diff --git a/Oracle/PCORI_MEDS_SCHEMA_CHANGE_ora.sql b/Oracle/PCORI_MEDS_SCHEMA_CHANGE_ora.sql
deleted file mode 100644
index 139f479..0000000
--- a/Oracle/PCORI_MEDS_SCHEMA_CHANGE_ora.sql
+++ /dev/null
@@ -1,50 +0,0 @@
-alter table pcornet_med add PCORI_NDC varchar2(12);
-UPDATE PCORNET_MED set pcori_ndc = pcori_basecode where length(pcori_basecode)=11 and c_hlevel>2 and LOWER(sourcesystem_cd) not in ('integration_tool')
-and pcori_basecode not like 'N%';
- 
-alter table pcornet_med add PCORI_CUI varchar2(8);
-UPDATE pcornet_med set PCORI_CUI = PCORI_BASECODE where length(pcori_basecode)<11 and c_hlevel>2 and LOWER(sourcesystem_cd) not in ('integration_tool')
-and pcori_basecode not like 'N%' and m_applied_path='@';
- 
- 
-create table CUI_T  as
-select * from
-(
-with
-cui(c_fullname,pcori_cui,c_hlevel) as
-(
-    select c_fullname,pcori_cui,c_hlevel from pcornet_med where pcori_cui is not null
-   union all
-    select m.c_fullname, cui.pcori_cui, m.c_hlevel
-    from pcornet_med m inner join cui on cui.c_fullname=m.c_path where m.pcori_cui is null
-),
-cuid as
-( select c_fullname, pcori_cui, row_number() over (partition by C_FULLNAME order by c_hlevel desc)as rowno  from cui)
- 
-select DISTINCT cuid.c_fullname as c_fullname, cuid.pcori_cui as pcori_cui from cuid where cuid.rowno=1
-);
- 
-update pcornet_med x set x.pcori_cui =
-    (select pcori_cui  from CUI_T t where x.c_fullname = t.c_fullname)
-where x.pcori_cui is null;
- 
- 
- 
-create table NDC_T as
-select * from
-(
-with ndc(c_fullname,pcori_ndc,c_hlevel) as
-(
-    select c_fullname,pcori_ndc,c_hlevel from pcornet_med where pcori_ndc is not null
-   union all
-    select m.c_fullname,ndc.pcori_ndc,m.c_hlevel from pcornet_med m
-    inner join ndc on ndc.c_fullname=m.c_path where m.pcori_ndc is null
-),
-ndcd as ( select c_fullname,pcori_ndc, row_number() over (partition by C_FULLNAME order by c_hlevel desc) row from ndc)
- 
-select DISTINCT ndcd.c_fullname as c_fullname, ndcd.pcori_ndc as pcori_ndc from ndcd where ndcd.row=1
-);
- 
-update pcornet_med x set x.pcori_ndc =
-    (select pcori_ndc  from NDC_T t where x.c_fullname = t.c_fullname)
-where x.pcori_ndc is null;
\ No newline at end of file
diff --git a/Oracle/PCORNetInit.sql b/Oracle/PCORNetInit.sql
new file mode 100644
index 0000000..0e96fb7
--- /dev/null
+++ b/Oracle/PCORNetInit.sql
@@ -0,0 +1,987 @@
+-------------------------------------------------------------------------------------------
+-- PCORNetInit Script
+-- 
+-- This script prepares target load and intermidiary transform tables, helper
+-- functions and procedure, and synonyms and views of the source i2b2 source
+-- tables.
+-- 
+-- This script should be run as the initial step of running the i2p-transform,
+-- but has been seperated out from PCORNetLoader_ora.sql so that the former can
+-- be run without dropping all tables.
+--
+-- Created by: Michael Prittie (mprittie@kumc.edu)
+-- Adapted from original PCORNetLoader_ora.sql
+--------------------------------------------------------------------------------
+
+
+--------------------------------------------------------------------------------
+-- HELPER FUNCTIONS AND PROCEDURES
+--------------------------------------------------------------------------------
+
+create or replace PROCEDURE GATHER_TABLE_STATS(table_name VARCHAR2) AS 
+  BEGIN
+  DBMS_STATS.GATHER_TABLE_STATS (
+          ownname => 'PCORNET_CDM', -- This doesn't work as a parameter for some reason.
+          tabname => table_name,
+          estimate_percent => 50, -- Percentage picked somewhat arbitrarily
+          cascade => TRUE,
+          degree => 16 
+          );
+END GATHER_TABLE_STATS;
+/
+
+
+create or replace PROCEDURE PMN_DROPSQL(sqlstring VARCHAR2) AS 
+  BEGIN
+      EXECUTE IMMEDIATE sqlstring;
+  EXCEPTION
+      WHEN OTHERS THEN NULL;
+END PMN_DROPSQL;
+/
+
+
+create or replace FUNCTION PMN_IFEXISTS(objnamestr VARCHAR2, objtypestr VARCHAR2) RETURN BOOLEAN AS 
+cnt NUMBER;
+BEGIN
+  SELECT COUNT(*)
+   INTO cnt
+    FROM USER_OBJECTS
+  WHERE  upper(OBJECT_NAME) = upper(objnamestr)
+         and upper(object_type) = upper(objtypestr);
+  
+  IF( cnt = 0 )
+  THEN
+    --dbms_output.put_line('NO!');
+    return FALSE;  
+  ELSE
+   --dbms_output.put_line('YES!'); 
+   return TRUE;
+  END IF;
+
+END PMN_IFEXISTS;
+/
+
+
+create or replace PROCEDURE PMN_Execuatesql(sqlstring VARCHAR2) AS 
+BEGIN
+  EXECUTE IMMEDIATE sqlstring;
+  dbms_output.put_line(sqlstring);
+END PMN_ExecuateSQL;
+/
+
+
+--ACK: http://dba.stackexchange.com/questions/9441/how-to-catch-and-handle-only-specific-oracle-exceptions
+create or replace procedure create_error_table(table_name varchar2) as
+sqltext varchar2(4000); 
+
+begin
+  dbms_errlog.create_error_log(dml_table_name => table_name);
+EXCEPTION
+  WHEN OTHERS THEN
+    IF SQLCODE = -955 THEN
+      NULL; -- suppresses ORA-00955 exception ("name is already used by an existing object")
+    ELSE
+       RAISE;
+    END IF;
+-- Delete rows from a previous run in case the table already existed
+sqltext := 'delete from ERR$_' || table_name;
+PMN_Execuatesql(sqltext);
+end;
+/
+
+
+create or replace FUNCTION GETDATAMARTID RETURN VARCHAR2 IS 
+BEGIN 
+    RETURN '&&datamart_id';
+END;
+/
+
+
+CREATE OR REPLACE FUNCTION GETDATAMARTNAME RETURN VARCHAR2 AS 
+BEGIN 
+    RETURN '&&datamart_name';
+END;
+/
+
+
+CREATE OR REPLACE FUNCTION GETDATAMARTPLATFORM RETURN VARCHAR2 AS 
+BEGIN 
+    RETURN '02'; -- 01 is MSSQL, 02 is Oracle
+END;
+/
+
+
+BEGIN
+PMN_DROPSQL('DROP TABLE pcornet_codelist');
+END;
+/
+create table pcornet_codelist(codetype varchar2(20), code varchar2(50))
+/
+
+create or replace procedure pcornet_parsecode (codetype in varchar, codestring in varchar) as
+
+tex varchar(2000);
+pos number(9);
+readstate char(1) ;
+nextchar char(1) ;
+val varchar(50);
+
+begin
+
+val:='';
+readstate:='F';
+pos:=0;
+tex := codestring;
+FOR pos IN 1..length(tex)
+LOOP
+--	dbms_output.put_line(val);
+    	nextchar:=substr(tex,pos,1);
+	if nextchar!=',' then
+		if nextchar='''' then
+			if readstate='F' then
+				val:='';
+				readstate:='T';
+			else
+				insert into pcornet_codelist values (codetype,val);
+				val:='';
+				readstate:='F'  ;
+			end if;
+		else
+			if readstate='T' then
+				val:= val || nextchar;
+			end if;
+		end if;
+	end if;
+END LOOP;
+
+end pcornet_parsecode;
+/
+
+create or replace procedure pcornet_popcodelist as
+
+codedata varchar(2000);
+onecode varchar(20);
+codetype varchar(20);
+
+cursor getcodesql is
+select 'RACE',c_dimcode from pcornet_demo where c_fullname like '\PCORI\DEMOGRAPHIC\RACE%'
+union
+select 'SEX',c_dimcode from pcornet_demo where c_fullname like '\PCORI\DEMOGRAPHIC\SEX%'
+union
+select 'HISPANIC',c_dimcode from pcornet_demo where c_fullname like '\PCORI\DEMOGRAPHIC\HISPANIC%';
+
+begin
+open getcodesql;
+LOOP 
+	fetch getcodesql into codetype,codedata;
+	EXIT WHEN getcodesql%NOTFOUND ;
+ 	pcornet_parsecode (codetype,codedata );
+end loop;
+
+close getcodesql ;
+end pcornet_popcodelist;
+/
+
+
+--------------------------------------------------------------------------------
+-- I2B2 SYNONYMS, VIEWS, AND INTERMEDIARY TABLES
+--------------------------------------------------------------------------------
+
+
+CREATE OR REPLACE SYNONYM I2B2FACT FOR "&&i2b2_data_schema".OBSERVATION_FACT
+/
+
+CREATE OR REPLACE SYNONYM I2B2MEDFACT FOR OBSERVATION_FACT_MEDS
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE i2b2patient_list');
+END;
+/
+
+CREATE table i2b2patient_list as 
+select * from
+(
+select DISTINCT PATIENT_NUM from I2B2FACT where START_DATE > to_date('&&min_pat_list_date_dd_mon_rrrr','dd-mon-rrrr')
+) where ROWNUM<100000000
+/
+
+create or replace VIEW i2b2patient as select * from "&&i2b2_data_schema".PATIENT_DIMENSION where PATIENT_NUM in (select PATIENT_NUM from i2b2patient_list)
+/
+
+create or replace view i2b2visit as select * from "&&i2b2_data_schema".VISIT_DIMENSION where START_DATE >= to_date('&&min_visit_date_dd_mon_rrrr','dd-mon-rrrr') and (END_DATE is NULL or END_DATE < CURRENT_DATE) and (START_DATE <CURRENT_DATE)
+/
+
+CREATE OR REPLACE SYNONYM pcornet_med FOR  "&&i2b2_meta_schema".pcornet_med
+/
+
+CREATE OR REPLACE SYNONYM pcornet_lab FOR  "&&i2b2_meta_schema".pcornet_lab
+/
+
+CREATE OR REPLACE SYNONYM pcornet_diag FOR  "&&i2b2_meta_schema".pcornet_diag
+/
+
+CREATE OR REPLACE SYNONYM pcornet_demo FOR  "&&i2b2_meta_schema".pcornet_demo
+/
+
+CREATE OR REPLACE SYNONYM pcornet_proc FOR  "&&i2b2_meta_schema".pcornet_proc
+/
+
+CREATE OR REPLACE SYNONYM pcornet_vital FOR  "&&i2b2_meta_schema".pcornet_vital
+/
+
+CREATE OR REPLACE SYNONYM pcornet_enc FOR  "&&i2b2_meta_schema".pcornet_enc
+/
+
+
+--------------------------------------------------------------------------------
+-- DEMOGRAPHIC
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE demographic');
+END;
+/
+CREATE TABLE demographic(
+	PATID varchar(50) NOT NULL,
+	BIRTH_DATE date NULL,
+	BIRTH_TIME varchar(5) NULL,
+	SEX varchar(2) NULL,
+	HISPANIC varchar(2) NULL,
+	BIOBANK_FLAG varchar(1) DEFAULT 'N',
+	RACE varchar(2) NULL,
+	RAW_SEX varchar(50) NULL,
+	RAW_HISPANIC varchar(50) NULL,
+	RAW_RACE varchar(50) NULL
+)
+/
+
+
+--------------------------------------------------------------------------------
+-- ENROLLMENT
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE enrollment');
+END;
+/
+CREATE TABLE enrollment (
+	PATID varchar(50) NOT NULL,
+	ENR_START_DATE date NOT NULL,
+	ENR_END_DATE date NULL,
+	CHART varchar(1) NULL,
+	ENR_BASIS varchar(1) NOT NULL,
+	RAW_CHART varchar(50) NULL,
+	RAW_BASIS varchar(50) NULL
+)
+/
+
+
+--------------------------------------------------------------------------------
+-- ENCOUNTER
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE encounter');
+END;
+/
+CREATE TABLE encounter(
+	PATID varchar(50) NOT NULL,
+	ENCOUNTERID varchar(50) NOT NULL,
+	ADMIT_DATE date NULL,
+	ADMIT_TIME varchar(5) NULL,
+	DISCHARGE_DATE date NULL,
+	DISCHARGE_TIME varchar(5) NULL,
+	PROVIDERID varchar(50) NULL,
+	FACILITY_LOCATION varchar(3) NULL,
+	ENC_TYPE varchar(2) NOT NULL,
+	FACILITYID varchar(50) NULL,
+	DISCHARGE_DISPOSITION varchar(2) NULL,
+	DISCHARGE_STATUS varchar(2) NULL,
+	DRG varchar(3) NULL,
+	DRG_TYPE varchar(2) NULL,
+	ADMITTING_SOURCE varchar(2) NULL,
+	RAW_SITEID varchar (50) NULL,
+	RAW_ENC_TYPE varchar(50) NULL,
+	RAW_DISCHARGE_DISPOSITION varchar(50) NULL,
+	RAW_DISCHARGE_STATUS varchar(50) NULL,
+	RAW_DRG_TYPE varchar(50) NULL,
+	RAW_ADMITTING_SOURCE varchar(50) NULL
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE drg');
+END;
+/
+CREATE TABLE drg (
+  PATIENT_NUM NUMBER(38) NOT NULL, 
+  ENCOUNTER_NUM NUMBER(38) NOT NULL, 
+  DRG_TYPE VARCHAR2(2), 
+  DRG VARCHAR2(3), 
+  RN NUMBER
+)
+/
+
+
+--------------------------------------------------------------------------------
+-- DIAGNOSIS
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE diagnosis');
+END;
+/
+CREATE TABLE diagnosis(
+	DIAGNOSISID varchar(19)  primary key,
+	PATID varchar(50) NOT NULL,
+	ENCOUNTERID varchar(50) NOT NULL,
+	ENC_TYPE varchar(2) NULL,
+	ADMIT_DATE date NULL,
+	PROVIDERID varchar(50) NULL,
+	DX varchar(18) NOT NULL,
+	DX_TYPE varchar(2) NOT NULL,
+	DX_SOURCE varchar(2) NOT NULL,
+	PDX varchar(2) NULL,
+	RAW_DX varchar(50) NULL,
+	RAW_DX_TYPE varchar(50) NULL,
+	RAW_DX_SOURCE varchar(50) NULL,
+	RAW_ORIGDX varchar(50) NULL,
+	RAW_PDX varchar(50) NULL
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP sequence  diagnosis_seq');
+END;
+/
+create sequence  diagnosis_seq
+/
+
+create or replace trigger diagnosis_trg
+before insert on diagnosis
+for each row
+begin
+  select diagnosis_seq.nextval into :new.DIAGNOSISID from dual;
+end;
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE sourcefact');
+END;
+/
+
+CREATE TABLE SOURCEFACT  ( 
+	PATIENT_NUM  	NUMBER(38) NOT NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	PROVIDER_ID  	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL,
+	START_DATE   	DATE NOT NULL,
+	DXSOURCE     	VARCHAR2(50) NULL,
+	C_FULLNAME   	VARCHAR2(700) NOT NULL 
+	)
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE pdxfact');
+END;
+/
+
+CREATE TABLE PDXFACT  ( 
+	PATIENT_NUM  	NUMBER(38) NOT NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	PROVIDER_ID  	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL,
+	START_DATE   	DATE NOT NULL,
+	PDXSOURCE    	VARCHAR2(50) NULL,
+	C_FULLNAME   	VARCHAR2(700) NOT NULL 
+	)
+/
+
+--------------------------------------------------------------------------------
+-- PROCEDURES
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE procedures');
+END;
+/
+CREATE TABLE procedures(
+	PROCEDURESID varchar(19)  primary key,
+	PATID varchar(50) NOT NULL,
+	ENCOUNTERID varchar(50) NOT NULL,
+	ENC_TYPE varchar(2) NULL,
+	ADMIT_DATE date NULL,
+	PROVIDERID varchar(50) NULL,
+	PX_DATE date NULL,
+	PX varchar(11) NOT NULL,
+	PX_TYPE varchar(2) NOT NULL,
+	PX_SOURCE varchar(2) NULL,
+	RAW_PX varchar(50) NULL,
+	RAW_PX_TYPE varchar(50) NULL
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP sequence  procedures_seq');
+END;
+/
+create sequence  procedures_seq
+/
+
+create or replace trigger procedures_trg
+before insert on procedures
+for each row
+begin
+  select procedures_seq.nextval into :new.PROCEDURESID from dual;
+end;
+/
+
+
+--------------------------------------------------------------------------------
+-- VITAL
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE vital');
+END;
+/
+CREATE TABLE vital (
+	VITALID varchar(19)  primary key,
+	PATID varchar(50) NULL,
+	ENCOUNTERID varchar(50) NULL,
+	MEASURE_DATE date NULL,
+	MEASURE_TIME varchar(5) NULL,
+	VITAL_SOURCE varchar(2) NULL,
+	HT number(18, 0) NULL, --8, 0
+	WT number(18, 0) NULL, --8, 0
+	DIASTOLIC number(18, 0) NULL,--4, 0
+	SYSTOLIC number(18, 0) NULL, --4, 0
+	ORIGINAL_BMI number(18,0) NULL,--8, 0
+	BP_POSITION varchar(2) NULL,
+	SMOKING varchar (2),
+	TOBACCO varchar (2),
+	TOBACCO_TYPE varchar (2),
+	RAW_VITAL_SOURCE varchar(50) NULL,
+	RAW_HT varchar(50) NULL,
+	RAW_WT varchar(50) NULL,
+	RAW_DIASTOLIC varchar(50) NULL,
+	RAW_SYSTOLIC varchar(50) NULL,
+	RAW_BP_POSITION varchar(50) NULL,
+	RAW_SMOKING varchar (50),
+	Raw_TOBACCO varchar (50),
+	Raw_TOBACCO_TYPE varchar (50)
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP SEQUENCE vital_seq');
+END;
+/
+create sequence  vital_seq
+/
+
+create or replace trigger vital_trg
+before insert on vital
+for each row
+begin
+  select vital_seq.nextval into :new.VITALID from dual;
+end;
+/
+
+
+--------------------------------------------------------------------------------
+-- LAB_RESULT_CM
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE lab_result_cm');
+END;
+/
+CREATE TABLE lab_result_cm(
+	LAB_RESULT_CM_ID varchar(19)  primary key,
+	PATID varchar(50) NOT NULL,
+	ENCOUNTERID varchar(50) NULL,
+	LAB_NAME varchar(10) NULL,
+	SPECIMEN_SOURCE varchar(10) NULL,
+	LAB_LOINC varchar(10) NULL,
+	PRIORITY varchar(2) NULL,
+	RESULT_LOC varchar(2) NULL,
+	LAB_PX varchar(11) NULL,
+	LAB_PX_TYPE varchar(2) NULL,
+	LAB_ORDER_DATE date NULL,
+	SPECIMEN_DATE date NULL,
+	SPECIMEN_TIME varchar(5) NULL,
+	RESULT_DATE date NULL,
+	RESULT_TIME varchar(5) NULL,
+	RESULT_QUAL varchar(12) NULL,
+	RESULT_NUM number (18,5) NULL,
+	RESULT_MODIFIER varchar(2) NULL,
+	RESULT_UNIT varchar(11) NULL,
+	NORM_RANGE_LOW varchar(10) NULL,
+	NORM_MODIFIER_LOW varchar(2) NULL,
+	NORM_RANGE_HIGH varchar(10) NULL,
+	NORM_MODIFIER_HIGH varchar(2) NULL,
+	ABN_IND varchar(2) NULL,
+	RAW_LAB_NAME varchar(50) NULL,
+	RAW_LAB_CODE varchar(50) NULL,
+	RAW_PANEL varchar(50) NULL,
+	RAW_RESULT varchar(50) NULL,
+	RAW_UNIT varchar(50) NULL,
+	RAW_ORDER_DEPT varchar(50) NULL,
+	RAW_FACILITY_CODE varchar(50) NULL
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP SEQUENCE lab_result_cm_seq');
+END;
+/
+create sequence  lab_result_cm_seq
+/
+
+create or replace trigger lab_result_cm_trg
+before insert on lab_result_cm
+for each row
+begin
+  select lab_result_cm_seq.nextval into :new.LAB_RESULT_CM_ID from dual;
+end;
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE priority');
+END;
+/
+
+CREATE TABLE PRIORITY  ( 
+	PATIENT_NUM  	NUMBER(38) NOT NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	PROVIDER_ID  	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL,
+	START_DATE   	DATE NOT NULL,
+	PRIORITY     	VARCHAR2(50) NULL 
+	)
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE location');
+END;
+/
+
+CREATE TABLE LOCATION  ( 
+	PATIENT_NUM  	NUMBER(38) NOT NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	PROVIDER_ID  	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL,
+	START_DATE   	DATE NOT NULL,
+	RESULT_LOC   	VARCHAR2(50) NULL 
+	)
+/
+
+-- TODO: This seems to belong in h2p-mapping
+alter table "&&i2b2_meta_schema".pcornet_lab add (
+  pcori_specimen_source varchar2(1000) -- arbitrary
+  );
+
+
+--------------------------------------------------------------------------------
+-- CONDITION
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE condition');
+END;
+/
+CREATE TABLE condition(
+	CONDITIONID varchar(19)  primary key,
+	PATID varchar(50) NOT NULL,
+	ENCOUNTERID  varchar(50) NULL,
+	REPORT_DATE  date NULL,
+	RESOLVE_DATE  date NULL,
+	ONSET_DATE  date NULL,
+	CONDITION_STATUS varchar(2) NULL,
+	CONDITION varchar(18) NOT NULL,
+	CONDITION_TYPE varchar(2) NOT NULL,
+	CONDITION_SOURCE varchar(2) NOT NULL,
+	RAW_CONDITION_STATUS varchar(2) NULL,
+	RAW_CONDITION varchar(18) NULL,
+	RAW_CONDITION_TYPE varchar(2) NULL,
+	RAW_CONDITION_SOURCE varchar(2) NULL
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP sequence  condition_seq');
+END;
+/
+create sequence  condition_seq
+/
+
+create or replace trigger condition_trg
+before insert on condition
+for each row
+begin
+  select condition_seq.nextval into :new.CONDITIONID from dual;
+end;
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE sourcefact2');
+END;
+/
+
+CREATE TABLE SOURCEFACT2  ( 
+	PATIENT_NUM  	NUMBER(38) NOT NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	PROVIDER_ID  	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL,
+	START_DATE   	DATE NOT NULL,
+	DXSOURCE     	VARCHAR2(50) NULL,
+	C_FULLNAME   	VARCHAR2(700) NOT NULL 
+	)
+/
+
+
+--------------------------------------------------------------------------------
+-- PRO_CM
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE pro_cm');
+END;
+/
+CREATE TABLE pro_cm(
+	PRO_CM_ID varchar(19)  primary key,
+	PATID varchar(50) NOT NULL,
+	ENCOUNTERID  varchar(50) NULL,
+	PRO_ITEM varchar (7) NOT NULL,
+	PRO_LOINC varchar (10) NULL,
+	PRO_DATE date NOT NULL,
+	PRO_TIME varchar (5) NULL,
+	PRO_RESPONSE int NOT NULL,
+	PRO_METHOD varchar (2) NULL,
+	PRO_MODE varchar (2) NULL,
+	PRO_CAT varchar (2) NULL,
+	RAW_PRO_CODE varchar (50) NULL,
+	RAW_PRO_RESPONSE varchar (50) NULL
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP sequence  pro_cm_seq');
+END;
+/
+create sequence  pro_cm_seq
+/
+
+create or replace trigger pro_cm_trg
+before insert on pro_cm
+for each row
+begin
+  select pro_cm_seq.nextval into :new.PRO_CM_ID from dual;
+end;
+/
+
+
+--------------------------------------------------------------------------------
+-- PRESCRIBING
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE prescribing');
+END;
+/
+CREATE TABLE prescribing(
+	PRESCRIBINGID varchar(19)  primary key,
+	PATID varchar(50) NOT NULL,
+	ENCOUNTERID  varchar(50) NULL,
+	RX_PROVIDERID varchar(50) NULL, -- NOTE: The spec has a _ before the ID, but this is inconsistent.
+	RX_ORDER_DATE date NULL,
+	RX_ORDER_TIME varchar (5) NULL,
+	RX_START_DATE date NULL,
+	RX_END_DATE date NULL,
+	RX_QUANTITY int NULL,
+	RX_REFILLS int NULL,
+	RX_DAYS_SUPPLY int NULL,
+	RX_FREQUENCY varchar(2) NULL,
+	RX_BASIS varchar (2) NULL,
+	RXNORM_CUI int NULL,
+	RAW_RX_MED_NAME varchar (50) NULL,
+	RAW_RX_FREQUENCY varchar (50) NULL,
+	RAW_RXNORM_CUI varchar (50) NULL
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP sequence  prescribing_seq');
+END;
+/
+create sequence  prescribing_seq
+/
+
+create or replace trigger prescribing_trg
+before insert on prescribing
+for each row
+begin
+  select prescribing_seq.nextval into :new.PRESCRIBINGID from dual;
+end;
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE basis');
+END;
+/
+
+CREATE TABLE BASIS  ( 
+	PCORI_BASECODE	VARCHAR2(50) NULL,
+	C_FULLNAME    	VARCHAR2(700) NOT NULL,
+	INSTANCE_NUM  	NUMBER(18) NOT NULL,
+	START_DATE    	DATE NOT NULL,
+	PROVIDER_ID   	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD    	VARCHAR2(50) NOT NULL,
+	ENCOUNTER_NUM 	NUMBER(38) NOT NULL,
+	MODIFIER_CD   	VARCHAR2(100) NOT NULL 
+	)
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE freq');
+END;
+/
+
+CREATE TABLE FREQ  ( 
+	PCORI_BASECODE	VARCHAR2(50) NULL,
+	INSTANCE_NUM  	NUMBER(18) NOT NULL,
+	START_DATE    	DATE NOT NULL,
+	PROVIDER_ID   	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD    	VARCHAR2(50) NOT NULL,
+	ENCOUNTER_NUM 	NUMBER(38) NOT NULL,
+	MODIFIER_CD   	VARCHAR2(100) NOT NULL 
+	)
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE quantity');
+END;
+/
+
+CREATE TABLE QUANTITY  ( 
+	NVAL_NUM     	NUMBER(18,5) NULL,
+	INSTANCE_NUM 	NUMBER(18) NOT NULL,
+	START_DATE   	DATE NOT NULL,
+	PROVIDER_ID  	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	MODIFIER_CD  	VARCHAR2(100) NOT NULL 
+	)
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE refills');
+END;
+/
+
+CREATE TABLE REFILLS  ( 
+	NVAL_NUM     	NUMBER(18,5) NULL,
+	INSTANCE_NUM 	NUMBER(18) NOT NULL,
+	START_DATE   	DATE NOT NULL,
+	PROVIDER_ID  	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	MODIFIER_CD  	VARCHAR2(100) NOT NULL 
+	)
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE supply');
+END;
+/
+
+CREATE TABLE SUPPLY  ( 
+	NVAL_NUM     	NUMBER(18,5) NULL,
+	INSTANCE_NUM 	NUMBER(18) NOT NULL,
+	START_DATE   	DATE NOT NULL,
+	PROVIDER_ID  	VARCHAR2(50) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	MODIFIER_CD  	VARCHAR2(100) NOT NULL 
+	)
+/
+
+
+--------------------------------------------------------------------------------
+-- DISPENSING
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE dispensing');
+END;
+/
+CREATE TABLE dispensing(
+	DISPENSINGID varchar(19)  primary key,
+	PATID varchar(50) NOT NULL,
+	PRESCRIBINGID varchar(19)  NULL,
+	DISPENSE_DATE date NOT NULL,
+	NDC varchar (11) NOT NULL,
+	DISPENSE_SUP int, 
+	DISPENSE_AMT int, 
+	RAW_NDC varchar (50)
+)
+/
+
+BEGIN
+PMN_DROPSQL('DROP sequence  dispensing_seq');
+END;
+/
+create sequence  dispensing_seq
+/
+
+create or replace trigger dispensing_trg
+before insert on dispensing
+for each row
+begin
+  select dispensing_seq.nextval into :new.DISPENSINGID from dual;
+end;
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE DISP_SUPPLY');  --Changed the table 'supply' to the name 'disp_supply' to avoid conflicts with the prescribing procedure, Matthew Joss 8/16/16
+END;
+/
+
+CREATE TABLE DISP_SUPPLY  ( 
+	NVAL_NUM     	NUMBER(18,5) NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL 
+	)
+/
+
+BEGIN
+PMN_DROPSQL('DROP TABLE amount');
+END;
+/
+
+CREATE TABLE AMOUNT  ( 
+	NVAL_NUM     	NUMBER(18,5) NULL,
+	ENCOUNTER_NUM	NUMBER(38) NOT NULL,
+	CONCEPT_CD   	VARCHAR2(50) NOT NULL 
+	)
+/
+
+-- TODO: This seems to belong in h2p-mapping
+alter table "&&i2b2_meta_schema".pcornet_med add (
+  pcori_ndc varchar2(1000) -- arbitrary
+  );
+
+
+--------------------------------------------------------------------------------
+-- PCORNET_TRIAL
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE pcornet_trial');
+END;
+/
+CREATE TABLE pcornet_trial(
+	PATID varchar(50) NOT NULL,
+	TRIALID varchar(20) NOT NULL,
+	PARTICIPANTID varchar(50) NOT NULL,
+	TRIAL_SITEID varchar(50) NULL,
+	TRIAL_ENROLL_DATE date NULL,
+	TRIAL_END_DATE date NULL,
+	TRIAL_WITHDRAW_DATE date NULL,
+	TRIAL_INVITE_CODE varchar(20) NULL
+)
+/
+
+
+--------------------------------------------------------------------------------
+-- DEATH
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE death');
+END;
+/
+CREATE TABLE death(
+	PATID varchar(50) NOT NULL,
+	DEATH_DATE date NOT NULL,
+	DEATH_DATE_IMPUTE varchar(2) NULL,
+	DEATH_SOURCE varchar(2) NOT NULL,
+	DEATH_MATCH_CONFIDENCE varchar(2) NULL
+)
+/
+
+
+--------------------------------------------------------------------------------
+-- DEATH_CAUSE
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE death_cause');
+END;
+/
+CREATE TABLE death_cause(
+	PATID varchar(50) NOT NULL,
+	DEATH_CAUSE varchar(8) NOT NULL,
+	DEATH_CAUSE_CODE varchar(2) NOT NULL,
+	DEATH_CAUSE_TYPE varchar(2) NOT NULL,
+	DEATH_CAUSE_SOURCE varchar(2) NOT NULL,
+	DEATH_CAUSE_CONFIDENCE varchar(2) NULL
+)
+/
+
+
+--------------------------------------------------------------------------------
+-- HARVEST
+--------------------------------------------------------------------------------
+
+BEGIN
+PMN_DROPSQL('DROP TABLE harvest');
+END;
+/
+CREATE TABLE harvest(
+	NETWORKID varchar(10) NOT NULL,
+	NETWORK_NAME varchar(20) NULL,
+	DATAMARTID varchar(10) NOT NULL,
+	DATAMART_NAME varchar(20) NULL,
+	DATAMART_PLATFORM varchar(2) NULL,
+	CDM_VERSION numeric(8, 2) NULL,
+	DATAMART_CLAIMS varchar(2) NULL,
+	DATAMART_EHR varchar(2) NULL,
+	BIRTH_DATE_MGMT varchar(2) NULL,
+	ENR_START_DATE_MGMT varchar(2) NULL,
+	ENR_END_DATE_MGMT varchar(2) NULL,
+	ADMIT_DATE_MGMT varchar(2) NULL,
+	DISCHARGE_DATE_MGMT varchar(2) NULL,
+	PX_DATE_MGMT varchar(2) NULL,
+	RX_ORDER_DATE_MGMT varchar(2) NULL,
+	RX_START_DATE_MGMT varchar(2) NULL,
+	RX_END_DATE_MGMT varchar(2) NULL,
+	DISPENSE_DATE_MGMT varchar(2) NULL,
+	LAB_ORDER_DATE_MGMT varchar(2) NULL,
+	SPECIMEN_DATE_MGMT varchar(2) NULL,
+	RESULT_DATE_MGMT varchar(2) NULL,
+	MEASURE_DATE_MGMT varchar(2) NULL,
+	ONSET_DATE_MGMT varchar(2) NULL,
+	REPORT_DATE_MGMT varchar(2) NULL,
+	RESOLVE_DATE_MGMT varchar(2) NULL,
+	PRO_DATE_MGMT varchar(2) NULL,
+	REFRESH_DEMOGRAPHIC_DATE date NULL,
+	REFRESH_ENROLLMENT_DATE date NULL,
+	REFRESH_ENCOUNTER_DATE date NULL,
+	REFRESH_DIAGNOSIS_DATE date NULL,
+	REFRESH_PROCEDURES_DATE date NULL,
+	REFRESH_VITAL_DATE date NULL,
+	REFRESH_DISPENSING_DATE date NULL,
+	REFRESH_LAB_RESULT_CM_DATE date NULL,
+	REFRESH_CONDITION_DATE date NULL,
+	REFRESH_PRO_CM_DATE date NULL,
+	REFRESH_PRESCRIBING_DATE date NULL,
+	REFRESH_PCORNET_TRIAL_DATE date NULL,
+	REFRESH_DEATH_DATE date NULL,
+	REFRESH_DEATH_CAUSE_DATE date NULL
+)
+/
+
+
diff --git a/Oracle/PCORNetLoader_ora.sql b/Oracle/PCORNetLoader_ora.sql
index f58ff44..6c672bc 100644
--- a/Oracle/PCORNetLoader_ora.sql
+++ b/Oracle/PCORNetLoader_ora.sql
@@ -20,744 +20,6 @@
 --undef network_id;
 --undef network_name;
 
