The very first commit

.gitattributes

+/mvnw text eol=lf
+*.cmd text eol=crlf

.gitignore

+HELP.md
+target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+
+### STS ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### IntelliJ IDEA ###
+.idea
+*.iws
+*.iml
+*.ipr
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/

.mvn/wrapper/maven-wrapper.properties

+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you 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
+#
+#   http://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.
+wrapperVersion=3.3.2
+distributionType=only-script
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.9/apache-maven-3.9.9-bin.zip

UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt

+"hahahahahahaha"
\ No newline at end of file

UserselidrAppDataLocalTemp³661.263675-references.txt

+"heeeeeeeeeeeeeeeeeeej"
\ No newline at end of file

mvnw

+#!/bin/sh
+# ----------------------------------------------------------------------------
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you 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
+#
+#    http://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.
+# ----------------------------------------------------------------------------
+
+# ----------------------------------------------------------------------------
+# Apache Maven Wrapper startup batch script, version 3.3.2
+#
+# Optional ENV vars
+# -----------------
+#   JAVA_HOME - location of a JDK home dir, required when download maven via java source
+#   MVNW_REPOURL - repo url base for downloading maven distribution
+#   MVNW_USERNAME/MVNW_PASSWORD - user and password for downloading maven
+#   MVNW_VERBOSE - true: enable verbose log; debug: trace the mvnw script; others: silence the output
+# ----------------------------------------------------------------------------
+
+set -euf
+[ "${MVNW_VERBOSE-}" != debug ] || set -x
+
+# OS specific support.
+native_path() { printf %s\\n "$1"; }
+case "$(uname)" in
+CYGWIN* | MINGW*)
+  [ -z "${JAVA_HOME-}" ] || JAVA_HOME="$(cygpath --unix "$JAVA_HOME")"
+  native_path() { cygpath --path --windows "$1"; }
+  ;;
+esac
+
+# set JAVACMD and JAVACCMD
+set_java_home() {
+  # For Cygwin and MinGW, ensure paths are in Unix format before anything is touched
+  if [ -n "${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"
+      JAVACCMD="$JAVA_HOME/jre/sh/javac"
+    else
+      JAVACMD="$JAVA_HOME/bin/java"
+      JAVACCMD="$JAVA_HOME/bin/javac"
+
+      if [ ! -x "$JAVACMD" ] || [ ! -x "$JAVACCMD" ]; then
+        echo "The JAVA_HOME environment variable is not defined correctly, so mvnw cannot run." >&2
+        echo "JAVA_HOME is set to \"$JAVA_HOME\", but \"\$JAVA_HOME/bin/java\" or \"\$JAVA_HOME/bin/javac\" does not exist." >&2
+        return 1
+      fi
+    fi
+  else
+    JAVACMD="$(
+      'set' +e
+      'unset' -f command 2>/dev/null
+      'command' -v java
+    )" || :
+    JAVACCMD="$(
+      'set' +e
+      'unset' -f command 2>/dev/null
+      'command' -v javac
+    )" || :
+
+    if [ ! -x "${JAVACMD-}" ] || [ ! -x "${JAVACCMD-}" ]; then
+      echo "The java/javac command does not exist in PATH nor is JAVA_HOME set, so mvnw cannot run." >&2
+      return 1
+    fi
+  fi
+}
+
+# hash string like Java String::hashCode
+hash_string() {
+  str="${1:-}" h=0
+  while [ -n "$str" ]; do
+    char="${str%"${str#?}"}"
+    h=$(((h * 31 + $(LC_CTYPE=C printf %d "'$char")) % 4294967296))
+    str="${str#?}"
+  done
+  printf %x\\n $h
+}
+
+verbose() { :; }
+[ "${MVNW_VERBOSE-}" != true ] || verbose() { printf %s\\n "${1-}"; }
+
+die() {
+  printf %s\\n "$1" >&2
+  exit 1
+}
+
+trim() {
+  # MWRAPPER-139:
+  #   Trims trailing and leading whitespace, carriage returns, tabs, and linefeeds.
+  #   Needed for removing poorly interpreted newline sequences when running in more
+  #   exotic environments such as mingw bash on Windows.
+  printf "%s" "${1}" | tr -d '[:space:]'
+}
+
+# parse distributionUrl and optional distributionSha256Sum, requires .mvn/wrapper/maven-wrapper.properties
+while IFS="=" read -r key value; do
+  case "${key-}" in
+  distributionUrl) distributionUrl=$(trim "${value-}") ;;
+  distributionSha256Sum) distributionSha256Sum=$(trim "${value-}") ;;
+  esac
+done <"${0%/*}/.mvn/wrapper/maven-wrapper.properties"
+[ -n "${distributionUrl-}" ] || die "cannot read distributionUrl property in ${0%/*}/.mvn/wrapper/maven-wrapper.properties"
+
+case "${distributionUrl##*/}" in
+maven-mvnd-*bin.*)
+  MVN_CMD=mvnd.sh _MVNW_REPO_PATTERN=/maven/mvnd/
+  case "${PROCESSOR_ARCHITECTURE-}${PROCESSOR_ARCHITEW6432-}:$(uname -a)" in
+  *AMD64:CYGWIN* | *AMD64:MINGW*) distributionPlatform=windows-amd64 ;;
+  :Darwin*x86_64) distributionPlatform=darwin-amd64 ;;
+  :Darwin*arm64) distributionPlatform=darwin-aarch64 ;;
+  :Linux*x86_64*) distributionPlatform=linux-amd64 ;;
+  *)
+    echo "Cannot detect native platform for mvnd on $(uname)-$(uname -m), use pure java version" >&2
+    distributionPlatform=linux-amd64
+    ;;
+  esac
+  distributionUrl="${distributionUrl%-bin.*}-$distributionPlatform.zip"
+  ;;
+maven-mvnd-*) MVN_CMD=mvnd.sh _MVNW_REPO_PATTERN=/maven/mvnd/ ;;
+*) MVN_CMD="mvn${0##*/mvnw}" _MVNW_REPO_PATTERN=/org/apache/maven/ ;;
+esac
+
+# apply MVNW_REPOURL and calculate MAVEN_HOME
+# maven home pattern: ~/.m2/wrapper/dists/{apache-maven-<version>,maven-mvnd-<version>-<platform>}/<hash>
+[ -z "${MVNW_REPOURL-}" ] || distributionUrl="$MVNW_REPOURL$_MVNW_REPO_PATTERN${distributionUrl#*"$_MVNW_REPO_PATTERN"}"
