commit fe0f431d4df0eac84d277af2cd54cf9006f8e3bb Author: Paul-Christian Volkmer Date: Thu Jun 19 13:37:55 2025 +0200 Initial commit diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..581bf51 --- /dev/null +++ b/.gitignore @@ -0,0 +1,39 @@ +.gradle +build/ +!gradle/wrapper/gradle-wrapper.jar +!**/src/main/**/build/ +!**/src/test/**/build/ + +### IntelliJ IDEA ### +.idea/ +*.iws +*.iml +*.ipr +out/ +!**/src/main/**/out/ +!**/src/test/**/out/ + +### Eclipse ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache +bin/ +!**/src/main/**/bin/ +!**/src/test/**/bin/ + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ + +### VS Code ### +.vscode/ + +### Mac OS ### +.DS_Store diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..0a04128 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,165 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 3, 29 June 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. + + + This version of the GNU Lesser General Public License incorporates +the terms and conditions of version 3 of the GNU General Public +License, supplemented by the additional permissions listed below. + + 0. Additional Definitions. + + As used herein, "this License" refers to version 3 of the GNU Lesser +General Public License, and the "GNU GPL" refers to version 3 of the GNU +General Public License. + + "The Library" refers to a covered work governed by this License, +other than an Application or a Combined Work as defined below. + + An "Application" is any work that makes use of an interface provided +by the Library, but which is not otherwise based on the Library. +Defining a subclass of a class defined by the Library is deemed a mode +of using an interface provided by the Library. + + A "Combined Work" is a work produced by combining or linking an +Application with the Library. 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Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + + Each version is given a distinguishing version number. If the +Library as you received it specifies that a certain numbered version +of the GNU Lesser General Public License "or any later version" +applies to it, you have the option of following the terms and +conditions either of that published version or of any later version +published by the Free Software Foundation. If the Library as you +received it does not specify a version number of the GNU Lesser +General Public License, you may choose any version of the GNU Lesser +General Public License ever published by the Free Software Foundation. + + If the Library as you received it specifies that a proxy can decide +whether future versions of the GNU Lesser General Public License shall +apply, that proxy's public statement of acceptance of any version is +permanent authorization for you to choose that version for the +Library. diff --git a/README.md b/README.md new file mode 100644 index 0000000..9ba4063 --- /dev/null +++ b/README.md @@ -0,0 +1,4 @@ +# Datenextraktion aus den Onkostar DNPM-Formularen + +Ziel dieser Library ist die Bereitstellung von Methoden zum Laden von Daten der DNPM-Formulare aus der Onkostar-Datenbank +und dem Mapping in das DNPM-Datenmodell 2.1. diff --git a/build.gradle.kts b/build.gradle.kts new file mode 100644 index 0000000..7dd08fc --- /dev/null +++ b/build.gradle.kts @@ -0,0 +1,60 @@ +plugins { + id("java") + id("java-library") +} + +group = "dev.pcvolkmer.onco" +version = "0.1.0-SNAPSHOT" + +var versions = mapOf( + "mtb-dto" to "0.1.0-SNAPSHOT", + "junit" to "5.13.1", + "assertj" to "3.27.3", + "mockito" to "5.18.0" +) + +java { + toolchain { + languageVersion = JavaLanguageVersion.of(11) + } +} + +configurations { + all { + resolutionStrategy { + cacheChangingModulesFor(5, "minutes") + } + } +} + +repositories { + maven { + url = uri("https://git.dnpm.dev/api/packages/public-snapshots/maven") + } + maven { + url = uri("https://git.dnpm.dev/api/packages/public/maven") + } + mavenCentral() +} + +dependencies { + api("dev.pcvolkmer.mv64e:mtb-dto:${versions["mtb-dto"]}") { isChanging = true } + implementation("org.springframework:spring-jdbc") { + version { + strictly("[4.3.8.RELEASE, )") + // Current Onkostar 2.14.0 dependendcy + prefer("4.3.8.RELEASE") + } + } + + testImplementation(platform("org.junit:junit-bom:${versions["junit"]}")) + testImplementation("org.junit.jupiter:junit-jupiter") + testImplementation("org.assertj:assertj-core:${versions["assertj"]}") + testImplementation("org.mockito:mockito-core:${versions["mockito"]}") + testImplementation("org.mockito:mockito-junit-jupiter:${versions["mockito"]}") + testRuntimeOnly("org.junit.platform:junit-platform-launcher") +} + +tasks.test { + useJUnitPlatform() +} diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 0000000..249e583 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..3f732bb --- /dev/null +++ b/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,6 @@ +#Thu Jun 19 10:34:56 CEST 2025 +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew new file mode 100755 index 0000000..1b6c787 --- /dev/null +++ b/gradlew @@ -0,0 +1,234 @@ +#!