PostreSQL support

edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_EID_TABLE.sql

@@ -4,8 +4,7 @@ BEGIN
     EXECUTE 'create table ' ||  tempPatientMappingTableName || ' (
         ENCOUNTER_MAP_ID        varchar(200) NOT NULL,
         ENCOUNTER_MAP_ID_SOURCE     varchar(50) NOT NULL,
-        PROJECT_ID              VARCHAR(50) NOT NULL,
-        PATIENT_MAP_ID          varchar(200), 
+        PATIENT_MAP_ID          varchar(200),
         PATIENT_MAP_ID_SOURCE   varchar(50), 
         ENCOUNTER_ID            varchar(200) NOT NULL,
         ENCOUNTER_ID_SOURCE     varchar(50) ,

edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_VISIT_TABLE.sql

@@ -5,7 +5,6 @@ BEGIN
     EXECUTE 'create table ' ||  tempTableName || ' (
         encounter_id                    varchar(200) not null,
         encounter_id_source             varchar(50) not null, 
-        project_id                      varchar(50) not null,
         patient_id                      varchar(200) not null,
         patient_id_source               varchar(50) not null,
         encounter_num                   numeric(38,0), 

edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/INSERT_EID_MAP_FROMTEMP.sql

@@ -98,7 +98,7 @@ and coalesce(encounter_mapping.update_date,to_date(''01-JAN-1900'',''DD-MON-YYYY
 
     -- insert new mapping records i.e flagged P
     EXECUTE ' insert into encounter_mapping (encounter_ide,encounter_ide_source,encounter_ide_status,encounter_num,patient_ide,patient_ide_source,update_date,download_date,import_date,sourcesystem_cd,upload_id,project_id) 
-    SELECT encounter_map_id,encounter_map_id_source,encounter_map_id_status,encounter_num,patient_map_id,patient_map_id_source,update_date,download_date,Now(),sourcesystem_cd,' || upload_id || ' , project_id
+    SELECT encounter_map_id,encounter_map_id_source,encounter_map_id_status,encounter_num,patient_map_id,patient_map_id_source,update_date,download_date,Now(),sourcesystem_cd,' || upload_id || ' , ''@'' project_id
     FROM ' || tempEidTableName || '  
     WHERE process_status_flag = ''P'' ' ; 
     EXCEPTION

edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/INSERT_ENCOUNTERVISIT_FROMTEMP.sql

@@ -35,14 +35,13 @@ BEGIN
         , distinctTemp.patient_id_source
         , ''A''
         ,  '|| upload_id ||'
-        , distinctTemp.project_id
+        , ''@''  project_id
         FROM 
         (SELECT 
             distinct encounter_id
             , encounter_id_source
             , patient_id
             , patient_id_source 
-            , project_id
             FROM ' || tempTableName || '  temp
             WHERE 
             NOT EXISTS (SELECT encounter_ide 

edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/INSERT_PID_MAP_FROMTEMP.sql

