[Task]: Snowflake JDBC Driver Support

.gitignore

@@ -0,0 +1,3 @@
+**/.DS_Store
+**/.vscode
+**/.idea

edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/data_build.xml

@@ -16,6 +16,7 @@ $Id: data_build.xml,v 1.3 2010/05/23 20:21:51 rk903 Exp $
 			<pathelement location="../../ojdbc8.jar" />
 			<pathelement location="../../mssql-jdbc-8.2.2.jre8.jar"/>
 			<pathelement location="../../postgresql-42.2.14.jar"/>
+			<pathelement location="../../snowflake-jdbc-3.13.30.jar"/>
 		</path>
 	</target>
 
@@ -169,5 +170,3 @@ $Id: data_build.xml,v 1.3 2010/05/23 20:21:51 rk903 Exp $
 
 
 </project>
-
-

edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/db.properties

@@ -17,9 +17,17 @@ db.project=demo
 #db.project=demo
 
 # Database setup parameters for PostgreSQL, uncomment to use and comment out Oracle
-#db.type=postgresql
-#db.username=i2b2demodata
-#db.password=demouser
-#db.driver=org.postgresql.Driver
-#db.url=jdbc:postgresql://localhost:5432/i2b2
-#db.project=demo
+# db.type=postgresql
+# db.username=i2b2demodata
+# db.password=demouser
+# db.driver=org.postgresql.Driver
+# db.url=jdbc:postgresql://localhost:5432/i2b2
+# db.project=demo
+
+# Database setup parameters for Snowflake, uncomment to use and comment out Oracle
+# db.type=snowflake
+# db.username=I2B2_ETL_USER
+# db.password=demouser
+# db.driver=net.snowflake.client.jdbc.SnowflakeDriver
+# db.url=jdbc:snowflake://<account>.us-east-2.aws.snowflakecomputing.com/?db=I2B2_DEV&schema=I2B2DATA&warehouse=I2B2_ETL_WH&role=I2B2&CLIENT_RESULT_COLUMN_CASE_INSENSITIVE=true
+# db.project=act

edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/crc_create_datamart_snowflake.sql

