fix: Use logical references (#41)

* update consumer id and topic names * fix: use logical references * docs: update README * remove unused narrative feature * ci: fix linting
diz-unimr · Jul 30, 2024 · 40d1380 · 40d1380
1 parent fb26e7d
commit 40d1380
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diff --git a/README.md b/README.md
@@ -66,7 +66,7 @@ update consumer group is deleted.
 On startup, the application checks the configured mapping version and
 determines a diff between the mappings of the current and the last used
 mapping version. This data is stored in the Kafka topic `mapping` with the key
-`lab-update`.
+`aim-lab-update`.
 
 In case there are no changes or the mapping versions used are equal, the
 update processor is not started.
@@ -104,8 +104,8 @@ tags can be found at the [Container Registry](https://github.com/orgs/diz-unimr/
 
 ## Development
 
-A [test setup](dev/compose.yaml) and [test data provider](dev/compose-data.yaml)
-is available for development purposes.
+A [test setup](dev/compose.yaml) with test data is available for development
+purposes.
 
 ### Builds
 

diff --git a/dev/compose-data.yaml b/dev/compose-data.yaml
diff --git a/dev/compose.yaml b/dev/compose.yaml
@@ -1,5 +1,3 @@
-version: "3.7"
-
 name: lab-to-fhir
 
 services:
@@ -30,6 +28,11 @@ services:
       KAFKA_COMPRESSION_TYPE: gzip
     depends_on:
       - zoo
+    healthcheck:
+      test: kafka-topics --bootstrap-server kafka:9092 --list
+      interval: 30s
+      timeout: 10s
+      retries: 3
 
   akhq:
     image: tchiotludo/akhq:0.19.0
@@ -44,3 +47,14 @@ services:
       - "9000:8080"
     depends_on:
       - kafka
+
+  lab-data-loader:
+    image: confluentinc/cp-kafkacat:7.0.1
+    entrypoint: ["/bin/bash", "-c"]
+    command: >
+      "kafkacat -b kafka:19092 -K: -t laboratory -P -l /data/lab-data.ndjson"
+    volumes:
+      - ./lab-data.ndjson:/data/lab-data.ndjson:ro
+    depends_on:
+      kafka:
+        condition: service_healthy
diff --git a/src/main/java/de/unimarburg/diz/labtofhir/configuration/FhirProperties.java b/src/main/java/de/unimarburg/diz/labtofhir/configuration/FhirProperties.java
@@ -9,21 +9,11 @@
 public class FhirProperties {
 
     private final Systems systems = new Systems();
-    @NotNull
-    private Boolean generateNarrative;
 
     public Systems getSystems() {
         return systems;
     }
 
-    public Boolean getGenerateNarrative() {
-        return generateNarrative;
-    }
-
-    public void setGenerateNarrative(Boolean generateNarrative) {
-        this.generateNarrative = generateNarrative;
-    }
-
     public static class Systems {
 
 

diff --git a/src/main/java/de/unimarburg/diz/labtofhir/configuration/MappingUpdateConfiguration.java b/src/main/java/de/unimarburg/diz/labtofhir/configuration/MappingUpdateConfiguration.java
@@ -22,8 +22,8 @@
 @Configuration
 public class MappingUpdateConfiguration {
 
-    private static final Logger LOG = LoggerFactory.getLogger(
-        MappingUpdateConfiguration.class);
+    private static final Logger LOG =
+        LoggerFactory.getLogger(MappingUpdateConfiguration.class);
     private static final long MAX_CONSUMER_POLL_DURATION_SECONDS = 10L;
 
     @Bean("mappingInfo")
@@ -33,10 +33,7 @@ public MappingInfo buildMappingUpdate(LoincMapper loincMapper,
         Producer<String, MappingUpdate> producer)
         throws ExecutionException, InterruptedException, IOException {
         // check versions
-        var configuredVersion = loincMapper
-            .getMap()
-            .getMetadata()
-            .getVersion();
+        var configuredVersion = loincMapper.getMap().getMetadata().getVersion();
 
         // 1. consume latest from (mapping) update topic
         var lastUpdate = getLastMappingUpdate(consumer);
@@ -54,13 +51,12 @@ public MappingInfo buildMappingUpdate(LoincMapper loincMapper,
 
         // 2. check if already on latest
         if (Objects.equals(configuredVersion, lastUpdate.getVersion())) {
-            LOG.info("Configured mapping version ({}) matches last version "
-                    + "({}). " + "No update necesssary", configuredVersion,
+            LOG.info(
+                "Configured mapping version ({}) matches last version ({}). "
+                    + "No update necesssary", configuredVersion,
                 lastUpdate.getVersion());
 
-            if (!labOffsets
-                .updateOffsets()
-                .isEmpty()) {
+            if (!labOffsets.updateOffsets().isEmpty()) {
                 // update in progress, continue
                 return new MappingInfo(lastUpdate, true);
             }
@@ -72,36 +68,29 @@ public MappingInfo buildMappingUpdate(LoincMapper loincMapper,
         // get last version's mapping
         var lastMap = LoincMapper.getSwlLoincMapping(
             ResourceHelper.getMappingFile(lastUpdate.getVersion(),
-                mappingProperties
-                    .getLoinc()
-                    .getCredentials()
-                    .getUser(), mappingProperties
-                    .getLoinc()
-                    .getCredentials()
-                    .getPassword(), mappingProperties
-                    .getLoinc()
-                    .getProxy(), mappingProperties
-                    .getLoinc()
-                    .getLocal()));
+                mappingProperties.getLoinc().getCredentials().getUser(),
+                mappingProperties.getLoinc().getCredentials().getPassword(),
+                mappingProperties.getLoinc().getProxy(),
+                mappingProperties.getLoinc().getLocal()));
         // ceate diff
-        var updates = loincMapper
-            .getMap()
-            .diff(lastMap);
-        var update = new MappingUpdate(configuredVersion,
-            lastUpdate.getVersion(), updates);
+        var updates = loincMapper.getMap().diff(lastMap);
+        var update =
+            new MappingUpdate(configuredVersion, lastUpdate.getVersion(),
+                updates);
 
         // save new mapping update
         saveMappingUpdate(producer, update);
 
         return new MappingInfo(update, false);
     }
 
+    @SuppressWarnings("checkstyle:LineLength")
     private void saveMappingUpdate(Producer<String, MappingUpdate> producer,
         MappingUpdate mappingUpdate)
         throws ExecutionException, InterruptedException {
 
-        producer
-            .send(new ProducerRecord<>("mapping", "lab-update", mappingUpdate))
+        producer.send(
+                new ProducerRecord<>("mapping", "aim-lab-update", mappingUpdate))
             .get();
     }
 
@@ -124,8 +113,7 @@ private MappingUpdate getLastMappingUpdate(
 
             var record = consumer
                 .poll(Duration.ofSeconds(MAX_CONSUMER_POLL_DURATION_SECONDS))
-                .iterator()
-                .next();
+                .iterator().next();
 
             consumer.unsubscribe();
             return record.value();