Update deps (#6)

sevenreup · web-flow · commit cd8ab971fac2 · 2025-01-22T10:57:25.000+02:00
* update

* fix dependency crash

* update kotlin version

* Add clean all future dates route
diff --git a/.idea/kotlinc.xml b/.idea/kotlinc.xml
diff --git a/Dockerfile b/Dockerfile
@@ -1,13 +1,13 @@
 # Stage 1: Cache Gradle dependencies
-FROM gradle:7.6.1-jdk17 AS cache
+FROM gradle:7.6.3-jdk17 AS cache
 RUN mkdir -p /home/gradle/cache_home
 ENV GRADLE_USER_HOME /home/gradle/cache_home
 COPY . /home/gradle/app/
 WORKDIR /home/gradle/app
 RUN gradle clean build -i --stacktrace
 
 # Stage 2: Build Application
-FROM gradle:7.6.1-jdk17 AS build
+FROM gradle:7.6.3-jdk17 AS build
 COPY --from=cache /home/gradle/cache_home /home/gradle/.gradle
 COPY . /usr/src/app/
 WORKDIR /usr/src/app
diff --git a/core/src/main/kotlin/org/dtree/fhir/core/fixes/CarePlanFixes.kt b/core/src/main/kotlin/org/dtree/fhir/core/fixes/CarePlanFixes.kt
@@ -12,6 +12,7 @@ import org.dtree.fhir.core.utils.*
 import io.github.cdimascio.dotenv.Dotenv
 import io.github.cdimascio.dotenv.dotenv
 import kotlinx.coroutines.runBlocking
+import org.dtree.fhir.core.di.FhirProvider
 import org.dtree.fhir.core.utils.extractId
 import org.dtree.fhir.core.utils.isCompleted
 import org.dtree.fhir.core.utils.isStarted
@@ -42,7 +43,7 @@ class CarePlanFixes {
         dotenv = dotenv {
             directory = projectRoot
         }
-        fhirClient = FhirClient(dotenv, iParser)
+        fhirClient = FhirClient(dotenv, FhirProvider())
     }
 
     fun fixEnteredInErrorCarePlan(projectRoot: String) {
diff --git a/core/src/main/kotlin/org/dtree/fhir/core/uploader/FileUploader.kt b/core/src/main/kotlin/org/dtree/fhir/core/uploader/FileUploader.kt
@@ -13,6 +13,7 @@ import org.dtree.fhir.core.utils.Logger
 import org.dtree.fhir.core.utils.readFile
 import io.github.cdimascio.dotenv.Dotenv
 import io.github.cdimascio.dotenv.dotenv
+import org.dtree.fhir.core.di.FhirProvider
 import org.hl7.fhir.r4.context.SimpleWorkerContext
 import org.hl7.fhir.r4.model.Bundle
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent
@@ -45,7 +46,7 @@ class FileUploader() {
         val configManager = ProjectConfigManager()
         projectConfig = configManager.loadProjectConfig(projectRoot, directoryPath)
         processExcludedPaths(projectRoot)
-        uploader = FhirClient(dotenv, iParser)
+        uploader = FhirClient(dotenv, FhirProvider())
         fetchFiles(
             directoryPath, mapOf(
                 Pair(projectConfig.structureMapLocation, "map"),
diff --git a/core/src/main/kotlin/org/dtree/fhir/core/uploader/LocationHierarchyUploader.kt b/core/src/main/kotlin/org/dtree/fhir/core/uploader/LocationHierarchyUploader.kt
@@ -11,6 +11,7 @@ import org.dtree.fhir.core.utils.*
 import io.github.cdimascio.dotenv.Dotenv
 import io.github.cdimascio.dotenv.dotenv
 import kotlinx.coroutines.runBlocking
+import org.dtree.fhir.core.di.FhirProvider
 import org.dtree.fhir.core.utils.extractId
 import org.dtree.fhir.core.utils.logicalId
 import org.hl7.fhir.r4.context.SimpleWorkerContext
@@ -36,7 +37,7 @@ class LocationHierarchyUploader {
             dotenv = dotenv {
                 directory = projectRoot
             }
-            fhirClient = FhirClient(dotenv, iParser)
+            fhirClient = FhirClient(dotenv, FhirProvider())
             val list = fhirClient.searchResources<Location>(count = batchSize) {
 
