-- ------------------------------------------------------------------
-- Title: Antibiotic prescriptions
--
-- Adapted from the MIMIC-IV upstream
--   concepts/medication/antibiotic.sql
-- and ported to MIMIC-III v1.3 vanilla PostgreSQL.
--
-- PORT NOTES:
--   1. MIMIC-III `prescriptions` has DATE-precision `startdate` /
--      `enddate` instead of MIMIC-IV's TIMESTAMP `starttime` /
--      `stoptime`.  We carry these through unchanged; downstream
--      consumers (suspicion_of_infection.sql) treat the antibiotic
--      time as the start-of-day timestamp of `startdate`.
--   2. MIMIC-III `prescriptions` already has a populated `icustay_id`
--      column on most rows, so we can pick the ICU stay directly
--      rather than recomputing from `intime`/`outtime`.  We still
--      back-fill it from `icustays` where missing, the same way
--      MIMIC-IV does.
-- ------------------------------------------------------------------

DROP TABLE IF EXISTS antibiotic;
CREATE TABLE antibiotic AS

WITH abx AS
(
  SELECT DISTINCT
         drug
       , route
       , CASE
           WHEN LOWER(drug) LIKE '%adoxa%'           THEN 1
           WHEN LOWER(drug) LIKE '%ala-tet%'         THEN 1
           WHEN LOWER(drug) LIKE '%alodox%'          THEN 1
           WHEN LOWER(drug) LIKE '%amikacin%'        THEN 1
           WHEN LOWER(drug) LIKE '%amikin%'          THEN 1
           WHEN LOWER(drug) LIKE '%amoxicill%'       THEN 1
           WHEN LOWER(drug) LIKE '%amphotericin%'    THEN 1
           WHEN LOWER(drug) LIKE '%anidulafungin%'   THEN 1
           WHEN LOWER(drug) LIKE '%ancef%'           THEN 1
           WHEN LOWER(drug) LIKE '%clavulanate%'     THEN 1
           WHEN LOWER(drug) LIKE '%ampicillin%'      THEN 1
           WHEN LOWER(drug) LIKE '%augmentin%'       THEN 1
           WHEN LOWER(drug) LIKE '%avelox%'          THEN 1
           WHEN LOWER(drug) LIKE '%avidoxy%'         THEN 1
           WHEN LOWER(drug) LIKE '%azactam%'         THEN 1
           WHEN LOWER(drug) LIKE '%azithromycin%'    THEN 1
           WHEN LOWER(drug) LIKE '%aztreonam%'       THEN 1
           WHEN LOWER(drug) LIKE '%axetil%'          THEN 1
           WHEN LOWER(drug) LIKE '%bactocill%'       THEN 1
           WHEN LOWER(drug) LIKE '%bactrim%'         THEN 1
           WHEN LOWER(drug) LIKE '%bactroban%'       THEN 1
           WHEN LOWER(drug) LIKE '%bethkis%'         THEN 1
           WHEN LOWER(drug) LIKE '%biaxin%'          THEN 1
           WHEN LOWER(drug) LIKE '%bicillin l-a%'    THEN 1
           WHEN LOWER(drug) LIKE '%cayston%'         THEN 1
           WHEN LOWER(drug) LIKE '%cefazolin%'       THEN 1
           WHEN LOWER(drug) LIKE '%cedax%'           THEN 1
           WHEN LOWER(drug) LIKE '%cefoxitin%'       THEN 1
           WHEN LOWER(drug) LIKE '%ceftazidime%'     THEN 1
           WHEN LOWER(drug) LIKE '%cefaclor%'        THEN 1
           WHEN LOWER(drug) LIKE '%cefadroxil%'      THEN 1
           WHEN LOWER(drug) LIKE '%cefdinir%'        THEN 1
           WHEN LOWER(drug) LIKE '%cefditoren%'      THEN 1
           WHEN LOWER(drug) LIKE '%cefepime%'        THEN 1
           WHEN LOWER(drug) LIKE '%cefotan%'         THEN 1
           WHEN LOWER(drug) LIKE '%cefotetan%'       THEN 1
           WHEN LOWER(drug) LIKE '%cefotaxime%'      THEN 1
           WHEN LOWER(drug) LIKE '%ceftaroline%'     THEN 1
           WHEN LOWER(drug) LIKE '%cefpodoxime%'     THEN 1
           WHEN LOWER(drug) LIKE '%cefpirome%'       THEN 1
           WHEN LOWER(drug) LIKE '%cefprozil%'       THEN 1
           WHEN LOWER(drug) LIKE '%ceftibuten%'      THEN 1
           WHEN LOWER(drug) LIKE '%ceftin%'          THEN 1
           WHEN LOWER(drug) LIKE '%ceftriaxone%'     THEN 1
           WHEN LOWER(drug) LIKE '%cefuroxime%'      THEN 1
