Commit 6e6ef243 authored by cossins's avatar cossins
Browse files

change CDM configuration README

parent b00228b1
......@@ -103,7 +103,9 @@ The next step (https://github.com/OHDSI/WebAPI/wiki/CDM-Configuration) is to con
* Results: cohort results
* Temp: temp table
In our configuration, CDM and Vocab are in the same schema (OMOP), Results are in the OMOP_COHORT schema and TEMP in the OMOP_TEMP schema.
In our configuration, CDM and Vocab are in the same schema (OMOP), Results are in the OMOP_COHORT schema and TEMP in the OMOP_TEMP schema. The OMOP_COHORT user can read the OMOP schema but it can't write in the TEMP schema. So only 2 schemas are used by WebAPI:
* OMOP_COHORT to write Results and Temp tables
* OMOP (patient level data)
We go back to pgAdmin to enter data in the webapi.source and webapi.source_daimon tables.
The following commands were executed:
......@@ -112,41 +114,36 @@ The following commands were executed:
TRUNCATE TABLE webapi.source CASCADE
TRUNCATE TABLE webapi.source_daimon CASCADE
-- CDM
-- SOURCE OMOP_COHORT
INSERT INTO webapi.source (source_id, source_name, source_key, source_connection, source_dialect, username, password)
SELECT nextval('webapi.source_sequence'), 'OMOP', 'OMOP', 'jdbc:oracle:thin:@{IP}:{PORT}:INFOPAT', 'oracle','OMOP','{PASSWORD}';
SELECT nextval('webapi.source_sequence'), 'OMOP_COHORT', 'OMOP_COHORT', 'jdbc:oracle:thin:@{IP}:{PORT}:INFOPAT', 'oracle','OMOP_COHORT','{PASSWORD}';
-- CDM (OMOP schema)
INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority)
SELECT nextval('webapi.source_sequence'), source_id, 0, 'cdm', 0
SELECT nextval('webapi.source_sequence'), source_id, 0, 'OMOP', 0
FROM webapi.source
WHERE source_key = 'OMOP'
WHERE source_key = 'OMOP_COHORT'
;
-- VOCAB
-- VOCAB (OMOP schema)
INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority)
SELECT nextval('webapi.source_sequence'), source_id, 1, 'vocab', 1
SELECT nextval('webapi.source_sequence'), source_id, 1, 'OMOP', 1
FROM webapi.source
WHERE source_key = 'OMOP'
WHERE source_key = 'OMOP_COHORT'
;
-- RESULTS
INSERT INTO webapi.source (source_id, source_name, source_key, source_connection, source_dialect, username, password)
SELECT nextval('webapi.source_sequence'), 'OMOP_COHORT', 'OMOP_COHORT', 'jdbc:oracle:thin:@{IP}:{PORT}:INFOPAT', 'oracle','OMOP_COHORT','{PASSWORD}';
-- RESULTS (OMOP_COHORT schema)
INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority)
SELECT nextval('webapi.source_sequence'), source_id, 2, 'results', 1
SELECT nextval('webapi.source_sequence'), source_id, 2, 'OMOP_COHORT', 1
FROM webapi.source
WHERE source_key = 'OMOP_COHORT'
;
-- TEMP
INSERT INTO webapi.source (source_id, source_name, source_key, source_connection, source_dialect, username, password)
SELECT nextval('webapi.source_sequence'), 'OMOP_TEMP', 'OMOP_TEMP', 'jdbc:oracle:thin:@{IP}:{PORT}:INFOPAT', 'oracle','OMOP_TEMP','{PASSWORD}';
-- TEMP (OMOP_COHORT schema)
INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority)
SELECT nextval('webapi.source_sequence'), source_id, 5, 'temp', 0
SELECT nextval('webapi.source_sequence'), source_id, 5, 'OMOP_COHORT', 0
FROM webapi.source
WHERE source_key = 'OMOP_TEMP'
WHERE source_key = 'OMOP_COHORT'
;
-- check:
......@@ -189,3 +186,9 @@ END; -- newline and /
Then, we needed to split the commands concerning the OMOP_COHORT schema and the OMOP_TEMP schema.
Excecuting the script was very long (multiple hours).
## Atlas
We cloned the github repository, moved to the latest release (v2.8.0)
```bash
git clone https://github.com/OHDSI/Atlas.git
git checkout refs/tags/v2.8.0
```
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