feat: add interface for ConditionRepository methods

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/OncoAnalyticsMonitorApplication.kt

@@ -1,6 +1,6 @@
 package dev.pcvolkmer.oncoanalytics.monitor
 
-import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository
+import dev.pcvolkmer.oncoanalytics.monitor.conditions.InMemoryConditionRepository
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics
 import org.springframework.boot.autoconfigure.SpringBootApplication
 import org.springframework.boot.runApplication
@@ -18,18 +18,18 @@ class OncoAnalyticsMonitorApplication {
     }
 
     @Bean
-    fun obdsXmlConditionRepository(): ConditionInMemoryRepository {
+    fun obdsXmlConditionRepository(): InMemoryConditionRepository {
-        return ConditionInMemoryRepository()
+        return InMemoryConditionRepository()
     }
 
     @Bean
-    fun fhirObdsConditionRepository(): ConditionInMemoryRepository {
+    fun fhirObdsConditionRepository(): InMemoryConditionRepository {
-        return ConditionInMemoryRepository()
+        return InMemoryConditionRepository()
     }
 
     @Bean
-    fun fhirPseudonymizedConditionRepository(): ConditionInMemoryRepository {
+    fun fhirPseudonymizedConditionRepository(): InMemoryConditionRepository {
-        return ConditionInMemoryRepository()
+        return InMemoryConditionRepository()
     }
 
 }

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/ConditionRepository.kt

@@ -0,0 +1,32 @@
+package dev.pcvolkmer.oncoanalytics.monitor.conditions
+
+/**
+ * Interface declaring a data repository to hold (latest) conditions
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1.0
+ */
+interface ConditionRepository {
+
+    /**
+     * Save condition if no newer condition (by id and version) is present
+     *
+     * @param condition The condition to be saved
+     * @return Will return true if successful
+     */
+    fun saveIfNewerVersion(condition: Condition): Boolean
+
+    /**
+     * Save condition without any checks
+     *
+     * @param condition The condition to be saved
+     * @return Will return true if successful
+     */
+    fun save(condition: Condition): Boolean
+
+    /**
+     * Return all saved conditions
+     */
+    fun findAll(): List<Condition>
+
+}

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/InMemoryConditionRepository.kt

@@ -2,6 +2,12 @@ package dev.pcvolkmer.oncoanalytics.monitor.conditions
 
 import org.apache.commons.codec.digest.DigestUtils
 
+/**
+ * Type to be used for the condition ID
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1.0
+ */
 @JvmInline
 value class ConditionId(val value: String) {
     companion object {
@@ -11,13 +17,30 @@ value class ConditionId(val value: String) {
     }
 }
 
+/**
+ * A condition
+ *
+ * @property id The conditions unique ID
+ * @property icd10 The ICD10 code of the related diagnosis
+ * @property version (if present) The version of the related oBDS message or zero
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1.0
+ */
 data class Condition(val id: ConditionId, val icd10: String, val version: Int = 0)
 
-class ConditionInMemoryRepository {
+/**
+ * In memory implementation of a ConditionRepository
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1.0
+ * @see ConditionRepository
+ */
+class InMemoryConditionRepository : ConditionRepository {
 
     private val conditions = mutableMapOf<ConditionId, Condition>()
 
-    fun saveIfNewerVersion(condition: Condition): Boolean {
+    override fun saveIfNewerVersion(condition: Condition): Boolean {
         if ((this.conditions[condition.id]?.version ?: 0) < condition.version) {
             this.conditions[condition.id] = condition
             return true
@@ -25,12 +48,12 @@ class ConditionInMemoryRepository {
         return false
     }
 
-    fun save(condition: Condition): Boolean {
+    override fun save(condition: Condition): Boolean {
         this.conditions[condition.id] = condition
         return true
     }
 
-    fun findAll(): List<Condition> {
+    override fun findAll(): List<Condition> {
         return conditions.values.toList()
     }
 

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/Statistics.kt

@@ -1,8 +1,26 @@
 package dev.pcvolkmer.oncoanalytics.monitor.conditions
 
+/**
+ * A statistics summary
+ *
+ * @property name The name of the statistics e.g. the source of data
+ * @property entries A list of entries containing information for each ICD10 code group
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1.0
+ */
 data class Statistics(
     val name: String,
     val entries: List<StatisticsEntry>
 )
 
+/**
+ * A statistics entry
+ *
+ * @property name The name of the ICD10 code group
+ * @property count Number of recognized oBDS or FHIR messages for the OCD10 code group
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1.0
+ */
 data class StatisticsEntry(val name: String, val count: Int)

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/helpers.kt

@@ -1,6 +1,6 @@
 package dev.pcvolkmer.oncoanalytics.monitor
 
-import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository
+import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.StatisticsEntry
 