           WHEN LOWER(drug) LIKE '%cephalexin%'      THEN 1
           WHEN LOWER(drug) LIKE '%cephalothin%'     THEN 1
           WHEN LOWER(drug) LIKE '%cephapririn%'     THEN 1
           WHEN LOWER(drug) LIKE '%chloramphenicol%' THEN 1
           WHEN LOWER(drug) LIKE '%cipro%'           THEN 1
           WHEN LOWER(drug) LIKE '%ciprofloxacin%'   THEN 1
           WHEN LOWER(drug) LIKE '%claforan%'        THEN 1
           WHEN LOWER(drug) LIKE '%clarithromycin%'  THEN 1
           WHEN LOWER(drug) LIKE '%cleocin%'         THEN 1
           WHEN LOWER(drug) LIKE '%clindamycin%'     THEN 1
           WHEN LOWER(drug) LIKE '%cubicin%'         THEN 1
           WHEN LOWER(drug) LIKE '%dicloxacillin%'   THEN 1
           WHEN LOWER(drug) LIKE '%dirithromycin%'   THEN 1
           WHEN LOWER(drug) LIKE '%doryx%'           THEN 1
           WHEN LOWER(drug) LIKE '%doxycy%'          THEN 1
           WHEN LOWER(drug) LIKE '%duricef%'         THEN 1
           WHEN LOWER(drug) LIKE '%dynacin%'         THEN 1
           WHEN LOWER(drug) LIKE '%ery-tab%'         THEN 1
           WHEN LOWER(drug) LIKE '%eryped%'          THEN 1
           WHEN LOWER(drug) LIKE '%eryc%'            THEN 1
           WHEN LOWER(drug) LIKE '%erythrocin%'      THEN 1
           WHEN LOWER(drug) LIKE '%erythromycin%'    THEN 1
           WHEN LOWER(drug) LIKE '%factive%'         THEN 1
           WHEN LOWER(drug) LIKE '%flagyl%'          THEN 1
           WHEN LOWER(drug) LIKE '%fortaz%'          THEN 1
           WHEN LOWER(drug) LIKE '%furadantin%'      THEN 1
           WHEN LOWER(drug) LIKE '%garamycin%'       THEN 1
           WHEN LOWER(drug) LIKE '%gentamicin%'      THEN 1
           WHEN LOWER(drug) LIKE '%kanamycin%'       THEN 1
           WHEN LOWER(drug) LIKE '%keflex%'          THEN 1
           WHEN LOWER(drug) LIKE '%kefzol%'          THEN 1
           WHEN LOWER(drug) LIKE '%ketek%'           THEN 1
           WHEN LOWER(drug) LIKE '%levaquin%'        THEN 1
           WHEN LOWER(drug) LIKE '%levofloxacin%'    THEN 1
           WHEN LOWER(drug) LIKE '%lincocin%'        THEN 1
           WHEN LOWER(drug) LIKE '%linezolid%'       THEN 1
           WHEN LOWER(drug) LIKE '%macrobid%'        THEN 1
           WHEN LOWER(drug) LIKE '%macrodantin%'     THEN 1
           WHEN LOWER(drug) LIKE '%maxipime%'        THEN 1
           WHEN LOWER(drug) LIKE '%mefoxin%'         THEN 1
           WHEN LOWER(drug) LIKE '%metronidazole%'   THEN 1
           WHEN LOWER(drug) LIKE '%meropenem%'       THEN 1
           WHEN LOWER(drug) LIKE '%methicillin%'     THEN 1
           WHEN LOWER(drug) LIKE '%minocin%'         THEN 1
           WHEN LOWER(drug) LIKE '%minocycline%'     THEN 1
           WHEN LOWER(drug) LIKE '%monodox%'         THEN 1
           WHEN LOWER(drug) LIKE '%monurol%'         THEN 1
           WHEN LOWER(drug) LIKE '%morgidox%'        THEN 1
           WHEN LOWER(drug) LIKE '%moxatag%'         THEN 1
           WHEN LOWER(drug) LIKE '%moxifloxacin%'    THEN 1
           WHEN LOWER(drug) LIKE '%mupirocin%'       THEN 1
           WHEN LOWER(drug) LIKE '%myrac%'           THEN 1
           WHEN LOWER(drug) LIKE '%nafcillin%'       THEN 1
           WHEN LOWER(drug) LIKE '%neomycin%'        THEN 1
           WHEN LOWER(drug) LIKE '%nicazel doxy 30%' THEN 1
           WHEN LOWER(drug) LIKE '%nitrofurantoin%'  THEN 1
           WHEN LOWER(drug) LIKE '%norfloxacin%'     THEN 1
           WHEN LOWER(drug) LIKE '%noroxin%'         THEN 1
           WHEN LOWER(drug) LIKE '%ocudox%'          THEN 1
           WHEN LOWER(drug) LIKE '%ofloxacin%'       THEN 1
           WHEN LOWER(drug) LIKE '%omnicef%'         THEN 1
           WHEN LOWER(drug) LIKE '%oracea%'          THEN 1
           WHEN LOWER(drug) LIKE '%oraxyl%'          THEN 1