/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/master/subprojects/plugins/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 + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit + +APP_NAME="Gradle" +APP_BASE_NAME=${0##*/} + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD=maximum + +warn () { + echo "$*" +} >&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: $JAVA_HOME + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +else + JAVACMD=java + which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." +fi + +# Increase the maximum file descriptors if we can. +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$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 + +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# 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..107acd3 --- /dev/null +++ b/gradlew.bat @@ -0,0 +1,89 @@ +@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=. +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%" == "0" goto execute + +echo. +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto execute + +echo. +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +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%"=="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! +if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 +exit /b 1 + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega diff --git a/settings.gradle.kts b/settings.gradle.kts new file mode 100644 index 0000000..42d6866 --- /dev/null +++ b/settings.gradle.kts @@ -0,0 +1 @@ +rootProject.name = "mv64e-onkostar-data" diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/DataMapper.java b/src/main/java/dev/pcvolkmer/onco/datamapper/DataMapper.java new file mode 100644 index 0000000..5db752b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/DataMapper.java @@ -0,0 +1,19 @@ +package dev.pcvolkmer.onco.datamapper; + +/** + * General interface for all data mappers + * + * @since 0.1 + * @author Paul-Christian Volkmer + * @param The destination type + */ +public interface DataMapper { + + /** + * Loads a data set from database and maps it into destination data type + * @param id The database id of the root procedure data set + * @return The data set to be loaded + */ + T getById(int id); + +} diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/KpaDiagnosisDataMapper.java b/src/main/java/dev/pcvolkmer/onco/datamapper/KpaDiagnosisDataMapper.java new file mode 100644 index 0000000..2ec2599 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/KpaDiagnosisDataMapper.java @@ -0,0 +1,63 @@ +package dev.pcvolkmer.onco.datamapper; + +import dev.pcvolkmer.mv64e.mtb.Coding; +import dev.pcvolkmer.mv64e.mtb.Mtb; +import dev.pcvolkmer.mv64e.mtb.MtbDiagnosis; +import dev.pcvolkmer.onco.datamapper.datacatalogues.Kpa; +import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException; +import org.springframework.jdbc.core.JdbcTemplate; + +import javax.sql.DataSource; +import java.sql.SQLException; + +/** + * Mapper class to load and map diagnosis data from database table 'dk_dnpm_kpa' + * + * @author Paul-Christian Volkmer + * @since 0.1 + */ +public class KpaDiagnosisDataMapper implements DataMapper { + + private final JdbcTemplate jdbcTemplate; + + KpaDiagnosisDataMapper(final JdbcTemplate jdbcTemplate) { + this.jdbcTemplate = jdbcTemplate; + } + + /** + * Create instance of the mapper class + * + * @param dataSource The datasource to be used + * @return The initialized mapper + */ + public static KpaDiagnosisDataMapper create(final DataSource dataSource) { + return new KpaDiagnosisDataMapper(new JdbcTemplate(dataSource)); + } + + /** + * Loads and maps a diagnosis using the kpa procedures database id + * + * @param id The database id of the procedure data set + * @return The loaded MtbDiagnosis file + */ + @Override + public MtbDiagnosis