New version - with styles

UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt

-"hahahahahahaha"
\ No newline at end of file

UserselidrAppDataLocalTemp³661.263675-references.txt

-"heeeeeeeeeeeeeeeeeeej"
\ No newline at end of file

pom.xml

@@ -28,6 +28,8 @@
     </scm>
     <properties>
         <java.version>17</java.version>
+        <lombok.version>1.18.36</lombok.version>
+
     </properties>
 
     <!-- -->
@@ -41,32 +43,21 @@
 
     <dependencies>
         <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-data-jpa</artifactId>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <version>${lombok.version}</version>
+            <scope>provided</scope>
         </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>
+            <artifactId>spring-boot-starter-data-jpa</artifactId>
         </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>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-web</artifactId>
         </dependency>
-        -->
 
         <dependency>
             <groupId>com.h2database</groupId>
@@ -79,8 +70,6 @@
             <artifactId>spring-boot-starter-webflux</artifactId>
         </dependency>
 
-
-
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-test</artifactId>
@@ -93,12 +82,14 @@
             <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>
@@ -147,14 +138,6 @@
             <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>
@@ -183,13 +166,22 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.11.0</version>
                 <configuration>
+                    <failOnError>false</failOnError>
+
                     <annotationProcessorPaths>
                         <path>
                             <groupId>org.mapstruct</groupId>
                             <artifactId>mapstruct-processor</artifactId>
                             <version>1.6.3</version>
                         </path>
+
+                        <path>
+                            <groupId>org.projectlombok</groupId>
+                            <artifactId>lombok</artifactId>
+                            <version>${lombok.version}</version>
+                        </path>
                     </annotationProcessorPaths>
+
                 </configuration>
             </plugin>
         </plugins>

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

 package com.dre0059.articleprocessor;
 
+import com.dre0059.articleprocessor.config.GrobidProperties;
+import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.http.MediaType;
 import org.springframework.stereotype.Service;
 import org.springframework.web.reactive.function.BodyInserters;
@@ -14,9 +16,10 @@ import java.io.File;
 public class GrobidClient {
     private final WebClient webClient;
 
-    public GrobidClient() {
-        this.webClient = WebClient.builder()
-                .baseUrl("http://158.196.98.65:8080")   // URL kde beží GROBID server
+  public GrobidClient(GrobidProperties grobidProperties) {
+
+    this.webClient = WebClient.builder()
+                .baseUrl(grobidProperties.getHost())   // URL kde beží GROBID server
                 .build();
     }
 

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

 package com.dre0059.articleprocessor.apacheTika;
 
-import org.apache.pdfbox.pdmodel.PDDocument;
-import org.apache.pdfbox.text.PDFTextStripper;
-import org.springframework.stereotype.Component;
-
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
-
-import static com.lowagie.text.html.HtmlTagMap.isTitle;
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.text.PDFTextStripper;
+import org.springframework.stereotype.Component;
 
 @Component
 public class PDFbox {

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

 package com.dre0059.articleprocessor.apacheTika;
 
-import org.apache.tika.Tika;
-import org.apache.tika.exception.TikaException;
-
-import javax.sound.midi.Soundbank;
-import java.io.*;
-import java.util.ArrayList;
+import java.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 {

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

@@ -4,48 +4,64 @@ import com.dre0059.articleprocessor.dto.DocumentDto;
 import com.dre0059.articleprocessor.dto.SimpleDocumentDto;
 import com.dre0059.articleprocessor.service.DocumentService;
 import java.util.List;
+import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseBody;
 
-@Controller()
-@RequestMapping("/api/document")
+@Controller
+@RequestMapping
 public class DocumentController {
 
   private final DocumentService documentService;
 
-
   public DocumentController(DocumentService documentService) {
     this.documentService = documentService;
   }
 
-  @GetMapping("/{id}")
+  @GetMapping("/api/documents/{id}")
   public ResponseEntity<DocumentDto> getDocumentById(@PathVariable Long id) {
     return ResponseEntity.ok(documentService.getDocumentById(id));
   }
 
-  @GetMapping("/references/{id}")
+  @GetMapping(
+    value = "/api/documents/{id}/content",
+    produces = MediaType.APPLICATION_PDF_VALUE
+  )
+  public @ResponseBody byte[] getDocumentContentById(@PathVariable Long id) {
+    return documentService.getDocumentContentById(id).getContent();
+  }
+
+  @GetMapping("/api/documents/{id}/references")
   public ResponseEntity<List<SimpleDocumentDto>> getReferencesFromDocument(@PathVariable Long id) {
-    return ResponseEntity.ok(documentService.getDocumentReferences(id));
+    return ResponseEntity.ok(documentService.getReferencedDocumentsById(id));
   }
 
