/
OMOP CDM vocabulary load - PostgreSQL.sql
63 lines (43 loc) · 3.07 KB
/
OMOP CDM vocabulary load - PostgreSQL.sql
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
/*********************************************************************************
# Copyright 2014 Observational Health Data Sciences and Informatics
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
********************************************************************************/
/************************
####### # # ####### ###### ##### ###### # # #######
# # ## ## # # # # # # # # ## ## # # #
# # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ######
# # # # # # # # # # # # # # #
# # # # # # # # # # # # # # # # #
####### # # ####### # ##### ###### # # ## #####
Script to load the common data model, version 5.0 vocabulary tables for PostgreSQL database on Windows (MS-DOS style file paths)
The database account running this script must have the "superuser" permission in the database.
Notes
1) There is no data file load for the SOURCE_TO_CONCEPT_MAP table because that table is deprecated in CDM version 5.0
2) This script assumes the CDM version 5 vocabulary zip file has been unzipped into the "C:\CDMV5VOCAB" directory.
3) If you unzipped your CDM version 5 vocabulary files into a different directory then replace all file paths below, with your directory path.
4) Truncate each table that will be lodaed below, before running this script.
last revised: 5 Dec 2014
author: Lee Evans
*************************/
COPY DRUG_STRENGTH FROM 'C:\CDMV5VOCAB\DRUG_STRENGTH.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT FROM 'C:\CDMV5VOCAB\CONCEPT.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT_RELATIONSHIP FROM 'C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT_ANCESTOR FROM 'C:\CDMV5VOCAB\CONCEPT_ANCESTOR.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT_SYNONYM FROM 'C:\CDMV5VOCAB\CONCEPT_SYNONYM.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY VOCABULARY FROM 'C:\CDMV5VOCAB\VOCABULARY.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY RELATIONSHIP FROM 'C:\CDMV5VOCAB\RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT_CLASS FROM 'C:\CDMV5VOCAB\CONCEPT_CLASS.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY DOMAIN FROM 'C:\CDMV5VOCAB\DOMAIN.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;