@@ -0,0 +1,208 @@
+/*********************************************************
+*         SNOWFLAKE SCRIPT TO CREATE DATA TABLES
+*         MD SABER HOSSAIN	7/14/2023
+/*        University of Missouri-Columbia			
+**********************************************************/
+
+
+-------------------------------------------------------------------------------------------
+-- create ENCOUNTER_MAPPING table with clustered PK on ENCOUNTER_IDE, ENCOUNTER_IDE_SOURCE 
+-------------------------------------------------------------------------------------------
+
+CREATE TABLE ENCOUNTER_MAPPING ( 
+    ENCOUNTER_IDE       	VARCHAR(200)  NOT NULL,
+    ENCOUNTER_IDE_SOURCE	VARCHAR(50)  NOT NULL,
+    PROJECT_ID              VARCHAR(50) NOT NULL,
+    ENCOUNTER_NUM			INT NOT NULL,
+    PATIENT_IDE         	VARCHAR(200) NOT NULL,
+    PATIENT_IDE_SOURCE  	VARCHAR(50) NOT NULL,
+    ENCOUNTER_IDE_STATUS	VARCHAR(50) NULL,
+    UPLOAD_DATE         	TIMESTAMP NULL,
+    UPDATE_DATE             TIMESTAMP NULL,
+    DOWNLOAD_DATE       	TIMESTAMP NULL,
+    IMPORT_DATE             TIMESTAMP NULL,
+    SOURCESYSTEM_CD         VARCHAR(50) NULL,
+    UPLOAD_ID               INT NULL
+ )
+;
+
+-------------------------------------------------------------------------------------
+-- create PATIENT_MAPPING table with clustered PK on PATIENT_IDE, PATIENT_IDE_SOURCE
+-------------------------------------------------------------------------------------
+
+CREATE TABLE PATIENT_MAPPING ( 
+    PATIENT_IDE         VARCHAR(200)  NOT NULL,
+    PATIENT_IDE_SOURCE	VARCHAR(50)  NOT NULL,
+    PATIENT_NUM       	INT NOT NULL,
+    PATIENT_IDE_STATUS	VARCHAR(50) NULL,
+    PROJECT_ID          VARCHAR(50) NOT NULL,
+    UPLOAD_DATE       	TIMESTAMP NULL,
+    UPDATE_DATE       	TIMESTAMP NULL,
+    DOWNLOAD_DATE     	TIMESTAMP NULL,
+    IMPORT_DATE         TIMESTAMP NULL,
+    SOURCESYSTEM_CD   	VARCHAR(50) NULL,
+    UPLOAD_ID         	INT NULL
+ )
+;
+
+------------------------------------------------------------------------------
+-- create CODE_LOOKUP table with clustered PK on TABLE_CD, COLUMN_CD, CODE_CD 
+------------------------------------------------------------------------------
+
+CREATE TABLE CODE_LOOKUP ( 
+    TABLE_CD            VARCHAR(100) NOT NULL,
+    COLUMN_CD           VARCHAR(100) NOT NULL,
+    CODE_CD             VARCHAR(50) NOT NULL,
+    NAME_CHAR           VARCHAR(650) NULL,
+    LOOKUP_BLOB         TEXT NULL, 
+    UPLOAD_DATE       	TIMESTAMP NULL,
+    UPDATE_DATE         TIMESTAMP NULL,
+    DOWNLOAD_DATE     	TIMESTAMP NULL,
+    IMPORT_DATE         TIMESTAMP NULL,
+    SOURCESYSTEM_CD   	VARCHAR(50) NULL,
+    UPLOAD_ID         	INT NULL
+	)
+;
+
+--------------------------------------------------------------------
+-- create CONCEPT_DIMENSION table with clustered PK on CONCEPT_PATH 
+--------------------------------------------------------------------
+
+CREATE TABLE CONCEPT_DIMENSION ( 
+	CONCEPT_PATH   		VARCHAR(700) NOT NULL,
+	CONCEPT_CD     		VARCHAR(50) NULL,
+	NAME_CHAR      		VARCHAR(2000) NULL,
+	CONCEPT_BLOB   		TEXT NULL,
+	UPDATE_DATE    		TIMESTAMP NULL,
+	DOWNLOAD_DATE  		TIMESTAMP NULL,
+	IMPORT_DATE    		TIMESTAMP NULL,
+	SOURCESYSTEM_CD		VARCHAR(50) NULL,
+    UPLOAD_ID			INT NULL
+	)
+;
+
+
+---------------------------------------------------------------------------------------------------------------------------------------
+-- create OBSERVATION_FACT table with NONclustered PK on ENCOUNTER_NUM, CONCEPT_CD, PROVIDER_ID, START_DATE, MODIFIER_CD, INSTANCE_NUM 
+---------------------------------------------------------------------------------------------------------------------------------------
+CREATE TABLE OBSERVATION_FACT ( 
+	ENCOUNTER_NUM  		INT NOT NULL,
+	PATIENT_NUM    		INT NOT NULL,
+	CONCEPT_CD     		VARCHAR(50) NOT NULL,
+	PROVIDER_ID    		VARCHAR(50) NOT NULL,
+	START_DATE     		TIMESTAMP NOT NULL,
+	MODIFIER_CD    		VARCHAR(100) default '@' NOT NULL,
+	INSTANCE_NUM		INT default (1) NOT NULL,
