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University of Wisconsin MSSQL to Oracle CDM conversion #12

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554f0f7
apply security and schema changes for i2p-transform
keithwanta Mar 17, 2016
099c736
update current_schema
keithwanta Mar 17, 2016
4dc25a7
MSSQL changes based on Oracle updates
keithwanta Mar 17, 2016
b00346d
had incorrect schema
keithwanta Mar 17, 2016
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7 changes: 6 additions & 1 deletion Release/Oracle/create_oracle_metadata_tables.sql
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
alter session set current_schema=I2B2METADATA; -- match i2b2 DDL scripts

--------------------------------------------------------
-- DDL for Table PCORNET_MED
--------------------------------------------------------
Expand Down Expand Up @@ -28,7 +30,9 @@ CREATE TABLE PCORNET_MED (
"M_EXCLUSION_CD" VARCHAR2(25) NULL,
"C_PATH" VARCHAR2(700) NULL,
"C_SYMBOL" VARCHAR2(50) NULL,
"PCORI_BASECODE" VARCHAR2(50) NULL
"PCORI_BASECODE" VARCHAR2(50) NULL,
"PCORI_NDC" VARCHAR2(12) NULL,
"PCORI_CUI" NUMBER NULL
)
;
CREATE INDEX META_FULLNAME_PCORNET_MED_IDX ON PCORNET_MED(C_FULLNAME)
Expand Down Expand Up @@ -352,3 +356,4 @@ CREATE INDEX META_HLEVEL_PCORNET_VITAL_IDX ON PCORNET_VITAL(C_HLEVEL)
;
CREATE INDEX META_SYNONYM_PCORNET_VITAL_IDX ON PCORNET_VITAL(C_SYNONYM_CD)
;

16 changes: 16 additions & 0 deletions Release/Oracle/i2p-transform_permissions.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
-- SCILHS\i2p-transform\PopMedNet-i2b2 Transform Documentation.md > 'Preparing the PopMedNet database' section

-- ASSUMES:
-- SCILHS\i2p-transform/Oracle/PCORI_MEDS_SCHEMA_CHANGE_ora.sql > Do not run old version of this with ALTER TABLE commands!

-- 'I2B2METADATA' is name of stock i2b2 ONT cell (I2B2METADATA schema)
alter session set current_schema=I2B2METADATA;

-- 'cdm' is name of user who needs access to 'CDM' schema
grant all on PCORNET_DEMO to cdm;
grant all on PCORNET_DIAG to cdm;
grant all on PCORNET_MED to cdm;
grant all on PCORNET_PROC to cdm;
grant all on PCORNET_ENROLL to cdm;
grant all on PCORNET_VITAL to cdm;
grant all on PCORNET_ENC to cdm;
88 changes: 46 additions & 42 deletions Release/SqlServer/create_sqlserver_metadata_tables.sql
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
USE [I2B2METADATA]; -- use this database
-- replace '[dbo]' occurrences with '[I2B2METADATA]' if using a single i2b2 database in MSSQL

--------------------------------------------------------
-- DDL for Table pcornet_med
Expand Down Expand Up @@ -29,24 +31,26 @@ CREATE TABLE [dbo].[pcornet_med] (
"C_PATH" VARCHAR(700) NULL,
"C_SYMBOL" VARCHAR(50) NULL,
"PCORI_BASECODE" VARCHAR(50) NULL
)
"PCORI_NDC" VARCHAR2(12) NULL,
"PCORI_CUI" INT NULL
)
;
CREATE INDEX META_FULLNAME_pcornet_med_IDX ON pcornet_med(C_FULLNAME)
CREATE INDEX [dbo].META_FULLNAME_pcornet_med_IDX ON [dbo].pcornet_med(C_FULLNAME)

@jklann jklann Mar 23, 2016

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Isn't dbo a SqlServer-only thing?

