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miracum / fhir-gateway

A thin layer between FHIR REST clients and resource processing pipelines.
Apache License 2.0
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application.yml doesn't allow error free start when SERVICES_PSQL_ENABLED is false #98

Closed UKFr-DIZ closed 10 months ago

UKFr-DIZ commented 11 months ago

Hi,

Error description

when using the given default docker-compose.yml and set SERVICES_PSQL_ENABLED false, the start of the container fails, because of an setting in the application.yml.

start up log. 

.... 
gateway-1             | 2023-12-01 12:08:08.939  INFO --- [           main] com.zaxxer.hikari.HikariDataSource       : HikariPool-1 - Starting...
gateway-1             | 2023-12-01 12:08:09.116  INFO --- [           main] com.zaxxer.hikari.pool.HikariPool        : HikariPool-1 - Added connection conn0: url=jdbc:h2:mem:05d8e72e-3558-4220-9d9a-75b79f6835f0 user=SA
gateway-1             | 2023-12-01 12:08:09.118  INFO --- [           main] com.zaxxer.hikari.HikariDataSource       : HikariPool-1 - Start completed.
gateway-1             | 2023-12-01 12:08:09.138  WARN --- [           main] ConfigServletWebServerApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'fhirController' defined in file [/opt/fhir-gateway/BOOT-INF/classes/org/miracum/etl/fhirgateway/controllers/FhirController.class]: Unsatisfied dependency expressed through constructor parameter 1: Error creating bean with name 'resourcePipeline' defined in file [/opt/fhir-gateway/BOOT-INF/classes/org/miracum/etl/fhirgateway/processors/ResourcePipeline.class]: Unsatisfied dependency expressed through constructor parameter 0: Error creating bean with name 'postgresFhirResourceRepository' defined in file [/opt/fhir-gateway/BOOT-INF/classes/org/miracum/etl/fhirgateway/stores/PostgresFhirResourceRepository.class]: Unsatisfied dependency expressed through constructor parameter 1: Error creating bean with name 'dataSourceScriptDatabaseInitializer' defined in class path resource [org/springframework/boot/autoconfigure/sql/init/DataSourceInitializationConfiguration.class]: Failed to execute SQL script statement #1 of class path resource [schema.sql]: CREATE TABLE IF NOT EXISTS resources ( id bigserial PRIMARY KEY, fhir_id varchar(64) NOT NULL, type varchar(64) NOT NULL, data jsonb NOT NULL, created_at timestamp NOT NULL DEFAULT NOW(), last_updated_at timestamp NOT NULL DEFAULT NOW(), is_deleted boolean NOT NULL DEFAULT FALSE, CONSTRAINT fhir_id_unique UNIQUE (fhir_id, type) )
gateway-1             | 2023-12-01 12:08:09.138  INFO --- [           main] com.zaxxer.hikari.HikariDataSource       : HikariPool-1 - Shutdown initiated...
gateway-1             | 2023-12-01 12:08:09.145  INFO --- [           main] com.zaxxer.hikari.HikariDataSource       : HikariPool-1 - Shutdown completed.
gateway-1             | 2023-12-01 12:08:09.148  INFO --- [           main] o.apache.catalina.core.StandardService   : Stopping service [Tomcat]
gateway-1             | 2023-12-01 12:08:09.166  INFO --- [           main] .s.b.a.l.ConditionEvaluationReportLogger :
gateway-1             |
gateway-1             | Error starting ApplicationContext. To display the condition evaluation report re-run your application with 'debug' enabled.
gateway-1             | 2023-12-01 12:08:09.181 ERROR --- [           main] o.s.boot.SpringApplication               : Application run failed
gateway-1             |
gateway-1             | org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'fhirController' defined in file [/opt/fhir-gateway/BOOT-INF/classes/org/miracum/etl/fhirgateway/controllers/FhirController.class]: Unsatisfied dependency expressed through constructor parameter 1: Error creating bean with name 'resourcePipeline' defined in file [/opt/fhir-gateway/BOOT-INF/classes/org/miracum/etl/fhirgateway/processors/ResourcePipeline.class]: Unsatisfied dependency expressed through constructor parameter 0: Error creating bean with name 'postgresFhirResourceRepository' defined in file [/opt/fhir-gateway/BOOT-INF/classes/org/miracum/etl/fhirgateway/stores/PostgresFhirResourceRepository.class]: Unsatisfied dependency expressed through constructor parameter 1: Error creating bean with name 'dataSourceScriptDatabaseInitializer' defined in class path resource [org/springframework/boot/autoconfigure/sql/init/DataSourceInitializationConfiguration.class]: Failed to execute SQL script statement #1 of class path resource [schema.sql]: CREATE TABLE IF NOT EXISTS resources ( id bigserial PRIMARY KEY, fhir_id varchar(64) NOT NULL, type varchar(64) NOT NULL, data jsonb NOT NULL, created_at timestamp NOT NULL DEFAULT NOW(), last_updated_at timestamp NOT NULL DEFAULT NOW(), is_deleted boolean NOT NULL DEFAULT FALSE, CONSTRAINT fhir_id_unique UNIQUE (fhir_id, type) )
gateway-1             |         at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:801) ~[spring-beans-6.0.13.jar:6.0.13]

Cause:

https://github.com/miracum/fhir-gateway/blob/002dcfa629245b2eb4c5049e8ac863f1b0d95a8d/src/main/resources/application.yml#L79 The SPRING_SQL_INIT_MODE variable or rather spring app setting is set to always which causes the startup of the gateway trying to execute a SQL schema init script, on a none existing DB as far as I understand.

Solution

Set SPRING_SQL_INIT_MODE to never, so the SQL script is disabled, when wanting to deactivate the DB output. Maybe you have a better solution to it, but the setting used to be on never in previous versions.

I would add to the SPRING_SERVICE_PSQL_ENABLED config in the docu, that the second attribute has to be set addtionally if the DB is to be deactivated.

chgl commented 10 months ago

Thanks for reporting and the suggestion! I've updated the docs according to your suggestion.