+	VALTYPE_CD     		VARCHAR(50) NULL,
+	TVAL_CHAR      		VARCHAR(255) NULL,
+	NVAL_NUM       		DECIMAL(18,5) NULL,
+	VALUEFLAG_CD   		VARCHAR(50) NULL,
+	QUANTITY_NUM   		DECIMAL(18,5) NULL,
+	UNITS_CD       		VARCHAR(50) NULL,
+	END_DATE       		TIMESTAMP NULL,
+	LOCATION_CD    		VARCHAR(50) NULL,
+	OBSERVATION_BLOB	TEXT NULL,
+	CONFIDENCE_NUM 		DECIMAL(18,5) NULL,
+	UPDATE_DATE    		TIMESTAMP NULL,
+	DOWNLOAD_DATE  		TIMESTAMP NULL,
+	IMPORT_DATE    		TIMESTAMP NULL,
+	SOURCESYSTEM_CD		VARCHAR(50) NULL, 
+    UPLOAD_ID         	INT NULL,
+    TEXT_SEARCH_INDEX   NUMBER(38, 0) NOT NULL
+	)
+;
+
+-------------------------------------------------------------------
+-- create PATIENT_DIMENSION table with clustered PK on PATIENT_NUM 
+-------------------------------------------------------------------
+
+CREATE TABLE PATIENT_DIMENSION ( 
+	PATIENT_NUM      	INT NOT NULL,
+	VITAL_STATUS_CD  	VARCHAR(50) NULL,
+	BIRTH_DATE       	DATE NULL,
+	DEATH_DATE       	DATE NULL,
+	SEX_CD           	VARCHAR(2) NULL,
+	LANGUAGE_CD      	VARCHAR(3) NULL,
+	HISPANIC			VARCHAR(2) NULL,
+	RACE_CD          	VARCHAR(50) NULL,
+	MARITAL_STATUS_CD	VARCHAR(50) NULL,
+	AGE_IN_YEARS_NUM	INT NULL default null,
+	RELIGION_CD      	VARCHAR(50) NULL default null,
+	ZIP_CD           	VARCHAR(10) NULL default null,
+	STATECITYZIP_PATH	VARCHAR(700) NULL default null,
+	INCOME_CD			VARCHAR(50) NULL default null,
+	PATIENT_BLOB     	TEXT NULL default null,
+	UPDATE_DATE      	DATE NULL,
+	DOWNLOAD_DATE    	DATE NULL,
+	IMPORT_DATE      	DATE NULL,
+	SOURCESYSTEM_CD  	VARCHAR(50) NULL,
+	UPLOAD_ID        	INT NULL
+	)
+;
+
+
+
+-----------------------------------------------------------------------------------
+-- create PROVIDER_DIMENSION table with clustered PK on PROVIDER_PATH, PROVIDER_ID 
+-----------------------------------------------------------------------------------
+
+CREATE TABLE PROVIDER_DIMENSION ( 
+	PROVIDER_ID        		 			VARCHAR(50) NOT NULL,
+	PROVIDER_SEX						VARCHAR(2)  NULL,
+	PROVIDER_PATH  		VARCHAR(700) NOT NULL default '@',
+	NAME_CHAR      		VARCHAR(850) NULL default null,
+	PROVIDER_BLOB  		TEXT NULL,
+	PROVIDER_SPECIALTY_PRIMARY       	VARCHAR(50) NULL,
+	PROVIDER_NPI 				 		VARCHAR(8) NULL,
+	PROVIDER_NPI_FLAG					VARCHAR(1) NULL,			
+	RAW_PROVIDER_SPECIALTY_PRIMARY		VARCHAR(50) NULL,
+	UPDATE_DATE     	DATE NULL,
+	DOWNLOAD_DATE       DATE NULL,
+	IMPORT_DATE         DATE NULL,
+	SOURCESYSTEM_CD     VARCHAR(50) NULL,
+	UPLOAD_ID        	INT NULL
+	)
+;
+
+-------------------------------------------------------------------
+-- create VISIT_DIMENSION table with clustered PK on ENCOUNTER_NUM 
+-------------------------------------------------------------------
+
+CREATE TABLE VISIT_DIMENSION ( 
+	ENCOUNTER_NUM       INT NOT NULL,
+	PATIENT_NUM        	INT NOT NULL,
+	PROVIDER_ID         VARCHAR(50) NOT NULL,
+	START_DATE          DATE NULL,
+	END_DATE            DATE NULL,
+	ENC_TYPE            VARCHAR(2) NULL,
+	LENGTH_OF_STAY      INT NULL,
+	ACTIVE_STATUS_CD	VARCHAR(50) default null,
+	INOUT_CD       		VARCHAR(50) NULL default null,
+	LOCATION_CD    		VARCHAR(50) NULL default null,
+	LOCATION_PATH  		VARCHAR(900) NULL default null,
+	VISIT_BLOB     		TEXT NULL default null,
+	UPDATE_DATE         DATE NULL,
+	DOWNLOAD_DATE       DATE NULL,
+	IMPORT_DATE         DATE NULL,
+	SOURCESYSTEM_CD     VARCHAR(50) NULL,
+	UPLOAD_ID       	INT NULL
+	)
+;
+
+
+------------------------------------------------------------
+-- create MODIFIER_DIMENSION table with PK on MODIFIER_PATH 
+------------------------------------------------------------
+
+CREATE TABLE MODIFIER_DIMENSION ( 
+	MODIFIER_PATH   	VARCHAR(700) NOT NULL,
+	MODIFIER_CD     	VARCHAR(50) NULL,
+	NAME_CHAR      		VARCHAR(2000) NULL,
+	MODIFIER_BLOB   	TEXT NULL,
+	UPDATE_DATE    		TIMESTAMP NULL,
+	DOWNLOAD_DATE  		TIMESTAMP NULL,
+	IMPORT_DATE    		TIMESTAMP NULL,
+	SOURCESYSTEM_CD		VARCHAR(50) NULL,
+    UPLOAD_ID			INT NULL
+	)
+;