+distributionUrlName="${distributionUrl##*/}"
+distributionUrlNameMain="${distributionUrlName%.*}"
+distributionUrlNameMain="${distributionUrlNameMain%-bin}"
+MAVEN_USER_HOME="${MAVEN_USER_HOME:-${HOME}/.m2}"
+MAVEN_HOME="${MAVEN_USER_HOME}/wrapper/dists/${distributionUrlNameMain-}/$(hash_string "$distributionUrl")"
+
+exec_maven() {
+  unset MVNW_VERBOSE MVNW_USERNAME MVNW_PASSWORD MVNW_REPOURL || :
+  exec "$MAVEN_HOME/bin/$MVN_CMD" "$@" || die "cannot exec $MAVEN_HOME/bin/$MVN_CMD"
+}
+
+if [ -d "$MAVEN_HOME" ]; then
+  verbose "found existing MAVEN_HOME at $MAVEN_HOME"
+  exec_maven "$@"
+fi
+
+case "${distributionUrl-}" in
+*?-bin.zip | *?maven-mvnd-?*-?*.zip) ;;
+*) die "distributionUrl is not valid, must match *-bin.zip or maven-mvnd-*.zip, but found '${distributionUrl-}'" ;;
+esac
+
+# prepare tmp dir
+if TMP_DOWNLOAD_DIR="$(mktemp -d)" && [ -d "$TMP_DOWNLOAD_DIR" ]; then
+  clean() { rm -rf -- "$TMP_DOWNLOAD_DIR"; }
+  trap clean HUP INT TERM EXIT
+else
+  die "cannot create temp dir"
+fi
+
+mkdir -p -- "${MAVEN_HOME%/*}"
+
+# Download and Install Apache Maven
+verbose "Couldn't find MAVEN_HOME, downloading and installing it ..."
+verbose "Downloading from: $distributionUrl"
+verbose "Downloading to: $TMP_DOWNLOAD_DIR/$distributionUrlName"
+
+# select .zip or .tar.gz
+if ! command -v unzip >/dev/null; then
+  distributionUrl="${distributionUrl%.zip}.tar.gz"
+  distributionUrlName="${distributionUrl##*/}"
+fi
+
+# verbose opt
+__MVNW_QUIET_WGET=--quiet __MVNW_QUIET_CURL=--silent __MVNW_QUIET_UNZIP=-q __MVNW_QUIET_TAR=''
+[ "${MVNW_VERBOSE-}" != true ] || __MVNW_QUIET_WGET='' __MVNW_QUIET_CURL='' __MVNW_QUIET_UNZIP='' __MVNW_QUIET_TAR=v
+
+# normalize http auth
+case "${MVNW_PASSWORD:+has-password}" in
+'') MVNW_USERNAME='' MVNW_PASSWORD='' ;;
+has-password) [ -n "${MVNW_USERNAME-}" ] || MVNW_USERNAME='' MVNW_PASSWORD='' ;;
+esac
+
+if [ -z "${MVNW_USERNAME-}" ] && command -v wget >/dev/null; then
+  verbose "Found wget ... using wget"
+  wget ${__MVNW_QUIET_WGET:+"$__MVNW_QUIET_WGET"} "$distributionUrl" -O "$TMP_DOWNLOAD_DIR/$distributionUrlName" || die "wget: Failed to fetch $distributionUrl"
+elif [ -z "${MVNW_USERNAME-}" ] && command -v curl >/dev/null; then
+  verbose "Found curl ... using curl"
+  curl ${__MVNW_QUIET_CURL:+"$__MVNW_QUIET_CURL"} -f -L -o "$TMP_DOWNLOAD_DIR/$distributionUrlName" "$distributionUrl" || die "curl: Failed to fetch $distributionUrl"
+elif set_java_home; then
+  verbose "Falling back to use Java to download"
+  javaSource="$TMP_DOWNLOAD_DIR/Downloader.java"
+  targetZip="$TMP_DOWNLOAD_DIR/$distributionUrlName"
+  cat >"$javaSource" <<-END
+	public class Downloader extends java.net.Authenticator
+	{
+	  protected java.net.PasswordAuthentication getPasswordAuthentication()
+	  {
+	    return new java.net.PasswordAuthentication( System.getenv( "MVNW_USERNAME" ), System.getenv( "MVNW_PASSWORD" ).toCharArray() );
+	  }
+	  public static void main( String[] args ) throws Exception
+	  {
+	    setDefault( new Downloader() );
+	    java.nio.file.Files.copy( java.net.URI.create( args[0] ).toURL().openStream(), java.nio.file.Paths.get( args[1] ).toAbsolutePath().normalize() );
+	  }
+	}
+	END
+  # For Cygwin/MinGW, switch paths to Windows format before running javac and java
+  verbose " - Compiling Downloader.java ..."
+  "$(native_path "$JAVACCMD")" "$(native_path "$javaSource")" || die "Failed to compile Downloader.java"
+  verbose " - Running Downloader.java ..."
+  "$(native_path "$JAVACMD")" -cp "$(native_path "$TMP_DOWNLOAD_DIR")" Downloader "$distributionUrl" "$(native_path "$targetZip")"
+fi
+
+# If specified, validate the SHA-256 sum of the Maven distribution zip file
+if [ -n "${distributionSha256Sum-}" ]; then
+  distributionSha256Result=false
+  if [ "$MVN_CMD" = mvnd.sh ]; then
+    echo "Checksum validation is not supported for maven-mvnd." >&2
+    echo "Please disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." >&2
+    exit 1
+  elif command -v sha256sum >/dev/null; then
+    if echo "$distributionSha256Sum  $TMP_DOWNLOAD_DIR/$distributionUrlName" | sha256sum -c >/dev/null 2>&1; then
+      distributionSha256Result=true
+    fi
+  elif command -v shasum >/dev/null; then
+    if echo "$distributionSha256Sum  $TMP_DOWNLOAD_DIR/$distributionUrlName" | shasum -a 256 -c >/dev/null 2>&1; then
+      distributionSha256Result=true
+    fi
+  else
+    echo "Checksum validation was requested but neither 'sha256sum' or 'shasum' are available." >&2
+    echo "Please install either command, or disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." >&2
+    exit 1
+  fi
+  if [ $distributionSha256Result = false ]; then
+    echo "Error: Failed to validate Maven distribution SHA-256, your Maven distribution might be compromised." >&2
+    echo "If you updated your Maven version, you need to update the specified distributionSha256Sum property." >&2
+    exit 1
+  fi
+fi
+
+# unzip and move
+if command -v unzip >/dev/null; then
+  unzip ${__MVNW_QUIET_UNZIP:+"$__MVNW_QUIET_UNZIP"} "$TMP_DOWNLOAD_DIR/$distributionUrlName" -d "$TMP_DOWNLOAD_DIR" || die "failed to unzip"
+else
+  tar xzf${__MVNW_QUIET_TAR:+"$__MVNW_QUIET_TAR"} "$TMP_DOWNLOAD_DIR/$distributionUrlName" -C "$TMP_DOWNLOAD_DIR" || die "failed to untar"
+fi
+printf %s\\n "$distributionUrl" >"$TMP_DOWNLOAD_DIR/$distributionUrlNameMain/mvnw.url"
+mv -- "$TMP_DOWNLOAD_DIR/$distributionUrlNameMain" "$MAVEN_HOME" || [ -d "$MAVEN_HOME" ] || die "fail to move MAVEN_HOME"
+
+clean || :
+exec_maven "$@"

