From ebe1559a351ece67605567f6d8f14ae339347917 Mon Sep 17 00:00:00 2001
From: dre0059 <eliska.dreveniakova@vsb.cz>
Date: Fri, 14 Feb 2025 15:37:28 +0100
Subject: [PATCH] The very first commit
---
.gitattributes | 2 +
.gitignore | 33 +++
.mvn/wrapper/maven-wrapper.properties | 19 ++
...e_safety_immunology_virolog-references.txt | 1 +
...ocalTemp\302\263661.263675-references.txt" | 1 +
mvnw | 259 ++++++++++++++++++
mvnw.cmd | 149 ++++++++++
pdf_database.db | 0
pom.xml | 175 ++++++++++++
.../ArticleProcessorApplication.java | 13 +
.../articleprocessor/GrobidClient.java | 44 +++
.../articleprocessor/apacheTika/PDFbox.java | 40 +++
.../apacheTika/ReferencesScanner.java | 177 ++++++++++++
.../controller/FileUploadController.java | 105 +++++++
.../articleprocessor/model/Author.java | 36 +++
.../articleprocessor/model/Document.java | 62 +++++
.../model/DocumentMetadata.java | 37 +++
.../articleprocessor/model/Reference.java | 41 +++
.../repository/AuthorRepository.java | 12 +
.../repository/DocumentRepository.java | 15 +
.../repository/ReferenceRepository.java | 9 +
.../service/DocumentService.java | 4 +
.../service/MetadataParser.java | 70 +++++
.../service/ReferenceService.java | 4 +
.../articleprocessor/service/TEIparser.java | 95 +++++++
src/main/resources/application.properties | 44 +++
.../resources/templates/upload-success.html | 88 ++++++
src/main/resources/templates/upload.html | 83 ++++++
.../ArticleProcessorApplicationTests.java | 13 +
29 files changed, 1631 insertions(+)
create mode 100644 .gitattributes
create mode 100644 .gitignore
create mode 100644 .mvn/wrapper/maven-wrapper.properties
create mode 100644 UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt
create mode 100644 "UserselidrAppDataLocalTemp\302\263661.263675-references.txt"
create mode 100644 mvnw
create mode 100644 mvnw.cmd
create mode 100644 pdf_database.db
create mode 100644 pom.xml
create mode 100644 src/main/java/com/dre0059/articleprocessor/ArticleProcessorApplication.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/GrobidClient.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/model/Author.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/model/Document.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/model/DocumentMetadata.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/model/Reference.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/repository/AuthorRepository.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/repository/DocumentRepository.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/repository/ReferenceRepository.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/service/DocumentService.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/service/MetadataParser.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java
create mode 100644 src/main/java/com/dre0059/articleprocessor/service/TEIparser.java
create mode 100644 src/main/resources/application.properties
create mode 100644 src/main/resources/templates/upload-success.html
create mode 100644 src/main/resources/templates/upload.html
create mode 100644 src/test/java/com/dre0059/articleprocessor/ArticleProcessorApplicationTests.java
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..3b41682
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+/mvnw text eol=lf
+*.cmd text eol=crlf
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..549e00a
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,33 @@
+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/
diff --git a/.mvn/wrapper/maven-wrapper.properties b/.mvn/wrapper/maven-wrapper.properties
new file mode 100644
index 0000000..d58dfb7
--- /dev/null
+++ b/.mvn/wrapper/maven-wrapper.properties
@@ -0,0 +1,19 @@
+# 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
diff --git a/UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt b/UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt
new file mode 100644
index 0000000..e4e16e4
--- /dev/null
+++ b/UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt
@@ -0,0 +1 @@
+"hahahahahahaha"
\ No newline at end of file