-create or replace PROCEDURE GATHER_TABLE_STATS(table_name VARCHAR2) AS 
-  BEGIN
-  DBMS_STATS.GATHER_TABLE_STATS (
-          ownname => 'PCORNET_CDM', -- This doesn't work as a parameter for some reason.
-          tabname => table_name,
-          estimate_percent => 50, -- Percentage picked somewhat arbitrarily
-          cascade => TRUE,
-          degree => 16 
-          );
-END GATHER_TABLE_STATS;
-/
-
-create or replace PROCEDURE PMN_DROPSQL(sqlstring VARCHAR2) AS 
-  BEGIN
-      EXECUTE IMMEDIATE sqlstring;
-  EXCEPTION
-      WHEN OTHERS THEN NULL;
-END PMN_DROPSQL;
-/
-
-create or replace FUNCTION PMN_IFEXISTS(objnamestr VARCHAR2, objtypestr VARCHAR2) RETURN BOOLEAN AS 
-cnt NUMBER;
-BEGIN
-  SELECT COUNT(*)
-   INTO cnt
-    FROM USER_OBJECTS
-  WHERE  upper(OBJECT_NAME) = upper(objnamestr)
-         and upper(object_type) = upper(objtypestr);
-  
-  IF( cnt = 0 )
-  THEN
-    --dbms_output.put_line('NO!');
-    return FALSE;  
-  ELSE
-   --dbms_output.put_line('YES!'); 
-   return TRUE;
-  END IF;
-
-END PMN_IFEXISTS;
-/
-
-
-create or replace PROCEDURE PMN_Execuatesql(sqlstring VARCHAR2) AS 
-BEGIN
-  EXECUTE IMMEDIATE sqlstring;
-  dbms_output.put_line(sqlstring);
-END PMN_ExecuateSQL;
-/
-
---ACK: http://dba.stackexchange.com/questions/9441/how-to-catch-and-handle-only-specific-oracle-exceptions
-create or replace procedure create_error_table(table_name varchar2) as
-sqltext varchar2(4000); 
-
-begin
-  dbms_errlog.create_error_log(dml_table_name => table_name);
-EXCEPTION
-  WHEN OTHERS THEN
-    IF SQLCODE = -955 THEN
-      NULL; -- suppresses ORA-00955 exception ("name is already used by an existing object")
-    ELSE
-       RAISE;
-    END IF;
--- Delete rows from a previous run in case the table already existed
-sqltext := 'delete from ERR$_' || table_name;
-PMN_Execuatesql(sqltext);
-end;
-/
-
-
-
-
-
-
-CREATE OR REPLACE SYNONYM I2B2FACT FOR "&&i2b2_data_schema".OBSERVATION_FACT
-/
-
-CREATE OR REPLACE SYNONYM I2B2MEDFACT FOR OBSERVATION_FACT_MEDS
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE i2b2patient_list');
-END;
-/
-
-CREATE table i2b2patient_list as 
-select * from
-(
-select DISTINCT PATIENT_NUM from I2B2FACT where START_DATE > to_date('&&min_pat_list_date_dd_mon_rrrr','dd-mon-rrrr')
-) where ROWNUM<100000000
-/
-
-create or replace VIEW i2b2patient as select * from "&&i2b2_data_schema".PATIENT_DIMENSION where PATIENT_NUM in (select PATIENT_NUM from i2b2patient_list)
-/
-
-create or replace view i2b2visit as select * from "&&i2b2_data_schema".VISIT_DIMENSION where START_DATE >= to_date('&&min_visit_date_dd_mon_rrrr','dd-mon-rrrr') and (END_DATE is NULL or END_DATE < CURRENT_DATE) and (START_DATE <CURRENT_DATE)
-/
-
-
-CREATE OR REPLACE SYNONYM pcornet_med FOR  "&&i2b2_meta_schema".pcornet_med
-/
-
-CREATE OR REPLACE SYNONYM pcornet_lab FOR  "&&i2b2_meta_schema".pcornet_lab
-/
-
-CREATE OR REPLACE SYNONYM pcornet_diag FOR  "&&i2b2_meta_schema".pcornet_diag
-/
-
-CREATE OR REPLACE SYNONYM pcornet_demo FOR  "&&i2b2_meta_schema".pcornet_demo
-/
-
-CREATE OR REPLACE SYNONYM pcornet_proc FOR  "&&i2b2_meta_schema".pcornet_proc
-/
-
-CREATE OR REPLACE SYNONYM pcornet_vital FOR  "&&i2b2_meta_schema".pcornet_vital
-/
-
-CREATE OR REPLACE SYNONYM pcornet_enc FOR  "&&i2b2_meta_schema".pcornet_enc
-/
-
-create or replace FUNCTION GETDATAMARTID RETURN VARCHAR2 IS 
-BEGIN 
-    RETURN '&&datamart_id';
-END;
-/
-
-CREATE OR REPLACE FUNCTION GETDATAMARTNAME RETURN VARCHAR2 AS 
-BEGIN 
-    RETURN '&&datamart_name';
-END;
-/
-
-CREATE OR REPLACE FUNCTION GETDATAMARTPLATFORM RETURN VARCHAR2 AS 
-BEGIN 
-    RETURN '02'; -- 01 is MSSQL, 02 is Oracle
-END;
-/
-
-/* TODO: Consider building the loyalty cohort as designed: 
-https://github.com/njgraham/SCILHS-utils/blob/master/LoyaltyCohort/LoyaltyCohort-ora.sql
-
-For now, let's count all patients for testing with the KUMC test patients.
-*/
-
---create or replace view i2b2loyalty_patients as (select patient_num,to_date('01-Jul-2010','dd-mon-rrrr') period_start,to_date('01-Jul-2014','dd-mon-rrrr') period_end from "&&i2b2_data_schema".loyalty_cohort_patient_summary where BITAND(filter_set, 61511) = 61511 and patient_num in (select patient_num from i2b2patient))
---/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE pcornet_codelist');
-END;
-/
-
-create table pcornet_codelist(codetype varchar2(20), code varchar2(50))
-/
-create or replace procedure pcornet_parsecode (codetype in varchar, codestring in varchar) as
-
-tex varchar(2000);
-pos number(9);
-readstate char(1) ;
-nextchar char(1) ;
-val varchar(50);
-
-begin
-
-val:='';
-readstate:='F';
-pos:=0;
-tex := codestring;
-FOR pos IN 1..length(tex)
-LOOP
---	dbms_output.put_line(val);
-    	nextchar:=substr(tex,pos,1);
-	if nextchar!=',' then
-		if nextchar='''' then
-			if readstate='F' then
-				val:='';
-				readstate:='T';
-			else
-				insert into pcornet_codelist values (codetype,val);
-				val:='';
-				readstate:='F'  ;
-			end if;
-		else
-			if readstate='T' then
-				val:= val || nextchar;
-			end if;
-		end if;
-	end if;
-END LOOP;
-
-end pcornet_parsecode;
-/
-
-
-
-create or replace procedure pcornet_popcodelist as
-
-codedata varchar(2000);
-onecode varchar(20);
-codetype varchar(20);
-
-cursor getcodesql is
-select 'RACE',c_dimcode from pcornet_demo where c_fullname like '\PCORI\DEMOGRAPHIC\RACE%'
-union
-select 'SEX',c_dimcode from pcornet_demo where c_fullname like '\PCORI\DEMOGRAPHIC\SEX%'
-union
-select 'HISPANIC',c_dimcode from pcornet_demo where c_fullname like '\PCORI\DEMOGRAPHIC\HISPANIC%';
-
-
-begin
-open getcodesql;
-LOOP 
-	fetch getcodesql into codetype,codedata;
-	EXIT WHEN getcodesql%NOTFOUND ;
- 	pcornet_parsecode (codetype,codedata );
-end loop;
-
-close getcodesql ;
-end pcornet_popcodelist;
-/
-
-
-
-
-BEGIN
-PMN_DROPSQL('DROP TABLE enrollment');
-END;
-/
-
-CREATE TABLE enrollment (
-	PATID varchar(50) NOT NULL,
-	ENR_START_DATE date NOT NULL,
-	ENR_END_DATE date NULL,
-	CHART varchar(1) NULL,
-	ENR_BASIS varchar(1) NOT NULL,
-	RAW_CHART varchar(50) NULL,
-	RAW_BASIS varchar(50) NULL
-)
-/
-
-
-
-BEGIN
-PMN_DROPSQL('DROP TABLE vital');
-END;
-/
-
-CREATE TABLE vital (
-	VITALID varchar(19)  primary key,
-	PATID varchar(50) NULL,
-	ENCOUNTERID varchar(50) NULL,
-	MEASURE_DATE date NULL,
-	MEASURE_TIME varchar(5) NULL,
-	VITAL_SOURCE varchar(2) NULL,
-	HT number(18, 0) NULL, --8, 0
-	WT number(18, 0) NULL, --8, 0
-	DIASTOLIC number(18, 0) NULL,--4, 0
-	SYSTOLIC number(18, 0) NULL, --4, 0
-	ORIGINAL_BMI number(18,0) NULL,--8, 0
-	BP_POSITION varchar(2) NULL,
-	SMOKING varchar (2),
-	TOBACCO varchar (2),
-	TOBACCO_TYPE varchar (2),
-	RAW_VITAL_SOURCE varchar(50) NULL,
-	RAW_HT varchar(50) NULL,
-	RAW_WT varchar(50) NULL,
-	RAW_DIASTOLIC varchar(50) NULL,
-	RAW_SYSTOLIC varchar(50) NULL,
-	RAW_BP_POSITION varchar(50) NULL,
-	RAW_SMOKING varchar (50),
-	Raw_TOBACCO varchar (50),
-	Raw_TOBACCO_TYPE varchar (50)
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP SEQUENCE vital_seq');
-END;
-/
-
-create sequence  vital_seq
-/
-
-create or replace trigger vital_trg
-before insert on vital
-for each row
-begin
-  select vital_seq.nextval into :new.VITALID from dual;
-end;
-/
-
-
-BEGIN
-PMN_DROPSQL('DROP TABLE procedures');
-END;
-/
-
-CREATE TABLE procedures(
-	PROCEDURESID varchar(19)  primary key,
-	PATID varchar(50) NOT NULL,
-	ENCOUNTERID varchar(50) NOT NULL,
-	ENC_TYPE varchar(2) NULL,
-	ADMIT_DATE date NULL,
-	PROVIDERID varchar(50) NULL,
-	PX_DATE date NULL,
-	PX varchar(11) NOT NULL,
-	PX_TYPE varchar(2) NOT NULL,
-	PX_SOURCE varchar(2) NULL,
-	RAW_PX varchar(50) NULL,
-	RAW_PX_TYPE varchar(50) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP sequence  procedures_seq');
-END;
-/
-
-create sequence  procedures_seq
-/
-
-create or replace trigger procedures_trg
-before insert on procedures
-for each row
-begin
-  select procedures_seq.nextval into :new.PROCEDURESID from dual;
-end;
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE diagnosis');
-END;
-/
-
-CREATE TABLE diagnosis(
-	DIAGNOSISID varchar(19)  primary key,
-	PATID varchar(50) NOT NULL,
-	ENCOUNTERID varchar(50) NOT NULL,
-	ENC_TYPE varchar(2) NULL,
-	ADMIT_DATE date NULL,
-	PROVIDERID varchar(50) NULL,
-	DX varchar(18) NOT NULL,
-	DX_TYPE varchar(2) NOT NULL,
-	DX_SOURCE varchar(2) NOT NULL,
-	PDX varchar(2) NULL,
-	RAW_DX varchar(50) NULL,
-	RAW_DX_TYPE varchar(50) NULL,
-	RAW_DX_SOURCE varchar(50) NULL,
-	RAW_ORIGDX varchar(50) NULL,
-	RAW_PDX varchar(50) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP sequence  diagnosis_seq');
-END;
-/
-create sequence  diagnosis_seq
-/
-
-create or replace trigger diagnosis_trg
-before insert on diagnosis
-for each row
-begin
-  select diagnosis_seq.nextval into :new.DIAGNOSISID from dual;
-end;
-/
-
-
-
-
-BEGIN
-PMN_DROPSQL('DROP TABLE lab_result_cm');
-END;
-/
-
-CREATE TABLE lab_result_cm(
-	LAB_RESULT_CM_ID varchar(19)  primary key,
-	PATID varchar(50) NOT NULL,
-	ENCOUNTERID varchar(50) NULL,
-	LAB_NAME varchar(10) NULL,
-	SPECIMEN_SOURCE varchar(10) NULL,
-	LAB_LOINC varchar(10) NULL,
-	PRIORITY varchar(2) NULL,
-	RESULT_LOC varchar(2) NULL,
-	LAB_PX varchar(11) NULL,
-	LAB_PX_TYPE varchar(2) NULL,
-	LAB_ORDER_DATE date NULL,
-	SPECIMEN_DATE date NULL,
-	SPECIMEN_TIME varchar(5) NULL,
-	RESULT_DATE date NULL,
-	RESULT_TIME varchar(5) NULL,
-	RESULT_QUAL varchar(12) NULL,
-	RESULT_NUM number (18,5) NULL,
-	RESULT_MODIFIER varchar(2) NULL,
-	RESULT_UNIT varchar(11) NULL,
-	NORM_RANGE_LOW varchar(10) NULL,
-	NORM_MODIFIER_LOW varchar(2) NULL,
-	NORM_RANGE_HIGH varchar(10) NULL,
-	NORM_MODIFIER_HIGH varchar(2) NULL,
-	ABN_IND varchar(2) NULL,
-	RAW_LAB_NAME varchar(50) NULL,
-	RAW_LAB_CODE varchar(50) NULL,
-	RAW_PANEL varchar(50) NULL,
-	RAW_RESULT varchar(50) NULL,
-	RAW_UNIT varchar(50) NULL,
-	RAW_ORDER_DEPT varchar(50) NULL,
-	RAW_FACILITY_CODE varchar(50) NULL
-)
-/
-
-
-BEGIN
-PMN_DROPSQL('DROP SEQUENCE lab_result_cm_seq');
-END;
-/
-
-create sequence  lab_result_cm_seq
-/
-
-create or replace trigger lab_result_cm_trg
-before insert on lab_result_cm
-for each row
-begin
-  select lab_result_cm_seq.nextval into :new.LAB_RESULT_CM_ID from dual;
-end;
-/
-
-
-BEGIN
-PMN_DROPSQL('DROP TABLE death');
-END;
-/
-CREATE TABLE death(
-	PATID varchar(50) NOT NULL,
-	DEATH_DATE date NOT NULL,
-	DEATH_DATE_IMPUTE varchar(2) NULL,
-	DEATH_SOURCE varchar(2) NOT NULL,
-	DEATH_MATCH_CONFIDENCE varchar(2) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE death_cause');
-END;
-/
-CREATE TABLE death_cause(
-	PATID varchar(50) NOT NULL,
-	DEATH_CAUSE varchar(8) NOT NULL,
-	DEATH_CAUSE_CODE varchar(2) NOT NULL,
-	DEATH_CAUSE_TYPE varchar(2) NOT NULL,
-	DEATH_CAUSE_SOURCE varchar(2) NOT NULL,
-	DEATH_CAUSE_CONFIDENCE varchar(2) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE dispensing');
-END;
-/
-CREATE TABLE dispensing(
-	DISPENSINGID varchar(19)  primary key,
-	PATID varchar(50) NOT NULL,
-	PRESCRIBINGID varchar(19)  NULL,
-	DISPENSE_DATE date NOT NULL,
-	NDC varchar (11) NOT NULL,
-	DISPENSE_SUP int, 
-	DISPENSE_AMT int, 
-	RAW_NDC varchar (50)
-)
-/
-
-
-BEGIN
-PMN_DROPSQL('DROP sequence  dispensing_seq');
-END;
-/
-create sequence  dispensing_seq
-/
-
-create or replace trigger dispensing_trg
-before insert on dispensing
-for each row
-begin
-  select dispensing_seq.nextval into :new.DISPENSINGID from dual;
-end;
-/
-
-
-
-
-
-
-
-
-
-
-BEGIN
-PMN_DROPSQL('DROP TABLE prescribing');
-END;
-/
-CREATE TABLE prescribing(
-	PRESCRIBINGID varchar(19)  primary key,
-	PATID varchar(50) NOT NULL,
-	ENCOUNTERID  varchar(50) NULL,
-	RX_PROVIDERID varchar(50) NULL, -- NOTE: The spec has a _ before the ID, but this is inconsistent.
-	RX_ORDER_DATE date NULL,
-	RX_ORDER_TIME varchar (5) NULL,
-	RX_START_DATE date NULL,
-	RX_END_DATE date NULL,
-	RX_QUANTITY int NULL,
-	RX_REFILLS int NULL,
-	RX_DAYS_SUPPLY int NULL,
-	RX_FREQUENCY varchar(2) NULL,
-	RX_BASIS varchar (2) NULL,
-	RXNORM_CUI int NULL,
-	RAW_RX_MED_NAME varchar (50) NULL,
-	RAW_RX_FREQUENCY varchar (50) NULL,
-	RAW_RXNORM_CUI varchar (50) NULL
-)
-/
-
-
-BEGIN
-PMN_DROPSQL('DROP sequence  prescribing_seq');
-END;
-/
-create sequence  prescribing_seq
-/
-
-create or replace trigger prescribing_trg
-before insert on prescribing
-for each row
-begin
-  select prescribing_seq.nextval into :new.PRESCRIBINGID from dual;
-end;
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE pcornet_trial');
-END;
-/
-CREATE TABLE pcornet_trial(
-	PATID varchar(50) NOT NULL,
-	TRIALID varchar(20) NOT NULL,
-	PARTICIPANTID varchar(50) NOT NULL,
-	TRIAL_SITEID varchar(50) NULL,
-	TRIAL_ENROLL_DATE date NULL,
-	TRIAL_END_DATE date NULL,
-	TRIAL_WITHDRAW_DATE date NULL,
-	TRIAL_INVITE_CODE varchar(20) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE condition');
-END;
-/
-CREATE TABLE condition(
-	CONDITIONID varchar(19)  primary key,
-	PATID varchar(50) NOT NULL,
-	ENCOUNTERID  varchar(50) NULL,
-	REPORT_DATE  date NULL,
-	RESOLVE_DATE  date NULL,
-	ONSET_DATE  date NULL,
-	CONDITION_STATUS varchar(2) NULL,
-	CONDITION varchar(18) NOT NULL,
-	CONDITION_TYPE varchar(2) NOT NULL,
-	CONDITION_SOURCE varchar(2) NOT NULL,
-	RAW_CONDITION_STATUS varchar(2) NULL,
-	RAW_CONDITION varchar(18) NULL,
-	RAW_CONDITION_TYPE varchar(2) NULL,
-	RAW_CONDITION_SOURCE varchar(2) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP sequence  condition_seq');
-END;
-/
-create sequence  condition_seq
-/
-
-create or replace trigger condition_trg
-before insert on condition
-for each row
-begin
-  select condition_seq.nextval into :new.CONDITIONID from dual;
-end;
-/
-
-
-
-BEGIN
-PMN_DROPSQL('DROP TABLE pro_cm');
-END;
-/
-CREATE TABLE pro_cm(
-	PRO_CM_ID varchar(19)  primary key,
-	PATID varchar(50) NOT NULL,
-	ENCOUNTERID  varchar(50) NULL,
-	PRO_ITEM varchar (7) NOT NULL,
-	PRO_LOINC varchar (10) NULL,
-	PRO_DATE date NOT NULL,
-	PRO_TIME varchar (5) NULL,
-	PRO_RESPONSE int NOT NULL,
-	PRO_METHOD varchar (2) NULL,
-	PRO_MODE varchar (2) NULL,
-	PRO_CAT varchar (2) NULL,
-	RAW_PRO_CODE varchar (50) NULL,
-	RAW_PRO_RESPONSE varchar (50) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP sequence  pro_cm_seq');
-END;
-/
-create sequence  pro_cm_seq
-/
-
-create or replace trigger pro_cm_trg
-before insert on pro_cm
-for each row
-begin
-  select pro_cm_seq.nextval into :new.PRO_CM_ID from dual;
-end;
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE harvest');
-END;
-/
-CREATE TABLE harvest(
-	NETWORKID varchar(10) NOT NULL,
-	NETWORK_NAME varchar(20) NULL,
-	DATAMARTID varchar(10) NOT NULL,
-	DATAMART_NAME varchar(20) NULL,
-	DATAMART_PLATFORM varchar(2) NULL,
-	CDM_VERSION numeric(8, 2) NULL,
-	DATAMART_CLAIMS varchar(2) NULL,
-	DATAMART_EHR varchar(2) NULL,
-	BIRTH_DATE_MGMT varchar(2) NULL,
-	ENR_START_DATE_MGMT varchar(2) NULL,
-	ENR_END_DATE_MGMT varchar(2) NULL,
-	ADMIT_DATE_MGMT varchar(2) NULL,
-	DISCHARGE_DATE_MGMT varchar(2) NULL,
-	PX_DATE_MGMT varchar(2) NULL,
-	RX_ORDER_DATE_MGMT varchar(2) NULL,
-	RX_START_DATE_MGMT varchar(2) NULL,
-	RX_END_DATE_MGMT varchar(2) NULL,
-	DISPENSE_DATE_MGMT varchar(2) NULL,
-	LAB_ORDER_DATE_MGMT varchar(2) NULL,
-	SPECIMEN_DATE_MGMT varchar(2) NULL,
-	RESULT_DATE_MGMT varchar(2) NULL,
-	MEASURE_DATE_MGMT varchar(2) NULL,
-	ONSET_DATE_MGMT varchar(2) NULL,
-	REPORT_DATE_MGMT varchar(2) NULL,
-	RESOLVE_DATE_MGMT varchar(2) NULL,
-	PRO_DATE_MGMT varchar(2) NULL,
-	REFRESH_DEMOGRAPHIC_DATE date NULL,
-	REFRESH_ENROLLMENT_DATE date NULL,
-	REFRESH_ENCOUNTER_DATE date NULL,
-	REFRESH_DIAGNOSIS_DATE date NULL,
-	REFRESH_PROCEDURES_DATE date NULL,
-	REFRESH_VITAL_DATE date NULL,
-	REFRESH_DISPENSING_DATE date NULL,
-	REFRESH_LAB_RESULT_CM_DATE date NULL,
-	REFRESH_CONDITION_DATE date NULL,
-	REFRESH_PRO_CM_DATE date NULL,
-	REFRESH_PRESCRIBING_DATE date NULL,
-	REFRESH_PCORNET_TRIAL_DATE date NULL,
-	REFRESH_DEATH_DATE date NULL,
-	REFRESH_DEATH_CAUSE_DATE date NULL
-)
-/
-
-
-
-BEGIN
-PMN_DROPSQL('DROP TABLE encounter');
-END;
-/
-CREATE TABLE encounter(
-	PATID varchar(50) NOT NULL,
-	ENCOUNTERID varchar(50) NOT NULL,
-	ADMIT_DATE date NULL,
-	ADMIT_TIME varchar(5) NULL,
-	DISCHARGE_DATE date NULL,
-	DISCHARGE_TIME varchar(5) NULL,
-	PROVIDERID varchar(50) NULL,
-	FACILITY_LOCATION varchar(3) NULL,
-	ENC_TYPE varchar(2) NOT NULL,
-	FACILITYID varchar(50) NULL,
-	DISCHARGE_DISPOSITION varchar(2) NULL,
-	DISCHARGE_STATUS varchar(2) NULL,
-	DRG varchar(3) NULL,
-	DRG_TYPE varchar(2) NULL,
-	ADMITTING_SOURCE varchar(2) NULL,
-	RAW_SITEID varchar (50) NULL,
-	RAW_ENC_TYPE varchar(50) NULL,
-	RAW_DISCHARGE_DISPOSITION varchar(50) NULL,
-	RAW_DISCHARGE_STATUS varchar(50) NULL,
-	RAW_DRG_TYPE varchar(50) NULL,
-	RAW_ADMITTING_SOURCE varchar(50) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE demographic');
-END;
-/
-CREATE TABLE demographic(
-	PATID varchar(50) NOT NULL,
-	BIRTH_DATE date NULL,
-	BIRTH_TIME varchar(5) NULL,
-	SEX varchar(2) NULL,
-	HISPANIC varchar(2) NULL,
-	BIOBANK_FLAG varchar(1) DEFAULT 'N',
-	RACE varchar(2) NULL,
-	RAW_SEX varchar(50) NULL,
-	RAW_HISPANIC varchar(50) NULL,
-	RAW_RACE varchar(50) NULL
-)
-/
-
-BEGIN
-PMN_DROPSQL('DROP TABLE i2pReport');
-END;
-/
-
-create table i2pReport (runid number, rundate date, concept varchar(20), sourceval number, destval number, diff number)
-/
-
-BEGIN
-insert into i2preport (runid) values (0);
-pcornet_popcodelist;
-END;
-/
 
