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medco-deployment/docker-images/i2b2-database/patches/pg_db_sql_temp_tables_fix.diff
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pg_db_sql_temp_tables_fix.diff
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diff --git a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_EID_TABLE.sql b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_EID_TABLE.sql
index 349a99f..9368907 100644
--- a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_EID_TABLE.sql
+++ b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_EID_TABLE.sql
@@ -4,7 +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,
+ PROJECT_ID VARCHAR(50) NOT NULL DEFAULT ''Demo'',
PATIENT_MAP_ID varchar(200),
PATIENT_MAP_ID_SOURCE varchar(50),
ENCOUNTER_ID varchar(200) NOT NULL,
@@ -21,7 +21,7 @@ BEGIN
EXECUTE 'CREATE INDEX idx_' || tempPatientMappingTableName || '_stateid_eid_id ON ' || tempPatientMappingTableName || ' (PROCESS_STATUS_FLAG)';
EXCEPTION
WHEN OTHERS THEN
- RAISE NOTICE '%%%', SQLSTATE, ' - ' , SQLERRM;
+ RAISE NOTICE '%%%', SQLSTATE || ' - ' || SQLERRM;
END;
$body$
LANGUAGE PLPGSQL;
diff --git a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_PATIENT_TABLE.sql b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_PATIENT_TABLE.sql
index c717821..7c675a5 100644
--- a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_PATIENT_TABLE.sql
+++ b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_PATIENT_TABLE.sql
@@ -27,7 +27,7 @@ BEGIN
EXECUTE 'CREATE INDEX idx_' || tempPatientDimensionTableName || '_pat_id ON ' || tempPatientDimensionTableName || ' (patient_id, patient_id_source,patient_num)';
EXCEPTION
WHEN OTHERS THEN
- RAISE NOTICE '%%%', SQLSTATE, ' - ' , SQLERRM;
+ RAISE NOTICE '%%%', SQLSTATE || ' - ' || SQLERRM;
END;
$body$
LANGUAGE PLPGSQL;
diff --git a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_PID_TABLE.sql b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_PID_TABLE.sql
index 1b6963c..988b88b 100644
--- a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_PID_TABLE.sql
+++ b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_PID_TABLE.sql
@@ -8,7 +8,7 @@ BEGIN
PATIENT_ID_STATUS varchar(50),
PATIENT_ID varchar(200),
PATIENT_ID_SOURCE varchar(50),
- PROJECT_ID VARCHAR(50) ,
+ PROJECT_ID VARCHAR(50) default ''Demo'',
PATIENT_NUM numeric(38,0),
PATIENT_MAP_ID_STATUS varchar(50),
PROCESS_STATUS_FLAG char(1),
@@ -24,7 +24,7 @@ BEGIN
(PROCESS_STATUS_FLAG)';
EXCEPTION
WHEN OTHERS THEN
- RAISE NOTICE '%%%', SQLSTATE, ' - ' , SQLERRM;
+ RAISE NOTICE '%%%', SQLSTATE || ' - ' || SQLERRM;
END;
$body$
LANGUAGE PLPGSQL;
diff --git a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_TABLE.sql b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_TABLE.sql
index 13f47ec..a939c81 100644
--- a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_TABLE.sql
+++ b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_TABLE.sql
@@ -11,7 +11,7 @@ BEGIN
patient_id_source varchar(50) not null,
provider_id varchar(50),
start_date timestamp,
- modifier_cd varchar(100),
+ modifier_cd varchar(100) not null DEFAULT ''@'',
instance_num numeric(18,0),
valtype_cd varchar(50),
tval_char varchar(255),
diff --git a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_VISIT_TABLE.sql b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_VISIT_TABLE.sql
index 83b56dd..48e39bf 100644
