The very first commit

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

+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> {
+}

src/main/java/com/dre0059/articleprocessor/service/DocumentService.java

+package com.dre0059.articleprocessor.service;
+
+public class DocumentService {
+}

src/main/java/com/dre0059/articleprocessor/service/MetadataParser.java

+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 získanie hodnôt 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;
+    }
+}

src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java

+package com.dre0059.articleprocessor.service;
+
+public class ReferenceService {
+}

src/main/java/com/dre0059/articleprocessor/service/TEIparser.java

+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;
+    }
+}

src/main/resources/application.properties

+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

src/main/resources/templates/upload-success.html

+<!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="${txtFilePath}"></a></p>
+<a href="/upload">Go back to upload another file</a>
+
+<p>Are the following references correct?</p>
+<button id="yesButton">Yes</button>
+<button id="noButton">No</button>
+
+<div id="references" style="display: block;">
+    <!-- Zobrazenie textu referencií -->
+    <div th:utext="${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 kliknutí 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 () {
+        // Získanie vybraného 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>

src/main/resources/templates/upload.html

+<!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>

src/test/java/com/dre0059/articleprocessor/ArticleProcessorApplicationTests.java

+package com.dre0059.articleprocessor;
+
+import org.junit.jupiter.api.Test;
+import org.springframework.boot.test.context.SpringBootTest;
+
+@SpringBootTest
+class ArticleProcessorApplicationTests {
+
+    @Test
+    void contextLoads() {
+    }
+
+}