 
 create or replace procedure PCORNetDemographic as 
@@ -896,7 +158,9 @@ union --6 -- NS, NR, nH
 begin    
 pcornet_popcodelist;
 
-PMN_DROPSQL('drop index demographic_patid');
+PMN_DROPSQL('drop index demographic_idx');
+
+execute immediate 'truncate table demographic';
 
 OPEN getsql;
 LOOP
@@ -908,7 +172,7 @@ FETCH getsql INTO sqltext;
 END LOOP;
 CLOSE getsql;
 
-execute immediate 'create index demographic_patid on demographic (PATID)';
+execute immediate 'create index demographic_idx on demographic (PATID)';
 GATHER_TABLE_STATS('DEMOGRAPHIC');
 
 end PCORNetDemographic; 
@@ -924,12 +188,26 @@ ORA-00904: "FACILITY_ID": invalid identifier
 ORA-00904: "LOCATION_ZIP": invalid identifier
 */
 create or replace procedure PCORNetEncounter as
-
-sqltext varchar2(4000);
 begin
 
-PMN_DROPSQL('drop index encounter_patid');
-PMN_DROPSQL('drop index encounter_encounterid');
+PMN_DROPSQL('drop index encounter_idx');
+PMN_DROPSQL('drop index drg_idx');
+
+execute immediate 'truncate table encounter';
+execute immediate 'truncate table drg';
+
+insert into drg
+select * from
+(select patient_num,encounter_num,drg_type, drg,row_number() over (partition by  patient_num, encounter_num order by drg_type desc) AS rn from
+(select patient_num,encounter_num,drg_type,max(drg) drg  from
+(select distinct f.patient_num,encounter_num,SUBSTR(c_fullname,22,2) drg_type,SUBSTR(pcori_basecode,INSTR(pcori_basecode, ':')+1,3) drg from i2b2fact f
+inner join demographic d on f.patient_num=d.patid
+inner join pcornet_enc enc on enc.c_basecode  = f.concept_cd
+and enc.c_fullname like ''\PCORI\ENCOUNTER\DRG\%'') drg1 group by patient_num,encounter_num,drg_type) drg) drg
+where rn=1;
+
+execute immediate 'create index drg_idx on drg (patient_num, encounter_num)';
+GATHER_TABLE_STATS('drg');
 
 insert into encounter(PATID,ENCOUNTERID,admit_date ,ADMIT_TIME , 
 		DISCHARGE_DATE ,DISCHARGE_TIME ,PROVIDERID ,FACILITY_LOCATION  
@@ -949,15 +227,7 @@ select distinct v.patient_num, v.encounter_num,
   drg.drg, drg_type, 
   CASE WHEN admitting_source IS NULL THEN 'NI' ELSE admitting_source END admitting_source
 from i2b2visit v inner join demographic d on v.patient_num=d.patid
-left outer join 
-   (select * from
-   (select patient_num,encounter_num,drg_type, drg,row_number() over (partition by  patient_num, encounter_num order by drg_type desc) AS rn from 
-   (select patient_num,encounter_num,drg_type,max(drg) drg  from
-    (select distinct f.patient_num,encounter_num,SUBSTR(c_fullname,22,2) drg_type,SUBSTR(pcori_basecode,INSTR(pcori_basecode, ':')+1,3) drg from i2b2fact f 
-     inner join demographic d on f.patient_num=d.patid
-     inner join pcornet_enc enc on enc.c_basecode  = f.concept_cd   
-      and enc.c_fullname like '\PCORI\ENCOUNTER\DRG\%') drg1 group by patient_num,encounter_num,drg_type) drg) drg
-     where rn=1) drg -- This section is bugfixed to only include 1 drg if multiple DRG types exist in a single encounter...
+left outer join drg -- This section is bugfixed to only include 1 drg if multiple DRG types exist in a single encounter...
   on drg.patient_num=v.patient_num and drg.encounter_num=v.encounter_num
 left outer join 
 -- Encounter type. Note that this requires a full table scan on the ontology table, so it is not particularly efficient.
@@ -965,8 +235,7 @@ left outer join
  inner join pcornet_enc e on c_dimcode like '%'''||inout_cd||'''%' and e.c_fullname like '\PCORI\ENCOUNTER\ENC_TYPE\%') enctype
   on enctype.patient_num=v.patient_num and enctype.encounter_num=v.encounter_num;
 
-execute immediate 'create index encounter_patid on encounter (PATID)';
-execute immediate 'create index encounter_encounterid on encounter (ENCOUNTERID)';
+execute immediate 'create index encounter_idx on encounter (PATID, ENCOUNTERID)';
 GATHER_TABLE_STATS('ENCOUNTER');
 
 end PCORNetEncounter;
@@ -974,41 +243,38 @@ end PCORNetEncounter;
 
 
 
-
 create or replace procedure PCORNetDiagnosis as
-sqltext varchar2(4000);
 begin
 
-PMN_DROPSQL('drop index diagnosis_patid');
-PMN_DROPSQL('drop index diagnosis_encounterid');
+PMN_DROPSQL('drop index diagnosis_idx');
+PMN_DROPSQL('drop index sourcefact_idx');
+PMN_DROPSQL('drop index pdxfact_idx');
 
-PMN_DROPSQL('DROP TABLE sourcefact'); -- associated indexes will be dropped as well
+execute immediate 'truncate table diagnosis';
+execute immediate 'truncate table sourcefact';
+execute immediate 'truncate table pdxfact';
 
-sqltext := 'create table sourcefact as '||
-	'select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, dxsource.pcori_basecode dxsource, dxsource.c_fullname '||
-	'from i2b2fact factline '||
-    'inner join encounter enc on enc.patid = factline.patient_num and enc.encounterid = factline.encounter_Num '||
-    'inner join pcornet_diag dxsource on factline.modifier_cd =dxsource.c_basecode '||
-	'where dxsource.c_fullname like ''\PCORI_MOD\CONDITION_OR_DX\%''';
-PMN_EXECUATESQL(sqltext);
+insert into table sourcefact
+	select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, dxsource.pcori_basecode dxsource, dxsource.c_fullname
+	from i2b2fact factline
+    inner join encounter enc on enc.patid = factline.patient_num and enc.encounterid = factline.encounter_Num
+    inner join pcornet_diag dxsource on factline.modifier_cd =dxsource.c_basecode
+	where dxsource.c_fullname like '\PCORI_MOD\CONDITION_OR_DX\%';
 
 execute immediate 'create index sourcefact_idx on sourcefact (patient_num, encounter_num, provider_id, concept_cd, start_date)';
 GATHER_TABLE_STATS('SOURCEFACT');
 
-PMN_DROPSQL('DROP TABLE pdxfact');
-
-sqltext := 'create table pdxfact as '||
-	'select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, dxsource.pcori_basecode pdxsource,dxsource.c_fullname  '||
-	'from i2b2fact factline '||
-    'inner join encounter enc on enc.patid = factline.patient_num and enc.encounterid = factline.encounter_Num '||
-    'inner join pcornet_diag dxsource on factline.modifier_cd =dxsource.c_basecode '||
-	'and dxsource.c_fullname like ''\PCORI_MOD\PDX\%''';
-PMN_EXECUATESQL(sqltext);
+insert into table pdxfact
+	select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, dxsource.pcori_basecode pdxsource,dxsource.c_fullname
+	from i2b2fact factline
+    inner join encounter enc on enc.patid = factline.patient_num and enc.encounterid = factline.encounter_Num
+    inner join pcornet_diag dxsource on factline.modifier_cd =dxsource.c_basecode
+	and dxsource.c_fullname like '\PCORI_MOD\PDX\%';
 
 execute immediate 'create index pdxfact_idx on pdxfact (patient_num, encounter_num, provider_id, concept_cd, start_date)';
 GATHER_TABLE_STATS('PDXFACT');
 
-insert into diagnosis (patid,			encounterid,	enc_type, admit_date, providerid, dx, dx_type, dx_source, pdx)
+insert into diagnosis (patid,	encounterid, enc_type, admit_date, providerid, dx, dx_type, dx_source, pdx)
 /* KUMC started billing with ICD10 on Oct 1, 2015. */
 with icd10_transition as (
   select date '2015-10-01' as cutoff from dual
@@ -1074,9 +340,7 @@ where (sourcefact.c_fullname like '\PCORI_MOD\CONDITION_OR_DX\DX_SOURCE\%' or so
 -- order by enc.admit_date desc
 ;
 
-
-execute immediate 'create index diagnosis_patid on diagnosis (PATID)';
-execute immediate 'create index diagnosis_encounterid on diagnosis (ENCOUNTERID)';
+execute immediate 'create index diagnosis_idx on diagnosis (PATID, ENCOUNTERID)';
 GATHER_TABLE_STATS('DIAGNOSIS');
 
 end PCORNetDiagnosis;
@@ -1084,66 +348,63 @@ end PCORNetDiagnosis;
 
 
 
-
-
 create or replace procedure PCORNetCondition as
-sqltext varchar2(4000);
 begin
 
-PMN_DROPSQL('drop index condition_patid');
-PMN_DROPSQL('drop index condition_encounterid');
+PMN_DROPSQL('drop index condition_idx');
+PMN_DROPSQL('drop index sourcefact2_idx');
+
+execute immediate 'truncate table condition';
+execute immediate 'truncate table sourcefact2';
 
 PMN_DROPSQL('DROP TABLE sourcefact2');
 
-sqltext := 'create table sourcefact2 as '||
-	'select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, dxsource.pcori_basecode dxsource, dxsource.c_fullname '||
-	'from i2b2fact factline '||
-    'inner join encounter enc on enc.patid = factline.patient_num and enc.encounterid = factline.encounter_Num '||
-    'inner join pcornet_diag dxsource on factline.modifier_cd =dxsource.c_basecode '||
-	'where dxsource.c_fullname like ''\PCORI_MOD\CONDITION_OR_DX\%''';
-PMN_EXECUATESQL(sqltext);
+insert into sourcefact2
+	select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, dxsource.pcori_basecode dxsource, dxsource.c_fullname
+	from i2b2fact factline
+    inner join encounter enc on enc.patid = factline.patient_num and enc.encounterid = factline.encounter_Num
+    inner join pcornet_diag dxsource on factline.modifier_cd =dxsource.c_basecode
+	where dxsource.c_fullname like '\PCORI_MOD\CONDITION_OR_DX\%';
+
+execute immediate 'create index sourcefact2_idx on sourcefact (patient_num, encounter_num, provider_id, concept_cd, start_date)';
+GATHER_TABLE_STATS('SOURCEFACT2');
 
 create_error_table('CONDITION');
 