@@ -1,67 +1,67 @@
-CREATE OR REPLACE FUNCTION insert_pid_map_fromtemp (tempPidTableName IN text,  upload_id IN bigint, 
-	errorMsg OUT text) 
+CREATE OR REPLACE FUNCTION insert_pid_map_fromtemp (tempPidTableName IN text,  upload_id IN bigint,
+	errorMsg OUT text)
 RETURNS text AS $body$
 DECLARE
 existingPatientNum varchar(32);
 maxPatientNum bigint;
 distinctPidCur REFCURSOR;
-disPatientId varchar(100); 
+disPatientId varchar(100);
 disPatientIdSource varchar(100);
 BEGIN
 	--delete the doublons
-	EXECUTE ' delete  from ' || tempPidTableName ||  ' t1  where 
-	oid > (select min(oid) from ' || tempPidTableName || ' t2 
+	EXECUTE ' delete  from ' || tempPidTableName ||  ' t1  where
+	oid > (select min(oid) from ' || tempPidTableName || ' t2
 		where t1.patient_map_id = t2.patient_map_id
 		and t1.patient_map_id_source = t2.patient_map_id_source) ';
 	LOCK TABLE  patient_mapping IN EXCLUSIVE MODE NOWAIT;
-	select max(patient_num) into STRICT  maxPatientNum from patient_mapping ; 
+	select max(patient_num) into STRICT  maxPatientNum from patient_mapping ;
 	-- set max patient num to zero of the value is null
-	if coalesce(maxPatientNum::text, '') = '' then 
+	if coalesce(maxPatientNum::text, '') = '' then
 		maxPatientNum := 0;
 	end if;
 	open distinctPidCur for EXECUTE 'SELECT distinct patient_id,patient_id_source from ' || tempPidTableName || '' ;
 	loop
 		FETCH distinctPidCur INTO disPatientId, disPatientIdSource;
-		IF NOT FOUND THEN EXIT; 
+		IF NOT FOUND THEN EXIT;
 	END IF; -- apply on distinctPidCur
 	-- dbms_output.put_line(disPatientId);
-	if  disPatientIdSource = 'HIVE'  THEN 
+	if  disPatientIdSource = 'HIVE'  THEN
 		begin
 			--check if hive number exist, if so assign that number to reset of map_id's within that pid
 			select patient_num into existingPatientNum from patient_mapping where patient_num = CAST(disPatientId AS numeric) and patient_ide_source = 'HIVE';
 			EXCEPTION  when NO_DATA_FOUND THEN
 				existingPatientNum := null;
 		end;
-		if (existingPatientNum IS NOT NULL AND existingPatientNum::text <> '') then 
+		if (existingPatientNum IS NOT NULL AND existingPatientNum::text <> '') then
 			EXECUTE ' update ' || tempPidTableName ||' set patient_num = CAST(patient_id AS numeric), process_status_flag = ''P''
 			where patient_id = $1 and not exists (select 1 from patient_mapping pm where pm.patient_ide = patient_map_id
 				and pm.patient_ide_source = patient_map_id_source)' using disPatientId;
-		else 
-			-- generate new patient_num i.e. take max(patient_num) + 1 
-			if maxPatientNum < CAST(disPatientId AS numeric) then 
+		else
+			-- generate new patient_num i.e. take max(patient_num) + 1
+			if maxPatientNum < CAST(disPatientId AS numeric) then
 				maxPatientNum := disPatientId;
 			end if ;
-			EXECUTE ' update ' || tempPidTableName ||' set patient_num = CAST(patient_id AS numeric), process_status_flag = ''P'' where 
+			EXECUTE ' update ' || tempPidTableName ||' set patient_num = CAST(patient_id AS numeric), process_status_flag = ''P'' where
 			patient_id = $1 and patient_id_source = ''HIVE'' and not exists (select 1 from patient_mapping pm where pm.patient_ide = patient_map_id
 				and pm.patient_ide_source = patient_map_id_source)' using disPatientId;
-		end if;    
+		end if;
 		-- test if record fectched
 		-- dbms_output.put_line(' HIVE ');
-	else 
+	else
 		begin
-			select patient_num into STRICT  existingPatientNum from patient_mapping where patient_ide = disPatientId and 
-			patient_ide_source = disPatientIdSource ; 
-			-- test if record fetched. 
+			select patient_num into STRICT  existingPatientNum from patient_mapping where patient_ide = disPatientId and
+			patient_ide_source = disPatientIdSource ;
+			-- test if record fetched.
 			EXCEPTION
 	WHEN NO_DATA_FOUND THEN
 		existingPatientNum := null;
 		end;
-		if (existingPatientNum IS NOT NULL AND existingPatientNum::text <> '') then 
+		if (existingPatientNum IS NOT NULL AND existingPatientNum::text <> '') then
 			EXECUTE ' update ' || tempPidTableName ||' set patient_num = CAST($1 AS numeric) , process_status_flag = ''P''
 			where patient_id = $2 and not exists (select 1 from patient_mapping pm where pm.patient_ide = patient_map_id
 				and pm.patient_ide_source = patient_map_id_source)' using  existingPatientNum,disPatientId;
-		else 
-			maxPatientNum := maxPatientNum + 1 ; 
+		else
+			maxPatientNum := maxPatientNum + 1 ;
 			EXECUTE 'insert into ' || tempPidTableName ||' (
 				patient_map_id
 				,patient_map_id_source
@@ -74,7 +74,7 @@ BEGIN
 				,download_date
 				,import_date
 				,sourcesystem_cd
-				,project_id) 
+				,project_id)
 			values(
 				$1
 				,''HIVE''
@@ -88,19 +88,19 @@ BEGIN
 				,Now()
 				,''edu.harvard.i2b2.crc''
 			,''HIVE''
-			)' using maxPatientNum,maxPatientNum,maxPatientNum; 
-			EXECUTE 'update ' || tempPidTableName ||' set patient_num =  $1 , process_status_flag = ''P'' 
-			where patient_id = $2 and  not exists (select 1 from 
+			)' using maxPatientNum,maxPatientNum,maxPatientNum;
+			EXECUTE 'update ' || tempPidTableName ||' set patient_num =  $1 , process_status_flag = ''P''
+			where patient_id = $2 and  not exists (select 1 from
 				patient_mapping pm where pm.patient_ide = patient_map_id
 				and pm.patient_ide_source = patient_map_id_source)' using maxPatientNum, disPatientId  ;
 		end if ;
 		-- dbms_output.put_line(' NOT HIVE ');
-	end if; 
+	end if;
 	END LOOP;
 	close distinctPidCur ;
 	-- do the mapping update if the update date is old
 EXECUTE ' UPDATE patient_mapping
-SET 
+SET
 patient_num = CAST(temp.patient_id AS numeric)
 ,patient_ide_status = temp.patient_map_id_status
 ,update_date = temp.update_date
@@ -109,17 +109,17 @@ patient_num = CAST(temp.patient_id AS numeric)
 ,sourcesystem_cd  = temp.sourcesystem_cd
 ,upload_id = ' || upload_id ||'
 FROM '|| tempPidTableName || '  temp
-WHERE 
-temp.patient_map_id = patient_mapping.patient_ide 
+WHERE
+temp.patient_map_id = patient_mapping.patient_ide
 and temp.patient_map_id_source = patient_mapping.patient_ide_source
 and temp.patient_id_source = ''HIVE''
-and coalesce(temp.process_status_flag::text, '''') = ''''  
+and coalesce(temp.process_status_flag::text, '''') = ''''
 and coalesce(patient_mapping.update_date,to_date(''01-JAN-1900'',''DD-MON-YYYY'')) <= coalesce(temp.update_date,to_date(''01-JAN-1900'',''DD-MON-YYYY''))
 ';
 	-- insert new mapping records i.e flagged P
 	EXECUTE ' insert into patient_mapping (patient_ide,patient_ide_source,patient_ide_status,patient_num,update_date,download_date,import_date,sourcesystem_cd,upload_id,project_id)
-	SELECT patient_map_id,patient_map_id_source,patient_map_id_status,patient_num,update_date,download_date,Now(),sourcesystem_cd,' || upload_id ||', project_id from '|| tempPidTableName || ' 
-	where process_status_flag = ''P'' ' ; 
+	SELECT patient_map_id,patient_map_id_source,patient_map_id_status,patient_num,update_date,download_date,Now(),sourcesystem_cd,' || upload_id ||', ''@'' project_id from '|| tempPidTableName || '
+	where process_status_flag = ''P'' ' ;
 	EXCEPTION WHEN OTHERS THEN
 		RAISE EXCEPTION 'An error was encountered - % -ERROR- %',SQLSTATE,SQLERRM;
 	END;