           WHEN LOWER(drug) LIKE '%oxacillin%'       THEN 1
           WHEN LOWER(drug) LIKE '%pc pen vk%'       THEN 1
           WHEN LOWER(drug) LIKE '%pce dispertab%'   THEN 1
           WHEN LOWER(drug) LIKE '%panixine%'        THEN 1
           WHEN LOWER(drug) LIKE '%pediazole%'       THEN 1
           WHEN LOWER(drug) LIKE '%penicillin%'      THEN 1
           WHEN LOWER(drug) LIKE '%periostat%'       THEN 1
           WHEN LOWER(drug) LIKE '%pfizerpen%'       THEN 1
           WHEN LOWER(drug) LIKE '%piperacillin%'    THEN 1
           WHEN LOWER(drug) LIKE '%tazobactam%'      THEN 1
           WHEN LOWER(drug) LIKE '%primsol%'         THEN 1
           WHEN LOWER(drug) LIKE '%proquin%'         THEN 1
           WHEN LOWER(drug) LIKE '%raniclor%'        THEN 1
           WHEN LOWER(drug) LIKE '%rifadin%'         THEN 1
           WHEN LOWER(drug) LIKE '%rifampin%'        THEN 1
           WHEN LOWER(drug) LIKE '%rocephin%'        THEN 1
           WHEN LOWER(drug) LIKE '%smz-tmp%'         THEN 1
           WHEN LOWER(drug) LIKE '%septra%'          THEN 1
           WHEN LOWER(drug) LIKE '%septra ds%'       THEN 1
           WHEN LOWER(drug) LIKE '%solodyn%'         THEN 1
           WHEN LOWER(drug) LIKE '%spectracef%'      THEN 1
           WHEN LOWER(drug) LIKE '%streptomycin%'    THEN 1
           WHEN LOWER(drug) LIKE '%sulfadiazine%'    THEN 1
           WHEN LOWER(drug) LIKE '%sulfamethoxazole%' THEN 1
           WHEN LOWER(drug) LIKE '%trimethoprim%'    THEN 1
           WHEN LOWER(drug) LIKE '%sulfatrim%'       THEN 1
           WHEN LOWER(drug) LIKE '%sulfisoxazole%'   THEN 1
           WHEN LOWER(drug) LIKE '%suprax%'          THEN 1
           WHEN LOWER(drug) LIKE '%synercid%'        THEN 1
           WHEN LOWER(drug) LIKE '%tazicef%'         THEN 1
           WHEN LOWER(drug) LIKE '%tetracycline%'    THEN 1
           WHEN LOWER(drug) LIKE '%timentin%'        THEN 1
           WHEN LOWER(drug) LIKE '%tobramycin%'      THEN 1
           WHEN LOWER(drug) LIKE '%unasyn%'          THEN 1
           WHEN LOWER(drug) LIKE '%vancocin%'        THEN 1
           WHEN LOWER(drug) LIKE '%vancomycin%'      THEN 1
           WHEN LOWER(drug) LIKE '%vantin%'          THEN 1
           WHEN LOWER(drug) LIKE '%vibativ%'         THEN 1
           WHEN LOWER(drug) LIKE '%vibra-tabs%'      THEN 1
           WHEN LOWER(drug) LIKE '%vibramycin%'      THEN 1
           WHEN LOWER(drug) LIKE '%zinacef%'         THEN 1
           WHEN LOWER(drug) LIKE '%zithromax%'       THEN 1
           WHEN LOWER(drug) LIKE '%zosyn%'           THEN 1
           WHEN LOWER(drug) LIKE '%zyvox%'           THEN 1
           ELSE 0
         END AS antibiotic
  FROM   prescriptions
  WHERE  drug_type NOT IN ('BASE')
    -- match upstream: NULL routes are excluded by the NOT IN.
    AND  route NOT IN ('OU','OS','OD','AU','AS','AD','TP')
    AND  LOWER(route) NOT LIKE '%ear%'
    AND  LOWER(route) NOT LIKE '%eye%'
    AND  LOWER(drug) NOT LIKE '%cream%'
    AND  LOWER(drug) NOT LIKE '%desensitization%'
    AND  LOWER(drug) NOT LIKE '%ophth oint%'
    AND  LOWER(drug) NOT LIKE '%gel%'
)
SELECT pr.subject_id
     , pr.hadm_id
     , COALESCE(pr.icustay_id, ie.icustay_id) AS icustay_id
     , pr.drug AS antibiotic
     , pr.route
     -- DATE-precision in MIMIC-III; downstream treats this as the
     -- start-of-day timestamp.
     , pr.startdate AS starttime
     , pr.enddate   AS stoptime
FROM   prescriptions pr
INNER  JOIN abx
       ON  pr.drug = abx.drug
       AND pr.route = abx.route
LEFT   JOIN icustays ie
       ON  pr.hadm_id = ie.hadm_id
       AND pr.startdate >= CAST(ie.intime  AS DATE)
       AND pr.startdate <= CAST(ie.outtime AS DATE)
WHERE  abx.antibiotic = 1;

CREATE INDEX IF NOT EXISTS antibiotic_idx
  ON antibiotic (subject_id, hadm_id, starttime);