             }
diff --git a/core/src/main/kotlin/org/dtree/fhir/core/uploader/general/FhirClient.kt b/core/src/main/kotlin/org/dtree/fhir/core/uploader/general/FhirClient.kt
@@ -13,6 +13,7 @@ import okhttp3.OkHttpClient
 import okhttp3.Response
 import okhttp3.logging.HttpLoggingInterceptor
 import org.apache.commons.net.ntp.TimeStamp
+import org.dtree.fhir.core.di.FhirProvider
 import org.dtree.fhir.core.models.PatientData
 import org.dtree.fhir.core.models.parsePatientResources
 import org.dtree.fhir.core.utils.Logger
@@ -27,10 +28,11 @@ import java.net.URI
 import java.util.concurrent.TimeUnit
 import kotlin.io.path.Path
 
-class FhirClient(private val dotenv: Dotenv, private val iParser: IParser) {
+class FhirClient(private val dotenv: Dotenv, private val provider: FhirProvider) {
     val fhirClient: IGenericClient
     private val okHttpClient: OkHttpClient
     val ctx: FhirContext = FhirContext.forR4()
+    val iParser = provider.parser
 
     init {
         okHttpClient = createOkHttpClient()
diff --git a/core/src/main/kotlin/org/dtree/fhir/core/uploader/localChanges/LocalChangesUploader.kt b/core/src/main/kotlin/org/dtree/fhir/core/uploader/localChanges/LocalChangesUploader.kt
@@ -17,6 +17,7 @@ import org.dtree.fhir.core.utils.*
 import io.github.cdimascio.dotenv.Dotenv
 import io.github.cdimascio.dotenv.dotenv
 import kotlinx.coroutines.runBlocking
+import org.dtree.fhir.core.di.FhirProvider
 import org.hl7.fhir.r4.context.SimpleWorkerContext
 import org.hl7.fhir.r4.model.Binary
 import org.hl7.fhir.r4.model.Bundle
@@ -49,7 +50,7 @@ class LocalChangesUploader(private val batchSize: Int = 10) {
             currentDir = filePath.getParentPath()
             val configManager = ProjectConfigManager()
             projectConfig = configManager.loadProjectConfig(projectRoot, filePath)
-            uploader = FhirClient(dotenv, iParser)
+            uploader = FhirClient(dotenv, FhirProvider())
             val data = filePath.readFile()
             val localChanges = gson.fromJson(data, LocalChangesModel::class.java)
             if (localChanges.changes.isNotEmpty()) {
diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
@@ -1,12 +1,12 @@
 [versions]
-ktor = "2.3.12" # Set your Ktor version
-kotlin = "2.0.10" # Set your Kotlin version
-koin = "3.5.6" # Set your Koin version
+ktor = "3.0.0" # Set your Ktor version
+kotlin = "2.1.0" # Set your Kotlin version
+koin = "4.1.0-Beta5" # Set your Koin version
 postgres = "42.5.1" # Set your PostgreSQL driver version
 h2 = "2.2.224" # Set your H2 version
 logback = "1.4.14" # Set your Logback version
 dotenv = "6.4.1" # Set the dotenv version
-swagger-ui = "2.9.0"
+swagger-ui = "4.1.5"
 jquery = "3.2.1"
 hapiFhir = "6.8.0"
 hapiFhirCore = "6.0.22"
@@ -37,7 +37,7 @@ ktor-server-resources = { module = "io.ktor:ktor-server-resources", version.ref
 ktor-serialization-gson = { module = "io.ktor:ktor-serialization-gson-jvm", version.ref = "ktor" }
 ktor-server-call-logging = { module = "io.ktor:ktor-server-call-logging-jvm", version.ref = "ktor" }
 ktor-server-auth-jwt = { module = "io.ktor:ktor-server-auth-jwt-jvm", version.ref = "ktor" }
-koin-ktor = { module = "io.insert-koin:koin-ktor", version.ref = "koin" }
+koin-ktor = { module = "io.insert-koin:koin-ktor3", version.ref = "koin" }
 koin-logger-slf4j = { module = "io.insert-koin:koin-logger-slf4j", version.ref = "koin" }
 ktor-serialization-json = { module = "io.ktor:ktor-serialization-kotlinx-json-jvm", version.ref = "ktor" }
 ktor-server-content-negotiation = { module = "io.ktor:ktor-server-content-negotiation-jvm", version.ref = "ktor" }
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/server/build.gradle.kts b/server/build.gradle.kts
@@ -16,7 +16,9 @@ tasks.test {
 }
 