diff --git "a/UserselidrAppDataLocalTemp\302\263661.263675-references.txt" "b/UserselidrAppDataLocalTemp\302\263661.263675-references.txt"
new file mode 100644
index 0000000..83c2742
--- /dev/null
+++ "b/UserselidrAppDataLocalTemp\302\263661.263675-references.txt"
@@ -0,0 +1 @@
+"heeeeeeeeeeeeeeeeeeej"
\ No newline at end of file
diff --git a/mvnw b/mvnw
new file mode 100644
index 0000000..19529dd
--- /dev/null
+++ b/mvnw
@@ -0,0 +1,259 @@
+#!/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 "$MAVEN_HOME" ] || die "fail to move MAVEN_HOME"
+
+clean || :
+exec_maven "$@"
diff --git a/mvnw.cmd b/mvnw.cmd
new file mode 100644
index 0000000..249bdf3
--- /dev/null
+++ b/mvnw.cmd
@@ -0,0 +1,149 @@
+<# : 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"
diff --git a/pdf_database.db b/pdf_database.db
new file mode 100644
index 0000000..e69de29
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..b83ae51
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,175 @@
+<?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 konkrétnà 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>
diff --git a/src/main/java/com/dre0059/articleprocessor/ArticleProcessorApplication.java b/src/main/java/com/dre0059/articleprocessor/ArticleProcessorApplication.java
new file mode 100644
index 0000000..53a5f87
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/ArticleProcessorApplication.java
@@ -0,0 +1,13 @@
+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);
+ }
+
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/GrobidClient.java b/src/main/java/com/dre0059/articleprocessor/GrobidClient.java
new file mode 100644
index 0000000..91ff786
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/GrobidClient.java
@@ -0,0 +1,44 @@
+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 bežà 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
diff --git a/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java b/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java
new file mode 100644
index 0000000..f520ae5
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java
@@ -0,0 +1,40 @@
+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());
+ }
+ }
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java b/src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java
new file mode 100644
index 0000000..279e405
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java
@@ -0,0 +1,177 @@
+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)"; // SamotnĂ© ÄŤĂslo 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+)"; // SamotnĂ© ÄŤĂslo 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");
+ }
+ }
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java b/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
new file mode 100644
index 0000000..91bfab5
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
@@ -0,0 +1,105 @@
+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 vyhodà len ERROR že nemožno správne spracovať
+// 2. ✅ !!! uloženie referencià do databázy
+// 3. prepojĂm referenciu s uloĹľenĂ˝mi ÄŤlánkami ???
+// 4. viac spraviĹĄ program USER-FRIENDLY - vĂ˝pis Ĺľe spracovávam document, vĂ˝pis Ĺľe dokument uĹľ je uloĹľenĂ˝, vĂ˝pis Ĺľe dokument sa uloĹľil a vypĂšem metadata pre overenie
+// 5. nesprávne vyťahovanie referencià - 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 referenciĂ 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")));
+ });
+ });
+ }
+
+
+}
+
+
+
diff --git a/src/main/java/com/dre0059/articleprocessor/model/Author.java b/src/main/java/com/dre0059/articleprocessor/model/Author.java
new file mode 100644
index 0000000..69329b9
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/model/Author.java
@@ -0,0 +1,36 @@
+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; }
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/model/Document.java b/src/main/java/com/dre0059/articleprocessor/model/Document.java
new file mode 100644
index 0000000..a017029
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/model/Document.java
@@ -0,0 +1,62 @@
