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👼 Automate schema creation #1

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👼 Automate schema creation #1

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3697505
👼 Automate schema creation.
psbrandt Jan 2, 2020
9a45495
👷🏼‍♂️ Add CI testing.
psbrandt Jan 2, 2020
937939b
📓 Add documentation.
psbrandt Jan 2, 2020
cebea7d
🎫 Add id_mapping migration and test.
psbrandt Jan 2, 2020
cd4c236
💩 Unfortunate observation_time workaround.
psbrandt Jan 3, 2020
1f483e5
🙈 Correct POM copy/paste error.
psbrandt Jan 3, 2020
c821fc8
😸 Relax measure_time requirement and only check in current schema.
psbrandt Jan 3, 2020
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20 changes: 20 additions & 0 deletions .travis.yml
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language: java
jdk:
- openjdk10

sudo: required
services:
- docker

# Fix for https://travis-ci.community/t/problematic-docker-compose-version-1-23-1/5362/3
before_install:
- sudo rm /usr/local/bin/docker-compose
- curl -L https://github.com/docker/compose/releases/download/1.24.1/docker-compose-Linux-x86_64 > docker-compose
- chmod +x docker-compose
- sudo mv docker-compose /usr/local/bin

install:
- mvn -Ptravis install -DskipTests=true -Dmaven.javadoc.skip=true -B -V

script:
- mvn test -Dskip.tests=false
35 changes: 35 additions & 0 deletions README.md
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# omoponfhir-omopv5-jpabase

<!-- TODO: Change this URL when merged -->
[![Build Status](https://travis-ci.org/PheMA/omoponfhir-omopv5-jpabase.svg?branch=flyway)](https://travis-ci.org/PheMA/omoponfhir-omopv5-jpabase)

Java library containing Hibernate JPA entities used by OMOP on FHIR.


## Schema Preparation

At least one table and one view need to be created to support mapping the OMOP CDM to FHIR. First, the `f_person` table
must be created to contain additional demographic information used by FHIR, but not typically stored in the OMOP CDM.
Second, since both the CDM `measurement` and `observation` tables map to the FHIR <kbd>Observation</kbd> resource, we
create a view called `f_observation_view`, which is a union of these two tables.

The PostgreSQL scripts for creating these two tables, as well as an index on `f_person` can be found in
[`src/main/resources/flyway/migrations/postgresql`](src/main/resources/flyway/migrations/postgresql).

### Automatic Schema Creation

To automatically create the necessary tables, or apply any updates implemented since you last ran the scripts, do the
following.

First, clone this repository:

```
git clone https://github.com/omoponfhir/omoponfhir-omopv5-jpabase.git
```

Then, use Maven and Flyway to apply the scripts for you:

```sh
mvn flyway:migrate -Ddatabase.url='jdbc:postgresql://localhost:5432/postgres?currentSchema=cdm' -Ddatabase.user=postgres -Ddatabase.password=postgres
```

Adjust the parameters as required. Importantly, ensure the correct schema is selected (`cdm` in the above example).
288 changes: 185 additions & 103 deletions pom.xml
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OR CONDITIONS OF ANY KIND, either express or implied. See the License for
the specific language governing permissions and limitations under the License. -->
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>

<groupId>edu.gatech.chai</groupId>
<artifactId>omoponfhir-omopv5-jpabase</artifactId>
<packaging>jar</packaging>
<version>1.1.2</version>
<name>omoponfhir-omopv5-jpabase</name>
<description>OMOP on FHIR JPABASE for OMOP version 5</description>
<url>http://maven.apache.org</url>
<groupId>edu.gatech.chai</groupId>
<artifactId>omoponfhir-omopv5-jpabase</artifactId>
<packaging>jar</packaging>
<version>1.1.2</version>
<name>omoponfhir-omopv5-jpabase</name>
<description>OMOP on FHIR JPABASE for OMOP version 5</description>
<url>http://maven.apache.org</url>

<licenses>
<license>
<name>Apache License, Version 2.0</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<licenses>
<license>
<name>Apache License, Version 2.0</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<hibernate_version>5.3.1.Final</hibernate_version>
<spring_version>5.0.8.RELEASE</spring_version>
<hibernate_version>5.3.1.Final</hibernate_version>
</properties>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<hibernate_version>5.3.1.Final</hibernate_version>
<spring_version>5.0.8.RELEASE</spring_version>
<hibernate_version>5.3.1.Final</hibernate_version>
<!-- For Flyway migrations -->
<flyway.version>6.1.3</flyway.version>
<postgres.driver.version>42.2.6</postgres.driver.version>
<database.url/>
<database.user/>
<database.password/>
<!-- Testing -->
<skip.tests>true</skip.tests>
<junit.jupiter.version>5.4.2</junit.jupiter.version>
<testcontainers.version>1.12.3</testcontainers.version>
</properties>

<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>javax.persistence</artifactId>
<version>2.2.0</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate_version}</version>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.20.0-GA</version>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>9.4.1211.jre7</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>net.jcip</groupId>
<artifactId>jcip-annotations</artifactId>
<version>1.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.json/json -->
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20180130</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.25</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.6</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.12.4</version>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>javax.persistence</artifactId>
<version>2.2.0</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate_version}</version>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.20.0-GA</version>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>9.4.1211.jre7</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>net.jcip</groupId>
<artifactId>jcip-annotations</artifactId>
<version>1.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.json/json -->
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20180130</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.25</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.6</version>
</dependency>
<!-- Testing -->
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>${flyway.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>${junit.jupiter.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
<version>${junit.jupiter.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>${junit.jupiter.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers</artifactId>
<version>${testcontainers.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<version>${testcontainers.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>postgresql</artifactId>
<version>${testcontainers.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.zaxxer</groupId>
<artifactId>HikariCP</artifactId>
<version>3.4.1</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.19.1</version>
<configuration>
<skipTests>${skip.tests}</skipTests>
</configuration>
<dependencies>
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-surefire-provider</artifactId>
<version>1.0.1</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-maven-plugin</artifactId>
<version>${flyway.version}</version>
<configuration>
<sqlMigrationSeparator>__</sqlMigrationSeparator>
<locations>
<location>filesystem:src/main/resources/flyway/migrations/postgresql</location>
</locations>
<url>${database.url}</url>
<user>${database.user}</user>
<password>${database.password}</password>
<baselineOnMigrate>true</baselineOnMigrate>
</configuration>
<dependencies>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgres.driver.version}</version>
</dependency>
</dependencies>
</plugin>
</plugins>
</build>
</project>
16 changes: 16 additions & 0 deletions src/main/resources/flyway/migrations/postgresql/V1.0.1__Create_f_person_table.pg.sql
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CREATE TABLE f_person
(
person_id INTEGER NOT NULL,
family_name VARCHAR(255),
given1_name VARCHAR(255),
given2_name VARCHAR(255),
prefix_name VARCHAR(255),
suffix_name VARCHAR(255),
preferred_language VARCHAR(255),
ssn VARCHAR(12),
active SMALLINT DEFAULT 1,
contact_point1 VARCHAR(255),
contact_point2 VARCHAR(255),
contact_point3 VARCHAR(255),
maritalstatus VARCHAR(255)
);
2 changes: 2 additions & 0 deletions src/main/resources/flyway/migrations/postgresql/V1.0.2__Create_f_person_index.pg.sql
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CREATE INDEX f_person_person_id_idx
ON f_person (person_id);
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