-sqltext := 'insert into condition (patid, encounterid, report_date, resolve_date, condition, condition_type, condition_status, condition_source) '||
-'select distinct factline.patient_num, min(factline.encounter_num) encounterid, min(factline.start_date) report_date, NVL(max(factline.end_date),null) resolve_date, diag.pcori_basecode,  '||
-'SUBSTR(diag.c_fullname,18,2) condition_type,   '||
-'	NVL2(max(factline.end_date) , ''RS'', ''NI'') condition_status,  '|| -- Imputed so might not be entirely accurate
-'	NVL(SUBSTR(max(dxsource),INSTR(max(dxsource), '':'')+1,2),''NI'') condition_source '||
-'from i2b2fact factline '||
-'inner join encounter enc on enc.patid = factline.patient_num and enc.encounterid = factline.encounter_Num '||
-'inner join pcornet_diag diag on diag.c_basecode  = factline.concept_cd    '||
-' left outer join sourcefact2 sf '||
-'on	factline.patient_num=sf.patient_num '||
-'and factline.encounter_num=sf.encounter_num '||
-'and factline.provider_id=sf.provider_id '||
-'and factline.concept_cd=sf.concept_Cd '||
-'and factline.start_date=sf.start_Date   '||
-'where diag.c_fullname like ''\PCORI\DIAGNOSIS\%'' '||
-'and sf.c_fullname like ''\PCORI_MOD\CONDITION_OR_DX\CONDITION_SOURCE\%'' '||
-'group by factline.patient_num, diag.pcori_basecode, diag.c_fullname ' ||
-'log errors into ERR$_CONDITION reject limit unlimited'
+insert into condition (patid, encounterid, report_date, resolve_date, condition, condition_type, condition_status, condition_source)
+select distinct factline.patient_num, min(factline.encounter_num) encounterid, min(factline.start_date) report_date, NVL(max(factline.end_date),null) resolve_date, diag.pcori_basecode,
+SUBSTR(diag.c_fullname,18,2) condition_type,
+	NVL2(max(factline.end_date) , 'RS', 'NI') condition_status, -- Imputed so might not be entirely accurate
+	NVL(SUBSTR(max(dxsource),INSTR(max(dxsource), ':')+1,2),'NI') condition_source
+from i2b2fact factline
+inner join encounter enc on enc.patid = factline.patient_num and enc.encounterid = factline.encounter_Num
+inner join pcornet_diag diag on diag.c_basecode  = factline.concept_cd
+ left outer join sourcefact2 sf
+on	factline.patient_num=sf.patient_num
+and factline.encounter_num=sf.encounter_num
+and factline.provider_id=sf.provider_id
+and factline.concept_cd=sf.concept_Cd
+and factline.start_date=sf.start_Date
+where diag.c_fullname like '\PCORI\DIAGNOSIS\%'
+and sf.c_fullname like '\PCORI_MOD\CONDITION_OR_DX\CONDITION_SOURCE\%'
+group by factline.patient_num, diag.pcori_basecode, diag.c_fullname
+log errors into ERR$_CONDITION reject limit unlimited
 ;
 
-PMN_EXECUATESQL(sqltext);
-
-execute immediate 'create index condition_patid on condition (PATID)';
-execute immediate 'create index condition_encounterid on condition (ENCOUNTERID)';
+execute immediate 'create index condition_idx on condition (PATID, ENCOUNTERID)';
+GATHER_TABLE_STATS('CONDITION');
 
 end PCORNetCondition;
 /
 
 
 
-
-
-
-
 create or replace procedure PCORNetProcedure as
 begin
 
-PMN_DROPSQL('drop index procedures_patid');
-PMN_DROPSQL('drop index procedures_encounterid');
+PMN_DROPSQL('drop index procedures_idx');
+
+execute immediate 'truncate table procedures';
 
 insert into procedures( 
 				patid,			encounterid,	enc_type, admit_date, px_date, providerid, px, px_type, px_source) 
@@ -1156,8 +417,7 @@ from i2b2fact fact
  inner join	pcornet_proc pr on pr.c_basecode  = fact.concept_cd   
 where pr.c_fullname like '\PCORI\PROCEDURE\%';
 
-execute immediate 'create index procedures_patid on procedures (PATID)';
-execute immediate 'create index procedures_encounterid on procedures (ENCOUNTERID)';
+execute immediate 'create index procedures_patid on procedures (PATID, ENCOUNTERID)';
 GATHER_TABLE_STATS('PROCEDURES');
 
 end PCORNetProcedure;
@@ -1172,8 +432,9 @@ end PCORNetProcedure;
 create or replace procedure PCORNetVital as
 begin
 
-PMN_DROPSQL('drop index vital_patid');
-PMN_DROPSQL('drop index vital_encounterid');
+PMN_DROPSQL('drop index vital_idx');
+
+execute immediate 'truncate table vital';
 
 -- jgk: I took out admit_date - it doesn't appear in the scheme. Now in SQLServer format - date, substring, name on inner select, no nested with. Added modifiers and now use only pathnames, not codes.
 insert into vital(patid, encounterid, measure_date, measure_time,vital_source,ht, wt, diastolic, systolic, original_bmi, bp_position,smoking,tobacco,tobacco_type)
@@ -1248,8 +509,7 @@ where ht is not null
   or tobacco is not null
 group by patid, encounterid, measure_date, measure_time, admit_date) y;
 
-execute immediate 'create index vital_patid on vital (PATID)';
-execute immediate 'create index vital_encounterid on vital (ENCOUNTERID)';
+execute immediate 'create index vital_idx on vital (PATID)';
 GATHER_TABLE_STATS('VITAL');
 
 end PCORNetVital;
@@ -1263,7 +523,9 @@ end PCORNetVital;
 create or replace procedure PCORNetEnroll as
 begin
 
-PMN_DROPSQL('drop index enrollment_patid');
+PMN_DROPSQL('drop index enrollment_idx');
+
+execute immediate 'truncate table enrollment';
 
 INSERT INTO enrollment(PATID, ENR_START_DATE, ENR_END_DATE, CHART, ENR_BASIS) 
 with pats_delta as (
@@ -1285,80 +547,40 @@ from enrolled enr
 join i2b2visit visit on enr.patient_num = visit.patient_num
 group by visit.patient_num;
 
-execute immediate 'create index enrollment_patid on enrollment (PATID)';
+execute immediate 'create index enrollment_idx on enrollment (PATID)';
 GATHER_TABLE_STATS('ENROLLMENT');
 
 end PCORNetEnroll;
 /
 
-/* TODO: When compiling PCORNetLabResultCM I got Error(106,17): 
-  PL/SQL: ORA-00942: table or view does not exist 
-apparently due to tables that the procedure references but also drops/recreates
-before reference.  Creating them outside the function solves the issue.  SQL
-copied from the function.
-
-In the same function, I got 
-  Error(63,123): PL/SQL: ORA-00904: "LAB"."PCORI_SPECIMEN_SOURCE": invalid identifier
-So, I just altered the table to have the referenced column.
-
-*/
-whenever sqlerror continue;
-drop table priority;
-drop table location;
-
-create table priority (
-  patient_num number(38,0),
-	encounter_num number(38,0),
-	provider_id varchar2(50 byte),
-	concept_cd varchar2(50 byte),
-	start_date date,
-	priority varchar2(50 byte)
-  );
-   
-create table location (	
-  patient_num number(38,0), 
-	encounter_num number(38,0), 
-	provider_id varchar2(50 byte), 
-	concept_cd varchar2(50 byte), 
-	start_date date, 
-	result_loc varchar2(50 byte)
-  );
-
-alter table "&&i2b2_meta_schema".pcornet_lab add (
-  pcori_specimen_source varchar2(1000) -- arbitrary
-  );
-whenever sqlerror exit;
 
 create or replace procedure PCORNetLabResultCM as
-sqltext varchar2(4000);
 begin
 
-PMN_DROPSQL('drop index lab_result_cm_patid');
-PMN_DROPSQL('drop index lab_result_cm_encounterid');
+PMN_DROPSQL('drop index lab_result_cm_idx');
+PMN_DROPSQL('drop index priority_idx');
+PMN_DROPSQL('drop index location_idx');
 
-PMN_DROPSQL('DROP TABLE priority');
+execute immediate 'truncate table priority';
+execute immediate 'truncate table location';
+execute immediate 'truncate table lab_result_cm';
 
-sqltext := 'create table priority as '||
-'(select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, lsource.pcori_basecode  PRIORITY  '||
-'from i2b2fact '||
-'inner join encounter enc on enc.patid = i2b2fact.patient_num and enc.encounterid = i2b2fact.encounter_Num '||
-'inner join pcornet_lab lsource on i2b2fact.modifier_cd =lsource.c_basecode '||
-'where c_fullname LIKE ''\PCORI_MOD\PRIORITY\%'') ';
-
-PMN_EXECUATESQL(sqltext);
+insert into priority
+select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, lsource.pcori_basecode PRIORITY
+from i2b2fact
+inner join encounter enc on enc.patid = i2b2fact.patient_num and enc.encounterid = i2b2fact.encounter_Num
+inner join pcornet_lab lsource on i2b2fact.modifier_cd =lsource.c_basecode
+where c_fullname LIKE '\PCORI_MOD\PRIORITY\%');
 
 execute immediate 'create index priority_idx on priority (patient_num, encounter_num, provider_id, concept_cd, start_date)';
 GATHER_TABLE_STATS('PRIORITY');
 
-PMN_DROPSQL('DROP TABLE location');
-sqltext := 'create table location as '||
-'(select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, lsource.pcori_basecode  RESULT_LOC '||
-'from i2b2fact '||
-'inner join encounter enc on enc.patid = i2b2fact.patient_num and enc.encounterid = i2b2fact.encounter_Num '||
-'inner join pcornet_lab lsource on i2b2fact.modifier_cd =lsource.c_basecode '||
-'where c_fullname LIKE ''\PCORI_MOD\RESULT_LOC\%'') ';
-
-PMN_EXECUATESQL(sqltext);
+insert into location
+select distinct patient_num, encounter_num, provider_id, concept_cd, start_date, lsource.pcori_basecode  RESULT_LOC
+from i2b2fact
+inner join encounter enc on enc.patid = i2b2fact.patient_num and enc.encounterid = i2b2fact.encounter_Num
+inner join pcornet_lab lsource on i2b2fact.modifier_cd =lsource.c_basecode
+where c_fullname LIKE '\PCORI_MOD\RESULT_LOC\%';
 
 execute immediate 'create index location_idx on location (patient_num, encounter_num, provider_id, concept_cd, start_date)';
 GATHER_TABLE_STATS('LOCATION');
@@ -1460,8 +682,8 @@ and M.start_date=l.start_Date
 WHERE m.ValType_Cd in ('N','T')
 and m.MODIFIER_CD='@';
 
-execute immediate 'create index lab_result_cm_patid on lab_result_cm (PATID)';
-execute immediate 'create index lab_result_cm_encounterid on lab_result_cm (ENCOUNTERID)';
+execute immediate 'create index lab_result_cm_idx on lab_result_cm (PATID, ENCOUNTERID)';
+GATHER_TABLE_STATS('LAB_RESULT_CM');
 
 END PCORNetLabResultCM;
 /
@@ -1472,6 +694,8 @@ END PCORNetLabResultCM;
 create or replace procedure PCORNetHarvest as
 begin
 
+execute immediate 'truncate table harvest';
+
 INSERT INTO harvest(NETWORKID, NETWORK_NAME, DATAMARTID, DATAMART_NAME, DATAMART_PLATFORM, CDM_VERSION, DATAMART_CLAIMS, DATAMART_EHR, BIRTH_DATE_MGMT, ENR_START_DATE_MGMT, ENR_END_DATE_MGMT, ADMIT_DATE_MGMT, DISCHARGE_DATE_MGMT, PX_DATE_MGMT, RX_ORDER_DATE_MGMT, RX_START_DATE_MGMT, RX_END_DATE_MGMT, DISPENSE_DATE_MGMT, LAB_ORDER_DATE_MGMT, SPECIMEN_DATE_MGMT, RESULT_DATE_MGMT, MEASURE_DATE_MGMT, ONSET_DATE_MGMT, REPORT_DATE_MGMT, RESOLVE_DATE_MGMT, PRO_DATE_MGMT, REFRESH_DEMOGRAPHIC_DATE, REFRESH_ENROLLMENT_DATE, REFRESH_ENCOUNTER_DATE, REFRESH_DIAGNOSIS_DATE, REFRESH_PROCEDURES_DATE, REFRESH_VITAL_DATE, REFRESH_DISPENSING_DATE, REFRESH_LAB_RESULT_CM_DATE, REFRESH_CONDITION_DATE, REFRESH_PRO_CM_DATE, REFRESH_PRESCRIBING_DATE, REFRESH_PCORNET_TRIAL_DATE, REFRESH_DEATH_DATE, REFRESH_DEATH_CAUSE_DATE) 
 	select '&&network_id', '&&network_name', getDataMartID(), getDataMartName(), getDataMartPlatform(), 3, hl.DATAMART_CLAIMS, hl.DATAMART_EHR, hl.BIRTH_DATE_MGMT, hl.ENR_START_DATE_MGMT, hl.ENR_END_DATE_MGMT, hl.ADMIT_DATE_MGMT, hl.DISCHARGE_DATE_MGMT, hl.PX_DATE_MGMT, hl.RX_ORDER_DATE_MGMT, hl.RX_START_DATE_MGMT, hl.RX_END_DATE_MGMT, hl.DISPENSE_DATE_MGMT, hl.LAB_ORDER_DATE_MGMT, hl.SPECIMEN_DATE_MGMT, hl.RESULT_DATE_MGMT, hl.MEASURE_DATE_MGMT, hl.ONSET_DATE_MGMT, hl.REPORT_DATE_MGMT, hl.RESOLVE_DATE_MGMT, hl.PRO_DATE_MGMT,
   case when (select count(*) from demographic) > 0 then current_date else null end REFRESH_DEMOGRAPHIC_DATE,
@@ -1495,137 +719,70 @@ end PCORNetHarvest;
 
 
 
-/* TODO: When compiling PCORNetPrescribing, I got Error(93,15): 
-  PL/SQL: ORA-00942: table or view does not exist
-At compile time, it's complaining about the fact tables don't exist that are 
-created in the function itself.  I created them ahead of time - SQL taken from
-the procedure.
-*/
-whenever sqlerror continue;
-drop table basis;
-drop table freq;
-drop table quantity;
-drop table refills;
-drop table supply;
-
-create table basis (
-  pcori_basecode varchar2(50 byte), 
-  c_fullname varchar2(700 byte), 
-  encounter_num number(38,0), 
-  concept_cd varchar2(50 byte),
-  instance_num number(18,0),
-  start_date date,
-  provider_id varchar2(50 byte),
-  modifier_cd varchar2(100 byte)
-  ) ;
-  
-create table freq (
-  pcori_basecode varchar2(50 byte), 
-  encounter_num number(38,0), 
-  concept_cd varchar2(50 byte),
-  instance_num number(18,0),
-  start_date date,
-  provider_id varchar2(50 byte),
-  modifier_cd varchar2(100 byte)
-  );
-
-create table quantity(
-  nval_num number(18,5), 
-  encounter_num number(38,0), 
-  concept_cd varchar2(50 byte),
-  instance_num number(18,0),
-  start_date date,
-  provider_id varchar2(50 byte),
-  modifier_cd varchar2(100 byte)
-  );
-  
-create table refills(
-  nval_num number(18,5), 
-  encounter_num number(38,0), 
-  concept_cd varchar2(50 byte),
-  instance_num number(18,0),
-  start_date date,
-  provider_id varchar2(50 byte),
-  modifier_cd varchar2(100 byte)
-  );
-
-create table supply(
-  nval_num number(18,5), 
-  encounter_num number(38,0), 
-  concept_cd varchar2(50 byte),
-  instance_num number(18,0),
-  start_date date,
-  provider_id varchar2(50 byte),
-  modifier_cd varchar2(100 byte)
-  );
-
-whenever sqlerror exit;
 
 create or replace procedure PCORNetPrescribing as
-sqltext varchar2(4000);
 begin
 
-PMN_DROPSQL('drop index prescribing_patid');
-PMN_DROPSQL('drop index prescribing_encounterid');
-
-
-PMN_DROPSQL('DROP TABLE basis');
-sqltext := 'create table basis as '||
-'(select pcori_basecode,c_fullname,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact basis '||
-'        inner join encounter enc on enc.patid = basis.patient_num and enc.encounterid = basis.encounter_Num '||
-'     join pcornet_med basiscode  '||
-'        on basis.modifier_cd = basiscode.c_basecode '||
-'        and basiscode.c_fullname like ''\PCORI_MOD\RX_BASIS\%'') ';
-PMN_EXECUATESQL(sqltext);
+PMN_DROPSQL('drop index prescribing_idx');
+PMN_DROPSQL('drop index basis_idx');
+PMN_DROPSQL('drop index freq_idx');
+PMN_DROPSQL('drop index quantity_idx');
+PMN_DROPSQL('drop index refills_idx');
+PMN_DROPSQL('drop index supply_idx');
+
+execute immediate 'truncate table prescribing';
+execute immediate 'truncate table basis';
+execute immediate 'truncate table freq';
+execute immediate 'truncate table quantity';
+execute immediate 'truncate table refills';
+execute immediate 'truncate table supply';
+
+insert into table basis
+select pcori_basecode,c_fullname,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact basis
+        inner join encounter enc on enc.patid = basis.patient_num and enc.encounterid = basis.encounter_Num
+     join pcornet_med basiscode
+        on basis.modifier_cd = basiscode.c_basecode
+        and basiscode.c_fullname like '\PCORI_MOD\RX_BASIS\%';
 
 execute immediate 'create unique index basis_idx on basis (instance_num, start_date, provider_id, concept_cd, encounter_num, modifier_cd)';
 GATHER_TABLE_STATS('BASIS');
 
-PMN_DROPSQL('DROP TABLE freq');
-sqltext := 'create table freq as '||
-'(select pcori_basecode,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact freq '||
-'        inner join encounter enc on enc.patid = freq.patient_num and enc.encounterid = freq.encounter_Num '||
-'     join pcornet_med freqcode  '||
-'        on freq.modifier_cd = freqcode.c_basecode '||
-'        and freqcode.c_fullname like ''\PCORI_MOD\RX_FREQUENCY\%'') ';
-PMN_EXECUATESQL(sqltext);
+insert into table freq
+select pcori_basecode,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact freq
+        inner join encounter enc on enc.patid = freq.patient_num and enc.encounterid = freq.encounter_Num
+     join pcornet_med freqcode
+        on freq.modifier_cd = freqcode.c_basecode
+        and freqcode.c_fullname like '\PCORI_MOD\RX_FREQUENCY\%';
 
 execute immediate 'create unique index freq_idx on freq (instance_num, start_date, provider_id, concept_cd, encounter_num, modifier_cd)';
 GATHER_TABLE_STATS('FREQ');
 
-PMN_DROPSQL('DROP TABLE quantity');
-sqltext := 'create table quantity as '||
-'(select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact quantity '||
-'        inner join encounter enc on enc.patid = quantity.patient_num and enc.encounterid = quantity.encounter_Num '||
-'     join pcornet_med quantitycode  '||
-'        on quantity.modifier_cd = quantitycode.c_basecode '||
-'        and quantitycode.c_fullname like ''\PCORI_MOD\RX_QUANTITY\'') ';
-
-PMN_EXECUATESQL(sqltext);
+insert into table quantity
+select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact quantity
+        inner join encounter enc on enc.patid = quantity.patient_num and enc.encounterid = quantity.encounter_Num
+     join pcornet_med quantitycode
+        on quantity.modifier_cd = quantitycode.c_basecode
+        and quantitycode.c_fullname like '\PCORI_MOD\RX_QUANTITY\';
 
 execute immediate 'create unique index quantity_idx on quantity (instance_num, start_date, provider_id, concept_cd, encounter_num, modifier_cd)';
 GATHER_TABLE_STATS('QUANTITY');
         
-PMN_DROPSQL('DROP TABLE refills');
-sqltext := 'create table refills as   '||
-'(select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact refills '||
-'        inner join encounter enc on enc.patid = refills.patient_num and enc.encounterid = refills.encounter_Num '||
-'     join pcornet_med refillscode  '||
-'        on refills.modifier_cd = refillscode.c_basecode '||
-'        and refillscode.c_fullname like ''\PCORI_MOD\RX_REFILLS\'') ';
-PMN_EXECUATESQL(sqltext);
+insert into table refills
+select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact refills
+        inner join encounter enc on enc.patid = refills.patient_num and enc.encounterid = refills.encounter_Num
+     join pcornet_med refillscode
+        on refills.modifier_cd = refillscode.c_basecode
+        and refillscode.c_fullname like '\PCORI_MOD\RX_REFILLS\';
 
 execute immediate 'create unique index refills_idx on refills (instance_num, start_date, provider_id, concept_cd, encounter_num, modifier_cd)';
 GATHER_TABLE_STATS('REFILLS');
         
-PMN_DROPSQL('DROP TABLE supply');  
-sqltext := 'create table supply as  '||
-'(select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact supply '||
-'        inner join encounter enc on enc.patid = supply.patient_num and enc.encounterid = supply.encounter_Num '||
-'     join pcornet_med supplycode  '||
-'        on supply.modifier_cd = supplycode.c_basecode '||
-'        and supplycode.c_fullname like ''\PCORI_MOD\RX_DAYS_SUPPLY\'')  ';
-PMN_EXECUATESQL(sqltext);
+insert into table supply
+select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd from i2b2medfact supply
+        inner join encounter enc on enc.patid = supply.patient_num and enc.encounterid = supply.encounter_Num
+     join pcornet_med supplycode
+        on supply.modifier_cd = supplycode.c_basecode
+        and supplycode.c_fullname like '\PCORI_MOD\RX_DAYS_SUPPLY\';
 
 execute immediate 'create unique index supply_idx on supply (instance_num, start_date, provider_id, concept_cd, encounter_num, modifier_cd)';
 GATHER_TABLE_STATS('SUPPLY');
@@ -1694,8 +851,7 @@ inner join encounter enc on enc.encounterid = m.encounter_Num
 
 where (basis.c_fullname is null or basis.c_fullname like '\PCORI_MOD\RX_BASIS\PR\%');
 
-execute immediate 'create index prescribing_patid on prescribing (PATID)';
-execute immediate 'create index prescribing_encounterid on prescribing (ENCOUNTERID)';
+execute immediate 'create index prescribing_idx on prescribing (PATID, ENCOUNTERID)';
 GATHER_TABLE_STATS('PRESCRIBING');
 
 end PCORNetPrescribing;
@@ -1703,33 +859,14 @@ end PCORNetPrescribing;
 
 
 
-/* TODO: When compiling PCORNetDispensing:
-
-Error(53,16): PL/SQL: ORA-00942: table or view does not exist (amount)
- - supply, also used, is created above in the prescribing function
-
-Also, Error(57,57): PL/SQL: ORA-00904: "MO"."PCORI_NDC": invalid identifier
-*/
-whenever sqlerror continue;
-drop table amount;
-
-create table amount(
-  nval_num number(18,5), 
-	encounter_num number(38,0), 
-	concept_cd varchar2(50 byte)
-  ); 
-
-alter table "&&i2b2_meta_schema".pcornet_med add (
-  pcori_ndc varchar2(1000) -- arbitrary
-  );
-whenever sqlerror exit;
 
 create or replace procedure PCORNetDispensing as
-sqltext varchar2(4000);
 begin
-/*
-PMN_DROPSQL('drop index dispensing_patid');
 
+PMN_DROPSQL('drop index dispensing_idx');
+
+execute immediate 'truncate table dispensing';
+/*
 PMN_DROPSQL('DROP TABLE supply');
 sqltext := 'create table supply as '||
 '(select nval_num,encounter_num,concept_cd from i2b2fact supply '||
@@ -1838,7 +975,8 @@ inner join encounter enc on enc.encounterid = m.encounter_Num
 group by m.encounter_num ,m.patient_num, m.start_date,  mo.pcori_ndc;
 */
 