@@ -32,7 +32,15 @@ val allKeys = listOf(
     "Other"
 )
 
-fun fetchStatistics(name: String, source: ConditionInMemoryRepository): Statistics {
+/**
+ * Fetch statistics using given ConditionRepository
+ *
+ * @see ConditionRepository
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1.0
+ */
+fun fetchStatistics(name: String, source: ConditionRepository): Statistics {
     fun mapIcd10Code(code: String): String {
         val c = when (code) {
             "D39.1", "D09.0", "D41.4" -> code
@@ -72,5 +80,7 @@ fun fetchStatistics(name: String, source: ConditionInMemoryRepository): Statisti
         .groupBy { mapIcd10Code(it.icd10) }
         .mapValues { it.value.size }
 
-    return Statistics(name, allKeys.map { StatisticsEntry(it, 0) }.map { StatisticsEntry(it.name, entries.getOrDefault(it.name, 0)) })
+    return Statistics(
+        name,
+        allKeys.map { StatisticsEntry(it, 0) }.map { StatisticsEntry(it.name, entries.getOrDefault(it.name, 0)) })
 }

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/FhirObdsTopicMonitor.kt

@@ -4,7 +4,7 @@ import ca.uhn.fhir.context.FhirContext
 import dev.pcvolkmer.oncoanalytics.monitor.StatisticsSink
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.Condition
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionId
-import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository
+import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
 import dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics
 import org.hl7.fhir.r4.model.Bundle
 import org.springframework.beans.factory.annotation.Qualifier
@@ -17,7 +17,7 @@ import org.springframework.stereotype.Component
 @Component
 class FhirObdsTopicMonitor(
     @Qualifier("fhirObdsConditionRepository")
-    private val conditionRepository: ConditionInMemoryRepository,
+    private val conditionRepository: ConditionRepository,
     statisticsEventProducer: StatisticsSink,
 ) : TopicMonitor(statisticsEventProducer) {
 

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/FhirPseudonymizedTopicMonitor.kt

@@ -4,7 +4,7 @@ import ca.uhn.fhir.context.FhirContext
 import dev.pcvolkmer.oncoanalytics.monitor.StatisticsSink
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.Condition
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionId
-import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository
+import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
 import dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics
 import org.hl7.fhir.r4.model.Bundle
 import org.springframework.beans.factory.annotation.Qualifier
@@ -17,7 +17,7 @@ import org.springframework.stereotype.Component
 @Component
 class FhirPseudonymizedTopicMonitor(
     @Qualifier("fhirPseudonymizedConditionRepository")
-    private val conditionRepository: ConditionInMemoryRepository,
+    private val conditionRepository: ConditionRepository,
     statisticsEventProducer: StatisticsSink,
 ) : TopicMonitor(statisticsEventProducer) {
 

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/ObdsXmlTopicMonitor.kt

@@ -7,7 +7,7 @@ import com.fasterxml.jackson.databind.ObjectMapper
 import dev.pcvolkmer.oncoanalytics.monitor.StatisticsSink
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.Condition
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionId
-import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository
+import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
 import dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics
 import org.springframework.beans.factory.annotation.Qualifier
 import org.springframework.kafka.annotation.KafkaListener
@@ -22,7 +22,7 @@ import javax.xml.xpath.XPathFactory
 @Component
 class ObdsXmlTopicMonitor(
     @Qualifier("obdsXmlConditionRepository")
-    private val conditionRepository: ConditionInMemoryRepository,
+    private val conditionRepository: ConditionRepository,
     private val objectMapper: ObjectMapper,
     statisticsEventProducer: StatisticsSink,
 ) : TopicMonitor(statisticsEventProducer) {

src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/StatisticsController.kt

@@ -1,6 +1,6 @@
 package dev.pcvolkmer.oncoanalytics.monitor.web
 
-import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository
+import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
 import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics
 import dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics
 import org.springframework.beans.factory.annotation.Qualifier
@@ -12,11 +12,11 @@ import org.springframework.web.bind.annotation.RestController
 @RequestMapping(path = ["/statistics"])
 class StatisticsController(
     @Qualifier("obdsXmlConditionRepository")
-    private val obdsXmlConditionRepository: ConditionInMemoryRepository,
+    private val obdsXmlConditionRepository: ConditionRepository,
     @Qualifier("fhirObdsConditionRepository")
-    private val fhirObdsConditionRepository: ConditionInMemoryRepository,
+    private val fhirObdsConditionRepository: ConditionRepository,
     @Qualifier("fhirPseudonymizedConditionRepository")
-    private val fhirPseudonymizedConditionRepository: ConditionInMemoryRepository,
+    private val fhirPseudonymizedConditionRepository: ConditionRepository,
 ) {
 
     @GetMapping(path = ["obdsxml"])