 tasks.withType<KotlinCompile> {
-    kotlinOptions.jvmTarget = "1.8"
+    kotlinOptions {
+        jvmTarget = "11"
+    }
 }
 
 application {
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/Application.kt b/server/src/main/kotlin/org/dtree/fhir/server/Application.kt
@@ -13,7 +13,7 @@ fun main(args: Array<String>) {
 fun Application.module() {
     val dotEnv = loadEnv()
 
+    configureFrameworks(dotEnv)
     configureSecurity()
     configureRouting()
-    configureFrameworks(dotEnv)
 }
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/controller/TracingController.kt b/server/src/main/kotlin/org/dtree/fhir/server/controller/TracingController.kt
@@ -1,21 +1,24 @@
 package org.dtree.fhir.server.controller
 
-import org.dtree.fhir.server.services.tracing.TracingListResults
+import org.dtree.fhir.server.core.models.PaginatedResponse
+import org.dtree.fhir.server.core.models.PaginationArgs
+import org.dtree.fhir.server.services.tracing.TracingResult
 import org.dtree.fhir.server.services.tracing.TracingService
 import org.dtree.fhir.server.services.tracing.TracingStatsResults
 import org.koin.core.component.KoinComponent
 import org.koin.core.component.inject
-import java.time.LocalDate
 
 class TracingControllerImpl : TracingController, BaseController(), KoinComponent {
     private val tracingService by inject<TracingService>()
     override fun getStats(id: String): TracingStatsResults {
         return tracingService.getStats(id)
     }
 
-    override fun getTracingList(facilityId: String, date: LocalDate): TracingListResults {
-        val result = tracingService.getTracingList(facilityId, date)
-        println(result.results.size)
+    override suspend fun getTracingList(
+        facilityId: String,
+        pagination: PaginationArgs
+    ): PaginatedResponse<TracingResult> {
+        val result = tracingService.getTracingList(facilityId, pagination)
         return result
     }
 
@@ -40,13 +43,22 @@ class TracingControllerImpl : TracingController, BaseController(), KoinComponent
             false
         }
     }
+
+    override suspend fun cleanFutureDateMissedAppointmentAll(): Boolean {
+        return try {
+            tracingService.cleanFutureDateMissedAppointmentAll()
+            true
+        } catch (e: Exception) {
+            println(e)
+            false
+        }
+    }
 }
 