-execute immediate 'create index dispensing_patid on dispensing (PATID)';
+execute immediate 'create index dispensing_idx on dispensing (PATID)';
+GATHER_TABLE_STATS('DISPENSING');
 
 end PCORNetDispensing;
 /
@@ -1854,8 +992,9 @@ end PCORNetDispensing;
 
 
 create or replace procedure PCORNetDeath as
-
 begin
+  
+execute immediate 'truncate table death';
 
 insert into death( patid, death_date, death_date_impute, death_source, death_match_confidence) 
 select distinct pat.patient_num, pat.death_date,
@@ -1885,116 +1024,149 @@ end;
 /
 
 
-create or replace PROCEDURE pcornetReport
-as
-i2b2pats  number;
-i2b2Encounters  number;
-i2b2facts number;
-i2b2dxs number;
-i2b2procs number;
-i2b2lcs number;
-
-pmnpats  number;
-encounters number;
-pmndx number;
-pmnprocs number;
-pmnfacts number;
-pmnenroll number;
-vital number;
-
-
-
-pmnlabs number;
-prescribings number;
-dispensings number;
-pmncond number;
-
-
-v_runid number;
+--------------------------------------------------------------------------------
+-- PCORNetPostProc procedure
+--
+-- Ideally this procedure would be empty, but as a matter of practice there are
+-- often post processing cleanup tasks that needs to be complete.  Such tasks
+-- should reside here with the goal of incorporating them into to the proper
+-- procedures above.
+--------------------------------------------------------------------------------
+create or replace procedure PCORNetPostProc as
 begin
-select count(*) into i2b2Pats   from i2b2patient;
-select count(*) into i2b2Encounters   from i2b2visit i inner join demographic d on i.patient_num=d.patid;
-
-
-select count(*) into pmnPats   from demographic;
-select count(*) into encounters   from encounter e ;
-select count(*) into pmndx   from diagnosis;
-select count(*) into pmnprocs  from procedures;
-
-select count(*) into pmncond from condition;
-select count(*) into pmnenroll  from enrollment;
-select count(*) into vital  from vital;
-select count(*) into pmnlabs from lab_result_cm;
-select count(*) into prescribings from prescribing;
-select count(*) into dispensings from dispensing;
-
-select max(runid) into v_runid from i2pReport;
-v_runid := v_runid + 1;
-insert into i2pReport values( v_runid, SYSDATE, 'Pats', i2b2pats, pmnpats, i2b2pats-pmnpats);
-insert into i2pReport values( v_runid, SYSDATE, 'Enrollment', i2b2pats, pmnenroll, i2b2pats-pmnpats);
-
-insert into i2pReport values(v_runid, SYSDATE, 'Encounters', i2b2Encounters, encounters, i2b2encounters-encounters);
-insert into i2pReport values(v_runid, SYSDATE, 'DX',		null,		pmndx,		null);
-insert into i2pReport values(v_runid, SYSDATE, 'PX',		null,		pmnprocs,	null);
-insert into i2pReport values(v_runid, SYSDATE, 'Condition',	null,		pmncond,	null);
-insert into i2pReport values(v_runid, SYSDATE, 'Vital',		null,		vital,	null);
-insert into i2pReport values(v_runid, SYSDATE, 'Labs',		null,		pmnlabs,	null);
-insert into i2pReport values(v_runid, SYSDATE, 'Prescribing',	null,		prescribings,null);
-insert into i2pReport values(v_runid, SYSDATE, 'Dispensing',	null,		dispensings,	null);
-
-end pcornetReport;
+  
+  /* Copy providerid from encounter table to diagnosis, procedures tables.
+  CDM specification says:
+    "Please note: This is a field replicated from the ENCOUNTER table."
+  */
+  merge into diagnosis d
+  using encounter e
+     on (d.encounterid = e.encounterid)
+  when matched then update set d.providerid = e.providerid;
+  
+  merge into procedures p
+  using encounter e
+     on (p.encounterid = e.encounterid)
+  when matched then update set p.providerid = e.providerid;
+  
+  merge into prescribing p
+  using encounter e
+     on (p.encounterid = e.encounterid)
+  when matched then update set p.rx_providerid = e.providerid;
+  
+  /* Currently in HERON, we have hight in cm and weight in oz (from visit vitals).
+  The CDM wants height in inches and weight in pounds. */
+  update vital v set v.ht = v.ht / 2.54;
+  update vital v set v.wt = v.wt / 16;
+  
+  /* Remove rows from the PRESCRIBING table where RX_* fields are null
+     TODO: Remove this when fixed in HERON
+   */
+  delete
+  from prescribing
+  where rx_basis is null
+    and rx_quantity is null
+    and rx_frequency is null
+    and rx_refills is null
+  ;
+  
+end PCORNetPostProc;
 /
 