getById(int id) { + var kpa = Kpa.create(this.jdbcTemplate); + var data = kpa.getById(id); + + var builder = MtbDiagnosis.builder(); + try { + builder + .id(data.getString("id")) + .code( + Coding.builder() + .code(data.getString("icd10")) + .build() + ); + } catch (SQLException e) { + throw new DataAccessException(e.getMessage()); + } + return builder.build(); + } + +} diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/MtbDataMapper.java b/src/main/java/dev/pcvolkmer/onco/datamapper/MtbDataMapper.java new file mode 100644 index 0000000..e6dbb38 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/MtbDataMapper.java @@ -0,0 +1,56 @@ +package dev.pcvolkmer.onco.datamapper; + +import dev.pcvolkmer.mv64e.mtb.Mtb; +import dev.pcvolkmer.onco.datamapper.datacatalogues.Kpa; +import org.springframework.jdbc.core.JdbcTemplate; + +import javax.sql.DataSource; + +/** + * Mapper class to load and map Mtb files from database + * + * @author Paul-Christian Volkmer + * @since 0.1 + */ +public class MtbDataMapper implements DataMapper { + + private final JdbcTemplate jdbcTemplate; + + MtbDataMapper(final JdbcTemplate jdbcTemplate) { + this.jdbcTemplate = jdbcTemplate; + } + + /** + * Create instance of the mapper class + * + * @param dataSource The datasource to be used + * @return The initialized mapper + */ + public static MtbDataMapper create(final DataSource dataSource) { + return new MtbDataMapper(new JdbcTemplate(dataSource)); + } + + /** + * Loads and maps a Mtb file using the root procedures database id + * + * @param id The database id of the root procedure data set + * @return The loaded Mtb file + */ + @Override + public Mtb getById(int id) { + return Mtb.builder().build(); + } + + /** + * Loads and maps a Mtb file using the case id + * + * @param caseId The case id + * @return The loaded Mtb file + */ + public Mtb getByCaseId(String caseId) { + var kpa = Kpa.create(this.jdbcTemplate); + return this.getById( + kpa.getProcedureIdByCaseId(caseId) + ); + } +} diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/Kpa.java b/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/Kpa.java new file mode 100644 index 0000000..0ec5c23 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/Kpa.java @@ -0,0 +1,86 @@ +package dev.pcvolkmer.onco.datamapper.datacatalogues; + +import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException; +import org.springframework.jdbc.core.JdbcTemplate; + +import java.sql.ResultSet; + +/** + * Load raw result sets from database table 'dk_dnpm_kpa' + * + * @author Paul-Christian Volkmer + * @since 0.1 + */ +public class Kpa { + + private final JdbcTemplate jdbcTemplate; + + private Kpa(JdbcTemplate jdbcTemplate) { + this.jdbcTemplate = jdbcTemplate; + } + + public static Kpa create(JdbcTemplate jdbcTemplate) { + return new Kpa(jdbcTemplate); + } + + /** + * Get procedure result set by procedure id + * @param id The procedure id + * @return The procedure id + */ + public ResultSet getById(int id) { + var result = this.jdbcTemplate.query( + "SELECT * FROM dk_dnpm_kpa id = ?", + (resultSet, i) -> resultSet, + id); + + if (result.isEmpty()) { + throw new DataAccessException("No record found for id: " + id); + } else if (result.size() > 1) { + throw new DataAccessException("Multiple records found for id: " + id); + } + + return result.get(0); + } + + /** + * Get procedure database id by case id + * @param caseId The case id + * @return The procedure id + */ + public int getProcedureIdByCaseId(String caseId) { + var result = this.jdbcTemplate.query( + "SELECT id FROM dk_dnpm_kpa WHERE fallnummermv = ?", + (resultSet, i) -> resultSet.getInt(1), + caseId); + + if (result.isEmpty()) { + throw new DataAccessException("No record found for case: " + caseId); + } else if (result.size() > 1) { + throw new DataAccessException("Multiple records found for case: " + caseId); + } + + return result.get(0); + } + + /** + * Get patient database id by case id + * @param caseId The case id + * @return The patients database id + */ + public int getPatientIdByCaseId(String caseId) { + var result = this.jdbcTemplate.query( + "SELECT patient_id FROM dk_dnpm_kpa JOIN prozedur ON (prozedur.id = dk_dnpm_kpa.id) WHERE fallnummermv = ?", + (resultSet, i) -> resultSet.getInt(1), + caseId); + + if (result.isEmpty()) { + throw new DataAccessException("No record found for case: " + caseId); + } else if (result.size() > 1) { + throw new DataAccessException("Multiple records