+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; }
+
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/model/DocumentMetadata.java b/src/main/java/com/dre0059/articleprocessor/model/DocumentMetadata.java
new file mode 100644
index 0000000..1aa86f9
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/model/DocumentMetadata.java
@@ -0,0 +1,37 @@
+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;
+ }
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/model/Reference.java b/src/main/java/com/dre0059/articleprocessor/model/Reference.java
new file mode 100644
index 0000000..5aae7ce
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/model/Reference.java
@@ -0,0 +1,41 @@
+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; }
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/repository/AuthorRepository.java b/src/main/java/com/dre0059/articleprocessor/repository/AuthorRepository.java
new file mode 100644
index 0000000..846a3fa
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/repository/AuthorRepository.java
@@ -0,0 +1,12 @@
+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);
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/repository/DocumentRepository.java b/src/main/java/com/dre0059/articleprocessor/repository/DocumentRepository.java
new file mode 100644
index 0000000..d68a201
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/repository/DocumentRepository.java
@@ -0,0 +1,15 @@
+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);
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/repository/ReferenceRepository.java b/src/main/java/com/dre0059/articleprocessor/repository/ReferenceRepository.java
new file mode 100644
index 0000000..f5cee29
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/repository/ReferenceRepository.java
@@ -0,0 +1,9 @@
+package com.dre0059.articleprocessor.repository;
+
+import com.dre0059.articleprocessor.model.Reference;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+import java.util.List;
+
+public interface ReferenceRepository extends JpaRepository<Reference, Long> {
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/service/DocumentService.java b/src/main/java/com/dre0059/articleprocessor/service/DocumentService.java
new file mode 100644
index 0000000..9b3c6ca
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/service/DocumentService.java
@@ -0,0 +1,4 @@
+package com.dre0059.articleprocessor.service;
+
+public class DocumentService {
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/service/MetadataParser.java b/src/main/java/com/dre0059/articleprocessor/service/MetadataParser.java
new file mode 100644
index 0000000..2cfc04b
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/service/MetadataParser.java
@@ -0,0 +1,70 @@
+package com.dre0059.articleprocessor.service;
+
+import com.dre0059.articleprocessor.model.Author;
+import com.dre0059.articleprocessor.model.Document;
+import com.dre0059.articleprocessor.repository.AuthorRepository;
+import com.dre0059.articleprocessor.repository.DocumentRepository;
+import com.dre0059.articleprocessor.repository.ReferenceRepository;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+@Service
+public class MetadataParser {
+
+ @Autowired
+ private DocumentRepository documentRepository;
+ @Autowired
+ private AuthorRepository authorRepository;
+
+ @Autowired
+ public MetadataParser(DocumentRepository documentRepository, AuthorRepository authorRepository) {
+ this.documentRepository = documentRepository;
+ this.authorRepository = authorRepository;
+ }
+
+ public Document parseBibTeX(String bibtexString) {
+ // Regular expression pre zĂskanie hodnĂ´t z BibTeX formátu
+ Pattern pattern = Pattern.compile("@.*?\\{.*?,\\s*author\\s*=\\s*\\{(.*?)\\},\\s*title\\s*=\\s*\\{(.*?)\\},\\s*doi\\s*=\\s*\\{(.*?)\\},\\s*abstract\\s*=\\s*\\{(.*?)\\}");
+ Matcher matcher = pattern.matcher(bibtexString);
+
+ if (matcher.find()) {
+ String authorsRaw = matcher.group(1);
+ String title = matcher.group(2);
+ String doi = matcher.group(3);
+ String abstractText = matcher.group(4);
+