 
-
-
-create or replace procedure pcornetloader as
+--------------------------------------------------------------------------------
+-- PCORNetLoader procedure
+--
+-- This procedure orchestrates the execution of the procedures defined above, 
+-- and consists of 13 steps.  Using the start_with_step parameter a step number
+-- can be provided to start at any point in the sequence.  This is helpful when
+-- an issue is encountered during execution and restart from the beginning is 
+-- undesirable.
+--
+-- Steps:
+-- 1 - PCORNetDemographic
+-- 2 - PCORNetEncounter
+-- 3 - PCORNetDiagnosis
+-- 4 - PCORNetCondition
+-- 5 - PCORNetProcedure
+-- 6 - PCORNetVital
+-- 7 - PCORNetEnroll
+-- 8 - PCORNetLabResultCM
+-- 9 - PCORNetPrescribing
+-- 10 - PCORNetDispensing
+-- 11 - PCORNetDeath
+-- 12 - PCORNetHarvest
+-- 13 - PCORNetPostProc
+--
+--------------------------------------------------------------------------------
+create or replace PROCEDURE PCORNetLoader(start_with_step VARCHAR2) AS
+start_with_step int;
 begin
----pcornetclear;
-PCORNetDemographic;
-PCORNetEncounter;
-PCORNetDiagnosis;
-PCORNetCondition;
-PCORNetProcedure; 
-PCORNetVital;
-PCORNetEnroll;
-PCORNetLabResultCM;
-PCORNetPrescribing;
-
-/* ORA-04068: existing state of packages has been discarded
-ORA-04065: not executed, altered or dropped stored procedure "PCORNETDISPENSING"
-ORA-06508: PL/SQL: could not find program unit being called: "PCORNETDISPENSING"
-ORA-06512: at "PCORNETLOADER", line 14
-ORA-06512: at line 2
-04068. 00000 -  "existing state of packages%s%s%s has been discarded"
-*Cause:    One of errors 4060 - 4067 when attempt to execute a stored
-           procedure.
-*Action:   Try again after proper re-initialization of any application's
-           state.
-
-The above error only happens when we call PCORNetDispensing _and_ PCORNetPrescribing
-from within pcornetloader.  When running either individually, the error does not
-happen.
-
-Skipping dispensing as per gpc-dev notes:
-http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20160223/8d79fa70/attachment-0001.pdf
-> LV: the dispensing side [?] is not mandatory? we just did Rx, since that
-> what we have in our i2b2
-*/
-PCORNetDispensing;
-PCORNetDeath;
-PCORNetHarvest;
-
-end pcornetloader;
-/
-
-
-BEGIN
-pcornetloader; --- you may want to run sql statements one by one in the pcornetloader procedure :)
-END;
-/
-
-select concept "Data Type",sourceval "From i2b2",destval "In PopMedNet", diff "Difference" from i2preport where RUNID = (select max(RUNID) from I2PREPORT);
-
-
-
+  
+  select step into start_with_step from (
+    select 1 step, 'PCORNetDemographic' proc from dual union
+    select 2 step, 'PCORNetEncounter' proc from dual union
+    select 3 step, 'PCORNetDiagnosis' proc from dual union
+    select 4 step, 'PCORNetCondition' proc from dual union
+    select 5 step, 'PCORNetProcedure' proc from dual union
+    select 6 step, 'PCORNetVital' proc from dual union
+    select 7 step, 'PCORNetEnroll' proc from dual union
+    select 8 step, 'PCORNetLabResultCM' proc from dual union
+    select 9 step, 'PCORNetPrescribing' proc from dual union
+    select 10 step, 'PCORNetDispensing' proc from dual union
+    select 11 step, 'PCORNetDeath' proc from dual union
+    select 12 step, 'PCORNetHarvest' proc from dual union
+    select 13 step, 'PCORNetPostProc' proc from dual
+  ) where proc=start_with;
+
+  if start_with_step = 1 then
+    PCORNetDemographic;
+  end if;
+  
+  if start_with_step >= 2 then
+    PCORNetEncounter;
+  end if;
+  
+  if start_with_step >= 3 then 
+    PCORNetDiagnosis;
+  end if;
+  
+  if start_with_step >= 4 then
+      PCORNetCondition;
+  end if;
+  
+  if start_with_step >= 5 then
+      PCORNetProcedure;
+  end if;
+  
+  if start_with_step >= 6 then
+      PCORNetVital;
+  end if;
+  
+  if start_with_step >= 7 then
+      PCORNetEnroll;
+  end if;
+  
+  if start_with _step >= 8 then
+      PCORNetLabResultCM;
+  end if;
+  
+  if start_with_step >= 9 then
+      PCORNetPrescribing;
+  end if;
+  
+  if start_with_step >= 10 then
+      PCORNetDispensing;
+  end if;
+  
+  if start_with_step >= 11 then
+      PCORNetDeath;
+  end if;
+  
+  if start_with_step >= 12 then
+      PCORNetHarvest;
+  end if;
+  
+  PCORNetPostProc;
+end PCORNetLoader;
+/
\ No newline at end of file
diff --git a/Oracle/cdm_postproc.sql b/Oracle/cdm_postproc.sql
deleted file mode 100644
index 54a26d2..0000000
--- a/Oracle/cdm_postproc.sql
+++ /dev/null
@@ -1,37 +0,0 @@
-/* Post-processing tasks against the CDM
-*/
-
-/* Copy providerid from encounter table to diagnosis, procedures tables.
-CDM specification says:
-  "Please note: This is a field replicated from the ENCOUNTER table."
-*/
-merge into diagnosis d
-using encounter e
-   on (d.encounterid = e.encounterid)
-when matched then update set d.providerid = e.providerid;
-
-merge into procedures p
-using encounter e
-   on (p.encounterid = e.encounterid)
-when matched then update set p.providerid = e.providerid;
-
-merge into prescribing p
-using encounter e
-   on (p.encounterid = e.encounterid)
-when matched then update set p.rx_providerid = e.providerid;
-
-/* Currently in HERON, we have hight in cm and weight in oz (from visit vitals).
-The CDM wants height in inches and weight in pounds. */
-update vital v set v.ht = v.ht / 2.54;
-update vital v set v.wt = v.wt / 16;
-
-/* Remove rows from the PRESCRIBING table where RX_* fields are null
-   TODO: Remove this when fixed in HERON
- */
-delete
-from pcornet_cdm.prescribing
-where rx_basis is null
-  and rx_quantity is null
-  and rx_frequency is null
-  and rx_refills is null
-;
\ No newline at end of file
diff --git a/Oracle/gather_table_stats.sql b/Oracle/gather_table_stats.sql
deleted file mode 100644
index 94f1a5e..0000000
--- a/Oracle/gather_table_stats.sql
+++ /dev/null
@@ -1,20 +0,0 @@
-/* Metadata table statistics - experimentation shows vastly better performance
-if this is done before the CDM transform.
-
-ACK: http://stackoverflow.com/questions/2242024/for-each-string-execute-a-function-procedure
-*/
-declare
-table_list sys.dbms_debug_vc2coll := sys.dbms_debug_vc2coll(
-  'PCORNET_DEMO', 'PCORNET_DIAG', 'PCORNET_ENC', 'PCORNET_ENROLL', 'PCORNET_LAB', 
-  'PCORNET_MED', 'PCORNET_PROC', 'PCORNET_VITAL');
-begin 
-  for t in table_list.first .. table_list.last
-  loop
-    DBMS_STATS.GATHER_TABLE_STATS (
-            ownname => '"&&i2b2_meta_schema"',
-            tabname => table_list(t),
-            estimate_percent => 40
-            );
-  end loop;
-end;
-/
diff --git a/Oracle/lab_loinc_mapping.csv b/Oracle/lab_loinc_mapping.csv
deleted file mode 100644
index 9338321..0000000
--- a/Oracle/lab_loinc_mapping.csv
+++ /dev/null
@@ -1,156 +0,0 @@
-"LOINC_CODE","LAB_NAME","PCORI_SPECIMEN_SOURCE"
-"13457-7","LDL",""
-"18261-8","LDL",""
-"2089-1","LDL",""
-"47213-4","LDL","SERUM, PLASMA, or SR_PLS"
-"47213-4","LDL","SERUM, PLASMA, or SR_PLS"
-"47213-4","LDL","SERUM, PLASMA, or SR_PLS"
-"49132-4","LDL",""
-"17855-8","A1C",""
-"17856-6","A1C","BLOOD"
-"4548-4","A1C","BLOOD"
-"59261-8","A1C",""
-"62388-4","A1C",""
-"2157-6","CK","SERUM, PLASMA, or SR_PLS"
-"2157-6","CK","SERUM, PLASMA, or SR_PLS"
-"2157-6","CK","SERUM, PLASMA, or SR_PLS"
-"2157-6","CK","SERUM, PLASMA, or SR_PLS"
-"50756-6","CK","BLOOD"
-"50756-6","CK","BLOOD"
-"50756-6","CK","BLOOD"
-"50756-6","CK","BLOOD"
-"13969-1","CK_MB","SERUM, PLASMA, or SR_PLS"
-"13969-1","CK_MB","SERUM, PLASMA, or SR_PLS"
-"13969-1","CK_MB","SERUM, PLASMA, or SR_PLS"
-"13969-1","CK_MB","SERUM, PLASMA, or SR_PLS"
-"2154-3","CK_MB","SERUM, PLASMA, or SR_PLS"
-"2154-3","CK_MB","SERUM, PLASMA, or SR_PLS"
-"2154-3","CK_MB","SERUM, PLASMA, or SR_PLS"
-"2154-3","CK_MB","SERUM, PLASMA, or SR_PLS"
-"32673-6","CK_MB","SERUM, PLASMA, or SR_PLS"
-"32673-6","CK_MB","SERUM, PLASMA, or SR_PLS"
-"32673-6","CK_MB","SERUM, PLASMA, or SR_PLS"
-"32673-6","CK_MB","SERUM, PLASMA, or SR_PLS"
-"49551-5","CK_MB","BLOOD"
-"49551-5","CK_MB","BLOOD"
-"49551-5","CK_MB","BLOOD"
-"49551-5","CK_MB","BLOOD"
-"12187-1","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"12187-1","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"12187-1","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"12187-1","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"12189-7","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"12189-7","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"12189-7","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"12189-7","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"20569-0","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"20569-0","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"20569-0","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"20569-0","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"49136-5","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"49136-5","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"49136-5","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"49136-5","CK_MBI","SERUM, PLASMA, or SR_PLS"
-"2160-0","CREATININE","SERUM, PLASMA, or SR_PLS"
-"38483-4","CREATININE","BLOOD"
-"14682-9","CREATININE","SERUM, PLASMA, or SR_PLS"
-"14682-9","CREATININE","SERUM, PLASMA, or SR_PLS"
-"14682-9","CREATININE","SERUM, PLASMA, or SR_PLS"
-"14682-9","CREATININE","SERUM, PLASMA, or SR_PLS"
-"21232-4","CREATININE","BLOOD"
-"21232-4","CREATININE","BLOOD"
-"21232-4","CREATININE","BLOOD"
-"21232-4","CREATININE","BLOOD"
-"35203-9","CREATININE","SERUM, PLASMA, or SR_PLS"
-"35203-9","CREATININE","SERUM, PLASMA, or SR_PLS"
-"35203-9","CREATININE","SERUM, PLASMA, or SR_PLS"
-"35203-9","CREATININE","SERUM, PLASMA, or SR_PLS"
-"44784-7","CREATININE","SERUM, PLASMA, or SR_PLS"
-"44784-7","CREATININE","SERUM, PLASMA, or SR_PLS"
-"44784-7","CREATININE","SERUM, PLASMA, or SR_PLS"
-"44784-7","CREATININE","SERUM, PLASMA, or SR_PLS"
-"59826-8","CREATININE","BLOOD"
-"59826-8","CREATININE","BLOOD"
-"59826-8","CREATININE","BLOOD"
-"59826-8","CREATININE","BLOOD"
-"14775-1","HGB","BLOOD"
-"14775-1","HGB","BLOOD"
-"14775-1","HGB","BLOOD"
-"14775-1","HGB","BLOOD"
-"20509-6","HGB","BLOOD"
-"20509-6","HGB","BLOOD"
-"20509-6","HGB","BLOOD"
-"20509-6","HGB","BLOOD"
-"30313-1","HGB","BLOOD"
-"30313-1","HGB","BLOOD"
-"30313-1","HGB","BLOOD"
-"30313-1","HGB","BLOOD"
-"30350-3","HGB","BLOOD"
-"30350-3","HGB","BLOOD"
-"30350-3","HGB","BLOOD"
-"30350-3","HGB","BLOOD"
-"30351-1","HGB","BLOOD"
-"30351-1","HGB","BLOOD"
-"30351-1","HGB","BLOOD"
-"30351-1","HGB","BLOOD"
-"30352-9","HGB","BLOOD"
-"30352-9","HGB","BLOOD"
-"30352-9","HGB","BLOOD"
-"30352-9","HGB","BLOOD"
-"55782-7","HGB","BLOOD"
-"55782-7","HGB","BLOOD"
-"55782-7","HGB","BLOOD"
-"55782-7","HGB","BLOOD"
-"59260-0","HGB","BLOOD"
-"59260-0","HGB","BLOOD"
-"59260-0","HGB","BLOOD"
-"59260-0","HGB","BLOOD"
-"718-7","HGB","BLOOD"
-"34714-6","INR","BLOOD"
-"34714-6","INR","BLOOD"
-"34714-6","INR","BLOOD"
-"34714-6","INR","BLOOD"
-"46418-0","INR","BLOOD"
-"46418-0","INR","BLOOD"
-"46418-0","INR","BLOOD"
-"46418-0","INR","BLOOD"
-"6301-6","INR","PPP"
-"6301-6","INR","PPP"
-"6301-6","INR","PPP"
-"6301-6","INR","PPP"
-"10839-9","TROP_I","SERUM, PLASMA, or SR_PLS"
-"10839-9","TROP_I","SERUM, PLASMA, or SR_PLS"
-"10839-9","TROP_I","SERUM, PLASMA, or SR_PLS"
-"10839-9","TROP_I","SERUM, PLASMA, or SR_PLS"
-"16255-2","TROP_I","SERUM, PLASMA, or SR_PLS"
-"16255-2","TROP_I","SERUM, PLASMA, or SR_PLS"
-"16255-2","TROP_I","SERUM, PLASMA, or SR_PLS"
-"16255-2","TROP_I","SERUM, PLASMA, or SR_PLS"
-"42757-5","TROP_I","BLOOD"
-"42757-5","TROP_I","BLOOD"
-"42757-5","TROP_I","BLOOD"
-"42757-5","TROP_I","BLOOD"
-"49563-0","TROP_I","SERUM, PLASMA, or SR_PLS"
-"49563-0","TROP_I","SERUM, PLASMA, or SR_PLS"
-"49563-0","TROP_I","SERUM, PLASMA, or SR_PLS"
-"49563-0","TROP_I","SERUM, PLASMA, or SR_PLS"
-"33204-9","TROP_T_QL","SERUM, PLASMA, or SR_PLS"
-"33204-9","TROP_T_QL","SERUM, PLASMA, or SR_PLS"
-"33204-9","TROP_T_QL","SERUM, PLASMA, or SR_PLS"
-"33204-9","TROP_T_QL","SERUM, PLASMA, or SR_PLS"
-"48426-1","TROP_T_QL","BLOOD"
-"48426-1","TROP_T_QL","BLOOD"
-"48426-1","TROP_T_QL","BLOOD"
-"48426-1","TROP_T_QL","BLOOD"
-"48425-3","TROP_T_QN","BLOOD"
-"48425-3","TROP_T_QN","BLOOD"
-"48425-3","TROP_T_QN","BLOOD"
-"48425-3","TROP_T_QN","BLOOD"
-"6597-9","TROP_T_QN","BLOOD"
-"6597-9","TROP_T_QN","BLOOD"
-"6597-9","TROP_T_QN","BLOOD"
-"6597-9","TROP_T_QN","BLOOD"
-"6598-7","TROP_T_QN","SERUM, PLASMA, or SR_PLS"
-"6598-7","TROP_T_QN","SERUM, PLASMA, or SR_PLS"
-"6598-7","TROP_T_QN","SERUM, PLASMA, or SR_PLS"
-"6598-7","TROP_T_QN","SERUM, PLASMA, or SR_PLS"
diff --git a/Oracle/load_pcornet_mapping.sh b/Oracle/load_pcornet_mapping.sh
deleted file mode 100644
index 651d6cc..0000000
--- a/Oracle/load_pcornet_mapping.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/bin/bash
-set -e
-
-# Expected environment variables
-# Database SID
-# export sid=
-
-# User and password for CDM user
-# export pcornet_cdm_user=
-# export pcornet_cdm=
-
-# Create/Load the local path mapping and ontology update tables
-sqlplus /nolog <<EOF
-connect ${pcornet_cdm_user}/${pcornet_cdm}
-
-set echo on;
-
-WHENEVER SQLERROR CONTINUE;
-drop table pcornet_mapping;
-drop table pcornet_ontology_updates;
-WHENEVER SQLERROR EXIT SQL.SQLCODE;
-
-start pcornet_mapping_ddl.sql
-start pcornet_ontology_updates_ddl.sql
-EOF
-
-ORACLE_SID=${sid} sqlldr ${pcornet_cdm_user}/${pcornet_cdm} control=pcornet_mapping.ctl data=pcornet_mapping.csv bad=pcornet_mapping.bad log=pcornet_mapping.log errors=0
-
-ORACLE_SID=${sid} sqlldr ${pcornet_cdm_user}/${pcornet_cdm} control=pcornet_ontology_updates.ctl data=pcornet_ontology_updates.csv bad=pcornet_ontology_updates.bad log=pcornet_ontology_updates.log errors=0
diff --git a/Oracle/ontology_fix_script_ora.sql b/Oracle/ontology_fix_script_ora.sql
deleted file mode 100644
index aed4c34..0000000
--- a/Oracle/ontology_fix_script_ora.sql
+++ /dev/null
@@ -1,41 +0,0 @@
---clean metadata
---Updated lcp@20141010
---AHA@20140925 and jgk@20141003 and lcp@20141007
--- fix problems with pcornet metadata pcori_basecode column so the code AHA writes creates valid popmednet data
-
--- 1) If you used the Mapper tool, then after running the integration step, run the following script to correct the pcori_basecode column.
-update integration
-set pcori_basecode = (select project_ont_mapping.destination_basecode from project_ont_mapping
-where integration.c_basecode = project_ont_mapping.source_basecode
-and integration.c_path = project_ont_mapping.destination_fullname
-)
-where exists (select 1 from project_ont_mapping
-where integration.c_basecode = project_ont_mapping.source_basecode
-and integration.c_path = project_ont_mapping.destination_fullname
-and project_ont_mapping.status_cd != 'D' or project_ont_mapping.status_cd is null)
-and integration.pcori_basecode is null
-/
-
--- 2) Run this script to fix some errors in pcori_basecode
-
--- Remove scheme prefixes
-update pcornet_demo set pcori_basecode=substr(pcori_basecode, instr(pcori_basecode,':')+1,100 )	 where c_fullname like '\PCORI\DEMOGRAPHIC\SEX\%'
-  or c_fullname like '\PCORI\DEMOGRAPHIC\RACE\%' or c_fullname like '\PCORI\DEMOGRAPHIC\HISPANIC\%'
-/
--- Fix a problem with the hispanic codes
-update pcornet_demo set pcori_basecode='Y' where pcori_basecode='HISPANIC' 
-/
-update pcornet_demo set pcori_basecode='N' where pcori_basecode='NOTHISPANIC'
-/
--- Scheme prefixes again
-update pcornet_diag set pcori_basecode=substr(pcori_basecode,  instr(pcori_basecode,':')+1,100 )
-  where c_fullname like '\PCORI\DIAGNOSIS\09\%' or c_fullname like '\PCORI_MOD\%'
-/
--- Data truncation errors occur if modifier folders have a pcori_basecode
-update pcornet_diag set pcori_basecode=null where c_visualattributes like 'O%'
-/
--- Scheme prefixes
-update pcornet_proc set pcori_basecode=substr(pcori_basecode,  instr(pcori_basecode,':')+1,100 )
-  where c_fullname like '\PCORI\PROCEDURE\09\%'
-/
-
diff --git a/Oracle/pcornet_mapping.csv b/Oracle/pcornet_mapping.csv
deleted file mode 100644
index 8d7e373..0000000
--- a/Oracle/pcornet_mapping.csv
+++ /dev/null
@@ -1,241 +0,0 @@
-pcori_path,local_path
-\PCORI_MOD\RX_BASIS\DI\,\Medication\Surescripts\Status\
-\PCORI_MOD\RX_QUANTITY\,\Medication\Surescripts\Amount\
-\PCORI_MOD\RX_DAYS_SUPPLY\,\Medication\Surescripts\Days Supply\
-\PCORI_MOD\RX_BASIS\PR\02\,\Medication\Inpatient\
-\PCORI_MOD\RX_BASIS\PR\OT\,\Medication\Other Orders\
-\PCORI_MOD\RX_BASIS\PR\01\,\Medication\Outpatient\
-\PCORI_MOD\RX_BASIS\PR\02\,\Medication\PRN Inpatient Order\
-\PCORI_MOD\PDX\P\,\Diagnosis\\modifier_dx\billing_diagnosis\discharge\discharge_primary\
-\PCORI_MOD\PDX\P\,\Diagnosis\Billing\Primary\
-\PCORI_MOD\CONDITION_OR_DX\DX_SOURCE\DI\,\Diagnosis\\modifier_dx\billing_diagnosis\discharge\
-\PCORI_MOD\CONDITION_OR_DX\DX_SOURCE\AD\,\Diagnosis\\modifier_dx\billing_diagnosis\admit\
-"\PCORI_MOD\CONDITION_OR_DX\DX_SOURCE\UN\","\Diagnosis\Billing\UHC_DIAGNOSIS\"
-"\PCORI_MOD\CONDITION_OR_DX\DX_SOURCE\FI\","\Diagnosis\Billing\UKP\"
-"\PCORI_MOD\PDX\X\","\Diagnosis\Billing\Primary\"
-"\PCORI_MOD\CONDITION_OR_DX\DX_SOURCE\FI\","\Diagnosis\\modifier_dx\billing_diagnosis\professional\"
-"\PCORI_MOD\PDX\X\","\Diagnosis\\modifier_dx\billing_diagnosis\professional\professional_primary\"
-\PCORI_MOD\CONDITION_OR_DX\CONDITION_SOURCE\HC\,\Diagnosis\Clinical\HOSPITAL_PL_YN\
-\PCORI_MOD\CONDITION_OR_DX\CONDITION_SOURCE\HC\,\Diagnosis\Clinical\PAT_ENC_DX\
-\PCORI_MOD\CONDITION_OR_DX\CONDITION_SOURCE\HC\,\Diagnosis\Clinical\PRINCIPAL_PL_YN\
-\PCORI_MOD\CONDITION_OR_DX\CONDITION_SOURCE\HC\,\Diagnosis\STATUS_C\ACTIVE\
-\PCORI_MOD\CONDITION_OR_DX\CONDITION_SOURCE\PR\,\Diagnosis\Clinical\MEDICAL_HISTORY_DX\
-\PCORI_MOD\CONDITION_OR_DX\CONDITION_SOURCE\RG\,\Diagnosis\NTDS\
-\PCORI\DEMOGRAPHIC\BIOBANK_FLAG\Y\,\i2b2\Specimens\
-\PCORI\DEMOGRAPHIC\HISPANIC\N\,"\i2b2\Demographics\Ethnicity\Non Hispanic, Latino or Spanish Origin\"
-\PCORI\DEMOGRAPHIC\HISPANIC\NI\,\i2b2\Demographics\Ethnicity\Not Recorded\
-\PCORI\DEMOGRAPHIC\HISPANIC\OT\,\i2b2\Demographics\Ethnicity\Other\
-\PCORI\DEMOGRAPHIC\HISPANIC\Y\,\i2b2\Demographics\Ethnicity\Hispanic\
-\PCORI\DEMOGRAPHIC\HISPANIC\Y\,\i2b2\Demographics\Ethnicity\Hispanic or Latino\
-\PCORI\DEMOGRAPHIC\HISPANIC\Y\,"\i2b2\Demographics\Ethnicity\Hispanic, Latino or Spanish Origin\"
-\PCORI\ENCOUNTER\ENC_TYPE\AV\,\i2b2\Visit Details\ENC_TYPE\AV\
-\PCORI\ENCOUNTER\ENC_TYPE\ED\,\i2b2\Visit Details\ENC_TYPE\ED\
-\PCORI\ENCOUNTER\ENC_TYPE\EI\,\i2b2\Visit Details\ENC_TYPE\EI\
-\PCORI\ENCOUNTER\ENC_TYPE\IP\,\i2b2\Visit Details\ENC_TYPE\IP\
-\PCORI\ENCOUNTER\ENC_TYPE\IS\,\i2b2\Visit Details\ENC_TYPE\IS\
-\PCORI\ENCOUNTER\ENC_TYPE\NI\,\i2b2\Visit Details\ENC_TYPE\NI\
-\PCORI\ENCOUNTER\ENC_TYPE\OA\,\i2b2\Visit Details\ENC_TYPE\OA\
-\PCORI\ENCOUNTER\ENC_TYPE\OT\,\i2b2\Visit Details\ENC_TYPE\OT\
-\PCORI\ENCOUNTER\ENC_TYPE\UN\,\i2b2\Visit Details\ENC_TYPE\UN\
-\PCORI\ENCOUNTER\ENC_TYPE\IP\,\i2b2\UHC\Visit Details\Length of Stay\Hospital\
-\PCORI\DEMOGRAPHIC\SEX\F\,\i2b2\Demographics\Gender\Female\
-\PCORI\DEMOGRAPHIC\SEX\M\,\i2b2\Demographics\Gender\Male\
-\PCORI\DEMOGRAPHIC\SEX\NI\,\i2b2\Demographics\Gender\Unknown\Unknown-@\
-\PCORI\DEMOGRAPHIC\SEX\UN\,\i2b2\Demographics\Gender\Unknown\Unknown-U\
-\PCORI\DEMOGRAPHIC\RACE\01\,\i2b2\Demographics\Race\American Indian or Alaskan Native\
-\PCORI\DEMOGRAPHIC\RACE\02\,\i2b2\Demographics\Race\Asian\
-\PCORI\DEMOGRAPHIC\RACE\03\,\i2b2\Demographics\Race\Black or African American\
-\PCORI\DEMOGRAPHIC\RACE\06\,\i2b2\Demographics\Race\Two Races\
-\PCORI\DEMOGRAPHIC\RACE\04\,\i2b2\Demographics\Race\Native Hawaiian or Other Pacific Islander\
-\PCORI\DEMOGRAPHIC\RACE\NI\,\i2b2\Demographics\Race\Not Recorded\
-\PCORI\DEMOGRAPHIC\RACE\OT\,\i2b2\Demographics\Race\Other\
-\PCORI\DEMOGRAPHIC\RACE\07\,\i2b2\Demographics\Race\Declined\
-\PCORI\DEMOGRAPHIC\RACE\05\,\i2b2\Demographics\Race\White or Caucasian\
-\PCORI\DIAGNOSIS\DX_TYPE\09\,\i2b2\Diagnoses\
-\PCORI\PROCEDURE\PX_TYPE\C4\,\i2b2\Procedures\PRC\Metathesaurus CPT Hierarchical Terms\
-\PCORI\PROCEDURE\PX_TYPE\09\,\i2b2\Procedures\PRC\ICD9 (Inpatient)\
-\PCORI\VITAL\HT\,\i2b2\Visit Details\Vitals\HEIGHT\
-\PCORI\VITAL\BP\DIASTOLIC\,\i2b2\Flowsheet\KU\GEN TMP CARD ECHO VITALS T:900426\KU GEN CARD GRP CV COMMON VITALS G:910000 I#2\BLOOD PRESSURE M:5 I#2\DIASTOLIC\
-\PCORI\VITAL\BP\SYSTOLIC\,\i2b2\Flowsheet\KU\GEN TMP CARD ECHO VITALS T:900426\KU GEN CARD GRP CV COMMON VITALS G:910000 I#2\BLOOD PRESSURE M:5 I#2\SYSTOLIC\
-\PCORI\VITAL\ORIGINAL_BMI\,\i2b2\Visit Details\Vitals\BMI\
-\PCORI\VITAL\WT\,\i2b2\Visit Details\Vitals\WEIGHT\
-\PCORI\VITAL\TOBACCO\SMOKING\YES\01\,\i2b2\History\Social History\Tobacco Usage\Smoking Tobacco Use\Current Every Day Smoker\
-\PCORI\VITAL\TOBACCO\SMOKING\YES\02\,\i2b2\History\Social History\Tobacco Usage\Smoking Tobacco Use\Current Some Day Smoker\
-\PCORI\VITAL\TOBACCO\SMOKING\03\,\i2b2\History\Social History\Tobacco Usage\Smoking Tobacco Use\Former Smoker\
-\PCORI\VITAL\TOBACCO\SMOKING\04\,\i2b2\History\Social History\Tobacco Usage\Smoking Tobacco Use\Never Smoker \
-\PCORI\VITAL\TOBACCO\SMOKING\YES\05\,"\i2b2\History\Social History\Tobacco Usage\Smoking Tobacco Use\Smoker, Current Status Unknown\"
-\PCORI\VITAL\TOBACCO\SMOKING\06\,\i2b2\History\Social History\Tobacco Usage\Smoking Tobacco Use\Unknown If Ever Smoked\
-\PCORI\VITAL\TOBACCO\SMOKING\YES\07\,\i2b2\History\Social History\Tobacco Usage\Smoking Tobacco Use\Heavy Tobacco Smoker\
-\PCORI\VITAL\TOBACCO\SMOKING\YES\08\,\i2b2\History\Social History\Tobacco Usage\Smoking Tobacco Use\Light Tobacco Smoker\
-\PCORI\VITAL\TOBACCO\02\01\,\i2b2\History\Social History\Tobacco Usage\Smokeless Tobacco Use\Current User\
-\PCORI\VITAL\TOBACCO\02\02\,\i2b2\History\Social History\Tobacco Usage\Smokeless Tobacco Use\Never Used\
-\PCORI\VITAL\TOBACCO\02\03\,\i2b2\History\Social History\Tobacco Usage\Smokeless Tobacco Use\Former User\
-\PCORI\VITAL\TOBACCO\UN\06\,\i2b2\History\Social History\Tobacco Usage\Not Asked\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\253\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\09\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\10\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\67\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\256\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\12\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\276\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\275\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\294\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\293\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\283\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\285\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\284\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\286\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\287\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\271\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\272\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\266\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\268\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\269\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\257\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\369\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\66\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\11\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\251\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\314\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\307\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\309\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\308\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\325\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\327\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\326\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\316\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\318\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\317\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\319\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\321\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\320\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\304\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\306\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\305\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\298\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\300\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\299\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\301\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\303\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\302\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\NI\,\i2b2\Visit Details\Discharge Disposition Codes\0\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\260\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\200\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\100\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\E\,\i2b2\Visit Details\Discharge Disposition Codes\20\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\43\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\06\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\01\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\261\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\50\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\51\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\68\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\254\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\259\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\258\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\07\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\15\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\366\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\262\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\63\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\64\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\255\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\264\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\65\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\62\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\250\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\02\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\03\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\30\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\263\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\252\
-\PCORI\ENCOUNTER\DISCHARGE_DISPOSITION\A\,\i2b2\Visit Details\Discharge Disposition Codes\365\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\IP\,\i2b2\Visit Details\Discharge Disposition Codes\253\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\SH\,\i2b2\Visit Details\Discharge Disposition Codes\09\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\67\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\256\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\257\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\369\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\66\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\11\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\251\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\NI\,\i2b2\Visit Details\Discharge Disposition Codes\0\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\260\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\200\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\100\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\43\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\HH\,\i2b2\Visit Details\Discharge Disposition Codes\06\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\HO\,\i2b2\Visit Details\Discharge Disposition Codes\01\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\HS\,\i2b2\Visit Details\Discharge Disposition Codes\261\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\HS\,\i2b2\Visit Details\Discharge Disposition Codes\50\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\HS\,\i2b2\Visit Details\Discharge Disposition Codes\51\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\RH\,\i2b2\Visit Details\Discharge Disposition Codes\68\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\254\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\259\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\RH\,\i2b2\Visit Details\Discharge Disposition Codes\258\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\AM\,\i2b2\Visit Details\Discharge Disposition Codes\07\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\AW\,\i2b2\Visit Details\Discharge Disposition Codes\15\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\AW\,\i2b2\Visit Details\Discharge Disposition Codes\366\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\IP\,\i2b2\Visit Details\Discharge Disposition Codes\262\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\IP\,\i2b2\Visit Details\Discharge Disposition Codes\63\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\NH\,\i2b2\Visit Details\Discharge Disposition Codes\64\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\255\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\RH\,\i2b2\Visit Details\Discharge Disposition Codes\264\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\OT\,\i2b2\Visit Details\Discharge Disposition Codes\65\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\RH\,\i2b2\Visit Details\Discharge Disposition Codes\62\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\HO\,\i2b2\Visit Details\Discharge Disposition Codes\250\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\IP\,\i2b2\Visit Details\Discharge Disposition Codes\02\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\NH\,\i2b2\Visit Details\Discharge Disposition Codes\03\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\SH\,\i2b2\Visit Details\Discharge Disposition Codes\30\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\IP\,\i2b2\Visit Details\Discharge Disposition Codes\263\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\HH\,\i2b2\Visit Details\Discharge Disposition Codes\252\
-\PCORI\ENCOUNTER\DISCHARGE_STATUS\HS\,\i2b2\Visit Details\Discharge Disposition Codes\365\
-\PCORI\ENCOUNTER\DRG\02\,\i2b2\UHC\Diagnosis\UHC MS-DRG\
-"\PCORI\ENCOUNTER\ENC_TYPE\AV\","\i2b2\Visit Details\Place of Service (IDX)\22\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\03\"
-"\PCORI\ENCOUNTER\ENC_TYPE\AV\","\i2b2\Visit Details\Place of Service (IDX)\26\"
-"\PCORI\ENCOUNTER\ENC_TYPE\AV\","\i2b2\Visit Details\Place of Service (IDX)\11\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\21\"
-"\PCORI\ENCOUNTER\ENC_TYPE\ED\","\i2b2\Visit Details\Place of Service (IDX)\23\"
-"\PCORI\ENCOUNTER\ENC_TYPE\IS\","\i2b2\Visit Details\Place of Service (IDX)\13\"
-"\PCORI\ENCOUNTER\ENC_TYPE\IS\","\i2b2\Visit Details\Place of Service (IDX)\65\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\34\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OT\","\i2b2\Visit Details\Place of Service (IDX)\25\"
-"\PCORI\ENCOUNTER\ENC_TYPE\IP\","\i2b2\Visit Details\Place of Service (IDX)\51\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\55\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\12\"
-"\PCORI\ENCOUNTER\ENC_TYPE\AV\","\i2b2\Visit Details\Place of Service (IDX)\20\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\52\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\72\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OT\","\i2b2\Visit Details\Place of Service (IDX)\9\"
-"\PCORI\ENCOUNTER\ENC_TYPE\IS\","\i2b2\Visit Details\Place of Service (IDX)\32\"
-"\PCORI\ENCOUNTER\ENC_TYPE\IS\","\i2b2\Visit Details\Place of Service (IDX)\33\"
-"\PCORI\ENCOUNTER\ENC_TYPE\AV\","\i2b2\Visit Details\Place of Service (IDX)\24\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OT\","\i2b2\Visit Details\Place of Service (IDX)\99\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\81\"
-"\PCORI\ENCOUNTER\ENC_TYPE\OA\","\i2b2\Visit Details\Place of Service (IDX)\56\"
-"\PCORI\ENCOUNTER\ENC_TYPE\IS\","\i2b2\Visit Details\Place of Service (IDX)\31\"
-"\PCORI\ENCOUNTER\ENC_TYPE\IS\","\i2b2\Visit Details\Place of Service (IDX)\54\"
-"\PCORI\ENCOUNTER\ENC_TYPE\AV\","\i2b2\Visit Details\Place of Service (IDX)\19\"
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\AV\,\i2b2\UHC\Visit Details\Admission Point Of Origin\21\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\AV\,\i2b2\UHC\Visit Details\Admission Point Of Origin\2\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\ED\,\i2b2\UHC\Visit Details\Admission Point Of Origin\7\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\HH\,\i2b2\UHC\Visit Details\Admission Point Of Origin\12\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\HH\,\i2b2\UHC\Visit Details\Admission Point Of Origin\11\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\HO\,\i2b2\UHC\Visit Details\Admission Point Of Origin\1\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\HS\,\i2b2\UHC\Visit Details\Admission Point Of Origin\22\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\IP\,\i2b2\UHC\Visit Details\Admission Point Of Origin\4\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\IP\,\i2b2\UHC\Visit Details\Admission Point Of Origin\10\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\IP\,\i2b2\UHC\Visit Details\Admission Point Of Origin\6\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\NI\,\i2b2\UHC\Visit Details\Admission Point Of Origin\9\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\NI\,\i2b2\UHC\Visit Details\Admission Point Of Origin\18\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\13\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\14\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\15\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\16\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\19\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\23\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\24\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\3\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\OT\,\i2b2\UHC\Visit Details\Admission Point Of Origin\8\
