commit 87ac9edb1e9b356405d6028f1a1798382a143bfa Author: Paul-Christian Volkmer Date: Mon Aug 5 19:23:58 2024 +0200 Initial commit diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..5a979af --- /dev/null +++ b/.gitignore @@ -0,0 +1,40 @@ +HELP.md +.gradle +build/ +!gradle/wrapper/gradle-wrapper.jar +!**/src/main/**/build/ +!**/src/test/**/build/ + +### STS ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache +bin/ +!**/src/main/**/bin/ +!**/src/test/**/bin/ + +### IntelliJ IDEA ### +.idea +*.iws +*.iml +*.ipr +out/ +!**/src/main/**/out/ +!**/src/test/**/out/ + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ + +### VS Code ### +.vscode/ + +### Kotlin ### +.kotlin diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..0ad25db --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published + by the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..97781c6 --- /dev/null +++ b/README.md @@ -0,0 +1,6 @@ +# onco-analytics-monitor + +Diese Anwendung überwacht die konfigurierten Topics, ermittelt die Anzahl der Conditions nach ICD10-Gruppe sortiert +und zeigt diese in Echtzeit an. + +![Screenshot](docs/screenshot.jpeg) diff --git a/build.gradle.kts b/build.gradle.kts new file mode 100644 index 0000000..5978aa4 --- /dev/null +++ b/build.gradle.kts @@ -0,0 +1,57 @@ +plugins { + id("org.springframework.boot") version "3.3.2" + id("io.spring.dependency-management") version "1.1.6" + id("org.graalvm.buildtools.native") version "0.10.2" + kotlin("jvm") version "1.9.24" + kotlin("plugin.spring") version "1.9.24" +} + +group = "dev.pcvolkmer.onco-analytics" +version = "0.0.1-SNAPSHOT" + +java { + toolchain { + languageVersion = JavaLanguageVersion.of(21) + } +} + +configurations { + compileOnly { + extendsFrom(configurations.annotationProcessor.get()) + } +} + +repositories { + mavenCentral() +} + +dependencies { + implementation("org.springframework.boot:spring-boot-starter-integration") + implementation("org.springframework.boot:spring-boot-starter-thymeleaf") + implementation("org.springframework.boot:spring-boot-starter-webflux") + implementation("com.fasterxml.jackson.module:jackson-module-kotlin") + implementation("io.projectreactor.kotlin:reactor-kotlin-extensions") + implementation("org.jetbrains.kotlin:kotlin-reflect") + implementation("org.jetbrains.kotlinx:kotlinx-coroutines-reactor") + implementation("org.springframework.kafka:spring-kafka") + implementation("commons-codec:commons-codec") + developmentOnly("org.springframework.boot:spring-boot-devtools") + developmentOnly("org.springframework.boot:spring-boot-docker-compose") + annotationProcessor("org.springframework.boot:spring-boot-configuration-processor") + testImplementation("org.springframework.boot:spring-boot-starter-test") + testImplementation("io.projectreactor:reactor-test") + testImplementation("org.jetbrains.kotlin:kotlin-test-junit5") + testImplementation("org.springframework.integration:spring-integration-test") + testImplementation("org.springframework.kafka:spring-kafka-test") + testRuntimeOnly("org.junit.platform:junit-platform-launcher") +} + +kotlin { + compilerOptions { + freeCompilerArgs.addAll("-Xjsr305=strict") + } +} + +tasks.withType { + useJUnitPlatform() +} diff --git a/dev-compose.yml b/dev-compose.yml new file mode 100644 index 0000000..7f8f37d --- /dev/null +++ b/dev-compose.yml @@ -0,0 +1,19 @@ +services: + + kafka: + image: bitnami/kafka + hostname: kafka + ports: + - "9092:9092" + - "9094:9094" + environment: + ALLOW_PLAINTEXT_LISTENER: "yes" + KAFKA_CFG_NODE_ID: "0" + KAFKA_CFG_PROCESS_ROLES: "controller,broker" + KAFKA_CFG_LISTENERS: PLAINTEXT://:9092,CONTROLLER://:9093,EXTERNAL://:9094 + KAFKA_CFG_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:9094 + KAFKA_CFG_LISTENER_SECURITY_PROTOCOL_MAP: CONTROLLER:PLAINTEXT,EXTERNAL:PLAINTEXT,PLAINTEXT:PLAINTEXT + KAFKA_CFG_INTER_BROKER_LISTENER_NAME: PLAINTEXT + KAFKA_CFG_AUTO_CREATE_TOPICS_ENABLE: true + KAFKA_CFG_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093 + KAFKA_CFG_CONTROLLER_LISTENER_NAMES: CONTROLLER diff --git a/docs/screenshot.jpeg b/docs/screenshot.jpeg new file mode 100644 index 0000000..4d20542 Binary files /dev/null and b/docs/screenshot.jpeg differ diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 0000000..e644113 Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 0000000..09523c0 --- /dev/null +++ b/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,7 @@ +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://services.gradle.org/distributions/gradle-8.9-bin.zip +networkTimeout=10000 +validateDistributionUrl=true +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew new file mode 100755 index 0000000..b740cf1 --- /dev/null +++ b/gradlew @@ -0,0 +1,249 @@ +#!