+ List<Author> authors = parseAuthors(authorsRaw);
+
+ Document document = new Document(title, null, doi, abstractText, null, null);
+ document.setAuthors(authors);
+
+ documentRepository.save(document);
+
+ for (Author author : authors) {
+ authorRepository.save(author);
+ }
+
+ return document;
+ }
+ return null;
+ }
+
+ private List<Author> parseAuthors(String authorsRaw) {
+ List<Author> authors = new ArrayList<>();
+ String[] authorNames = authorsRaw.split(" and ");
+ for (String fullName : authorNames) {
+ String[] nameParts = fullName.trim().split("\\s+", 2);
+ if (nameParts.length == 2) {
+ authors.add(new Author(nameParts[1], nameParts[0])); // Priezvisko, Meno
+ } else {
+ authors.add(new Author(nameParts[0], "")); // Ak meno nemá priezvisko
+ }
+ }
+ return authors;
+ }
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java b/src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java
new file mode 100644
index 0000000..4428ebb
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java
@@ -0,0 +1,4 @@
+package com.dre0059.articleprocessor.service;
+
+public class ReferenceService {
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/service/TEIparser.java b/src/main/java/com/dre0059/articleprocessor/service/TEIparser.java
new file mode 100644
index 0000000..b39d4bd
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/service/TEIparser.java
@@ -0,0 +1,95 @@
+package com.dre0059.articleprocessor.service;
+
+import com.dre0059.articleprocessor.model.DocumentMetadata;
+import com.dre0059.articleprocessor.model.Reference;
+import com.dre0059.articleprocessor.repository.DocumentRepository;
+import com.dre0059.articleprocessor.repository.ReferenceRepository;
+import org.springframework.stereotype.Service;
+import org.w3c.dom.*;
+import org.xml.sax.InputSource;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.List;
+
+@Service
+public class TEIparser {
+
+
+ private final ReferenceRepository referenceRepository;
+ private final DocumentRepository documentRepository;
+
+ public TEIparser(ReferenceRepository referenceRepository, DocumentRepository documentRepository) {
+ this.referenceRepository = referenceRepository;
+ this.documentRepository = documentRepository;
+ }
+
+ public void parseAndSaveToDB(String xmlContent, DocumentMetadata document) {
+ try {
+ List<Reference> references = parseReferencesFromXML(xmlContent, document);
+
+ if (!references.isEmpty()) {
+ referenceRepository.saveAll(references);
+ System.out.println("References successfully saved to DB");
+ } else {
+ System.out.println("No valid references found in XML.");
+ }
+ } catch (Exception e) {
+ System.err.println("Error parsing references: " + e.getMessage());
+ e.printStackTrace();
+ }
+ }
+
+ private List<Reference> parseReferencesFromXML(String xmlContent, DocumentMetadata document) {
+ List<Reference> references = new ArrayList<>();
+
+ try {
+ DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
+ dbFactory.setNamespaceAware(true);
+ DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
+ Document doc = dBuilder.parse(new InputSource(new StringReader(xmlContent)));
+
+ // <biblStruct> - bibliographical information (consists of all needed information)
+ NodeList biblStructs = doc.getElementsByTagNameNS("*", "biblStruct");
+
+ for (int i = 0; i < biblStructs.getLength(); i++) {
+ Element bibl = (Element) biblStructs.item(i);
+
+ String title = getTagValueNS("title", bibl, "Unknown Title");
+ String publisher = getTagValueNS("publisher", bibl, "Unknown Publisher");
+ String year = getTagValueNS("year", bibl, "Unknown Year");
+
+ List<String> authors = new ArrayList<>();
+ NodeList authorNodes = bibl.getElementsByTagNameNS("*", "author");
+
+ for (int j = 0; j < authorNodes.getLength(); j++) {
+ Element authorElement = (Element) authorNodes.item(j);
+ Element persName = (Element) authorElement.getElementsByTagNameNS("*", "persName");
+
+ if (persName != null) {
+ String forename = getTagValueNS("forename", persName, "");
+ String surname = getTagValueNS("surname", persName, "");
+ if (!forename.isEmpty() || !surname.isEmpty()) {
