker_out);", .con = conn)
  }

  return(sql_query)
}