/bin/sh + +# +# Copyright © 2015-2021 the original authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +############################################################################## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# +############################################################################## + +# Attempt to set APP_HOME + +# Resolve links: $0 may be a link +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac +done + +# This is normally unused +# shellcheck disable=SC2034 +APP_BASE_NAME=${0##*/} +# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036) +APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD=maximum + +warn () { + echo "$*" +} >&2 + +die () { + echo + echo "$*" + echo + exit 1 +} >&2 + +# OS specific support (must be 'true' or 'false'). +cygwin=false +msys=false +darwin=false +nonstop=false +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; +esac + +CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar + + +# Determine the Java command to use to start the JVM. +if [ -n "$JAVA_HOME" ] ; then + if [ -x "$JAVA_HOME/jre/sh/java" ] ; then + # IBM's JDK on AIX uses strange locations for the executables + JAVACMD=$JAVA_HOME/jre/sh/java + else + JAVACMD=$JAVA_HOME/bin/java + fi + if [ ! -x "$JAVACMD" ] ; then + die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +else + JAVACMD=java + if ! command -v java >/dev/null 2>&1 + then + die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +fi + +# Increase the maximum file descriptors if we can. +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC2039,SC3045 + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC2039,SC3045 + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac +fi + +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. + +# For Cygwin or MSYS, switch paths to Windows format before running java +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + + # Now convert the arguments - kludge to limit ourselves to /bin/sh + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) + fi + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg + done +fi + + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Collect all arguments for the java command: +# * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments, +# and any embedded shellness will be escaped. +# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be +# treated as '${Hostname}' itself on the command line. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Stop when "xargs" is not available. +if ! command -v xargs >/dev/null 2>&1 +then + die "xargs is not available" +fi + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# + +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' + +exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat new file mode 100644 index 0000000..7101f8e --- /dev/null +++ b/gradlew.bat @@ -0,0 +1,92 @@ +@rem +@rem Copyright 2015 the original author or authors. +@rem +@rem Licensed under the Apache License, Version 2.0 (the "License"); +@rem you may not use this file except in compliance with the License. +@rem You may obtain a copy of the License at +@rem +@rem https://www.apache.org/licenses/LICENSE-2.0 +@rem +@rem Unless required by applicable law or agreed to in writing, software +@rem distributed under the License is distributed on an "AS IS" BASIS, +@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +@rem See the License for the specific language governing permissions and +@rem limitations under the License. +@rem + +@if "%DEBUG%"=="" @echo off +@rem ########################################################################## +@rem +@rem Gradle startup script for Windows +@rem +@rem ########################################################################## + +@rem Set local scope for the variables with windows NT shell +if "%OS%"=="Windows_NT" setlocal + +set DIRNAME=%~dp0 +if "%DIRNAME%"=="" set DIRNAME=. +@rem This is normally unused +set APP_BASE_NAME=%~n0 +set APP_HOME=%DIRNAME% + +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + +@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" + +@rem Find java.exe +if defined JAVA_HOME goto findJavaFromJavaHome + +set JAVA_EXE=java.exe +%JAVA_EXE% -version >NUL 2>&1 +if %ERRORLEVEL% equ 0 goto execute + +echo. 1>&2 +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2 +echo. 1>&2 +echo Please set the JAVA_HOME variable in your environment to match the 1>&2 +echo location of your Java installation. 1>&2 + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto execute + +echo. 1>&2 +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2 +echo. 1>&2 +echo Please set the JAVA_HOME variable in your environment to match the 1>&2 +echo location of your Java installation. 1>&2 + +goto fail + +:execute +@rem Setup the command line + +set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + + +@rem Execute Gradle +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* + +:end +@rem End local scope for the variables with windows NT shell +if %ERRORLEVEL% equ 0 goto mainEnd + +:fail +rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of +rem the _cmd.exe /c_ return code! +set EXIT_CODE=%ERRORLEVEL% +if %EXIT_CODE% equ 0 set EXIT_CODE=1 +if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE% +exit /b %EXIT_CODE% + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega diff --git a/settings.gradle.kts b/settings.gradle.kts new file mode 100644 index 0000000..aa1e447 --- /dev/null +++ b/settings.gradle.kts @@ -0,0 +1 @@ +rootProject.name = "onco-analytics-monitor" diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/OncoAnalyticsMonitorApplication.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/OncoAnalyticsMonitorApplication.kt new file mode 100644 index 0000000..aef3875 --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/OncoAnalyticsMonitorApplication.kt @@ -0,0 +1,34 @@ +package dev.pcvolkmer.oncoanalytics.monitor + +import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository +import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics +import org.springframework.boot.autoconfigure.SpringBootApplication +import org.springframework.boot.runApplication +import org.springframework.context.annotation.Bean +import reactor.core.publisher.Sinks + +typealias StatisticsSink = Sinks.Many + +@SpringBootApplication +class OncoAnalyticsMonitorApplication { + + @Bean + fun statisticsEventProducer(): StatisticsSink { + return Sinks.many().multicast().onBackpressureBuffer() + } + + @Bean + fun obdsXmlConditionRepository(): ConditionInMemoryRepository { + return ConditionInMemoryRepository() + } + + @Bean + fun obdsFhirConditionRepository(): ConditionInMemoryRepository { + return ConditionInMemoryRepository() + } + +} + +fun main(args: Array) { + runApplication(*args) +} \ No newline at end of file diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/ConditionInMemoryRepository.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/ConditionInMemoryRepository.kt new file mode 100644 index 0000000..c274fa5 --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/ConditionInMemoryRepository.kt @@ -0,0 +1,32 @@ +package dev.pcvolkmer.oncoanalytics.monitor.conditions + +import org.apache.commons.codec.digest.DigestUtils + +@JvmInline +value class ConditionId(val value: String) + +data class Condition(val id: ConditionId, val version: Int, val icd10: String) { + companion object { + fun generateConditionId(patientId: String, tumorId: String): ConditionId { + return ConditionId(DigestUtils.sha256Hex("$patientId-$tumorId")) + } + } +} + +class ConditionInMemoryRepository { + + private val conditions = mutableMapOf() + + fun saveIfNewerVersion(condition: Condition): Boolean { + if ((this.conditions[condition.id]?.version ?: 0) < condition.version) { + this.conditions[condition.id] = condition + return true + } + return false + } + + fun findAll(): List { + return conditions.values.toList() + } + +} \ No newline at end of file diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/Statistics.