+ authors.add(forename + " " + surname);
+ }
+ }
+
+ }
+ references.add(new Document(title, year, doi, abstractText, pages, publisher));
+
+ }
+ } catch (Exception e) {
+ System.err.println("Failed to parse references XML: " + e.getMessage());
+ e.printStackTrace();
+ }
+
+ return references;
+ }
+
+ private static String getTagValueNS(String tagName, Element element, String defaultValue) {
+ NodeList nodeList = element.getElementsByTagNameNS("*", tagName);
+ return (nodeList.getLength() > 0) ? nodeList.item(0).getTextContent().trim() : defaultValue;
+ }
+}
diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
new file mode 100644
index 0000000..c1d0451
--- /dev/null
+++ b/src/main/resources/application.properties
@@ -0,0 +1,44 @@
+server.port=8080
+spring.application.name=articleProcessor
+
+#spring.datasource.url=jdbc:sqlite:pdf_database.db
+#spring.datasource.driver-class-name=org.sqlite.JDBC
+#spring.jpa.database-platform=org.hibernate.dialect.SQLiteDialect
+#spring.jpa.hibernate.ddl-auto=update
+
+#spring.datasource.url=jdbc:sqlite:"D:\\Bakalarka\\my_db\\first_database.db"
+#driverClassName=org.sqlite.JDBC
+#url=jdbc:sqlite:memory:myDb?cache=shared
+#username=sa
+#password=sa
+#spring.jpa.database-platform=org.hibernate.community.dialect.SQLiteDialect
+#spring.jpa.hibernate.ddl-auto=create-drop
+#spring.jpa.show-sql=true
+
+
+# SQLite database configuration
+#spring.datasource.url=jdbc:sqlite:pdf_database.db
+#spring.jpa.database-platform=org.hibernate.dialect.SQLiteDialect
+#spring.jpa.hibernate.ddl-auto=create-drop
+#spring.jpa.show-sql=true
+
+#spring.datasource.url=jdbc:h2:mem:testdb
+spring.datasource.url=jdbc:h2:file:/data/demo
+spring.datasource.driverClassName=org.h2.Driver
+spring.datasource.username=sa
+spring.datasource.password=password
+spring.jpa.database-platform=org.hibernate.dialect.H2Dialect
+spring.jpa.defer-datasource-initialization=true
+
+spring.h2.console.enabled=true
+
+spring.jpa.hibernate.ddl-auto=update
+spring.jpa.show-sql=true
+spring.jpa.properties.hibernate.format_sql=true
+
+spring.thymeleaf.prefix=classpath:/templates/
+spring.thymeleaf.suffix=.html
+
+# Spring MVC for uploading PDF files
+spring.servlet.multipart.max-file-size=5MB
+spring.servlet.multipart.max-request-size=5MB
diff --git a/src/main/resources/templates/upload-success.html b/src/main/resources/templates/upload-success.html
new file mode 100644
index 0000000..98923b0
--- /dev/null
+++ b/src/main/resources/templates/upload-success.html
@@ -0,0 +1,88 @@
+<!DOCTYPE html>
+<html xmlns:th="http://www.thymeleaf.org">
+<head>
+ <meta charset="UTF-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <title>Upload Success</title>
+</head>
+<body>
+<h1>Upload Successful</h1>
+<p th:text="${message}"></p>
+<p>Converted text file: <a th:href="@{${txtFilePath}}" th:text="${txtFilePath}"></a></p>
+<a href="/upload">Go back to upload another file</a>
+
+<p>Are the following references correct?</p>
+<button id="yesButton">Yes</button>
+<button id="noButton">No</button>
+
+<div id="references" style="display: block;">
+ <!-- Zobrazenie textu referenciĂ -->
+ <div th:utext="${referencesText}"></div>
+</div>
+
+<div id="fullText" style="display: none;">
+ <h3>Full text:</h3>
+ <pre th:utext="${fullText}" id="fullTextContent" style="border: 1px solid #ccc; padding: 10px; cursor: text;"></pre>
+ <button id="saveSelectedText">Save Selected References</button>
+</div>
+
+<button id="showReferences">Show saved references</button>
+<div id = "savedReferences" ></div>
+
+<script>
+ // Zobrazenie celého textu pri kliknutà na "No"
+ document.getElementById("noButton").addEventListener("click", function(){
+ document.getElementById("fullText").style.display = "block";
+ document.getElementById("references").style.display = "none";
+ });
+
+ // Uloženie vybraného textu
+ document.getElementById("saveSelectedText").addEventListener("click", function () {
+ // ZĂskanie vybranĂ©ho textu
+ const selection = window.getSelection().toString().trim();
+
+ if (!selection) {
+ alert("Please select some text to save.");
+ return;
