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Merge pull request #58 from Mandalka/fhirserver-http-basic-auth
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Support http basic auth in FHIR server sink (#8)
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@makampf
makampf authored Sep 7, 2023
2 parents a1105a2 + 15fa05a commit 9ca10b8
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Showing 5 changed files with 37 additions and 10 deletions.
5 changes: 4 additions & 1 deletion README.md
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Expand Up @@ -23,7 +23,7 @@ curl -d @tests/e2e/data/bundle.json -H "Content-Type: application/json" -X POST
To configure your deployment, you can change the following environment variables:

| Variable | Description | Default |
| ----------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------- |
|-------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------|
| SPRING_DATASOURCE_URL | JDBC URL of the Postgres DB to store the received FHIR resources, needs to be set to an empty variable if no PSQL db is to be connected to | jdbc:postgresql://fhir-db:5432/fhir |
| SPRING_DATASOURCE_USERNAME | Username of the Postgres DB | postgres |
| SPRING_DATASOURCE_PASSWORD | Password for the Postgres DB | postgres |
Expand All @@ -32,6 +32,9 @@ To configure your deployment, you can change the following environment variables
| SERVICES_LOINC_CONVERSIONS_URL | URL of the [LOINC conversion service](https://gitlab.miracum.org/miracum/etl/loinc-conversion) | <http://loinc-converter:8080/conversions> |
| SERVICES_FHIRSERVER_ENABLED | Whether to send received resources to a downstream FHIR server | false |
| SERVICES_FHIRSERVER_URL | URL of the FHIR server to send data to | <http://fhir-server:8080/fhir> |
| SERVICES_FHIRSERVER_AUTH_BASIC_ENABLED | Enable HTTP basic auth for sending data to FHIR server | false |
| SERVICES_FHIRSERVER_AUTH_BASIC_USERNAME | HTTP basic auth username of the FHIR server to send data to | `""` |
| SERVICES_FHIRSERVER_AUTH_BASIC_PASSWORD | HTTP basic auth password of the FHIR server to send data to | `""` |
| SERVICES_KAFKA_ENABLED | Enable reading FHIR resources from, and writing them back to a Kafka cluster | false |
| SERVICES_KAFKA_GENERATE_OUTPUT_TOPIC_MATCH_EXPRESSION | Allows for dynamically generating the Kafka output topic's name based on the input topic. Used to set a regular expression which is applied to the input topic and the first match is replaced with the value of `SERVICES_KAFKA_GENERATE_OUTPUT_TOPIC_REPLACE_WITH`. You can set this to `"^"` to add a prefix to the output topic. | `""` |

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18 changes: 18 additions & 0 deletions src/main/java/org/miracum/etl/fhirgateway/AppConfig.java
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Expand Up @@ -4,7 +4,9 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.okhttp.client.OkHttpRestfulClientFactory;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
import ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
Expand Down Expand Up @@ -69,6 +71,22 @@ public FhirContext fhirContext(
return fhirContext;
}

@Bean
IGenericClient fhirClient(
FhirContext fhirContext,
@Value("${services.fhirServer.auth.basic.username}") String username,
@Value("${services.fhirServer.auth.basic.password}") String password,
@Value("${services.fhirServer.auth.basic.enabled}") boolean isBasicAuthEnabled,
@Value("${services.fhirServer.url}") String fhirServerUrl) {
var client = fhirContext.newRestfulGenericClient(fhirServerUrl);

if (isBasicAuthEnabled) {
client.registerInterceptor(new BasicAuthInterceptor(username, password));
}

return client;
}

@Bean
public RestTemplate restTemplate(RestTemplateBuilder builder) {
return builder.build();
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10 changes: 3 additions & 7 deletions src/main/java/org/miracum/etl/fhirgateway/stores/FhirServerResourceRepository.java
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Expand Up @@ -9,7 +9,6 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.retry.RetryCallback;
import org.springframework.retry.RetryContext;
import org.springframework.retry.backoff.FixedBackOffPolicy;
Expand All @@ -32,19 +31,16 @@ public class FhirServerResourceRepository implements FhirResourceRepository {
private final RetryTemplate retryTemplate;

@Autowired
public FhirServerResourceRepository(
FhirContext fhirContext, @Value("${services.fhirServer.url}") String fhirServerUrl) {
public FhirServerResourceRepository(FhirContext fhirContext, IGenericClient client) {

this.fhirParser = fhirContext.newJsonParser();
this.client = fhirContext.newRestfulGenericClient(fhirServerUrl);
this.client = client;

this.retryTemplate = new RetryTemplate();

var fixedBackOffPolicy = new FixedBackOffPolicy();
fixedBackOffPolicy.setBackOffPeriod(5_000);
retryTemplate.setBackOffPolicy(fixedBackOffPolicy);

retryTemplate.setRetryPolicy(new SimpleRetryPolicy(5));

this.retryTemplate.registerListener(
new RetryListenerSupport() {
@Override
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7 changes: 6 additions & 1 deletion src/main/resources/application-dev.yml
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Expand Up @@ -13,8 +13,13 @@ services:
enabled: true
url: "http://localhost:5000/fhir"
fhirServer:
url: "http://localhost:8082/fhir"
enabled: false
url: "http://localhost:8082/fhir"
auth:
basic:
enabled: false
username: ""
password: ""
psql:
enabled: true
kafka:
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7 changes: 6 additions & 1 deletion src/main/resources/application.yml
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Expand Up @@ -88,8 +88,13 @@ services:
enabled: true
url: ""
fhirServer:
url: ""
enabled: false
url: ""
auth:
basic:
enabled: false
username: ""
password: ""
psql:
enabled: true
kafka:
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