--- a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_VISIT_TABLE.sql
+++ b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/CREATE_TEMP_VISIT_TABLE.sql
@@ -5,7 +5,7 @@ BEGIN
EXECUTE 'create table ' || tempTableName || ' (
encounter_id varchar(200) not null,
encounter_id_source varchar(50) not null,
- project_id varchar(50) not null,
+ project_id varchar(50) not null DEFAULT ''Demo'',
patient_id varchar(200) not null,
patient_id_source varchar(50) not null,
encounter_num numeric(38,0),
@@ -27,4 +27,4 @@ BEGIN
RAISE EXCEPTION 'An error was encountered - % -ERROR- %',SQLSTATE,SQLERRM;
END;
$body$
-LANGUAGE PLPGSQL;
\ No newline at end of file
+LANGUAGE PLPGSQL;
diff --git a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/INSERT_EID_MAP_FROMTEMP.sql b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/INSERT_EID_MAP_FROMTEMP.sql
index d2a8b25..21366d6 100644
--- a/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/INSERT_EID_MAP_FROMTEMP.sql
+++ b/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/postgresql/INSERT_EID_MAP_FROMTEMP.sql
@@ -8,6 +8,8 @@ maxEncounterNum bigint;
distinctEidCur REFCURSOR;
disEncounterId varchar(100);
disEncounterIdSource varchar(100);
+disPatientId varchar(100);
+disPatientIdSource varchar(100);
BEGIN
EXECUTE ' delete from ' || tempEidTableName || ' t1 where
@@ -21,9 +23,9 @@ BEGIN
if coalesce(maxEncounterNum::text, '') = '' then
maxEncounterNum := 0;
end if;
- open distinctEidCur for EXECUTE 'SELECT distinct encounter_id,encounter_id_source from ' || tempEidTableName ||' ' ;
+ open distinctEidCur for EXECUTE 'SELECT distinct encounter_id,encounter_id_source,patient_map_id,patient_map_id_source from ' || tempEidTableName ||' ' ;
loop
- FETCH distinctEidCur INTO disEncounterId, disEncounterIdSource;
+ FETCH distinctEidCur INTO disEncounterId, disEncounterIdSource,disPatientId,disPatientIdSource;
IF NOT FOUND THEN EXIT; END IF; -- apply on distinctEidCur
-- dbms_output.put_line(disEncounterId);
if disEncounterIdSource = 'HIVE' THEN
@@ -65,8 +67,8 @@ BEGIN
maxEncounterNum := maxEncounterNum + 1 ;
--TODO : add update colunn
EXECUTE ' insert into ' || tempEidTableName ||' (encounter_map_id,encounter_map_id_source,encounter_id,encounter_id_source,encounter_num,process_status_flag
- ,encounter_map_id_status,update_date,download_date,import_date,sourcesystem_cd,project_id)
- values($1,''HIVE'',$2,''HIVE'',$3,''P'',''A'',Now(),Now(),Now(),''edu.harvard.i2b2.crc'',''HIVE'')' using maxEncounterNum,maxEncounterNum,maxEncounterNum;
+ ,encounter_map_id_status,update_date,download_date,import_date,sourcesystem_cd,project_id,patient_map_id,patient_map_id_source)
+ values($1,''HIVE'',$2,''HIVE'',$3,''P'',''A'',Now(),Now(),Now(),''edu.harvard.i2b2.crc'',''HIVE'', $4, $5)' using maxEncounterNum,maxEncounterNum,maxEncounterNum,disPatientId,disPatientIdSource;
EXECUTE ' update ' || tempEidTableName ||' set encounter_num = $1 , process_status_flag = ''P''
where encounter_id = $2 and not exists (select 1 from
encounter_mapping em where em.encounter_ide = encounter_map_id
@@ -106,4 +108,4 @@ and coalesce(encounter_mapping.update_date,to_date(''01-JAN-1900'',''DD-MON-YYYY
RAISE EXCEPTION 'An error was encountered - % -ERROR- %',SQLSTATE,SQLERRM;
end;
$body$
- LANGUAGE PLPGSQL;
\ No newline at end of file
+ LANGUAGE PLPGSQL;
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