mvnw.cmd

+<# : batch portion
+@REM ----------------------------------------------------------------------------
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements.  See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership.  The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License.  You may obtain a copy of the License at
+@REM
+@REM    http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied.  See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM ----------------------------------------------------------------------------
+
+@REM ----------------------------------------------------------------------------
+@REM Apache Maven Wrapper startup batch script, version 3.3.2
+@REM
+@REM Optional ENV vars
+@REM   MVNW_REPOURL - repo url base for downloading maven distribution
+@REM   MVNW_USERNAME/MVNW_PASSWORD - user and password for downloading maven
+@REM   MVNW_VERBOSE - true: enable verbose log; others: silence the output
+@REM ----------------------------------------------------------------------------
+
+@IF "%__MVNW_ARG0_NAME__%"=="" (SET __MVNW_ARG0_NAME__=%~nx0)
+@SET __MVNW_CMD__=
+@SET __MVNW_ERROR__=
+@SET __MVNW_PSMODULEP_SAVE=%PSModulePath%
+@SET PSModulePath=
+@FOR /F "usebackq tokens=1* delims==" %%A IN (`powershell -noprofile "& {$scriptDir='%~dp0'; $script='%__MVNW_ARG0_NAME__%'; icm -ScriptBlock ([Scriptblock]::Create((Get-Content -Raw '%~f0'))) -NoNewScope}"`) DO @(
+  IF "%%A"=="MVN_CMD" (set __MVNW_CMD__=%%B) ELSE IF "%%B"=="" (echo %%A) ELSE (echo %%A=%%B)
+)
+@SET PSModulePath=%__MVNW_PSMODULEP_SAVE%
+@SET __MVNW_PSMODULEP_SAVE=
+@SET __MVNW_ARG0_NAME__=
+@SET MVNW_USERNAME=
+@SET MVNW_PASSWORD=
+@IF NOT "%__MVNW_CMD__%"=="" (%__MVNW_CMD__% %*)
+@echo Cannot start maven from wrapper >&2 && exit /b 1
+@GOTO :EOF
+: end batch / begin powershell #>
+
+$ErrorActionPreference = "Stop"
+if ($env:MVNW_VERBOSE -eq "true") {
+  $VerbosePreference = "Continue"
+}
+
+# calculate distributionUrl, requires .mvn/wrapper/maven-wrapper.properties
+$distributionUrl = (Get-Content -Raw "$scriptDir/.mvn/wrapper/maven-wrapper.properties" | ConvertFrom-StringData).distributionUrl
+if (!$distributionUrl) {
+  Write-Error "cannot read distributionUrl property in $scriptDir/.mvn/wrapper/maven-wrapper.properties"
+}
+
+switch -wildcard -casesensitive ( $($distributionUrl -replace '^.*/','') ) {
+  "maven-mvnd-*" {
+    $USE_MVND = $true
+    $distributionUrl = $distributionUrl -replace '-bin\.[^.]*$',"-windows-amd64.zip"
+    $MVN_CMD = "mvnd.cmd"
+    break
+  }
+  default {
+    $USE_MVND = $false
+    $MVN_CMD = $script -replace '^mvnw','mvn'
+    break
+  }
+}
+
+# apply MVNW_REPOURL and calculate MAVEN_HOME
+# maven home pattern: ~/.m2/wrapper/dists/{apache-maven-<version>,maven-mvnd-<version>-<platform>}/<hash>
+if ($env:MVNW_REPOURL) {
+  $MVNW_REPO_PATTERN = if ($USE_MVND) { "/org/apache/maven/" } else { "/maven/mvnd/" }
+  $distributionUrl = "$env:MVNW_REPOURL$MVNW_REPO_PATTERN$($distributionUrl -replace '^.*'+$MVNW_REPO_PATTERN,'')"
+}
+$distributionUrlName = $distributionUrl -replace '^.*/',''
+$distributionUrlNameMain = $distributionUrlName -replace '\.[^.]*$','' -replace '-bin$',''
+$MAVEN_HOME_PARENT = "$HOME/.m2/wrapper/dists/$distributionUrlNameMain"
+if ($env:MAVEN_USER_HOME) {