;
CREATE INDEX META_APPLIED_PATH_pcornet_med_IDX ON pcornet_med(M_APPLIED_PATH)
CREATE INDEX [dbo].META_APPLIED_PATH_pcornet_med_IDX ON [dbo].pcornet_med(M_APPLIED_PATH)
;
CREATE INDEX META_EXCLUSION_pcornet_med_IDX ON pcornet_med(M_EXCLUSION_CD)
CREATE INDEX [dbo].META_EXCLUSION_pcornet_med_IDX ON [dbo].pcornet_med(M_EXCLUSION_CD)
;
CREATE INDEX META_HLEVEL_pcornet_med_IDX ON pcornet_med(C_HLEVEL)
CREATE INDEX [dbo].META_HLEVEL_pcornet_med_IDX ON [dbo].pcornet_med(C_HLEVEL)
;
CREATE INDEX META_SYNONYM_pcornet_med_IDX ON pcornet_med(C_SYNONYM_CD)
CREATE INDEX [dbo].META_SYNONYM_pcornet_med_IDX ON [dbo].pcornet_med(C_SYNONYM_CD)
;

--------------------------------------------------------
-- DDL for Table PCORNET_DEMO
--------------------------------------------------------

CREATE TABLE PCORNET_DEMO (
CREATE TABLE [dbo].PCORNET_DEMO (
"C_HLEVEL" INT NOT NULL,
"C_FULLNAME" VARCHAR(700) NOT NULL,
"C_NAME" VARCHAR(2000) NOT NULL,
Expand Down Expand Up @@ -75,22 +79,22 @@ CREATE TABLE PCORNET_DEMO (
"PCORI_BASECODE" VARCHAR(50) NULL
)
;
CREATE INDEX META_FULLNAME_PCORNET_DEMO_IDX ON PCORNET_DEMO(C_FULLNAME)
CREATE INDEX [dbo].META_FULLNAME_PCORNET_DEMO_IDX ON [dbo].PCORNET_DEMO(C_FULLNAME)
;
CREATE INDEX META_APPLIED_PATH_PCORNET_DEMO_IDX ON PCORNET_DEMO(M_APPLIED_PATH)
CREATE INDEX [dbo].META_APPLIED_PATH_PCORNET_DEMO_IDX ON [dbo].PCORNET_DEMO(M_APPLIED_PATH)
;
CREATE INDEX META_EXCLUSION_PCORNET_DEMO_IDX ON PCORNET_DEMO(M_EXCLUSION_CD)
CREATE INDEX [dbo].META_EXCLUSION_PCORNET_DEMO_IDX ON [dbo].PCORNET_DEMO(M_EXCLUSION_CD)
;
CREATE INDEX META_HLEVEL_PCORNET_DEMO_IDX ON PCORNET_DEMO(C_HLEVEL)
CREATE INDEX [dbo].META_HLEVEL_PCORNET_DEMO_IDX ON [dbo].PCORNET_DEMO(C_HLEVEL)
;
CREATE INDEX META_SYNONYM_PCORNET_DEMO_IDX ON PCORNET_DEMO(C_SYNONYM_CD)
CREATE INDEX [dbo].META_SYNONYM_PCORNET_DEMO_IDX ON [dbo].PCORNET_DEMO(C_SYNONYM_CD)
;

--------------------------------------------------------
-- DDL for Table PCORNET_DIAG
--------------------------------------------------------

CREATE TABLE PCORNET_DIAG (
CREATE TABLE [dbo].PCORNET_DIAG (
"C_HLEVEL" INT NOT NULL,
"C_FULLNAME" VARCHAR(700) NOT NULL,
"C_NAME" VARCHAR(2000) NOT NULL,
Expand Down Expand Up @@ -119,22 +123,22 @@ CREATE TABLE PCORNET_DIAG (
"PCORI_BASECODE" VARCHAR(50) NULL
)
;
CREATE INDEX META_FULLNAME_PCORNET_DIAG_IDX ON PCORNET_DIAG(C_FULLNAME)
CREATE INDEX [dbo].META_FULLNAME_PCORNET_DIAG_IDX ON [dbo].PCORNET_DIAG(C_FULLNAME)
;
CREATE INDEX META_APPLIED_PATH_PCORNET_DIAG_IDX ON PCORNET_DIAG(M_APPLIED_PATH)
CREATE INDEX [dbo].META_APPLIED_PATH_PCORNET_DIAG_IDX ON [dbo].PCORNET_DIAG(M_APPLIED_PATH)
;
CREATE INDEX META_EXCLUSION_PCORNET_DIAG_IDX ON PCORNET_DIAG(M_EXCLUSION_CD)
CREATE INDEX [dbo].META_EXCLUSION_PCORNET_DIAG_IDX ON [dbo].PCORNET_DIAG(M_EXCLUSION_CD)
;
CREATE INDEX META_HLEVEL_PCORNET_DIAG_IDX ON PCORNET_DIAG(C_HLEVEL)
CREATE INDEX [dbo].META_HLEVEL_PCORNET_DIAG_IDX ON [dbo].PCORNET_DIAG(C_HLEVEL)
;
CREATE INDEX META_SYNONYM_PCORNET_DIAG_IDX ON PCORNET_DIAG(C_SYNONYM_CD)
CREATE INDEX [dbo].META_SYNONYM_PCORNET_DIAG_IDX ON [dbo].PCORNET_DIAG(C_SYNONYM_CD)
;