-\PCORI\ENCOUNTER\ADMITTING_SOURCE\SN\,\i2b2\UHC\Visit Details\Admission Point Of Origin\5\
diff --git a/Oracle/pcornet_mapping.ctl b/Oracle/pcornet_mapping.ctl
deleted file mode 100644
index eaaa936..0000000
--- a/Oracle/pcornet_mapping.ctl
+++ /dev/null
@@ -1,8 +0,0 @@
-options (errors=0, skip=1)
-load data
-truncate into table pcornet_mapping
-fields terminated by ',' optionally enclosed by '"'
-trailing nullcols(
-  PCORI_PATH,
-  LOCAL_PATH
-  )
\ No newline at end of file
diff --git a/Oracle/pcornet_mapping.sql b/Oracle/pcornet_mapping.sql
deleted file mode 100644
index eeb2a3f..0000000
--- a/Oracle/pcornet_mapping.sql
+++ /dev/null
@@ -1,692 +0,0 @@
-/* Adapted from work by Phillip Reeder at UTSW
-
-Map local terms as leaves under the PCORNet terms.
-*/
-
-/* Delete any existing mapped terms
-*/
-set echo on;
---select *
-delete 
-from "&&i2b2_meta_schema".PCORNET_VITAL where sourcesystem_cd='MAPPING';
-
-delete 
-from "&&i2b2_meta_schema".PCORNET_ENC where sourcesystem_cd='MAPPING';
-
-insert into "&&i2b2_meta_schema".PCORNET_VITAL
-SELECT PCORNET_VITAL.C_HLEVEL+1,
-  PCORNET_VITAL.C_FULLNAME || i2b2.c_basecode || '\' as  C_FULLNAME,
-  i2b2.c_basecode || ' ' || i2b2.c_name as C_NAME,
-  PCORNET_VITAL.C_SYNONYM_CD,
-  PCORNET_VITAL.C_VISUALATTRIBUTES,
-  PCORNET_VITAL.C_TOTALNUM,
-  i2b2.c_basecode as C_BASECODE,
-  PCORNET_VITAL.C_METADATAXML,
-  PCORNET_VITAL.C_FACTTABLECOLUMN,
-  PCORNET_VITAL.C_TABLENAME,
-  PCORNET_VITAL.C_COLUMNNAME,
-  PCORNET_VITAL.C_COLUMNDATATYPE,
-  PCORNET_VITAL.C_OPERATOR,
-  PCORNET_VITAL.C_FULLNAME || i2b2.c_basecode || '\' as  C_DIMCODE,
-  PCORNET_VITAL.C_COMMENT,
-  PCORNET_VITAL.C_TOOLTIP,
-  PCORNET_VITAL.M_APPLIED_PATH,
-  PCORNET_VITAL.UPDATE_DATE,
-  PCORNET_VITAL.DOWNLOAD_DATE,
-  PCORNET_VITAL.IMPORT_DATE,
-  'MAPPING' as SOURCESYSTEM_CD,
-  PCORNET_VITAL.VALUETYPE_CD,
-  PCORNET_VITAL.M_EXCLUSION_CD,
-  PCORNET_VITAL.C_PATH,
-  PCORNET_VITAL.C_SYMBOL,
-  PCORNET_VITAL.PCORI_BASECODE
-FROM "&&i2b2_meta_schema".PCORNET_VITAL join pcornet_mapping on pcornet_mapping.PCORI_PATH=PCORNET_VITAL.c_fullname and pcornet_mapping.local_path is not null
-join "&&i2b2_meta_schema"."&&terms_table" i2b2 on i2b2.c_fullname=pcornet_mapping.local_path;
-
-insert into "&&i2b2_meta_schema".PCORNET_ENC
-SELECT PCORNET_ENC.C_HLEVEL+1,
-  PCORNET_ENC.C_FULLNAME || i2b2.c_name || '\' as  C_FULLNAME,
-  i2b2.c_basecode || ' ' || i2b2.c_name as C_NAME,
-  PCORNET_ENC.C_SYNONYM_CD,
-  PCORNET_ENC.C_VISUALATTRIBUTES,
-  PCORNET_ENC.C_TOTALNUM,
-  i2b2.c_basecode as C_BASECODE,
-  PCORNET_ENC.C_METADATAXML,
-  PCORNET_ENC.C_FACTTABLECOLUMN,
-  PCORNET_ENC.C_TABLENAME,
-  PCORNET_ENC.C_COLUMNNAME,
-  PCORNET_ENC.C_COLUMNDATATYPE,
-  PCORNET_ENC.C_OPERATOR,
-  PCORNET_ENC.C_FULLNAME || i2b2.c_name || '\' as  C_DIMCODE,
-  PCORNET_ENC.C_COMMENT,
-  PCORNET_ENC.C_TOOLTIP,
-  PCORNET_ENC.M_APPLIED_PATH,
-  PCORNET_ENC.UPDATE_DATE,
-  PCORNET_ENC.DOWNLOAD_DATE,
-  PCORNET_ENC.IMPORT_DATE,
-  'MAPPING' as SOURCESYSTEM_CD,
-  PCORNET_ENC.VALUETYPE_CD,
-  PCORNET_ENC.M_EXCLUSION_CD,
-  PCORNET_ENC.C_PATH,
-  PCORNET_ENC.C_SYMBOL,
-  PCORNET_ENC.PCORI_BASECODE
-FROM "&&i2b2_meta_schema".PCORNET_ENC join pcornet_mapping on pcornet_mapping.PCORI_PATH=PCORNET_ENC.c_fullname and pcornet_mapping.local_path is not null
-join "&&i2b2_meta_schema"."&&terms_table" i2b2 on i2b2.c_fullname=pcornet_mapping.local_path;
-
-commit;
-
-/* Updates to PCORNet demographic ontology
- - Hispanic was added as a column, so updating code lists.
- 
-TODO: Consider making a pull request to the SCILHS ontology with the changes.
-See also: https://github.com/SCILHS/i2p-transform/issues/1
-*/
-delete
-from "&&i2b2_meta_schema".pcornet_demo where c_fullname in (
-  select c_fullname from pcornet_ontology_updates
-  where c_fullname like '\PCORI\DEMOGRAPHIC\%'
-  );
-insert into "&&i2b2_meta_schema".pcornet_demo (
-  select * from pcornet_ontology_updates where c_fullname like '\PCORI\DEMOGRAPHIC\%'
-  );
-
-/* Bugs in the SCILHS ontology
-*/
---https://github.com/SCILHS/scilhs-ontology/issues/11
-update "&&i2b2_meta_schema".pcornet_diag pd set pd.pcori_basecode = 'PDX:S' where c_fullname = '\PCORI_MOD\PDX\S\';
-update "&&i2b2_meta_schema".pcornet_diag pd set pd.pcori_basecode = 'PDX:P' where c_fullname = '\PCORI_MOD\PDX\P\';
-update "&&i2b2_meta_schema".pcornet_diag pd set pd.pcori_basecode = 'PDX:X' where c_fullname = '\PCORI_MOD\PDX\X\';
-
-
-/* Replace PCORNet ICD9, ICD10 diagnoses hierarchy with the local hierarchy filling in
-the pcornet_basecode with the expected values.
-*/
-
---select *
-delete 
-from "&&i2b2_meta_schema".PCORNET_DIAG
-where c_fullname like '\PCORI\DIAGNOSIS\09\%'
-   or c_fullname like '\PCORI\DIAGNOSIS\10\%'
-;
-
-
-insert into "&&i2b2_meta_schema".PCORNET_DIAG
--- TODO: Stop cheating by going back to Clarity
-with edg9 as (
-    select dx_id, code from clarity.edg_current_icd9@id
-)
-, edg10 as (
-    select dx_id, code from clarity.edg_current_icd10@id
-)
-, heron_dx as (
-  select case
-         when ht.c_basecode like 'KUH|DX_ID:%'
-         then to_number(replace(ht.c_basecode, 'KUH|DX_ID:', ''))
-         else null
-         end dx_id
-       , ht.*
-  from "&&i2b2_meta_schema"."&&terms_table" ht
-  where c_fullname like '\i2b2\Diagnoses\ICD%'
-)
-, terms_dxi as (
-  select case
-         when ht.c_basecode like 'ICD9:%' then replace(ht.c_basecode, 'ICD9:', '')
-         when ht.c_basecode like 'ICD10:%' then replace(ht.c_basecode, 'ICD10:', '')
-         when ht.c_basecode like 'KUH|DX_ID:%'
-          and ht.c_fullname like '\i2b2\Diagnoses\ICD9\%'
-              then edg9.code
-         when ht.c_basecode like 'KUH|DX_ID:%'
-          and ht.c_fullname like '\i2b2\Diagnoses\ICD10\%'
-              then edg10.code
-         end pcori_basecode
-       , ht.*
-  from heron_dx ht
-  left join edg9
-         on edg9.dx_id = ht.dx_id
-  left join edg10
-         on edg10.dx_id = ht.dx_id
-)
-select
-  td.c_hlevel,
-  replace(replace(td.c_fullname, '\i2b2\Diagnoses\ICD9\', '\PCORI\DIAGNOSIS\09\')
-                               , '\i2b2\Diagnoses\ICD10\', '\PCORI\DIAGNOSIS\10\') c_fullname, 
-  td.c_name, td.c_synonym_cd, td.c_visualattributes,
-  td.c_totalnum, td.c_basecode, td.c_metadataxml, td.c_facttablecolumn, td.c_tablename, 
-  td.c_columnname, td.c_columndatatype, td.c_operator, td.c_dimcode, td.c_comment, 
-  td.c_tooltip, td.m_applied_path, td.update_date, td.download_date, td.import_date, 
-  td.sourcesystem_cd, td.valuetype_cd, td.m_exclusion_cd, td.c_path, td.c_symbol,
-  td.pcori_basecode
-from terms_dxi td
-;
-
-
--- Other diagnosis mappings such as modifiers for PDX, DX_SOURCE.
-insert into "&&i2b2_meta_schema".PCORNET_DIAG
-SELECT pcornet_diag.C_HLEVEL+1,
-  pcornet_diag.C_FULLNAME || i2b2.c_basecode || '\' as  C_FULLNAME,
-  i2b2.c_basecode || ' ' || i2b2.c_name as C_NAME,
-  pcornet_diag.C_SYNONYM_CD,
-  pcornet_diag.C_VISUALATTRIBUTES,
-  pcornet_diag.C_TOTALNUM,
-  i2b2.c_basecode as C_BASECODE,
-  pcornet_diag.C_METADATAXML,
-  pcornet_diag.C_FACTTABLECOLUMN,
-  pcornet_diag.C_TABLENAME,
-  pcornet_diag.C_COLUMNNAME,
-  pcornet_diag.C_COLUMNDATATYPE,
-  pcornet_diag.C_OPERATOR,
-  pcornet_diag.C_FULLNAME || i2b2.c_basecode || '\' as  C_DIMCODE,
-  pcornet_diag.C_COMMENT,
-  pcornet_diag.C_TOOLTIP,
-  pcornet_diag.M_APPLIED_PATH,
-  pcornet_diag.UPDATE_DATE,
-  pcornet_diag.DOWNLOAD_DATE,
-  pcornet_diag.IMPORT_DATE,
-  'MAPPING' as SOURCESYSTEM_CD,
-  pcornet_diag.VALUETYPE_CD,
-  pcornet_diag.M_EXCLUSION_CD,
-  pcornet_diag.C_PATH,
-  pcornet_diag.C_SYMBOL,
-  pcornet_diag.PCORI_BASECODE
-FROM "&&i2b2_meta_schema".pcornet_diag join pcornet_mapping on pcornet_mapping.PCORI_PATH = pcornet_diag.c_fullname and pcornet_mapping.local_path is not null
-join "&&i2b2_meta_schema"."&&terms_table" i2b2 on i2b2.c_fullname like pcornet_mapping.local_path || '%';
-
-commit;
-
--- TODO may be better represented in pcornet_mapping.csv
-create or replace view proc_local_to_pcori as
-select           '\PCORI\PROCEDURE\09\' as pcori_path, '\i2b2\Procedures\PRC\ICD9 (Inpatient)\' as local_path from dual 
-union all select '\PCORI\PROCEDURE\10\' as pcori_path, '\i2b2\Procedures\ICD10\' as local_path from dual 
-union all select '\PCORI\PROCEDURE\C4\' as pcori_path, '\i2b2\Procedures\PRC\Metathesaurus CPT Hierarchical Terms\' as local_path from dual
-;
-
---select *
-delete
-from "&&i2b2_meta_schema".PCORNET_PROC p_proc
-where exists (select 1
-              from proc_local_to_pcori m
-              where p_proc.c_fullname like m.pcori_path || '%');
-
-insert into "&&i2b2_meta_schema".PCORNET_PROC
-select 
-  ht.c_hlevel, 
-  replace(ht.c_fullname, m.local_path, m.pcori_path) c_fullname, 
-  ht.c_name, ht.c_synonym_cd, ht.c_visualattributes,
-  ht.c_totalnum, ht.c_basecode, ht.c_metadataxml, ht.c_facttablecolumn, ht.c_tablename, 
-  ht.c_columnname, ht.c_columndatatype, ht.c_operator, ht.c_dimcode, ht.c_comment, 
-  ht.c_tooltip, ht.m_applied_path, ht.update_date, ht.download_date, ht.import_date, 
-  ht.sourcesystem_cd, ht.valuetype_cd, ht.m_exclusion_cd, ht.c_path, ht.c_symbol,
-  ht.c_basecode pcori_basecode
-from  "&&i2b2_meta_schema"."&&terms_table" ht
-join proc_local_to_pcori m on ht.c_fullname like m.local_path || '%'
-order by ht.c_hlevel;
-
-/* MS-DRGs
-*/
-delete 
-from "&&i2b2_meta_schema".PCORNET_ENC
-where c_fullname like '\PCORI\ENCOUNTER\DRG\02\%'
-;
-
-insert into "&&i2b2_meta_schema".PCORNET_ENC
-with drg_path_map as (
-  select local_path, local_path || '%' like_local_path, pcori_path, pcori_path || '%' like_pcori_path
-  from pcornet_mapping where pcori_path like '\PCORI\ENCOUNTER\DRG\02\%'
-  )
-select 
-  ht.c_hlevel, 
-  replace(ht.c_fullname, pm.local_path, pm.pcori_path) c_fullname, 
-  ht.c_name, ht.c_synonym_cd, ht.c_visualattributes,
-  ht.c_totalnum, ht.c_basecode, ht.c_metadataxml, ht.c_facttablecolumn, ht.c_tablename, 
-  ht.c_columnname, ht.c_columndatatype, ht.c_operator, ht.c_dimcode, ht.c_comment, 
-  ht.c_tooltip, ht.m_applied_path, ht.update_date, ht.download_date, ht.import_date, 
-  ht.sourcesystem_cd, ht.valuetype_cd, ht.m_exclusion_cd, ht.c_path, ht.c_symbol,
-  case when ht.c_basecode is not null 
-    then 'MSDRG:' || lpad(substr(ht.c_basecode, instr(ht.c_basecode, ':') + 1), 3, '0')
-  end pcori_basecode
-from 
-  "&&i2b2_meta_schema"."&&terms_table" ht
-cross join drg_path_map pm
-where c_fullname like pm.like_local_path
---order by c_hlevel 
-;
-
-/* The following is good for eyeballing the DRG alignment - the names seem to
-match exactly between UHC and the PCORNet ontology.
-*/
-/*
-with drg_path_map as (
-  select local_path, local_path || '%' like_local_path, pcori_path, pcori_path || '%' like_pcori_path
-  from pcornet_mapping where pcori_path like '\PCORI\ENCOUNTER\DRG\02\%'
-  ),
-pcornet_drgs as (
-  select replace(pe.pcori_basecode, 'MSDRG:', '') drg_code, pe.* 
-  from "&&i2b2_meta_schema".pcornet_enc pe
-  cross join drg_path_map dm
-  where pe.c_fullname like dm.like_pcori_path
-  ),
-local_drgs as (
-  select
-    replace(ht.c_basecode, 'UHC|UHCMSDRG:', '') drg_code, ht.*
-  from "&&i2b2_meta_schema"."&&terms_table" ht 
-  cross join drg_path_map dm
-  where ht.c_fullname like dm.like_local_path
-  )
-select pd.drg_code, pd.c_name, ld.c_name from pcornet_drgs pd
-join local_drgs ld on ld.drg_code = pd.drg_code;
-*/
-
-/* Admitting source: For i2p-transform, these values go in the visit dimension.
-To make them queryable from the web interface, insert the local terms under the
-PCORI parent.
-*/
-
-
-create or replace view admit_src_path_map as
-select local_path, local_path || '%' like_local_path, pcori_path, pcori_path || '%' like_pcori_path
-from pcornet_mapping where pcori_path like '\PCORI\ENCOUNTER\ADMITTING_SOURCE\%'
-;
-
-update "&&i2b2_meta_schema".PCORNET_ENC
-set c_visualattributes = 'FA' where c_fullname in (
-  select pcori_path from admit_src_path_map
-  );
-  
-insert into "&&i2b2_meta_schema".PCORNET_ENC
-select 
-  pe.c_hlevel + 1 c_hlevel,
-  pm.pcori_path || ht.c_basecode || '\' c_fullname,
-  ht.c_name, ht.c_synonym_cd, ht.c_visualattributes,
-  ht.c_totalnum, ht.c_basecode, ht.c_metadataxml, ht.c_facttablecolumn, ht.c_tablename, 
-  ht.c_columnname, ht.c_columndatatype, ht.c_operator, ht.c_dimcode, ht.c_comment, 
-  ht.c_tooltip, ht.m_applied_path, ht.update_date, ht.download_date, ht.import_date, 
-  'MAPPING' sourcesystem_cd, ht.valuetype_cd, ht.m_exclusion_cd, ht.c_path, ht.c_symbol,
-  pe.pcori_basecode
-from 
-  "&&i2b2_meta_schema"."&&terms_table" ht
-cross join admit_src_path_map pm
-join "&&i2b2_meta_schema".pcornet_enc pe on pe.c_fullname = pm.pcori_path
-where ht.c_fullname like pm.like_local_path
-order by c_hlevel
-;
-
-
-/* Medications
-This section takes the place of PCORI_MEDS_SCHEMA_CHANGE_ora.sql included in the
-SCILHS code.
-*/
-whenever sqlerror continue;
-alter table "&&i2b2_meta_schema".pcornet_med add (
-  pcori_cui varchar2(8)
-  );
-
-alter table "&&i2b2_meta_schema".pcornet_med add (
-  pcori_ndc varchar2(12)
-  );
-whenever sqlerror exit;
-
-delete 
-from "&&i2b2_meta_schema".PCORNET_MED
-where c_fullname like '\PCORI\MEDICATION\RXNORM_CUI\%'
-and c_fullname not like '\PCORI_MOD\%';
-
-update "&&i2b2_meta_schema".PCORNET_MED med
-set med.c_visualattributes = 'DAE' where c_fullname in (
-  select distinct pm.pcori_path
-  from pcornet_mapping pm
-  join "&&i2b2_meta_schema".PCORNET_MED med on med.c_fullname = pm.pcori_path
-  where  med.c_fullname like '\PCORI_MOD\%'
-  );
-  
-/* RX Frequency modifiers
-*/
-create or replace view rx_frequency_strs as
-select '\PCORI_MOD\RX_FREQUENCY\' freq_mod_path, 'RX_FREQUENCY:' freq_mod_pfx from dual;
-
-delete
-from "&&i2b2_meta_schema".PCORNET_MED pm
-where pm.c_fullname like (select strs.freq_mod_path || '%' from rx_frequency_strs strs);
-
-insert into "&&i2b2_meta_schema".pcornet_med
-select
-  c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum, 
-  c_basecode, c_metadataxml, c_facttablecolumn, c_tablename, c_columnname, 
-  c_columndatatype, c_operator, c_dimcode, c_comment, c_tooltip, m_applied_path, 
-  update_date, download_date, import_date, sourcesystem_cd, valuetype_cd, 
-  m_exclusion_cd, c_path, c_symbol, 
-  strs.freq_mod_pfx || substr(ht.c_fullname, length(strs.freq_mod_path) + 1, 2) pcori_basecode, 
-  null pcori_cui, null pcori_ndc
-from "&&i2b2_meta_schema"."&&terms_table" ht
-cross join rx_frequency_strs strs
-where ht.c_fullname like (select strs.freq_mod_path || '%' from rx_frequency_strs)
-and ht.m_exclusion_cd is null
-and ht.c_basecode is not null;
-  
-
-
-/** medication_id_to_best_rxcui
-
-Spec for PRESCRIBING.RXNORM_CUI says:
-
-  Where an RxNorm mapping exists for the source
-  medication, this field contains the RxNorm concept
-  identifier (CUI) at the highest possible specificity.
-
-  If more than one option exists for mapping, the
-  following ordered strategy may be adopted:
-  1)Semantic generic clinical drug
-  2)Semantic Branded clinical drug
-  3)Generic drug pack
-  4)Branded drug pack
-
-*/
-create or replace view medication_id_to_best_rxcui as
-with pcornet_spec as (
-  select '1) Semantic generic clinical drug (SCD)' spec_order, 1 ix, 'SCD' tty from dual union all
-  select '2) Semantic Branded clinical drug (SBC)', 2, 'SBD' from dual union all
-  select '3) Generic drug pack (GPCK)', 3, 'GPCK' from dual union all
-  select '4) Branded drug pack (BPCK)', 4, 'BPCK' from dual
-)
-, cui_pref as (  -- Rx concepts joined with spec order
-  select rxcui, str rxnorm_str, ix, spec_order
-  from rxnorm.rxnconso@id con
-  join pcornet_spec on pcornet_spec.tty = con.tty
-)
-/*
-  TODO: Consider changing HERON paths to be RXCUIs or including the RXCUI column
-  so that we don't have to reach back to the clarity_med_id_to_rxcui map. See
-  also https://informatics.gpcnetwork.org/trac/Project/ticket/390.
-*/
-, clarity_med_id_to_rxcui as (
-  select cmed.medication_id clarity_med_id, rxn.rxnorm_code rxcui, '1) Clarity'  dose_pref
-  from clarity.rxnorm_codes@id rxn
-  join clarity.clarity_medication@id cmed on cmed.medication_id = rxn.medication_id
-  union all
-  select clarity_med_id, rxcui, '2) GCN'
-  from "&&i2b2_etl_schema".clarity_med_id_to_rxcui_gcn@id
-  union all
-  select clarity_med_id, rxcui, '3) NDC'
-  from "&&i2b2_etl_schema".clarity_med_id_to_rxcui_ndc@id
-  union all
-  select to_number(clarity_medication_id), rxcui, '4) Manual Curation' --, con.tty, va_name, sdf_name
-  from "&&i2b2_etl_schema".med_map_manual_curation mmmc
-  join rxnorm.rxnconso@id con on con.rxaui = mmmc.sdf_rxaui
-)
-, med_map_pref as ( -- HERON clarity_med_id_to_rxcui joined with spec order
-    select distinct clarity_med_id medication_id
-         , med_map.rxcui, cui_pref.rxnorm_str, med_map.dose_pref
-         , coalesce(spec_order, '9) HERON mapping misc.') spec_order
-    from clarity_med_id_to_rxcui med_map
-    left join cui_pref on cui_pref.rxcui = med_map.rxcui
-)
-, med_map_best as (
-  -- Take the mapping with the best (i.e. min) spec_order and dose_pref, just like...
-  --  Taking the record with the max date
-  --  http://stackoverflow.com/a/8898142
-  -- This may result in multiple rxcuis per medication_id, so while we're
-  -- at it, take the minimum rxcui among those with the best spec_order.
-  select *
-  from (select medication_id, rxcui, rxnorm_str, spec_order, dose_pref
-             , rank() over (partition by medication_id order by spec_order, dose_pref, rxcui) rnk
-        from med_map_pref)
-  where rnk = 1
-)
-, all_med as (
-  select cd. concept_cd, max(name_char) name_char
-  from blueherondata.concept_dimension cd
-  where cd.concept_cd like 'KUH|MEDICATION_ID:%'
-  group by cd.concept_cd
-)
-select all_med.*, med_map_best.*
-from all_med
-left join med_map_best on all_med.concept_cd = 'KUH|MEDICATION_ID:' || med_map_best.medication_id
-;
-;
-/* Eyeball it:
-
-select *
-from medication_id_to_best_rxcui mitr
-join blueheronmetadata.counts_by_concept cbc on cbc.concept_cd = mitr.concept_cd
-order by facts desc
-;
-*/
-
-/* test cases (TODO: formalize these)
-
-Picking out just one row per CUI from RXNORM can be tricky; did we goof?
-select count(*), medication_id
-from medication_id_to_best_rxcui
-where medication_id is not null
-group by medication_id having count(*) > 1;
-
-How many of each spec_order?
-
-select count(*), spec_order, dose_pref from medication_id_to_best_rxcui
-group by spec_order, dose_pref order by 1 desc;
-
-27825	1) Semantic generic clinical drug (SCD)	1) Clarity
-17527	1) Semantic generic clinical drug (SCD)	2) GCN
- 3475		 *null* lots of IVP. TODO: med mixes
- 2888	9) HERON mapping misc.	2) GCN
- 2550	9) HERON mapping misc.	1) Clarity
-  421	1) Semantic generic clinical drug (SCD)	3) NDC
-  295	3) Generic drug pack (GPCK)	1) Clarity
-  177	3) Generic drug pack (GPCK)	2) GCN
-   97	2) Semantic Branded clinical drug (SBC)	3) NDC
-    4	9) HERON mapping misc.	3) NDC
-    2	4) Branded drug pack (BPCK)	3) NDC
-    1	3) Generic drug pack (GPCK)	3) NDC
-
-Be sure RXCUI for 0.4 ML ENOXAPARIN 100 MG/ML SC SYRG includes the 0.4 ML dose info:
-select concept_cd, name_char, rxcui, rxnorm_str, spec_order, dose_pref from medication_id_to_best_rxcui where concept_cd = 'KUH|MEDICATION_ID:85052'; -- -> 854235, 1) SCD
-
-select concept_cd, name_char, rxcui, rxnorm_str, spec_order, dose_pref from medication_id_to_best_rxcui where concept_cd = 'KUH|MEDICATION_ID:85051'; -- -> 854248, 1) SCD
-
-This one goes from "LEVOTHYROXINE PO" to "Levothyroxine Sodium 0.1 MG Oral Tablet"; is that right?
-select concept_cd, name_char, rxcui, rxnorm_str, spec_order, dose_pref from medication_id_to_best_rxcui where concept_cd = 'KUH|MEDICATION_ID:150171'; -- -> 892246,	1) SCD
-*/
-
-
-insert into "&&i2b2_meta_schema".PCORNET_MED
-with
-terms_rx as (
-  select 
-    best.rxcui mapped_rxcui, ht.*
-  from 
-    "&&i2b2_meta_schema"."&&terms_table" ht
-  left join medication_id_to_best_rxcui best on best.concept_cd = ht.c_basecode
-  where c_fullname like '\i2b2\Medications%'
-		and c_basecode not like 'NDC:%' -- We'll handle NDCs seperately below
-  	and ht.c_visualattributes not like '%H%'
-  )
-select
-  rx.c_hlevel + 1 c_hlevel, 
-  replace(rx.c_fullname, '\i2b2\Medications\', '\PCORI\MEDICATION\RXNORM_CUI\') c_fullname, 
-  rx.c_name, rx.c_synonym_cd, rx.c_visualattributes,
-  rx.c_totalnum, rx.c_basecode, rx.c_metadataxml, rx.c_facttablecolumn, rx.c_tablename, 
-  rx.c_columnname, rx.c_columndatatype, rx.c_operator, rx.c_dimcode, rx.c_comment, 
-  rx.c_tooltip, rx.m_applied_path, rx.update_date, rx.download_date, rx.import_date, 
-  rx.sourcesystem_cd, rx.valuetype_cd, rx.m_exclusion_cd, rx.c_path, rx.c_symbol,
-  rx.rxcui pcori_basecode, rx.rxcui pcori_cui, 
-  -- Don't worry about NDCs for now - used for dispensing
-  null pcori_ndc from (
-    select
-      trx.*,
-      case 
-        when trx.mapped_rxcui is not null then trx.mapped_rxcui
-        when trx.c_basecode like 'RXCUI:%' then replace(trx.c_basecode, 'RXCUI:', '')
-        else null 
-      end rxcui
-    from terms_rx trx
-    --order by trx.c_hlevel
-    ) rx;
-
--- Handle mapping NDC codes for DISPENSING
-insert into "&&i2b2_meta_schema".PCORNET_MED
-select
-	c_hlevel + 1 c_hlevel,
-	replace(c_fullname, '\i2b2\Medications\', '\PCORI\MEDICATION\RXNORM_CUI\') c_fullname,
-  c_name, c_synonym_cd, c_visualattributes,
-  c_totalnum, c_basecode, c_metadataxml, c_facttablecolumn, c_tablename,
-  c_columnname, c_columndatatype, c_operator, c_dimcode, c_comment,
-  c_tooltip, m_applied_path, update_date, download_date, import_date,
-  sourcesystem_cd, valuetype_cd, m_exclusion_cd, c_path, c_symbol,
-  null pcori_basecode, null pcori_cui,
-  substr(c_basecode, 5) pcori_ndc
-from "&&i2b2_meta_schema"."&&terms_table"
-where c_fullname like '\i2b2\Medications%'
-	and c_basecode like 'NDC:%'
-	and length(substr(c_basecode, 5)) < 12 -- Make sure we have 11 digit NDC
-;
-
-delete 
-from "&&i2b2_meta_schema".PCORNET_MED where sourcesystem_cd='MAPPING';
-
-
-insert into "&&i2b2_meta_schema".PCORNET_MED
-with med_mod_mapping as (
-  select distinct pcori_path, i2b2.c_fullname, i2b2.c_basecode, i2b2.c_name
-  FROM "&&i2b2_meta_schema".pcornet_med 
-  join pcornet_mapping on pcornet_mapping.PCORI_PATH = pcornet_med.c_fullname and pcornet_mapping.local_path is not null
-  join "&&i2b2_meta_schema"."&&terms_table" i2b2 on i2b2.c_fullname like pcornet_mapping.local_path || '%'
-  where i2b2.c_basecode is not null
-  )
-SELECT pcornet_med.C_HLEVEL+1,
-  pcornet_med.C_FULLNAME || med_mod_mapping.c_basecode || '\' as  C_FULLNAME,
-  med_mod_mapping.c_basecode || ' ' || med_mod_mapping.c_name as C_NAME,
-  pcornet_med.C_SYNONYM_CD,
-  pcornet_med.C_VISUALATTRIBUTES,
-  pcornet_med.C_TOTALNUM,
-  med_mod_mapping.c_basecode as C_BASECODE,
-  pcornet_med.C_METADATAXML,
-  pcornet_med.C_FACTTABLECOLUMN,
-  pcornet_med.C_TABLENAME,
-  pcornet_med.C_COLUMNNAME,
-  pcornet_med.C_COLUMNDATATYPE,
-  pcornet_med.C_OPERATOR,
-  pcornet_med.C_FULLNAME || med_mod_mapping.c_basecode || '\' as  C_DIMCODE,
-  pcornet_med.C_COMMENT,
-  pcornet_med.C_TOOLTIP,
-  pcornet_med.M_APPLIED_PATH,
-  pcornet_med.UPDATE_DATE,
-  pcornet_med.DOWNLOAD_DATE,
-  pcornet_med.IMPORT_DATE,
-  'MAPPING' as SOURCESYSTEM_CD,
-  pcornet_med.VALUETYPE_CD,
-  pcornet_med.M_EXCLUSION_CD,
-  pcornet_med.C_PATH,
-  pcornet_med.C_SYMBOL,
-  pcornet_med.PCORI_BASECODE,
-  null pcori_cui,
-  null pcori_ndc
-from med_mod_mapping
-join "&&i2b2_meta_schema".pcornet_med on med_mod_mapping.PCORI_PATH = pcornet_med.c_fullname
-;
-
-commit;
-
-/* Replace SCILHS PCORNet Labs hierarchy with our local LOINC hierarchy with
-   adjustment to make it "SCILHS like".
-*/
-
-/* Remove existing SCIHLS Labs hierarchy */
-truncate table "&&i2b2_meta_schema".pcornet_lab;
-
-/* Insert LOINC codes from local hierarchy, setting c_basecode to appropriate
-   LAB_NAME for common PCORNet labs. */
-insert into "&&i2b2_meta_schema".pcornet_lab
-select distinct
-  lc.C_HLEVEL,
-  replace(lc.C_FULLNAME, '\i2b2\Laboratory Tests\', '\PCORI\LAB_RESULT_CM\') c_fullname,
-  lc.C_NAME,
-  lc.C_SYNONYM_CD,
-  lc.C_VISUALATTRIBUTES,
-  lc.C_TOTALNUM,
-  case
-    when llm.lab_name is not null then 'LAB_NAME:'|| llm.lab_name
-    else lc.c_basecode
-  end c_basecode,
-  to_char(lc.C_METADATAXML),
-  lc.C_FACTTABLECOLUMN,
-  lc.C_TABLENAME,
-  lc.C_COLUMNNAME,
-  lc.C_COLUMNDATATYPE,
-  lc.C_OPERATOR,
-  lc.C_DIMCODE,
-  to_char(lc.C_COMMENT),
-  lc.C_TOOLTIP,
-  lc.M_APPLIED_PATH,
-  lc.UPDATE_DATE,
-  lc.DOWNLOAD_DATE,
-  lc.IMPORT_DATE,
-  lc.SOURCESYSTEM_CD,
-  lc.VALUETYPE_CD,
-  lc.M_EXCLUSION_CD,
-  lc.C_PATH,
-  lc.C_SYMBOL,
-  llm.pcori_specimen_source,
-  replace(lc.c_basecode, 'LOINC:', '') pcori_basecode
-from "&&i2b2_meta_schema"."&&terms_table" lc
-left outer join lab_loinc_mapping llm
-  on lc.c_basecode = ('LOINC:' || llm.loinc_code)
-where lc.c_basecode like 'LOINC:%'
-;
-
-/* Insert child KUH|COMPONENT_ID nodes, setting pcori_basecode, and c_path to
-   that of it's parent. */
-insert into "&&i2b2_meta_schema".pcornet_lab
-with parent_loinc_codes as ( -- LOINC codes with children LOINC codes
-  select p_loinc.*
-  from "&&i2b2_meta_schema"."&&terms_table" p_loinc
-  join "&&i2b2_meta_schema"."&&terms_table" c_loinc
-    on c_loinc.c_fullname like (p_loinc.c_fullname || '%')
-    and p_loinc.c_basecode like 'LOINC:%'
-    and c_loinc.c_basecode like 'LOINC:%'
-    and p_loinc.c_basecode!=c_loinc.c_basecode
-)
-, children_loinc_codes as ( -- LOINC codes without children LOINC codes
-  select clc.*
-  from "&&i2b2_meta_schema"."&&terms_table" clc
-  where clc.c_basecode like 'LOINC:%'
-    and clc.c_basecode not in (
-      select c_basecode from parent_loinc_codes
-  )
-)
-select distinct
-  ccc.C_HLEVEL,
-  replace(ccc.C_FULLNAME, '\i2b2\Laboratory Tests\', '\PCORI\LAB_RESULT_CM\') c_fullname,
-  ccc.C_NAME,
-  ccc.C_SYNONYM_CD,
-  ccc.C_VISUALATTRIBUTES,
-  ccc.C_TOTALNUM,
-  ccc.C_BASECODE,
-  to_char(ccc.C_METADATAXML),
-  ccc.C_FACTTABLECOLUMN,
-  ccc.C_TABLENAME,
-  ccc.C_COLUMNNAME,
-  ccc.C_COLUMNDATATYPE,
-  ccc.C_OPERATOR,
-  ccc.C_DIMCODE,
-  to_char(ccc.C_COMMENT),
-  ccc.C_TOOLTIP,
-  ccc.M_APPLIED_PATH,
-  ccc.UPDATE_DATE,
-  ccc.DOWNLOAD_DATE,
-  ccc.IMPORT_DATE,
-  ccc.SOURCESYSTEM_CD,
-  ccc.VALUETYPE_CD,
-  ccc.M_EXCLUSION_CD,
-  replace(clc.C_FULLNAME, '\i2b2\Laboratory Tests\', '\PCORI\LAB_RESULT_CM\') c_path,
-  ccc.C_SYMBOL,
-  llm.pcori_specimen_source,
-  replace(clc.c_basecode, 'LOINC:', '') pcori_basecode
-from children_loinc_codes clc
-join "&&i2b2_meta_schema"."&&terms_table" ccc
-  on ccc.c_fullname like (clc.c_fullname || '%')
-  and ccc.c_basecode like 'KUH|COMPONENT_ID:%' -- TODO: Generalize for other sites.
-left outer join lab_loinc_mapping llm
-  on clc.c_basecode = ('LOINC:' || llm.loinc_code)
-;
-
-commit;
-
diff --git a/Oracle/pcornet_mapping_ddl.sql b/Oracle/pcornet_mapping_ddl.sql
deleted file mode 100644
index 12d6e87..0000000
--- a/Oracle/pcornet_mapping_ddl.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-CREATE TABLE pcornet_mapping (
-    "PCORI_PATH"    VARCHAR2(2000),
-    "LOCAL_PATH"    VARCHAR2(2000)
-    );
diff --git a/Oracle/pcornet_ontology_updates.csv b/Oracle/pcornet_ontology_updates.csv
deleted file mode 100644
index b5c10e2..0000000
--- a/Oracle/pcornet_ontology_updates.csv
+++ /dev/null
@@ -1,9 +0,0 @@
-"C_HLEVEL","C_FULLNAME","C_NAME","C_SYNONYM_CD","C_VISUALATTRIBUTES","C_TOTALNUM","C_BASECODE","C_METADATAXML","C_FACTTABLECOLUMN","C_TABLENAME","C_COLUMNNAME","C_COLUMNDATATYPE","C_OPERATOR","C_DIMCODE","C_COMMENT","C_TOOLTIP","M_APPLIED_PATH","UPDATE_DATE","DOWNLOAD_DATE","IMPORT_DATE","SOURCESYSTEM_CD","VALUETYPE_CD","M_EXCLUSION_CD","C_PATH","C_SYMBOL","PCORI_BASECODE"
-2,"\PCORI\DEMOGRAPHIC\HISPANIC\","Ethnicity","N","CAE",,,"<?xml version=""1.0"" encoding=""UTF-8""?><ValueMetadata><Version>3.2</Version><CreationDateTime>2014-05-09T11:10:26.266-04:00</CreationDateTime><MaxStringLength/><DataType>Enum</DataType><Oktousevalues/><EnumValues><Val>No</Val><Val>Unknown</Val><Val>Yes</Val>    </EnumValues></ValueMetadata>","concept_cd","CONCEPT_DIMENSION","concept_path","T","like","\PCORI\DEMOGRAPHIC\HISPANIC\",,"Ethnicity","@","2014-05-09 11:10:28","2014-05-09 11:10:28","2014-05-09 11:10:28","PCORNET_CDM",,,"\PCORI\DEMOGRAPHIC\","HISPANIC",
-3,"\PCORI\DEMOGRAPHIC\HISPANIC\NI\","No information","N","LAE",,"ETHNICITY:NI",,"PATIENT_NUM","PATIENT_DIMENSION","ETHNICITY_CD","N","IS","NULL",,"No information: A data field is present in the source system, but the source value is null or blank.","@","2014-06-02 19:40:30","2014-06-02 19:40:30","2014-06-02 19:40:30","PCORNET_CDM",,,"\PCORI\DEMOGRAPHIC\HISPANIC\","NI","NI"
-3,"\PCORI\DEMOGRAPHIC\HISPANIC\N\","Non-Hispanic","N","LIE",,"ETHNICITY:NOTHISPANIC",,"PATIENT_NUM","PATIENT_DIMENSION","ETHNICITY_CD","T","IN","'N'",,"Non-Hispanic","@","2014-05-09 11:12:04","2014-05-09 11:12:04","2014-05-09 11:12:04","PCORNET_CDM",,,"\PCORI\DEMOGRAPHIC\HISPANIC\","N","N"
-3,"\PCORI\DEMOGRAPHIC\HISPANIC\OT\","Other","N","LAE",,"ETHNICITY:OT",,"PATIENT_NUM","PATIENT_DIMENSION","ETHNICITY_CD","T","IN","'OT'",,"Other: A data field is present in the source system, but the source value cannot be mapped to the CDM.","@","2014-06-02 19:44:16","2014-06-02 19:44:16","2014-06-02 19:44:16","PCORNET_CDM",,,"\PCORI\DEMOGRAPHIC\HISPANIC\","OT","OT"
-3,"\PCORI\DEMOGRAPHIC\HISPANIC\UN\","Unknown","N","LAE",,"ETHNICITY:UN",,"PATIENT_NUM","PATIENT_DIMENSION","ETHNICITY_CD","T","IN","'UN','u','unk'",,"Unknown: A data field is present in the source system, but the source value explicitly denotes an unknown value.","@","2014-06-02 19:43:08","2014-06-02 19:43:08","2014-06-02 19:43:08","PCORNET_CDM",,,"\PCORI\DEMOGRAPHIC\HISPANIC\","UN","UN"
-3,"\PCORI\DEMOGRAPHIC\HISPANIC\Y\","Hispanic","N","LAE",,"ETHNICITY:HISPANIC",,"PATIENT_NUM","PATIENT_DIMENSION","ETHNICITY_CD","T","IN","'Y','hib','his/black','his/white','hiw','hispanic'",,"A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. \ Hisptanic","@","2014-05-09 15:21:33","2014-05-09 11:11:12","2014-05-09 11:11:12","PCORNET_CDM",,,"\PCORI\DEMOGRAPHIC\HISPANIC\","Y","Y"
-3,"\PCORI\DEMOGRAPHIC\RACE\NI\","No information","N","LAE",,"RACE:NI",,"PATIENT_NUM","PATIENT_DIMENSION","RACE_CD","N","IS","'@'",,"No information: A data field is present in the source system, but the source value is null or blank.","@","2016-03-30 16:48:29","2016-03-30 16:48:29","2016-03-30 16:48:29","PCORNET_CDM",,"","\PCORI\DEMOGRAPHIC\RACE\","NI","NI"
-3,"\PCORI\DEMOGRAPHIC\RACE\OT\","Other","N","LAE",,"RACE:OT",,"PATIENT_NUM","PATIENT_DIMENSION","RACE_CD","T","IN","'OT','o','d','deferred'",,"Other: A data field is present in the source system, but the source value cannot be mapped to the CDM.","@","2016-03-30 16:48:29","2016-03-30 16:48:29","2016-03-30 16:48:29","PCORNET_CDM",,"","\PCORI\DEMOGRAPHIC\RACE\","OT","OT"
diff --git a/Oracle/pcornet_ontology_updates.ctl b/Oracle/pcornet_ontology_updates.ctl
deleted file mode 100644
index c0d966d..0000000
--- a/Oracle/pcornet_ontology_updates.ctl
+++ /dev/null
@@ -1,32 +0,0 @@
-options (direct=true, errors=0, skip=1)
-load data
-truncate into table PCORNET_ONTOLOGY_UPDATES
-fields terminated by ',' optionally enclosed by '"'
-trailing nullcols(
-  C_HLEVEL,
-  C_FULLNAME,
-  C_NAME CHAR(2000),
-  C_SYNONYM_CD,
-  C_VISUALATTRIBUTES,
-  C_TOTALNUM,
-  C_BASECODE,
-  C_METADATAXML CHAR(100000),
-  C_FACTTABLECOLUMN,
-  C_TABLENAME,
-  C_COLUMNNAME,
-  C_COLUMNDATATYPE,
-  C_OPERATOR,
-  C_DIMCODE CHAR(700),
-  C_COMMENT,
-  C_TOOLTIP CHAR(900),
-  M_APPLIED_PATH,
-  UPDATE_DATE DATE 'YYYY-MM-DD HH24:MI:SS',
-  DOWNLOAD_DATE DATE 'YYYY-MM-DD HH24:MI:SS',
-  IMPORT_DATE DATE 'YYYY-MM-DD HH24:MI:SS',
-  SOURCESYSTEM_CD,
-  VALUETYPE_CD,
-  M_EXCLUSION_CD,
-  C_PATH,
-  C_SYMBOL,
-  PCORI_BASECODE
-  )
\ No newline at end of file
diff --git a/Oracle/pcornet_ontology_updates_ddl.sql b/Oracle/pcornet_ontology_updates_ddl.sql
deleted file mode 100644
index 82ec392..0000000
--- a/Oracle/pcornet_ontology_updates_ddl.sql
+++ /dev/null
@@ -1,29 +0,0 @@
-CREATE TABLE pcornet_ontology_updates (
-	"C_HLEVEL"			NUMBER(22,0)	NOT NULL, 
-	"C_FULLNAME"			VARCHAR2(700)	NOT NULL, 
-	"C_NAME"			VARCHAR2(2000)	NOT NULL, 
-	"C_SYNONYM_CD"			CHAR(1)	NOT NULL, 
-	"C_VISUALATTRIBUTES"		CHAR(3)	NOT NULL, 
-	"C_TOTALNUM"			NUMBER(22,0)	NULL, 
-	"C_BASECODE"			VARCHAR2(50)	NULL, 
-	"C_METADATAXML"			CLOB	NULL, 
-	"C_FACTTABLECOLUMN"		VARCHAR2(50)	NOT NULL, 
-	"C_TABLENAME"			VARCHAR2(50)	NOT NULL, 
-	"C_COLUMNNAME"			VARCHAR2(50)	NOT NULL, 
-	"C_COLUMNDATATYPE"		VARCHAR2(50)	NOT NULL, 
-	"C_OPERATOR"			VARCHAR2(10)	NOT NULL, 
-	"C_DIMCODE"			VARCHAR2(700)	NOT NULL, 
-	"C_COMMENT"			CLOB	NULL, 
-	"C_TOOLTIP"			VARCHAR2(900)	NULL, 
-	"M_APPLIED_PATH"		VARCHAR2(700)	NOT NULL, 
-	"UPDATE_DATE"			DATE	NOT NULL, 
-	"DOWNLOAD_DATE"			DATE	NULL, 
-	"IMPORT_DATE"			DATE	NULL, 
-	"SOURCESYSTEM_CD"		VARCHAR2(50)	NULL, 
-	"VALUETYPE_CD"			VARCHAR2(50)	NULL,
-	"M_EXCLUSION_CD"		VARCHAR2(25) NULL,
-	"C_PATH"			VARCHAR2(700)   NULL,
-	"C_SYMBOL"			VARCHAR2(50)	NULL,
-	"PCORI_BASECODE"		VARCHAR2(50) NULL
-)
-;
diff --git a/Oracle/run-i2p-transform.sh b/Oracle/run-i2p-transform.sh
index f0a4b7b..ad1544e 100644
--- a/Oracle/run-i2p-transform.sh
+++ b/Oracle/run-i2p-transform.sh
@@ -1,32 +1,9 @@
 #!/bin/bash
 set -e
 