+  $MAVEN_HOME_PARENT = "$env:MAVEN_USER_HOME/wrapper/dists/$distributionUrlNameMain"
+}
+$MAVEN_HOME_NAME = ([System.Security.Cryptography.MD5]::Create().ComputeHash([byte[]][char[]]$distributionUrl) | ForEach-Object {$_.ToString("x2")}) -join ''
+$MAVEN_HOME = "$MAVEN_HOME_PARENT/$MAVEN_HOME_NAME"
+
+if (Test-Path -Path "$MAVEN_HOME" -PathType Container) {
+  Write-Verbose "found existing MAVEN_HOME at $MAVEN_HOME"
+  Write-Output "MVN_CMD=$MAVEN_HOME/bin/$MVN_CMD"
+  exit $?
+}
+
+if (! $distributionUrlNameMain -or ($distributionUrlName -eq $distributionUrlNameMain)) {
+  Write-Error "distributionUrl is not valid, must end with *-bin.zip, but found $distributionUrl"
+}
+
+# prepare tmp dir
+$TMP_DOWNLOAD_DIR_HOLDER = New-TemporaryFile
+$TMP_DOWNLOAD_DIR = New-Item -Itemtype Directory -Path "$TMP_DOWNLOAD_DIR_HOLDER.dir"
+$TMP_DOWNLOAD_DIR_HOLDER.Delete() | Out-Null
+trap {
+  if ($TMP_DOWNLOAD_DIR.Exists) {
+    try { Remove-Item $TMP_DOWNLOAD_DIR -Recurse -Force | Out-Null }
+    catch { Write-Warning "Cannot remove $TMP_DOWNLOAD_DIR" }
+  }
+}
+
+New-Item -Itemtype Directory -Path "$MAVEN_HOME_PARENT" -Force | Out-Null
+
+# Download and Install Apache Maven
+Write-Verbose "Couldn't find MAVEN_HOME, downloading and installing it ..."
+Write-Verbose "Downloading from: $distributionUrl"
+Write-Verbose "Downloading to: $TMP_DOWNLOAD_DIR/$distributionUrlName"
+
+$webclient = New-Object System.Net.WebClient
+if ($env:MVNW_USERNAME -and $env:MVNW_PASSWORD) {
+  $webclient.Credentials = New-Object System.Net.NetworkCredential($env:MVNW_USERNAME, $env:MVNW_PASSWORD)
+}
+[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12
+$webclient.DownloadFile($distributionUrl, "$TMP_DOWNLOAD_DIR/$distributionUrlName") | Out-Null
+
+# If specified, validate the SHA-256 sum of the Maven distribution zip file
+$distributionSha256Sum = (Get-Content -Raw "$scriptDir/.mvn/wrapper/maven-wrapper.properties" | ConvertFrom-StringData).distributionSha256Sum
+if ($distributionSha256Sum) {
+  if ($USE_MVND) {
+    Write-Error "Checksum validation is not supported for maven-mvnd. `nPlease disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties."
+  }
+  Import-Module $PSHOME\Modules\Microsoft.PowerShell.Utility -Function Get-FileHash
+  if ((Get-FileHash "$TMP_DOWNLOAD_DIR/$distributionUrlName" -Algorithm SHA256).Hash.ToLower() -ne $distributionSha256Sum) {
+    Write-Error "Error: Failed to validate Maven distribution SHA-256, your Maven distribution might be compromised. If you updated your Maven version, you need to update the specified distributionSha256Sum property."
+  }
+}
+
+# unzip and move
+Expand-Archive "$TMP_DOWNLOAD_DIR/$distributionUrlName" -DestinationPath "$TMP_DOWNLOAD_DIR" | Out-Null
+Rename-Item -Path "$TMP_DOWNLOAD_DIR/$distributionUrlNameMain" -NewName $MAVEN_HOME_NAME | Out-Null
+try {
+  Move-Item -Path "$TMP_DOWNLOAD_DIR/$MAVEN_HOME_NAME" -Destination $MAVEN_HOME_PARENT | Out-Null
+} catch {
+  if (! (Test-Path -Path "$MAVEN_HOME" -PathType Container)) {
+    Write-Error "fail to move MAVEN_HOME"
+  }
+} finally {
+  try { Remove-Item $TMP_DOWNLOAD_DIR -Recurse -Force | Out-Null }
+  catch { Write-Warning "Cannot remove $TMP_DOWNLOAD_DIR" }
+}
+
+Write-Output "MVN_CMD=$MAVEN_HOME/bin/$MVN_CMD"

pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>org.springframework.boot</groupId>
+        <artifactId>spring-boot-starter-parent</artifactId>
+        <version>3.4.0</version>
+        <relativePath/> <!-- lookup parent from repository -->
+    </parent>
+    <groupId>com.dre0059</groupId>
+    <artifactId>articleProcessor</artifactId>
+    <version>0.0.1-SNAPSHOT</version>
+    <name>articleProcessor</name>
+    <description>articleProcessor</description>
+    <url/>
+    <licenses>
+        <license/>
+    </licenses>
+    <developers>
+        <developer/>
+    </developers>
+    <scm>
+        <connection/>
+        <developerConnection/>
+        <tag/>
+        <url/>
+    </scm>
+    <properties>
+        <java.version>17</java.version>
+    </properties>
+
+    <!-- -->
+    <repositories>
+        <repository>
+            <id>grobid</id>
+            <name>GROBID DIY repo</name>
+            <url>https://grobid.s3.eu-west-1.amazonaws.com/repo/</url>
+        </repository>
+    </repositories>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-data-jpa</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-web</artifactId>
+        </dependency>
+
+        <!--<dependency>
+            <groupId>com.mysql</groupId>
+            <artifactId>mysql-connector-j</artifactId>
+            <scope>runtime</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.xerial</groupId>
+            <artifactId>sqlite-jdbc</artifactId>
+            <version>3.43.2.1</version>
+        </dependency>
+
+          <dependency>
+            <groupId>org.hibernate.orm</groupId>
+            <artifactId>hibernate-community-dialects</artifactId>
+            <version>6.2.12.Final</version>
+        </dependency>
+        -->
+
+        <dependency>
+            <groupId>com.h2database</groupId>
+            <artifactId>h2</artifactId>
+            <scope>runtime</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-webflux</artifactId>
+        </dependency>
+
+
+
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-test</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <!-- APACHE TIKA  -->
+        <dependency>
+            <groupId>org.apache.tika</groupId>
+            <artifactId>tika-core</artifactId>
+            <version>2.9.2</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.tika</groupId>
+            <artifactId>tika-parsers</artifactId>
+            <version>2.9.2</version>
+            <type>pom</type>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.tika</groupId>
+            <artifactId>tika-parser-pdf-module</artifactId>
+            <version>2.9.2</version>
+        </dependency>
+
+        <!-- PDF BOX -->
+        <dependency>
+            <groupId>org.apache.pdfbox</groupId>
+            <artifactId>pdfbox</artifactId>
+            <version>2.0.27</version> <!-- Môžete skontrolovať najnovšiu verziu -->
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-core</artifactId>
+            <version>2.23.1</version> <!-- zadejte konkrétní verzi, např. 2.19.0 -->
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-api</artifactId>
+            <version>2.23.1</version>
+        </dependency>
+
+        <!-- OCR TESSERACT -->
+        <dependency>
+            <groupId>net.sourceforge.tess4j</groupId>
+            <artifactId>tess4j</artifactId>
+            <version>4.3.0</version>
+        </dependency>
+        <!-- OCR - Optické rozpoznávanie znakov -->
+        <dependency>
+            <groupId>org.apache.tika</groupId>
+            <artifactId>tika-parsers-standard-package</artifactId>
+            <version>2.4.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.tika</groupId>
+            <artifactId>tika-parser-ocr-module</artifactId>
+            <version>2.9.2</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-thymeleaf</artifactId>
+        </dependency>
+
+        <!-- GROBID Dependencies - stará verzia
+        <dependency>
+            <groupId>org.grobid</groupId>
+            <artifactId>grobid-core</artifactId>
+            <version>0.8.1</version>
+        </dependency>
+        -->
+
+        <!-- Apache Commons IO (pre prácu so súbormi) -->
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.11.0</version>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.springframework.boot</groupId>
+                <artifactId>spring-boot-maven-plugin</artifactId>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>

src/main/java/com/dre0059/articleprocessor/ArticleProcessorApplication.java

+package com.dre0059.articleprocessor;
+
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+
+@SpringBootApplication
+public class ArticleProcessorApplication {
+
+    public static void main(String[] args) {
+        SpringApplication.run(ArticleProcessorApplication.class, args);
+    }
+
+}

src/main/java/com/dre0059/articleprocessor/GrobidClient.java

+package com.dre0059.articleprocessor;
+
+import org.springframework.http.MediaType;
+import org.springframework.stereotype.Service;
+import org.springframework.web.reactive.function.BodyInserters;
+import org.springframework.web.reactive.function.client.WebClient;
+import org.springframework.core.io.FileSystemResource;
+import reactor.core.publisher.Mono;
+
+import java.io.File;
+
+
+@Service
+public class GrobidClient {
+    private final WebClient webClient;
+
+    public GrobidClient() {
+        this.webClient = WebClient.builder()
+                .baseUrl("http://158.196.98.65:8080")   // URL kde beží GROBID server
+                .build();
+    }
+
+    // get METADATA of the file
+    public Mono<String> processHeader(File pdfFile){    // Mono - vráti jeden string, výsledok je JSON
+        return webClient.post()
+                .uri("/api/processHeaderDocument")
+                .contentType(MediaType.MULTIPART_FORM_DATA)
+                .body(BodyInserters.fromMultipartData("input", new FileSystemResource(pdfFile)))
+                .attribute("consolidateHeader", 1)
+                .retrieve()
+                .bodyToMono(String.class);
+    }
+
+    // spracuje REFERENCIE z PDF
+    public Mono<String> processReferences(File pdfFile){
+        return webClient.post()
+                .uri("/api/processReferences")
+                .contentType(MediaType.MULTIPART_FORM_DATA)
+                .body(BodyInserters.fromMultipartData("input", new FileSystemResource(pdfFile)))
+                .retrieve()
+                .bodyToMono(String.class);
+    }
+
+}
\ No newline at end of file

src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java

+package com.dre0059.articleprocessor.apacheTika;
+
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.text.PDFTextStripper;
+import org.springframework.stereotype.Component;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import static com.lowagie.text.html.HtmlTagMap.isTitle;
+
+@Component
+public class PDFbox {
+    private int countTXT = 0;
+    public int getCountTXT(){ return this.countTXT; }
+
+    public void toTXT(String inputPDFpath, String outputTXTpath){
+        File pdfFile = new File(inputPDFpath);
+
+        try(PDDocument document = PDDocument.load(pdfFile)){
+            PDFTextStripper pdfStripper = new PDFTextStripper();
+            String extractedText = pdfStripper.getText(document);
+
+            //String[] lines = extractedText.split("\n");
+            //StringBuilder contentWithHeaders = new StringBuilder();
+
+            try (FileWriter writer = new FileWriter(outputTXTpath)) {
+                writer.write(extractedText);
+                System.out.println("File was sucessfully saved to : " + outputTXTpath);
+                countTXT++;
+            } catch (IOException e) {
+                System.err.println("FAILURE - file was not saved : " + e.getMessage());
+            }
+
+        } catch (IOException ex) {
+            System.err.println("FAILURE - Problem kin reading file : " + ex.getMessage());
+        }
+    }
+}