--------------------------------------------------------
-- DDL for Table PCORNET_ENC
--------------------------------------------------------

CREATE TABLE PCORNET_ENC (
CREATE TABLE [dbo].PCORNET_ENC (
"C_HLEVEL" INT NOT NULL,
"C_FULLNAME" VARCHAR(700) NOT NULL,
"C_NAME" VARCHAR(2000) NOT NULL,
Expand Down Expand Up @@ -163,23 +167,23 @@ CREATE TABLE PCORNET_ENC (
"PCORI_BASECODE" VARCHAR(50) NULL
)
;
CREATE INDEX META_FULLNAME_PCORNET_ENC_IDX ON PCORNET_ENC(C_FULLNAME)
CREATE INDEX [dbo].META_FULLNAME_PCORNET_ENC_IDX ON [dbo].PCORNET_ENC(C_FULLNAME)
;
CREATE INDEX META_APPLIED_PATH_PCORNET_ENC_IDX ON PCORNET_ENC(M_APPLIED_PATH)
CREATE INDEX [dbo].META_APPLIED_PATH_PCORNET_ENC_IDX ON [dbo].PCORNET_ENC(M_APPLIED_PATH)
;
CREATE INDEX META_EXCLUSION_PCORNET_ENC_IDX ON PCORNET_ENC(M_EXCLUSION_CD)
CREATE INDEX [dbo].META_EXCLUSION_PCORNET_ENC_IDX ON [dbo].PCORNET_ENC(M_EXCLUSION_CD)
;
CREATE INDEX META_HLEVEL_PCORNET_ENC_IDX ON PCORNET_ENC(C_HLEVEL)
CREATE INDEX [dbo].META_HLEVEL_PCORNET_ENC_IDX ON [dbo].PCORNET_ENC(C_HLEVEL)
;
CREATE INDEX META_SYNONYM_PCORNET_ENC_IDX ON PCORNET_ENC(C_SYNONYM_CD)
CREATE INDEX [dbo].META_SYNONYM_PCORNET_ENC_IDX ON [dbo].PCORNET_ENC(C_SYNONYM_CD)
;


--------------------------------------------------------
-- DDL for Table PCORNET_ENROLL
--------------------------------------------------------

CREATE TABLE PCORNET_ENROLL (
CREATE TABLE [dbo].PCORNET_ENROLL (
"C_HLEVEL" INT NOT NULL,
"C_FULLNAME" VARCHAR(700) NOT NULL,
"C_NAME" VARCHAR(2000) NOT NULL,
Expand Down Expand Up @@ -208,23 +212,23 @@ CREATE TABLE PCORNET_ENROLL (
"PCORI_BASECODE" VARCHAR(50) NULL
)
;
CREATE INDEX META_FULLNAME_PCORNET_ENROLL_IDX ON PCORNET_ENROLL(C_FULLNAME)
CREATE INDEX [dbo].META_FULLNAME_PCORNET_ENROLL_IDX ON [dbo].PCORNET_ENROLL(C_FULLNAME)
;
CREATE INDEX META_APPLIED_PATH_PCORNET_ENROLL_IDX ON PCORNET_ENROLL(M_APPLIED_PATH)
CREATE INDEX [dbo].META_APPLIED_PATH_PCORNET_ENROLL_IDX ON [dbo].PCORNET_ENROLL(M_APPLIED_PATH)
;
CREATE INDEX META_EXCLUSION_PCORNET_ENROLL_IDX ON PCORNET_ENROLL(M_EXCLUSION_CD)
CREATE INDEX [dbo].META_EXCLUSION_PCORNET_ENROLL_IDX ON [dbo].PCORNET_ENROLL(M_EXCLUSION_CD)
;
CREATE INDEX META_HLEVEL_PCORNET_ENROLL_IDX ON PCORNET_ENROLL(C_HLEVEL)
CREATE INDEX [dbo].META_HLEVEL_PCORNET_ENROLL_IDX ON [dbo].PCORNET_ENROLL(C_HLEVEL)
;
CREATE INDEX META_SYNONYM_PCORNET_ENROLL_IDX ON PCORNET_ENROLL(C_SYNONYM_CD)
CREATE INDEX [dbo].META_SYNONYM_PCORNET_ENROLL_IDX ON [dbo].PCORNET_ENROLL(C_SYNONYM_CD)
;


