change CDM configuration README

README.md

@@ -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
+```