src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java

+package com.dre0059.articleprocessor.apacheTika;
+
+import org.apache.tika.Tika;
+import org.apache.tika.exception.TikaException;
+
+import javax.sound.midi.Soundbank;
+import java.io.*;
+import java.util.ArrayList;
+import java.util.Scanner;
+import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+
+public class ReferencesScanner {
+
+    // private Vector<String> references;
+    // notFound is just for TESTING
+    private int notFound;
+    private int notParsed;
+    public int getNotFound(){
+        return this.notFound;
+    }
+    public int getNotParsed(){ return this.notParsed; }
+
+
+    public boolean findReferences(String filepath, String outputPath) {
+        Tika tika = new Tika();
+        String content;
+
+        try {
+            content = tika.parseToString(new File(filepath));
+            String[] lines = content.split("\\r?\\n"); // split text to lines
+
+            boolean found = false;
+            StringBuilder referencesData = new StringBuilder();
+
+            // Regular expression for "References" and variations
+
+            String regex = "\\b[Rr][Ee][Ff][Ee][Rr][Ee][Nn][Cc][Ee][Ss]?\\b|" +
+                    "\\b[Nn][Oo][Tt][Ee][Ss]?\\s+[Aa][Nn][Dd]\\s+[Rr][Ee][Ff][Ee][Rr][Ee][Nn][Cc][Ee][Ss]?\\b";
+
+            // the most suitable for finding the references
+            //String regex = "(?i)(\\d*\\s*References|References|R\\s*E\\s*F\\s*E\\s*R\\s*E\\s*N\\s*C\\s*E\\s*S|Notes\\s+and\\s+References|RE[FE]*R[EE]*N[C]*E[S]*|^\\s*REFERENCES\\s*$)";
+            Pattern pattern = Pattern.compile(regex);
+
+            for (String line : lines) {
+                if (found) {
+                    // TODO : FURTHER READING is in the end of the line and in the beggining of the other line (this below is not working)
+                    if (line.contains("APPENDIX") || line.contains("Appendix") || line.contains("FURTHER\nREADING"))
+                        break;
+                    // Append lines of references
+                    referencesData.append(line).append(System.lineSeparator());
+                } else {
+                    // Check if line contains references
+                    Matcher matcher = pattern.matcher(line);
+                    if (matcher.find()) {
+                        found = true; // Reference found
+                        referencesData.append(line).append(System.lineSeparator());
+                    }
+                }
+            }
+
+            // Save references to TXT file
+            if (found) {
+                try (FileWriter writer = new FileWriter(outputPath)) {
+                    writer.write(referencesData.toString());
+                    System.out.println("References found and saved to " + outputPath);
+                } catch (IOException e) {
+                    e.printStackTrace();
+                }
+                return true; // Return true indicating references were found
+            } else {
+                System.out.println("References NOT found in file: " + filepath);
+                notFound++;
+                return false; // Return false indicating no references were found
+            }
+
+        } catch (IOException | TikaException e) {
+            e.printStackTrace();
+            return false; // Return false if an exception occurs
+        }
+    }
+    // parse references to vector
+    public Vector<String> parseReferences(String inputReferencesPath, String outputPath) throws IOException {
+        Vector<String> parsedReferences = new Vector<>();
+
+        FileInputStream stream = null;
+        try{
+            stream = new FileInputStream(inputReferencesPath);
+        } catch (FileNotFoundException e) {
+            throw new RuntimeException("File not found " + inputReferencesPath, e);
+        }
+
+        Scanner scanner = new Scanner(stream);
+        String line = null;
+
+        int index = 1;  // number of current reference
+        boolean found = false;     // used for lines behind found reference
+
+        while (scanner.hasNextLine()){
+            // first reference (from second until the last, it will be true - because we dont wanna go to another line, we wanna stay on line with next [ i ] )
+            if(!found)
+                line = scanner.nextLine();
+
+            // regex for patterns : 1 1. (1) [1] ... s* - spaces
+            //String regex = "(\\(\\s*\\b" + index + "\\b\\s*\\))|(\\[\\s*\\b " + index +"\\b\\s*\\])|(\\b" + index + "\\b\\s*\\.)|(\\b" + index + "\\b)";
+
+            String regex = "(\\(\\s*" + index + "\\s*\\))"        // Formát (index)
+                    + "|(\\[\\s*" + index + "\\s*\\])"      // Formát [index]
+                    + "|(\\b" + index + "\\b\\s*\\.)"       // Formát index.
+                    + "|(\\b" + index + "\\b)";             // Samotné číslo index
+
+
+            Pattern pattern = Pattern.compile(regex);   // regular expression
+            Matcher matcher = pattern.matcher(line);    // matcher for comparing regular exrpession
+
+            // [ i ] found, add reference
+            if(matcher.find()){
+                StringBuilder currReference = new StringBuilder();
+                currReference.append(line); // append line which contains [ 1 ]
+
+                index++;    // regex searches for 2 instead of 1
+                //regex = "(\\(\\s*\\b" + index + "\\b\\s*\\))|(\\[\\s*\\b " + index +"\\b\\s*\\])|(\\b" + index + "\\b\\s*\\.)|(\\b" + index + "\\b\\s+)"; // [ 2 ]
+                regex = "(\\(\\s*" + index + "\\s*\\))"        // Formát (index)
+                        + "|(\\[\\s*" + index + "\\s*\\])"      // Formát [index]
+                        + "|(\\b" + index + "\\b\\s*\\.)"       // Formát index.
+                        + "|(\\b" + index + "\\b\\s+)";             // Samotné číslo index
+
+                pattern = Pattern.compile(regex);
+
+                //line = scanner.nextLine();
+                //matcher = pattern.matcher(line);    // looking for [ 2 ] on the next line
+
+                while(scanner.hasNextLine()){ // all lines without regex (these lines belong to first reference)
+                    line = scanner.nextLine();
+                    matcher = pattern.matcher(line);    // looking for [ 2 ] on the next line
+
+                    if(matcher.find()){     // [ 2 ] was found
+                        found = true;
+                        break;
+                    }
+                    currReference.append(" ").append(line); // [ 2 ] was not found, lines belong to the first reference
+                }
+                //System.out.println("Match was found\n");
+
+                parsedReferences.add(currReference.toString());     // add the whole reference [ 1 ] to vector
+            }
+        }
+
+        scanner.close();
+
+        int i = 0;
+        try(FileWriter writer = new FileWriter(outputPath)) {
+            for (String ref : parsedReferences) {
+                i++;
+                writer.write(i + ". " + ref + "\n");
+                //System.out.println(i + " " + ref);
+            }
+        }catch (IOException e){
+            e.printStackTrace();
+        }
+
+        if(!(parsedReferences.size() > 0)){
+            notParsed++;
+            System.out.println("References NOT parsed in file: " + inputReferencesPath);
+        }
+        return parsedReferences;
+    }
+
+    // pslit reference and get NAME and year out of it
+    public void splitReferences(Vector<String> oneDocumentReferences){
+        for(String ref : oneDocumentReferences){
+            System.out.println(ref + "\n");
+        }
+    }
+}