edu.harvard.i2b2.data/Release_1-7/NewInstall/Hivedata/scripts/crc_db_lookup_postgresql_insert_data.sql

@@ -1,4 +1,4 @@
 INSERT INTO CRC_DB_LOOKUP(c_domain_id, c_project_path, c_owner_id, c_db_fullschema, c_db_datasource, c_db_servertype, c_db_nicename, c_db_tooltip, c_comment, c_entry_date, c_change_date, c_status_cd)
-  VALUES('i2b2demo', '/Demo/', '@', 'public', 'java:/QueryToolDemoDS', 'POSTGRESQL', 'Demo', NULL, NULL, NULL, NULL, NULL);
+  VALUES('i2b2demo', '/Demo/', '@', 'i2b2demodata', 'java:/QueryToolDemoDS', 'POSTGRESQL', 'Demo', NULL, NULL, NULL, NULL, NULL);
 
 

edu.harvard.i2b2.data/Release_1-7/NewInstall/Hivedata/scripts/im_db_lookup_postgresql_insert_data.sql

@@ -1,2 +1,2 @@
 INSERT INTO IM_DB_LOOKUP(c_domain_id, c_project_path, c_owner_id, c_db_fullschema, c_db_datasource, c_db_servertype, c_db_nicename, c_db_tooltip, c_comment, c_entry_date, c_change_date, c_status_cd)
-  VALUES('i2b2demo', 'Demo/', '@', 'public', 'java:/IMDemoDS', 'POSTGRESQL', 'IM', NULL, NULL, NULL, NULL, NULL);
+  VALUES('i2b2demo', 'Demo/', '@', 'i2b2imdata', 'java:/IMDemoDS', 'POSTGRESQL', 'IM', NULL, NULL, NULL, NULL, NULL);

edu.harvard.i2b2.data/Release_1-7/NewInstall/Hivedata/scripts/ont_db_lookup_postgresql_insert_data.sql

@@ -1,2 +1,2 @@
 INSERT INTO ONT_DB_LOOKUP(c_domain_id, c_project_path, c_owner_id, c_db_fullschema, c_db_datasource, c_db_servertype, c_db_nicename, c_db_tooltip, c_comment, c_entry_date, c_change_date, c_status_cd)
-  VALUES('i2b2demo', 'Demo/', '@', 'public', 'java:/OntologyDemoDS', 'POSTGRESQL', 'Metadata', NULL, NULL, NULL, NULL, NULL);
+  VALUES('i2b2demo', 'Demo/', '@', 'i2b2metadata', 'java:/OntologyDemoDS', 'POSTGRESQL', 'Metadata', NULL, NULL, NULL, NULL, NULL);

edu.harvard.i2b2.data/Release_1-7/NewInstall/Hivedata/scripts/work_db_lookup_postgresql_insert_data.sql

@@ -1,2 +1,2 @@
 INSERT INTO WORK_DB_LOOKUP(c_domain_id, c_project_path, c_owner_id, c_db_fullschema, c_db_datasource, c_db_servertype, c_db_nicename, c_db_tooltip, c_comment, c_entry_date, c_change_date, c_status_cd)
-  VALUES('i2b2demo', 'Demo/', '@', 'public', 'java:/WorkplaceDemoDS', 'POSTGRESQL', 'Workplace', NULL, NULL, NULL, NULL, NULL);
+  VALUES('i2b2demo', 'Demo/', '@', 'i2b2workdata', 'java:/WorkplaceDemoDS', 'POSTGRESQL', 'Workplace', NULL, NULL, NULL, NULL, NULL);