diff --git a/README.md b/README.md
index 5fae8e81c19fb79afaf82459b9aad305626770bb..3e72bffb55890061553a91bd73dce3e95749c413 100644
--- a/README.md
+++ b/README.md
@@ -10,94 +10,3 @@
-
-
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://gitlab.vsb.cz/dre0059/articleprocessor-grobid-version-1.0.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://gitlab.vsb.cz/dre0059/articleprocessor-grobid-version-1.0/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
diff --git a/data/demo.mv.db b/data/demo.mv.db
index cea7e2f55842f2283c6d0fe9a7f2ac0bb6d50a00..2035600e8f6a6054a336c3d8b089cb45303629bb 100644
Binary files a/data/demo.mv.db and b/data/demo.mv.db differ
diff --git a/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java b/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java
deleted file mode 100644
index fb4481081e0dd42f1e96d43d8e85244e1aaa42cb..0000000000000000000000000000000000000000
--- a/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package com.dre0059.articleprocessor.apacheTika;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import org.apache.pdfbox.pdmodel.PDDocument;
-import org.apache.pdfbox.text.PDFTextStripper;
-import org.springframework.stereotype.Component;
-
-@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
deleted file mode 100644
index d02dafd2cf1b4fded61e144a79348c52f0204bb2..0000000000000000000000000000000000000000
--- a/src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java
+++ /dev/null
@@ -1,178 +0,0 @@
-package com.dre0059.articleprocessor.apacheTika;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Scanner;
-import java.util.Vector;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import org.apache.tika.Tika;
-import org.apache.tika.exception.TikaException;
-
-
-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 ÄÃslo 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 ÄÃslo 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/resources/static/js/scripts.js b/src/main/resources/static/js/scripts.js
deleted file mode 100644
index 0a1726ad0d68d7a6c6832a893a7585d8a09d7d42..0000000000000000000000000000000000000000
--- a/src/main/resources/static/js/scripts.js
+++ /dev/null
@@ -1,7 +0,0 @@
-/*!
-* Start Bootstrap - Landing Page v6.0.6 (https://startbootstrap.com/theme/landing-page)
-* Copyright 2013-2023 Start Bootstrap
-* Licensed under MIT (https://github.com/StartBootstrap/startbootstrap-landing-page/blob/master/LICENSE)
-*/
-// This file is intentionally blank
-// Use this file to add JavaScript to your project
\ No newline at end of file
diff --git a/src/main/resources/templates/upload-success.html b/src/main/resources/templates/upload-success.html
deleted file mode 100644
index 9beeb4f11e76946a30adfa550d0b9f057666fbd6..0000000000000000000000000000000000000000
--- a/src/main/resources/templates/upload-success.html
+++ /dev/null
@@ -1,89 +0,0 @@
-<!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>
- <link rel="icon" type="image/x-icon" href="assets/favicon.ico" />
-</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 referencià -->
- <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 () {
- // ZÃskanie 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>
diff --git a/src/main/resources/templates/view-pdf.html b/src/main/resources/templates/view-pdf.html
index 1723fdb8ad973d7474b2e7bba6828c15e8ab72da..b0b94e878b7d26d8445693f9cbdf62ff77fa0065 100644
--- a/src/main/resources/templates/view-pdf.html
+++ b/src/main/resources/templates/view-pdf.html
@@ -55,7 +55,7 @@
<a class="nav-link" href="/view">View all</a>
</li>
<li class="nav-item">
- <a class="nav-link" href="/upload">Statistics</a>
+ <a class="nav-link" href="/statistics">Statistics</a>
</li>
<li class="nav-item">
<a class="nav-link" href="/upload">About project</a>