OMOP <-> FHIR mapper
Omopfhirmap is a command-line tool for mapping a OHDSI cohort, defined in ATLAS, to a FHIR bundle that can be optionally submitted to a FHIR server for processing. Conversely, it can process a FHIR bundle and add resources to an existing CDM database ignoring duplicates. Unlike GT-FHIR2, the OMOP on FHIR Project at Georgia Tech omopfhirmap does not expose OMOP database as FHIR endpoints.
mvn clean install spring-boot:repackage
```shell script
java -jar
### Examples* *java -jar target/omopfhirmap-0.0.1.jar help** *java -jar target/omopfhirmap-0.0.1.jar tofhirbundle 2 test-fhir.json --spring.config.location=application.properties*This will convert the cohort defined in Atlas with an ID of 2(looks in the cohort table in results schema) and writes the FHIR (collection) bundle.* *java -jar target/omopfhirmap-0.0.1.jar toomop test-fhir.json 3 --spring.config.location=application.properties*Imports the FHIR bundle in the above file, creates persons,observations, measurements, procedure and visit occurences.Finally it creates a new cohort with ID 3 (Can be seen in Atlas)* Sample application.properties
spring.main.banner-mode=off
logging.level.org.springframework=ERROR
logging.level.root=ERROR
logging.level.org.foo.bar.baz=INFO
spring.jpa.hibernate.ddl-auto=none
spring.datasource.initialization-mode=always
spring.datasource.platform=postgres
spring.datasource.url=jdbc
//localhost:5432/username_db?currentSchema=synpuf_results,synpuf5,ohdsi
spring.datasource.username=username
spring.datasource.password=secret
spring.jpa.properties.hibernate.jdbc.lob.non_contextual_creation=true
omopfhir.system.name=mySystem
```