+ }
+
+ // Poslanie vybraného textu na server
+ fetch('/saveReferences', {
+ method: 'POST',
+ headers: {
+ 'Content-Type': 'application/json',
+ },
+ body: JSON.stringify({ selectedText: selection }),
+ })
+ .then(response => {
+ if (response.ok) {
+ alert("Selected references saved successfully.");
+ } else {
+ return response.text().then(err => { throw new Error(err); });
+ }
+ })
+ .catch(error => console.error("Error saving references:", error));
+ });
+
+ document.getElementById("showReferences").addEventListener("click", function () {
+ fetch('/getReferences')
+ .then(response => {
+ if(!response.ok) {
+ return response.text().then(err => {
+ throw new Error(err);
+ });
+ }
+ return response.text(); // references as one string
+ })
+ .then(data => {
+ const savedReferencesDiv = document.getElementById("savedReferences");
+ console.log(data);
+ savedReferencesDiv.innerHTML = data.replace(/\n/g, '<br>'); // replace newLine for HTML tag
+ })
+ .catch(error => console.error("Error fetching references: ", error));
+ });
+
+
+</script>
+</body>
+</html>
diff --git a/src/main/resources/templates/upload.html b/src/main/resources/templates/upload.html
new file mode 100644
index 0000000..dd6b70a
--- /dev/null
+++ b/src/main/resources/templates/upload.html
@@ -0,0 +1,83 @@
+<!DOCTYPE html>
+<html xmlns:th="http://www.thymeleaf.org">
+ <head>
+ <meta charset="UTF-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <title>Upload PDF</title>
+ <script src = "https://code.jquery.com/jquery-3.6.0.min.js"></script>
+ <style>
+ #pdf-preview {
+ width: 500px;
+ height: 600px;
+ border: 1px solid #ddd;
+ margin-top: 10px;
+ }
+ </style>
+ </head>
+
+ <body>
+ <h1>Upload your PDF</h1>
+
+ <!-- formular na nahravanie PDF -->
+
+ <form action="/api/grobid/upload" method="post" id = "uploadForm" enctype = "multipart/form-data">
+ <label for="fileInput">Choose PDF file:</label>
+ <input type = "file" id = "fileInput" name = "file" accept="application/pdf">
+ <button type = "submit">Upload & Process the PDF</button>
+ </form>
+
+ <!-- zobrazenie PDF -->
+ <div id="pdf-container">
+ <iframe id="pdf-preview" src="" style="display: none;"></iframe>
+ </div>
+
+ <!-- JSON výstup -->
+ <div id = "response-containter" style="display: none;">
+ <h3>Response : </h3>
+ <pre id = "json-output"></pre>
+ </div>
+
+ <!-- .js na zobrazenie PDF -->
+ <script>
+ document.getElementById('fileInput').addEventListener('change', function(event){
+ const file = event.target.files[0];
+ if(file && file.type === 'application/pdf'){
+ const fileURL = URL.createObjectURL(file);
+ document.getElementById('pdf-preview').src = fileURL;
+ document.getElementById('pdf-preview').style.display = 'block';
+ } else {
+ alert ('Please, choose valid PDF file.');
+ }
+ });
+
+ // AJAX for sending a file
+ $('#uploadForm').submit(function(event) {
+ event.preventDefault();
+ const fileInput = $('#fileInput')[0].files[0];
+
+ if(!fileInput){
+ alert("Please select a PDF file first.");
+ return;
+ }
+
+ const formData = new FormData();
+ formData.append("file", fileInput);
+
+ $.ajax({
+ url: "/api/grobid/upload",
+ type : "POST",
+ data : formData,
+ processData : false,
+ contentType : false,
+ success : function(response){
+ $('#json-output').text(JSON.stringify(response, null, 4));
+ $('#response-containter').show();
+ },
+ error: function(){
+ alert("Error processing PDF.");
+ }
+ });
+ });
+ </script>
+ </body>
+</html>
diff --git a/src/test/java/com/dre0059/articleprocessor/ArticleProcessorApplicationTests.java b/src/test/java/com/dre0059/articleprocessor/ArticleProcessorApplicationTests.java
new file mode 100644
index 0000000..9bb5c39
--- /dev/null
+++ b/src/test/java/com/dre0059/articleprocessor/ArticleProcessorApplicationTests.java
@@ -0,0 +1,13 @@
+package com.dre0059.articleprocessor;
+
+import org.junit.jupiter.api.Test;
+import org.springframework.boot.test.context.SpringBootTest;
+
+@SpringBootTest
+class ArticleProcessorApplicationTests {
+
+ @Test
+ void contextLoads() {
+ }
+
+}
--
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