found for case: " + caseId); + } + + return result.get(0); + } + +} diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/exceptions/DataAccessException.java b/src/main/java/dev/pcvolkmer/onco/datamapper/exceptions/DataAccessException.java new file mode 100644 index 0000000..41191e7 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/exceptions/DataAccessException.java @@ -0,0 +1,13 @@ +package dev.pcvolkmer.onco.datamapper.exceptions; + +/** + * Exception to be thrown if no or unexpected multiple data sets where found + * + * @author Paul-Christian Volkmer + * @since 0.1 + */ +public class DataAccessException extends RuntimeException { + public DataAccessException(String message) { + super(message); + } +} diff --git a/src/test/java/dev/pcvolkmer/onco/datamapper/KpaDiagnosisDataMapperTest.java b/src/test/java/dev/pcvolkmer/onco/datamapper/KpaDiagnosisDataMapperTest.java new file mode 100644 index 0000000..07c97bb --- /dev/null +++ b/src/test/java/dev/pcvolkmer/onco/datamapper/KpaDiagnosisDataMapperTest.java @@ -0,0 +1,63 @@ +package dev.pcvolkmer.onco.datamapper; + +import dev.pcvolkmer.mv64e.mtb.MtbDiagnosis; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.jdbc.core.RowMapper; + +import javax.sql.DataSource; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.List; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.*; +import static org.mockito.Mockito.doAnswer; + +@ExtendWith(MockitoExtension.class) +class KpaDiagnosisDataMapperTest { + + JdbcTemplate jdbcTemplate; + + KpaDiagnosisDataMapper dataMapper; + + @BeforeEach + void setUp(@Mock JdbcTemplate jdbcTemplate) { + this.jdbcTemplate = jdbcTemplate; + this.dataMapper = new KpaDiagnosisDataMapper(jdbcTemplate); + } + + @Test + void shouldCreateDataMapper(@Mock DataSource dataSource) { + assertThat(MtbDataMapper.create(dataSource)).isNotNull(); + } + + @Test + void shouldUseKpaProcedureId(@Mock ResultSet resultSet) throws SQLException { + doAnswer(invocationOnMock -> { + var columnName = invocationOnMock.getArgument(0, String.class); + switch (columnName) { + case "id": + return "1"; + case "icd10": + return "F79.9"; + default: + return null; + } + }).when(resultSet).getString(anyString()); + + doAnswer(invocationOnMock -> List.of(resultSet)) + .when(jdbcTemplate) + .query(anyString(), any(RowMapper.class), anyInt()); + + var actual = this.dataMapper.getById(1); + assertThat(actual).isInstanceOf(MtbDiagnosis.class); + assertThat(actual.getId()).isEqualTo("1"); + assertThat(actual.getCode().getCode()).isEqualTo("F79.9"); + } + +} diff --git a/src/test/java/dev/pcvolkmer/onco/datamapper/MtbDataMapperTest.java b/src/test/java/dev/pcvolkmer/onco/datamapper/MtbDataMapperTest.java new file mode 100644 index 0000000..0eddf4d --- /dev/null +++ b/src/test/java/dev/pcvolkmer/onco/datamapper/MtbDataMapperTest.java @@ -0,0 +1,71 @@ +package dev.pcvolkmer.onco.datamapper; + +import dev.pcvolkmer.mv64e.mtb.Mtb; +import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.jdbc.core.RowMapper; + +import javax.sql.DataSource; + +import java.util.List; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.doAnswer; + +@ExtendWith(MockitoExtension.class) +class MtbDataMapperTest { + + JdbcTemplate jdbcTemplate; + + MtbDataMapper mtbDataMapper; + + @BeforeEach + void setUp(@Mock JdbcTemplate jdbcTemplate) { + this.jdbcTemplate = jdbcTemplate; + this.mtbDataMapper = new MtbDataMapper(jdbcTemplate); + } + + @Test + void shouldCreateDataMapper(@Mock DataSource dataSource) { + assertThat(MtbDataMapper.create(dataSource)).isNotNull(); + } + + @Test + void shouldUseKpaProcedureId() { + doAnswer(invocationOnMock -> List.of(1)) + .when(jdbcTemplate) + .query(anyString(), any(RowMapper.class), anyString()); + + var actual = this.mtbDataMapper.getByCaseId("16000123"); + assertThat(actual).isInstanceOf(Mtb.class); + } + + @Test + void shouldThrowExceptionIfNoKpaProcedureFound() { + var ex = assertThrows(DataAccessException.class, () -> { + this.mtbDataMapper.getByCaseId("16000123"); + }); + assertThat(ex).hasMessage("No record found for case: 16000123"); + } + + @Test + void shouldThrowExceptionIfMultipleKpaProceduresFound() { + doAnswer(invocationOnMock -> List.of(1, 2)) + .when(jdbcTemplate) + .query(anyString(), any(RowMapper.class), anyString()); + + var ex = assertThrows(DataAccessException.class, () -> { + this.mtbDataMapper.getByCaseId("16000123"); + }); + assertThat(ex).hasMessage("Multiple records found for case: 16000123"); + } + +}