--------------------------------------------------------
-- DDL for Table PCORNET_PROC
--------------------------------------------------------

CREATE TABLE PCORNET_PROC (
CREATE TABLE [dbo].PCORNET_PROC (
"C_HLEVEL" INT NOT NULL,
"C_FULLNAME" VARCHAR(700) NOT NULL,
"C_NAME" VARCHAR(2000) NOT NULL,
Expand Down Expand Up @@ -253,22 +257,22 @@ CREATE TABLE PCORNET_PROC (
"PCORI_BASECODE" VARCHAR(50) NULL
)
;
CREATE INDEX META_FULLNAME_PCORNET_PROC_IDX ON PCORNET_PROC(C_FULLNAME)
CREATE INDEX [dbo].META_FULLNAME_PCORNET_PROC_IDX ON [dbo].PCORNET_PROC(C_FULLNAME)
;
CREATE INDEX META_APPLIED_PATH_PCORNET_PROC_IDX ON PCORNET_PROC(M_APPLIED_PATH)
CREATE INDEX [dbo].META_APPLIED_PATH_PCORNET_PROC_IDX ON [dbo].PCORNET_PROC(M_APPLIED_PATH)
;
CREATE INDEX META_EXCLUSION_PCORNET_PROC_IDX ON PCORNET_PROC(M_EXCLUSION_CD)
CREATE INDEX [dbo].META_EXCLUSION_PCORNET_PROC_IDX ON [dbo].PCORNET_PROC(M_EXCLUSION_CD)
;
CREATE INDEX META_HLEVEL_PCORNET_PROC_IDX ON PCORNET_PROC(C_HLEVEL)
CREATE INDEX [dbo].META_HLEVEL_PCORNET_PROC_IDX ON [dbo].PCORNET_PROC(C_HLEVEL)
;
CREATE INDEX META_SYNONYM_PCORNET_PROC_IDX ON PCORNET_PROC(C_SYNONYM_CD)
CREATE INDEX [dbo].META_SYNONYM_PCORNET_PROC_IDX ON [dbo].PCORNET_PROC(C_SYNONYM_CD)
;

--------------------------------------------------------
-- DDL for Table PCORNET_VITAL
--------------------------------------------------------

CREATE TABLE PCORNET_VITAL (
CREATE TABLE [dbo].PCORNET_VITAL (
"C_HLEVEL" INT NOT NULL,
"C_FULLNAME" VARCHAR(700) NOT NULL,
"C_NAME" VARCHAR(2000) NOT NULL,
Expand Down Expand Up @@ -297,13 +301,13 @@ CREATE TABLE PCORNET_VITAL (
"PCORI_BASECODE" VARCHAR(50) NULL
)
;
CREATE INDEX META_FULLNAME_PCORNET_VITAL_IDX ON PCORNET_VITAL(C_FULLNAME)
CREATE INDEX [dbo].META_FULLNAME_PCORNET_VITAL_IDX ON [dbo].PCORNET_VITAL(C_FULLNAME)
;
CREATE INDEX META_APPLIED_PATH_PCORNET_VITAL_IDX ON PCORNET_VITAL(M_APPLIED_PATH)
CREATE INDEX [dbo].META_APPLIED_PATH_PCORNET_VITAL_IDX ON [dbo].PCORNET_VITAL(M_APPLIED_PATH)
;
CREATE INDEX META_EXCLUSION_PCORNET_VITAL_IDX ON PCORNET_VITAL(M_EXCLUSION_CD)
CREATE INDEX [dbo].META_EXCLUSION_PCORNET_VITAL_IDX ON [dbo].PCORNET_VITAL(M_EXCLUSION_CD)
;
CREATE INDEX META_HLEVEL_PCORNET_VITAL_IDX ON PCORNET_VITAL(C_HLEVEL)
CREATE INDEX [dbo].META_HLEVEL_PCORNET_VITAL_IDX ON [dbo].PCORNET_VITAL(C_HLEVEL)
;
CREATE INDEX META_SYNONYM_PCORNET_VITAL_IDX ON PCORNET_VITAL(C_SYNONYM_CD)
CREATE INDEX [dbo].META_SYNONYM_PCORNET_VITAL_IDX ON [dbo].PCORNET_VITAL(C_SYNONYM_CD)
;