src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java

+package com.dre0059.articleprocessor.controller;
+
+import com.dre0059.articleprocessor.GrobidClient;
+import com.dre0059.articleprocessor.model.DocumentMetadata;
+import com.dre0059.articleprocessor.service.MetadataParser;
+import com.dre0059.articleprocessor.repository.DocumentRepository;
+import com.dre0059.articleprocessor.repository.ReferenceRepository;
+import com.dre0059.articleprocessor.service.TEIparser;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.ui.Model;
+import org.springframework.web.bind.annotation.*;
+import org.springframework.web.multipart.MultipartFile;
+import reactor.core.publisher.Mono;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+// TODO :
+//  1. ✅ nefunguje mi správne uloženie článku, pokiaľ už článok v DBS je, aktuálne mi vyhodí len ERROR že nemožno správne spracovať
+//  2. ✅ !!! uloženie referencií do databázy
+//  3. prepojím referenciu s uloženými článkami ???
+//  4. viac spraviť program USER-FRIENDLY - výpis že spracovávam document, výpis že dokument už je uložený, výpis že dokument sa uložil a vypíšem metadata pre overenie
+//  5. nesprávne vyťahovanie referencií - referencie ktoré sa odkazujú na nejaký web, nie sú spracované
+
+@Controller
+@RequestMapping("/api/grobid")
+public class FileUploadController {
+    private static final Logger logger = LoggerFactory.getLogger(FileUploadController.class);
+    private final GrobidClient grobidClient;
+    private final DocumentRepository metadataRepository;
+    private final ReferenceRepository referenceRepository;
+
+    public FileUploadController(GrobidClient grobidClient, DocumentRepository metadataRepository, ReferenceRepository referenceRepository) {
+        this.grobidClient = grobidClient;
+        this.metadataRepository = metadataRepository;
+        this.referenceRepository = referenceRepository;
+    }
+
+    @GetMapping("/upload")
+    public String showUploadForm(Model model) {
+        return "upload";  // vracia upload.html
+    }
+
+    @PostMapping("/upload")
+    @ResponseBody
+    public Mono<ResponseEntity<Map<String, String>>> handleFileUpload(@RequestParam("file") MultipartFile file) {
+        logger.info("Received file: {}", file.getOriginalFilename());
+
+        return Mono.fromCallable(() -> {
+            Path tempFile = Files.createTempFile("upload-", ".pdf");
+            file.transferTo(tempFile.toFile());
+            return tempFile.toFile();
+        }).flatMap(pdfFile -> {
+            Mono<String> metadataMono = grobidClient.processHeader(pdfFile);
+            Mono<String> referencesMono = grobidClient.processReferences(pdfFile);
+
+            return Mono.zip(metadataMono, referencesMono)
+                    .flatMap(result -> {
+                        String metadataJson = result.getT1();
+                        String referencesXml = result.getT2();
+
+                        String title = MetadataParser.extractTitle(metadataJson);
+                        List<String> authors = MetadataParser.extractAuthors(metadataJson);
+
+                        return Mono.justOrEmpty(metadataRepository.findByTitle(title))
+                                .map(existing -> {
+                                    logger.warn("Article with title '{}' already exists!", title);
+                                    return ResponseEntity.status(HttpStatus.CONFLICT)
+                                            .body(Map.of("error", "Article is already in database."));
+                                })
+                                .switchIfEmpty(Mono.fromCallable(() -> {
+                                    DocumentMetadata doc = new DocumentMetadata(title, authors);
+                                    metadataRepository.save(doc);
+
+                                    // Spracovanie referencií cez TEIparser
+                                    TEIparser teiParser = new TEIparser(referenceRepository);
+                                    teiParser.parseAndSaveToDB(referencesXml, doc);
+
+                                    Map<String, String> response = new HashMap<>();
+                                    response.put("metadata", metadataJson);
+                                    response.put("references", referencesXml);
+
+                                    return ResponseEntity.ok(response);
+                                }));
+                    })
+                    .onErrorResume(e -> {
+                        logger.error("Error processing PDF", e);
+                        return Mono.just(ResponseEntity.internalServerError().body(Map.of("error", "Failed to process PDF")));
+                    });
+        });
+    }
+
+
+}
+
+
+