 interface TracingController {
     fun getStats(id: String): TracingStatsResults
-
-    fun getTracingList(facilityId: String, date: LocalDate): TracingListResults
-
+    suspend fun getTracingList(facilityId: String, pagination: PaginationArgs): PaginatedResponse<TracingResult>
     suspend fun setPatientsEnteredInError(patients: List<String>): Boolean
     suspend fun cleanFutureDateMissedAppointment(facilityId: String): Boolean
+    suspend fun cleanFutureDateMissedAppointmentAll(): Boolean
 }
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/core/cache/CacheManager.kt b/server/src/main/kotlin/org/dtree/fhir/server/core/cache/CacheManager.kt
@@ -0,0 +1,37 @@
+package org.dtree.fhir.server.core.cache
+
+import kotlinx.coroutines.sync.Mutex
+import kotlinx.coroutines.sync.withLock
+import java.time.Instant
+
+data class CacheEntry<T>(
+    val data: List<T>,
+    val timestamp: Instant
+)
+
+class CacheManager<T>(
+    private val ttlSeconds: Long = 300 // 5 minutes default TTL
+) {
+    private val cache = mutableMapOf<String, CacheEntry<T>>()
+    private val mutex = Mutex()
+
+    suspend fun get(key: String): List<T>? {
+        return mutex.withLock {
+            val entry = cache[key] ?: return null
+
+            // Check if cache is expired
+            if (Instant.now().minusSeconds(ttlSeconds).isAfter(entry.timestamp)) {
+                cache.remove(key)
+                return null
+            }
+
+            entry.data
+        }
+    }
+
+    suspend fun set(key: String, data: List<T>) {
+        mutex.withLock {
+            cache[key] = CacheEntry(data, Instant.now())
+        }
+    }
+}
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/core/cache/CacheService.kt b/server/src/main/kotlin/org/dtree/fhir/server/core/cache/CacheService.kt
@@ -0,0 +1,4 @@
+package org.dtree.fhir.server.core.cache
+
+class CacheService {
+}
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/core/cache/PaginationUtil.kt b/server/src/main/kotlin/org/dtree/fhir/server/core/cache/PaginationUtil.kt
@@ -0,0 +1,27 @@
+package org.dtree.fhir.server.core.cache
+
+import org.dtree.fhir.server.core.models.PaginatedResponse
+import kotlin.math.ceil
+
+class PaginationUtil<T> {
+    fun paginate(items: List<T>, page: Int, pageSize: Int): PaginatedResponse<T> {
+        val totalItems = items.size
+        val totalPages = ceil(totalItems.toDouble() / pageSize).toInt()
+        val startIndex = (page - 1) * pageSize
+        val endIndex = minOf(startIndex + pageSize, totalItems)
+
+        val paginatedItems = if (startIndex < totalItems) {
+            items.subList(startIndex, endIndex)
+        } else {
+            emptyList()
+        }
+
+        return PaginatedResponse(
+            items = paginatedItems,
+            page = page,
+            pageSize = pageSize,
+            totalItems = totalItems,
+            totalPages = totalPages
+        )
+    }
+}
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/core/models/PaginatedResponse.kt b/server/src/main/kotlin/org/dtree/fhir/server/core/models/PaginatedResponse.kt
@@ -0,0 +1,9 @@
+package org.dtree.fhir.server.core.models
+
+data class PaginatedResponse<T>(
+    val items: List<T>,
+    val page: Int,
+    val pageSize: Int,
+    val totalItems: Int,
+    val totalPages: Int
+)
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/core/models/PaginationArgs.kt b/server/src/main/kotlin/org/dtree/fhir/server/core/models/PaginationArgs.kt
@@ -0,0 +1,19 @@
+package org.dtree.fhir.server.core.models
+
+data class PaginationArgs(
+    val all: Boolean = false,
+    val page: Int = 0,
+    val pageSize: Int = 0,
+) {
+    companion object {
+        fun parse(params:io.ktor.http.Parameters): PaginationArgs {
+            val all = params["all"]?.toBoolean() ?: true
+            val page = params["page"]?.toInt() ?: 0
+            val pageSize = params["pageSize"]?.toInt() ?: 0
+
+            return PaginationArgs(
+                all = all, page = page, pageSize = pageSize
+            )
+        }
+    }
+}
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/plugins/Frameworks.kt b/server/src/main/kotlin/org/dtree/fhir/server/plugins/Frameworks.kt
@@ -9,6 +9,7 @@ import org.dtree.fhir.server.plugins.injection.ModulesInjection
 import org.dtree.fhir.server.services.injection.ServicesInjection
 import org.dtree.fhir.server.util.LocalDateAdapter
 import org.dtree.fhir.server.util.LocalDateTimeTypeAdapter
+import org.koin.core.logger.Level
 import org.koin.dsl.module
 import org.koin.ktor.plugin.Koin
 import org.koin.logger.slf4jLogger
@@ -23,10 +24,11 @@ fun Application.configureFrameworks(dotEnv: Dotenv) {
         }
     }
     install(Koin) {
-        slf4jLogger()
+        slf4jLogger(level = Level.DEBUG)
         modules(module {
             single { dotEnv }
             single { FhirProvider() }
         }, ModulesInjection.koinBeans, ServicesInjection.koinBeans)
+
     }
 }
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/plugins/Routing.kt b/server/src/main/kotlin/org/dtree/fhir/server/plugins/Routing.kt
@@ -21,10 +21,6 @@ import org.dtree.fhir.server.plugins.tracing.tracingModule
 fun Application.configureRouting() {
     install(Resources)
     install(SwaggerUI) {
-        swagger {
-            swaggerUrl = "swagger-ui"
-            forwardRoot = true
-        }
         info {
             title = "Example API"
             version = "latest"
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/plugins/injection/ModulesInjection.kt b/server/src/main/kotlin/org/dtree/fhir/server/plugins/injection/ModulesInjection.kt
@@ -17,6 +17,7 @@ import org.dtree.fhir.server.controller.StatsController
 import org.dtree.fhir.server.controller.StatsControllerImpl
 import org.dtree.fhir.server.controller.TracingController
 import org.dtree.fhir.server.controller.TracingControllerImpl
+import org.koin.core.module.dsl.bind
 import org.koin.dsl.module
 
