add README.md

README.md

+# Installation of WebAPI and Atlas 
+
+We describe how we installed WebAPI and Atlas
+
+## System Configuration:
+
+### OS
+DISTRIB_ID=Ubuntu
+DISTRIB_RELEASE=18.04
+DISTRIB_CODENAME=bionic
+DISTRIB_DESCRIPTION="Ubuntu 18.04.5 LTS"
+
+### Docker
+Docker version 19.03.14
+
+## Docker-compose
+docker-compose version 1.25.4
+
+### Java
+openjdk 11.0.9.1 2020-11-04
+OpenJDK Runtime Environment (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04)
+OpenJDK 64-Bit Server VM (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04, mixed mode, sharing)
+
+### Maven
+Apache Maven 3.6.0
+Maven home: /usr/share/maven
+Java version: 1.8.0_275, vendor: Private Build, runtime: /usr/lib/jvm/java-8-openjdk-amd64/jre
+Default locale: fr_FR, platform encoding: UTF-8
+OS name: "linux", version: "5.4.0-58-generic", arch: "amd64", family: "unix"
+
+### pgAdmin
+Version
+4.24
+Copyright
+Copyright (C) 2013 - 2020, The pgAdmin Development Team
+Python Version
+3.8.3 (default, May 20 2020, 20:46:20) [GCC 9.2.0]
+Flask Version
+1.0.2
+Application Mode
+Server
+
+### postGres
+postgres (PostgreSQL) 12.1 (Debian 12.1-1.pgdg100+1)
+
+## WebAPI
+We launched 3 services: PostgreSQL, pgadmin and tomcat:
+```bash
+docker-compose up -d
+```
+
+We followed the instructions to install WebAPI: https://github.com/OHDSI/WebAPI/wiki/WebAPI-Installation-Guide
+
+### WebAPI Database
+We used PostgreSQL for WebAPI database storage. pgAdmin was used to configure PostgreSQL.  
+We created the different roles in the pgAdmin interface. 
+
+#### pgAdmin interface
+After login, create a new Server: 
+
+* Name: ohdsi
+* Host: webapi_postgres (container name, see docker-compose.yml)
+* Port: 5432
+* Username: postgres (by default, not an environment variable)
+* Password: ${POSTGRES_PASSWORD}
+
+
+### Build WebAPI
+
+We cloned the github repository, moved to the latest release (v2.8.0)
+```bash
+git clone https://github.com/OHDSI/WebAPI.git
+git checkout refs/tags/v2.8.0
+```
+
+Then copy the WebAPIConfig to WebAPI folder:
+```bash
+cp ./WebAPIConfig ./WebAPI
+```
+
+Then enters the folder and compile the project with maven:
+```bash
+mvn clean package -DskipTests -s WebAPIConfig/settings.xml -P webapi-postgresql
+```
+
+Then we moved it to the tomcat with the configuration files: 
+```bash
+docker cp web.xml webapi_tomcat:/usr/local/tomcat/webapps.dist/manager/WEB-INF
+docker cp tomcat-users.xml webapi_tomcat:/usr/local/tomcat/conf
+docker cp target/WebAPI.war webapi_tomcat:/usr/local/tomcat/webapps
+docker logs webapi_tomcat -f
+```
+
+Check installation by going to: http://localhost:8080/WebAPI/info
+
+
+### CMD Configuration
+
+#### WebAPI
+The next step (https://github.com/OHDSI/WebAPI/wiki/CDM-Configuration) is to configure WebAPI to connect to:
+* CDM: containing patient level data
+* Vocab: OMOP vocabulary
+* 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.  
+
+We go back to pgAdmin to enter data in the webapi.source and webapi.source_daimon tables.  
+The following commands were executed:
+
+```sql
+TRUNCATE TABLE webapi.source CASCADE
+TRUNCATE TABLE webapi.source_daimon CASCADE
+
+-- CDM
+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}';
+
+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
+FROM webapi.source
+WHERE source_key = 'OMOP'
+;
+
+-- VOCAB
+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
+FROM webapi.source
+WHERE source_key = 'OMOP'
+;
+
+-- 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}';
+
+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
+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}';
+
+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
+FROM webapi.source
+WHERE source_key = 'OMOP_TEMP'
+;
+
+-- check:
+SELECT * FROM webapi.source;
+SELECT * FROM webapi.source_daimon;
+```
+
+Check sources: http://localhost:8080/WebAPI/source/sources
+
+#### Oracle
+
+(This script is handy to delete all tables in a schema:)
+```sql
+SELECT 'DROP TABLE "' || TABLE_NAME || '" CASCADE CONSTRAINTS;' FROM user_tables;
+```
+
+By going to: http://localhost:8080/WebAPI/ddl/results?dialect=oracle&schema=OMOP_COHORT&vocabSchema=OMOP&tempSchema=OMOP_TEMP=initConceptHierarchy=true  
+We get the Oracle scripts to execute to create new tables in our OMOP_COHORT and OMOP_TEMP schema
+
+We tried to execute all the commands in Oracle SQL developer but we got an error because of the BEGIN-END syntax. We needed to replace all 
+```sql
+END;
+```
+
+by 
+
+```sql
+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).
+