-# Expected environment variables (put there by Jenkins, etc.)
-
-# Database SID
-#export sid=
-# User and password for CDM user
-#export pcornet_cdm_user=
-#export pcornet_cdm=
-
-#export i2b2_data_schema=
-#export i2b2_meta_schema=
-#export datamart_id=
-#export datamart_name=
-#export network_id=
-#export network_name=
-# export i2b2_etl_schema=
-# export min_pat_list_date_dd_mon_rrrr=
-# export min_visit_date_dd_mon_rrrr=
-# export enrollment_months_back=36
-
-# All i2b2 terms - used for local path mapping
-#export terms_table=
-
 python load_csv.py harvest_local harvest_local.csv harvest_local.ctl pcornet_cdm_user pcornet_cdm
 python load_csv.py PMN_LabNormal pmn_labnormal.csv pmn_labnormal.ctl pcornet_cdm_user pcornet_cdm
 python load_csv.py lab_loinc_mapping lab_loinc_mapping.csv lab_loinc_mapping.ctl pcornet_cdm_user pcornet_cdm
-. ./load_pcornet_mapping.sh
 
 # Run some tests
 sqlplus /nolog <<EOF
@@ -59,11 +36,13 @@ select rxcui from "&&i2b2_etl_schema".clarity_med_id_to_rxcui@id where 1=0;
 select case when qty > 0 then 1 else 1/0 end obs_fact_meds_populated from (
   select count(*) qty from observation_fact_meds
   );
-
 EOF
 
 
-# Insert local terms as leaves of the PCORNet terms and run the transform
+########### Initialize Schema ###########
+if [ ${initialize_schema} == 'true' ]
+then
+
 sqlplus /nolog <<EOF
 connect ${pcornet_cdm_user}/${pcornet_cdm}
 
@@ -72,25 +51,37 @@ set timing on;
 set linesize 3000;
 set pagesize 5000;
 
-WHENEVER SQLERROR CONTINUE;
-
-drop table DEMOGRAPHIC;
-drop table ENROLLMENT;
-drop table ENCOUNTER;
-drop table DIAGNOSIS;
-drop table PROCEDURES;
-drop table VITAL;
-drop table DISPENSING;
-drop table LAB_RESULT_CM;
-drop table CONDITION;
-drop table PRO_CM;
-drop table PRESCRIBING;
-drop table PCORNET_TRIAL;
-drop table DEATH;
-drop table DEATH_CAUSE;
-drop table HARVEST;
+define i2b2_data_schema=${i2b2_data_schema}
+define i2b2_meta_schema=${i2b2_meta_schema}
+define i2b2_etl_schema=${i2b2_etl_schema}
+define datamart_id=${datamart_id}
+define datamart_name=${datamart_name}
+define network_id=${network_id}
+define network_name=${network_name}
+define terms_table=${terms_table}
+define min_pat_list_date_dd_mon_rrrr=${min_pat_list_date_dd_mon_rrrr}
+define min_visit_date_dd_mon_rrrr=${min_visit_date_dd_mon_rrrr}
+define enrollment_months_back=${enrollment_months_back}
+define pcornet_cdm_user=${pcornet_cdm_user}
 
-WHENEVER SQLERROR EXIT SQL.SQLCODE;
+-- Prepare for transform
+start PCORNetInit.sql
+EOF
+
+fi
+
+
+########### Load Transform Procedures ###########
+if [ ${load_procedures} == 'true' ]
+then
+
+sqlplus /nolog <<EOF
+connect ${pcornet_cdm_user}/${pcornet_cdm}
+
+set echo on;
+set timing on;
+set linesize 3000;
+set pagesize 5000;
 
 define i2b2_data_schema=${i2b2_data_schema}
 define i2b2_meta_schema=${i2b2_meta_schema}
@@ -105,17 +96,38 @@ define min_visit_date_dd_mon_rrrr=${min_visit_date_dd_mon_rrrr}
 define enrollment_months_back=${enrollment_months_back}
 define pcornet_cdm_user=${pcornet_cdm_user}
 
--- Local terminology mapping
-start pcornet_mapping.sql
+-- Define transform procedures
+start PCORNetLoader_ora.sql
+EOF
 
--- Prepare for transform
-start gather_table_stats.sql
+fi
 
--- SCILHS transform
-start PCORNetLoader_ora.sql
 
--- Post-process steps
-start cdm_postproc.sql
+########### Exectute Transform ########### 
+sqlplus /nolog <<EOF
+connect ${pcornet_cdm_user}/${pcornet_cdm}
+
+set echo on;
+set timing on;
+set linesize 3000;
+set pagesize 5000;
+
+-- Run transform
+execute PCORNetLoader('${start_with}');
+EOF
+
+
+########### Run Stats / Tests ###########
+sqlplus /nolog <<EOF
+connect ${pcornet_cdm_user}/${pcornet_cdm}
+
+set echo on;
+set timing on;
+set linesize 3000;
+set pagesize 5000;
+
+define pcornet_cdm_user=${pcornet_cdm_user}
+define i2b2_data_schema=${i2b2_data_schema}
 
 -- Report stats
 start cdm_stats.sql