 object ModulesInjection {
@@ -29,15 +30,14 @@ object ModulesInjection {
             fetcher.getRepository()
             fetcher
         }
-        single<StatsController> { StatsControllerImpl() }
-        single<TracingController> { TracingControllerImpl() }
-        single<AppointmentController> { AppointmentControllerImpl() }
-        single<CarePlanController> { CarePlanControllerImpl() }
-        single<TasksController> { TasksControllerImpl() }
-        single<PatientController> { PatientControllerImpl() }
-
-        single<FhirClient> { FhirClient(this.get<Dotenv>(), this.get<FhirProvider>().parser) }
+        singleOf(::StatsControllerImpl) { bind<StatsController>() }
+        singleOf(::TracingControllerImpl) { bind<TracingController>() }
+        singleOf(::AppointmentControllerImpl) { bind<AppointmentController>() }
+        singleOf(::CarePlanControllerImpl) { bind<CarePlanController>() }
+        singleOf(::TasksControllerImpl) { bind<TasksController>() }
+        singleOf(::PatientControllerImpl) { bind<PatientController>() }
 
+        singleOf(::FhirClient)
         singleOf(::ResponseGenerator)
     }
 }
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/plugins/tracing/Tracing.kt b/server/src/main/kotlin/org/dtree/fhir/server/plugins/tracing/Tracing.kt
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/plugins/tracing/TracingModule.kt b/server/src/main/kotlin/org/dtree/fhir/server/plugins/tracing/TracingModule.kt
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/services/tracing/TracingService.kt b/server/src/main/kotlin/org/dtree/fhir/server/services/tracing/TracingService.kt
diff --git a/server/src/main/kotlin/org/dtree/fhir/server/services/tracing/TracingStatsResults.kt b/server/src/main/kotlin/org/dtree/fhir/server/services/tracing/TracingStatsResults.kt

Original file line number	Diff line number	Diff line change
`@@ -16,7 +16,9 @@ tasks.test {`
`16`	`16`	`}`
`17`	`17`
`18`	`18`	`tasks.withType<KotlinCompile> {`
`19`		`- kotlinOptions.jvmTarget = "1.8"`
	`19`	`+ kotlinOptions {`
	`20`	`+ jvmTarget = "11"`
	`21`	`+ }`
`20`	`22`	`}`
`21`	`23`
`22`	`24`	`application {`