add constraints and indices

Author: alistairewj

mimic-ed/buildmimic/postgres/constraint.sql

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+---------------------------
+---------------------------
+-- Creating Primary Keys --
+---------------------------
+---------------------------
+
+ALTER TABLE mimic_ed.edstays DROP CONSTRAINT IF EXISTS edstays_pk CASCADE;
+ALTER TABLE mimic_ed.edstays
+ADD CONSTRAINT edstays_pk
+  PRIMARY KEY (stay_id);
+
+ALTER TABLE mimic_ed.diagnosis DROP CONSTRAINT IF EXISTS diagnosis_pk CASCADE;
+ALTER TABLE mimic_ed.diagnosis
+ADD CONSTRAINT diagnosis_pk
+  PRIMARY KEY (stay_id, seq_num);
+
+ALTER TABLE mimic_ed.medrecon DROP CONSTRAINT IF EXISTS medrecon_pk CASCADE;
+ALTER TABLE mimic_ed.medrecon
+ADD CONSTRAINT medrecon_pk
+  PRIMARY KEY (stay_id, charttime, name);
+
+ALTER TABLE mimic_ed.pyxis DROP CONSTRAINT IF EXISTS pyxis_pk CASCADE;
+ALTER TABLE mimic_ed.pyxis
+ADD CONSTRAINT pyxis_pk
+  PRIMARY KEY (stay_id, charttime, name);
+
+ALTER TABLE mimic_ed.triage DROP CONSTRAINT IF EXISTS triage_pk CASCADE;
+ALTER TABLE mimic_ed.triage
+ADD CONSTRAINT triage_pk
+  PRIMARY KEY (stay_id);
+
+ALTER TABLE mimic_ed.vitalsign DROP CONSTRAINT IF EXISTS vitalsign_pk CASCADE;
+ALTER TABLE mimic_ed.vitalsign
+ADD CONSTRAINT vitalsign_pk
+  PRIMARY KEY (stay_id, charttime);
+
+---------------------------
+---------------------------
+-- Creating Foreign Keys --
+---------------------------
+---------------------------
+
+ALTER TABLE mimic_ed.diagnosis DROP CONSTRAINT IF EXISTS diagnosis_edstays_fk CASCADE;
+ALTER TABLE mimic_ed.diagnosis
+ADD CONSTRAINT diagnosis_edstays_fk
+  FOREIGN KEY (stay_id)
+  REFERENCES mimic_ed.edstays (stay_id);
+
+ALTER TABLE mimic_ed.medrecon DROP CONSTRAINT IF EXISTS medrecon_edstays_fk CASCADE;
+ALTER TABLE mimic_ed.medrecon
+ADD CONSTRAINT medrecon_edstays_fk
+  FOREIGN KEY (stay_id)
+  REFERENCES mimic_ed.edstays (stay_id);
+
+ALTER TABLE mimic_ed.pyxis DROP CONSTRAINT IF EXISTS pyxis_edstays_fk CASCADE;
+ALTER TABLE mimic_ed.pyxis
+ADD CONSTRAINT pyxis_edstays_fk
+  FOREIGN KEY (stay_id)
+  REFERENCES mimic_ed.edstays (stay_id);
+
+ALTER TABLE mimic_ed.triage DROP CONSTRAINT IF EXISTS triage_edstays_fk CASCADE;
+ALTER TABLE mimic_ed.triage
+ADD CONSTRAINT triage_edstays_fk
+  FOREIGN KEY (stay_id)
+  REFERENCES mimic_ed.edstays (stay_id);
+
+ALTER TABLE mimic_ed.vitalsign DROP CONSTRAINT IF EXISTS vitalsign_edstays_fk CASCADE;
+ALTER TABLE mimic_ed.vitalsign
+ADD CONSTRAINT vitalsign_edstays_fk
+  FOREIGN KEY (stay_id)
+  REFERENCES mimic_ed.edstays (stay_id);

mimic-ed/buildmimic/postgres/index.sql

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+----------------------------------------
+----------------------------------------
+-- Indexes for the MIMIC-IV-ED module --
+----------------------------------------
+----------------------------------------
+
+-- patients
+DROP INDEX IF EXISTS patients_idx01;
+CREATE INDEX patients_idx01
+  ON patients (anchor_age);
+
+DROP INDEX IF EXISTS patients_idx02;
+CREATE INDEX patients_idx02
+  ON patients (anchor_year);
+
+-- admissions
+ 
+DROP INDEX IF EXISTS admissions_idx01;
+CREATE INDEX admissions_idx01
+  ON admissions (admittime, dischtime, deathtime);
+
+-- transfers
+
+DROP INDEX IF EXISTS transfers_idx01;
+CREATE INDEX transfers_idx01
+  ON transfers (hadm_id);
+
+DROP INDEX IF EXISTS transfers_idx02;
+CREATE INDEX transfers_idx02
+  ON transfers (intime);
+
+DROP INDEX IF EXISTS transfers_idx03;
+CREATE INDEX transfers_idx03
+  ON transfers (careunit);