src/main/java/com/dre0059/articleprocessor/model/Author.java

+package com.dre0059.articleprocessor.model;
+
+import jakarta.persistence.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Entity
+@Table(name = "authors")
+public class Author {
+
+    @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    private Long id;
+
+    private String name;
+    private String surname;
+
+    @ManyToMany(mappedBy = "authors")
+    private List<Document> documents = new ArrayList<Document>();
+
+    public Author(){}
+    public Author(String name, String surname) {
+        this.name = name;
+        this.surname = surname;
+    }
+
+    public Long getId() { return id; }
+    public String getName() { return name; }
+    public String getSurname() { return surname; }
+    public List<Document> getDocuments() { return documents; }
+
+    public void setName(String name) { this.name = name; }
+    public void setSurname(String surname) { this.surname = surname; }
+    public void setDocuments(List<Document> documents) { this.documents = documents; }
+}

src/main/java/com/dre0059/articleprocessor/model/Document.java

+package com.dre0059.articleprocessor.model;
+
+import jakarta.persistence.*;
+import org.hibernate.annotations.CollectionId;
+import com.dre0059.articleprocessor.model.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Entity
+@Table(name = "documents")
+public class Document {
+
+    @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    private Long id;
+
+    private String title;
+    private Integer year;
+    private String doi;
+
+    @Column(name = "abstractText")
+    private String abstractText;
+
+    private Integer pages;
+    private String publisher;
+
+    @OneToMany(mappedBy = "fromDocument", cascade = CascadeType.ALL)
+    private List<Reference> references = new ArrayList<>();
+
+    @ManyToMany
+    @JoinTable(
+            name = "document_author",
+            joinColumns = @JoinColumn(name = "ID_document"),
+            inverseJoinColumns = @JoinColumn(name = "ID_author")
+    )
+    private List<Author> authors = new ArrayList<>();
+
+    public Document() {}
+
+    public Document(String title, Integer year, String doi, String abstractText, Integer pages, String publisher) {
+        this.title = title;
+        this.year = year;
+        this.doi = doi;
+        this.abstractText = abstractText;
+        this.pages = pages;
+        this.publisher = publisher;
+    }
+
+    public Long getId() { return id; }
+    public String getTitle() { return title; }
+    public Integer getYear() { return year; }
+    public String getDoi() { return doi; }
+    public String getAbstractText() { return abstractText; }
+    public Integer getPages() { return pages; }
+    public String getPublisher() { return publisher; }
+    public List<Reference> getReferences() { return references; }
+    public List<Author> getAuthors() { return authors; }
+
+    public void setAuthors(List<Author> authors) { this.authors = authors; }
+
+}

src/main/java/com/dre0059/articleprocessor/model/DocumentMetadata.java

+package com.dre0059.articleprocessor.model;
+
+import jakarta.persistence.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Entity // DBS table
+@Table (name = "DOCUMENT_METADATA", uniqueConstraints = @UniqueConstraint(columnNames = "title"))
+public class DocumentMetadata {
+    @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY) // ID is generated automatically
+    private Long id;
+
+    private String title;
+
+    @ElementCollection  // pomocna tabulka authors
+    private List<String> authors = new ArrayList<>();
+
+    // needed for Hibernate for right instances in DBS
+    public DocumentMetadata() {}
+
+    public DocumentMetadata(String title, List<String> authors) {
+        this.title = title;
+        this.authors = authors;
+    }
+
+    public Long getId(){
+        return id;
+    }
+    public String getTitle(){
+        return title;
+    }
+    public List<String> getAuthors(){
+        return authors;
+    }
+}

src/main/java/com/dre0059/articleprocessor/model/Reference.java

+package com.dre0059.articleprocessor.model;
+
+import jakarta.persistence.*;
+
+import javax.print.Doc;
+import java.util.List;
+
+@Entity
+@Table(name = "references")
+public class Reference {
+    @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    private Long id;
+
+    // number or letters in reference list
+    private String orderNumber;
+
+    @ManyToOne(cascade = CascadeType.ALL)
+    @JoinColumn(name = "ID_fromDocument")
+    private Document fromDocument;
+
+    @ManyToOne(cascade = CascadeType.ALL)
+    @JoinColumn(name = "ID_toDocument")
+    private Document toDocument;
+
+    public Reference() {}
+    public Reference(String orderNumber, Document fromDocument, Document toDocument) {
+        this.orderNumber = orderNumber;
+        this.fromDocument = fromDocument;
+        this.toDocument = toDocument;
+    }
+
+    public String getOrderNumber() { return orderNumber; }
+    public Document getFromDocument() { return fromDocument; }
+    public Document getToDocument() { return toDocument; }
+    public Long getId() { return id; }
+
+    public void setFromDocument(Document fromDocument) { this.fromDocument = fromDocument; }
+    public void setToDocument(Document toDocument) { this.toDocument = toDocument; }
+    public void setOrderNumber(String orderNumber) { this.orderNumber = orderNumber; }
+}

src/main/java/com/dre0059/articleprocessor/repository/AuthorRepository.java

+package com.dre0059.articleprocessor.repository;
+
+import com.dre0059.articleprocessor.model.Author;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+
+import java.util.Optional;
+
+@Repository
+public interface AuthorRepository extends JpaRepository<Author, Long> {
+    Optional<Author> findByFullname(String name, String surname);
+}

src/main/java/com/dre0059/articleprocessor/repository/DocumentRepository.java

+package com.dre0059.articleprocessor.repository;
+
+import com.dre0059.articleprocessor.model.DocumentMetadata;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+import org.w3c.dom.Document;
+
+import java.util.Optional;
+
+// uklada extrahovane data
+@Repository
+public interface DocumentRepository extends JpaRepository<Document, Long> {
+    Optional<Document> findByTitleAndAuthorsSurname(String title, String surname);
+}