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/Statistics.kt new file mode 100644 index 0000000..745ce59 --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/conditions/Statistics.kt @@ -0,0 +1,8 @@ +package dev.pcvolkmer.oncoanalytics.monitor.conditions + +data class Statistics( + val name: String, + val entries: List +) + +data class StatisticsEntry(val name: String, val count: Int) \ No newline at end of file diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/helpers.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/helpers.kt new file mode 100644 index 0000000..853b30b --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/helpers.kt @@ -0,0 +1,75 @@ +package dev.pcvolkmer.oncoanalytics.monitor + +import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository +import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics +import dev.pcvolkmer.oncoanalytics.monitor.conditions.StatisticsEntry + +val allKeys = listOf( + "C00-C14", + "C15", + "C16", + "C18-C21", + "C22", + "C23-C24", + "C25", + "C32", + "C33-C34", + "C50, D05", + "C53, D06", + "C54-C55", + "C56, D39.1", + "C61", + "C62", + "C64", + "C67, D09.0, D41.4", + "C70-C72", + "C73", + "C81", + "C82-C88, C96", + "C90", + "C91-C95", + "Other" +) + +fun fetchStatistics(name: String, source: ConditionInMemoryRepository): Statistics { + fun mapIcd10Code(code: String): String { + val c = when (code) { + "D39.1", "D09.0", "D41.4" -> code + else -> code.split('.').first() + } + + return when (c) { + "C00", "C01", "C02", "C03", "C04", "C05", "C06", "C07", "C08", "C09", "C10", "C11", "C12", "C13", "C14" -> "C00-C14" + "C15" -> "C15" + "C16" -> "C16" + "C18", "C19", "C20", "C21" -> "C18-C21" + "C22" -> "C22" + "C23", "C24" -> "C23-C24" + "C25" -> "C25" + "C32" -> "C32" + "C33", "C34" -> "C33-C34" + "C43" -> "C43" + "C50", "D05" -> "C50, D05" + "C53", "D06" -> "C53, D06" + "C54", "C55" -> "C54-C55" + "C56", "D39.1" -> "C56, D39.1" + "C61" -> "C61" + "C62" -> "C62" + "C64" -> "C64" + "C67", "D09.0", "D41.4" -> "C67, D09.0, D41.4" + "C70", "C71", "C72" -> "C70-C72" + "C73" -> "C73" + "C81" -> "C81" + "C82", "C83", "C84", "C85", "C86", "C87", "C88", "C96" -> "C82-C88, C96" + "C90" -> "C90" + "C91", "C92", "C93", "C94", "C95" -> "C91-C95" + else -> "Other" + } + } + + val entries = source.findAll() + .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)) }) +} \ No newline at end of file diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/ObdsXmlTopicMonitor.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/ObdsXmlTopicMonitor.kt new file mode 100644 index 0000000..c4e4a4e --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/ObdsXmlTopicMonitor.kt @@ -0,0 +1,79 @@ +package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners + +import com.fasterxml.jackson.annotation.JsonAlias +import com.fasterxml.jackson.annotation.JsonCreator +import com.fasterxml.jackson.annotation.JsonIgnoreProperties +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.ConditionInMemoryRepository +import dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics +import org.springframework.beans.factory.annotation.Qualifier +import org.springframework.kafka.annotation.KafkaListener +import org.springframework.kafka.support.KafkaHeaders +import org.springframework.messaging.handler.annotation.Header +import org.springframework.messaging.handler.annotation.Payload +import org.springframework.stereotype.Component +import org.xml.sax.InputSource +import java.io.StringReader +import javax.xml.xpath.XPathFactory + +@Component +class ObdsXmlTopicMonitor( + @Qualifier("obdsXmlConditionRepository") + private val conditionRepository: ConditionInMemoryRepository, + private val objectMapper: ObjectMapper, + statisticsEventProducer: StatisticsSink, +) : TopicMonitor(statisticsEventProducer) { + + @KafkaListener(topicPattern = "input.