From 554f0f78698021addb13803bde88ac848b23dd65 Mon Sep 17 00:00:00 2001 From: Keith Wanta Date: Thu, 17 Mar 2016 11:58:52 -0500 Subject: [PATCH 1/4] apply security and schema changes for i2p-transform --- Release/Oracle/create_oracle_metadata_tables.sql | 7 ++++++- Release/Oracle/i2p-transform_permissions.sql | 13 +++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 Release/Oracle/i2p-transform_permissions.sql diff --git a/Release/Oracle/create_oracle_metadata_tables.sql b/Release/Oracle/create_oracle_metadata_tables.sql index 535e639..522a2e7 100644 --- a/Release/Oracle/create_oracle_metadata_tables.sql +++ b/Release/Oracle/create_oracle_metadata_tables.sql @@ -1,3 +1,5 @@ +alter session set current_schema=I2B2METADATA; -- match i2b2 DDL scripts + -------------------------------------------------------- -- DDL for Table PCORNET_MED -------------------------------------------------------- @@ -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) @@ -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) ; + diff --git a/Release/Oracle/i2p-transform_permissions.sql b/Release/Oracle/i2p-transform_permissions.sql new file mode 100644 index 0000000..077b3ab --- /dev/null +++ b/Release/Oracle/i2p-transform_permissions.sql @@ -0,0 +1,13 @@ +-- 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! +-- 'cdm' is name of user in CDM v3 database or 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; From 099c73673bcce14cddd962bf026317390175080b Mon Sep 17 00:00:00 2001 From: Keith Wanta Date: Thu, 17 Mar 2016 12:04:52 -0500 Subject: [PATCH 2/4] update current_schema --- Release/Oracle/i2p-transform_permissions.sql | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Release/Oracle/i2p-transform_permissions.sql b/Release/Oracle/i2p-transform_permissions.sql index 077b3ab..2d03342 100644 --- a/Release/Oracle/i2p-transform_permissions.sql +++ b/Release/Oracle/i2p-transform_permissions.sql @@ -2,8 +2,11 @@ -- ASSUMES: -- SCILHS\i2p-transform/Oracle/PCORI_MEDS_SCHEMA_CHANGE_ora.sql > Do not run old version of this with ALTER TABLE commands! --- 'cdm' is name of user in CDM v3 database or schema +-- 'CDM' is name of schema +alter session set current_schema=CDM; + +-- '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; From 4dc25a7680f56340b155b6e15da4a3f586550294 Mon Sep 17 00:00:00 2001 From: Keith Wanta Date: Thu, 17 Mar 2016 12:20:25 -0500 Subject: [PATCH 3/4] MSSQL changes based on Oracle updates --- Release/Oracle/i2p-transform_permissions.sql | 4 +- .../create_sqlserver_metadata_tables.sql | 88 ++++++++++--------- 2 files changed, 48 insertions(+), 44 deletions(-) diff --git a/Release/Oracle/i2p-transform_permissions.sql b/Release/Oracle/i2p-transform_permissions.sql index 2d03342..64703b6 100644 --- a/Release/Oracle/i2p-transform_permissions.sql +++ b/Release/Oracle/i2p-transform_permissions.sql @@ -3,8 +3,8 @@ -- ASSUMES: -- SCILHS\i2p-transform/Oracle/PCORI_MEDS_SCHEMA_CHANGE_ora.sql > Do not run old version of this with ALTER TABLE commands! --- 'CDM' is name of schema -alter session set current_schema=CDM; +-- 'I2B2DEMODATA' is name of stock i2b2 CRC schema +alter session set current_schema=I2B2DEMODATA; -- 'cdm' is name of user who needs access to 'CDM' schema grant all on PCORNET_DEMO to cdm; diff --git a/Release/SqlServer/create_sqlserver_metadata_tables.sql b/Release/SqlServer/create_sqlserver_metadata_tables.sql index d4c3013..e7996e2 100644 --- a/Release/SqlServer/create_sqlserver_metadata_tables.sql +++ b/Release/SqlServer/create_sqlserver_metadata_tables.sql @@ -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 @@ -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) ; -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, @@ -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, @@ -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, @@ -163,15 +167,15 @@ 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) ; @@ -179,7 +183,7 @@ CREATE INDEX META_SYNONYM_PCORNET_ENC_IDX ON 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, @@ -208,15 +212,15 @@ 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) ; @@ -224,7 +228,7 @@ CREATE INDEX META_SYNONYM_PCORNET_ENROLL_IDX ON 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, @@ -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, @@ -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) ; From b00346daff2d8a9ae62e8fee97a2157ee1ef4535 Mon Sep 17 00:00:00 2001 From: Keith Wanta Date: Thu, 17 Mar 2016 13:45:58 -0500 Subject: [PATCH 4/4] had incorrect schema --- Release/Oracle/i2p-transform_permissions.sql | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Release/Oracle/i2p-transform_permissions.sql b/Release/Oracle/i2p-transform_permissions.sql index 64703b6..ec8febb 100644 --- a/Release/Oracle/i2p-transform_permissions.sql +++ b/Release/Oracle/i2p-transform_permissions.sql @@ -3,8 +3,8 @@ -- ASSUMES: -- SCILHS\i2p-transform/Oracle/PCORI_MEDS_SCHEMA_CHANGE_ora.sql > Do not run old version of this with ALTER TABLE commands! --- 'I2B2DEMODATA' is name of stock i2b2 CRC schema -alter session set current_schema=I2B2DEMODATA; +-- '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;