*") + override fun handleTopicRecord( + @Header(KafkaHeaders.RECEIVED_TOPIC) topic: String, + @Header(KafkaHeaders.RECEIVED_TIMESTAMP) timestamp: Long, + @Header(KafkaHeaders.RECEIVED_KEY) key: String, + @Payload payload: String, + ) { + try { + val p = objectMapper.readValue(payload, Record::class.java) + val xPath = XPathFactory.newDefaultInstance().newXPath() + + // Use local-name() due to XML namespace + val patientId = xPath.evaluate( + "//*[local-name()='Patienten_Stammdaten']/@Patient_ID", + InputSource(StringReader(p.payload.data)) + ) + val tumorId = xPath.evaluate( + "//*[local-name()='Tumorzuordnung']/@Tumor_ID", + InputSource(StringReader(p.payload.data)) + ) + val icd10 = xPath.evaluate( + "//*[local-name()='Primaertumor_ICD_Code']/text()", + InputSource(StringReader(p.payload.data)) + ) + + val updated = conditionRepository.saveIfNewerVersion( + Condition( + Condition.generateConditionId(patientId, tumorId), + p.payload.version, + icd10 + ) + ) + + if (updated) { + sendUpdatedStatistics(fetchStatistics("obdsxml", conditionRepository)) + } + } catch (e: Exception) { + // Ignore + } + } + + @JsonIgnoreProperties(ignoreUnknown = true) + class Record @JsonCreator constructor(val payload: RecordPayload) + + class RecordPayload @JsonCreator constructor( + @JsonAlias("ID") val id: Int, + @JsonAlias("YEAR") val year: String, + @JsonAlias("VERSIONSNUMMER") val version: Int, + @JsonAlias("XML_DATEN") val data: String + ) +} \ No newline at end of file diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/TopicMonitor.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/TopicMonitor.kt new file mode 100644 index 0000000..4ca0d34 --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/topiclisteners/TopicMonitor.kt @@ -0,0 +1,21 @@ +package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners + +import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics +import org.apache.kafka.common.TopicPartition +import org.springframework.kafka.listener.ConsumerSeekAware +import org.springframework.kafka.listener.ConsumerSeekAware.ConsumerSeekCallback +import reactor.core.publisher.Sinks + +abstract class TopicMonitor(private val statisticsEventProducer: Sinks.Many) : ConsumerSeekAware { + + abstract fun handleTopicRecord(topic: String, timestamp: Long, key: String, payload: String) + + fun sendUpdatedStatistics(statistics: Statistics) { + statisticsEventProducer.emitNext(statistics) { _, _ -> false } + } + + override fun onPartitionsAssigned(assignments: MutableMap, callback: ConsumerSeekCallback) { + callback.seekToBeginning(assignments.keys) + } + +} \ No newline at end of file diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/EventStreamController.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/EventStreamController.kt new file mode 100644 index 0000000..8e6e0dd --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/EventStreamController.kt @@ -0,0 +1,23 @@ +package dev.pcvolkmer.oncoanalytics.monitor.web + +import dev.pcvolkmer.oncoanalytics.monitor.StatisticsSink +import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics +import org.springframework.http.MediaType +import org.springframework.http.codec.ServerSentEvent +import org.springframework.web.bind.annotation.GetMapping +import org.springframework.web.bind.annotation.RestController +import reactor.core.publisher.Flux + +@RestController +class EventStreamController( + private val statisticsEventProducer: StatisticsSink, +) { + + @GetMapping(path = ["/events"], produces = [MediaType.TEXT_EVENT_STREAM_VALUE]) + fun eventStream(): Flux> { + return statisticsEventProducer.asFlux().map { + ServerSentEvent.builder(it).event(it.name).build() + }.doOnComplete { println("X") } + } + +} \ No newline at end of file diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/HomeController.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/HomeController.kt new file mode 100644 index 0000000..28072bc --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/HomeController.kt @@ -0,0 +1,14 @@ +package dev.pcvolkmer.oncoanalytics.monitor.web + +import org.springframework.stereotype.Controller +import org.springframework.web.bind.annotation.GetMapping + +@Controller +class HomeController { + + @GetMapping + fun index(): String { + return "index" + } + +} \ No newline at end of file diff --git a/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/StatisticsController.kt b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/StatisticsController.kt new file mode 100644 index 0000000..6d126ce --- /dev/null +++ b/src/main/kotlin/dev/pcvolkmer/oncoanalytics/monitor/web/StatisticsController.kt @@ -0,0 +1,30 @@ +package dev.pcvolkmer.oncoanalytics.monitor.web + +import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionInMemoryRepository +import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics +import dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics +import org.springframework.beans.factory.annotation.Qualifier +import org.springframework.web.bind.annotation.GetMapping +import org.springframework.web.bind.annotation.RequestMapping +import org.springframework.web.bind.annotation.RestController + +@RestController +@RequestMapping(path = ["/statistics"]) +class StatisticsController( + @Qualifier("obdsXmlConditionRepository") + private val obdsXmlConditionRepository: ConditionInMemoryRepository, + @Qualifier("obdsFhirConditionRepository") + private val obdsFhirConditionRepository: ConditionInMemoryRepository, +) { + + @GetMapping(path = ["obdsxml"]) + fun obdsxmlStatistics(): Statistics { + return fetchStatistics("obdsxml", obdsXmlConditionRepository) + } + + @GetMapping(path = ["obdsfhir"]) + fun obdsfhirStatistics(): Statistics { + return fetchStatistics("obdfhir", obdsFhirConditionRepository) + } + +} \ No newline at end of file diff --git a/src/main/resources/application-dev.yml b/src/main/resources/application-dev.yml new file mode 100644 index 0000000..80bc974 --- /dev/null +++ b/src/main/resources/application-dev.yml @@ -0,0 +1,8 @@ +spring: + application: + name: onco-analytics-monitor + + docker: + compose: + file: dev-compose.yml + diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml new file mode 100644 index 0000000..9a29b4c --- /dev/null +++ b/src/main/resources/application.yml @@ -0,0 +1,18 @@ +spring: + application: + name: onco-analytics-monitor + + kafka: + consumer: + group-id: ${spring.application.name} + + web: + resources: + cache: + cachecontrol: + max-age: 1d + chain: + strategy: + content: + enabled: true + paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg \ No newline at end of file diff --git a/src/main/resources/static/images/db.png b/src/main/resources/static/images/db.png new file mode 100644 index 0000000..663862d Binary files /dev/null and b/src/main/resources/static/images/db.png differ diff --git a/src/main/resources/static/images/job.png b/src/main/resources/static/images/job.png new file mode 100644 index 0000000..f624bef Binary files /dev/null and b/src/main/resources/static/images/job.png differ diff --git a/src/main/resources/static/images/kafka.png b/src/main/resources/static/images/kafka.png new file mode 100644 index 0000000..daf45d8 Binary files /dev/null and b/src/main/resources/static/images/kafka.png differ diff --git a/src/main/resources/static/images/topic.png b/src/main/resources/static/images/topic.png new file mode 100644 index 0000000..600cc82 Binary files /dev/null and b/src/main/resources/static/images/topic.png differ diff --git a/src/main/resources/templates/index.html b/src/main/resources/templates/index.html new file mode 100644 index 0000000..505999f --- /dev/null +++ b/src/main/resources/templates/index.html @@ -0,0 +1,185 @@ + + + + + onco-analytics-monitor + + + + +
+ +
+

onco-analytics-monitor

+

+ Überwachung der einzelnen Kafka Topics und enthaltener Conditions - aufgeteilt nach ICD10-Gruppe. +

+
+ +
+
+ +
Onkostar Database
+
+
+
+ +
Kafka Connect
+
+
+
+ +
Kafka Topic oBDS XML
+
+
+
+
+
+
+ +
oBDS-to-fhir
+
+
+
+ +
Kafka Topic oBDS FHIR
+
+
+
+
+
+ +
+ + + + + \ No newline at end of file diff --git a/src/test/kotlin/dev/pcvolkmer/oncoanalytics/monitor/OncoAnalyticsMonitorApplicationTests.kt b/src/test/kotlin/dev/pcvolkmer/oncoanalytics/monitor/OncoAnalyticsMonitorApplicationTests.kt new file mode 100644 index 0000000..1c47f36 --- /dev/null +++ b/src/test/kotlin/dev/pcvolkmer/oncoanalytics/monitor/OncoAnalyticsMonitorApplicationTests.kt @@ -0,0 +1,13 @@ +package dev.pcvolkmer.oncoanalytics.monitor + +import org.junit.jupiter.api.Test +import org.springframework.boot.test.context.SpringBootTest + +@SpringBootTest +class OncoAnalyticsMonitorApplicationTests { + + @Test + fun contextLoads() { + } + +}