   @GetMapping("/view/{id}")
-  public String viewPdf(Model model, @PathVariable("id") Long id) {
-    var references = documentService.getDocumentReferences(id);
+  public String viewDocument(Model model, @PathVariable("id") Long id) {
+    var references = documentService.getReferencedDocumentsById(id);
 
+    if (documentService.getDocumentById(id) == null) {
+      throw new IllegalArgumentException("Document with ID " + id + " not found.");
+    }
+
+    model.addAttribute("documentId", id);
     model.addAttribute("references", references);
+    model.addAttribute("docTitle", documentService.getDocumentById(id).getTitle());
+
 
     return "view-pdf";
   }
 
   @GetMapping("/view")
-  public String viewPdf(Model model) {
-    var references = documentService.getAllReferences();
+  public String viewAllDocuments(Model model) {
+    var documents = documentService.getAllDocuments();
 
-    model.addAttribute("references", references);
+    model.addAttribute("documents", documents);
 
     return "view-all";
   }

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

 package com.dre0059.articleprocessor.controller;
 
 import com.dre0059.articleprocessor.GrobidClient;
-import com.dre0059.articleprocessor.model.Category;
-import com.dre0059.articleprocessor.repository.CategoryRepository;
+import com.dre0059.articleprocessor.service.CategoryService;
 import com.dre0059.articleprocessor.service.HeaderService;
-
 import com.dre0059.articleprocessor.service.ReferenceService;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
 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.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.ResponseBody;
 import org.springframework.web.multipart.MultipartFile;
 
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.util.List;
-import java.util.Optional;
-
 @Controller
-@RequestMapping("/api/grobid")
+@RequestMapping
 public class FileUploadController {
     private final GrobidClient grobidClient;
     private final HeaderService headerService;
     private final ReferenceService referenceService;
-    private final CategoryRepository categoryRepository;
+    private final CategoryService categoryService;
 
-    public FileUploadController(GrobidClient grobidClient, HeaderService headerService, ReferenceService referenceService, CategoryRepository categoryRepository) {
+    public FileUploadController(GrobidClient grobidClient, HeaderService headerService, ReferenceService referenceService, CategoryService categoryService) {
         this.grobidClient = grobidClient;
         this.headerService = headerService;
         this.referenceService = referenceService;
-        this.categoryRepository = categoryRepository;
+        this.categoryService = categoryService;
     }
 
     @GetMapping("/upload")
     public String showUploadForm(Model model) {
-        List<Category> categories = categoryRepository.findAll();
+        var categories = categoryService.getAll();
         model.addAttribute("categories", categories);
         return "upload";  // vracia upload.html
     }
 
-    @PostMapping("/upload")
+    @PostMapping("/api/upload")
     @ResponseBody
-    public ResponseEntity<String> handleFileUpload(@RequestParam("file") MultipartFile file, @RequestParam("category") String category) {
+    public ResponseEntity<String> handleFileUpload(@RequestParam("file") MultipartFile file, @RequestParam("categoryId") String categoryId) {
         if (file.isEmpty()) {
             return ResponseEntity.badRequest().body("No file uploaded!");
         }
 
-        System.out.println("Received file: " + file.getOriginalFilename());
-        System.out.println("Received category: " + category);
-
         try {
-            // Vytvorenie dočasného súboru
+            System.out.println("Processing file " + file.getOriginalFilename());
             File tmpFile = File.createTempFile("article-", ".pdf");
 
             // save data from file to tmpFile
@@ -60,26 +56,19 @@ public class FileUploadController {
              } catch (IOException e) {
                 return ResponseEntity.internalServerError().body("FAILURE - cannot process file : " + e.getMessage());
             }
+            //System.out.println("File written to temporary location. ");
 
             String header = grobidClient.processHeader(tmpFile);
-            String references = grobidClient.processReferences(tmpFile);
+            //System.out.println("GROBID Header processed: " + header);
 
-            String categoryId = category.substring(0, 3);
-            Optional<Category> categoryOptional = categoryRepository.findById(categoryId);
+            String references = grobidClient.processReferences(tmpFile);
+            //System.out.println("GROBID Reference processed: " + references);
 
-            System.out.println("ID category is : " + categoryId);
-            System.out.println("Optional category is : " + categoryOptional);
-            if (category.isEmpty()) {
-                return ResponseEntity.badRequest().body("Invalid category ID!");
-            }
+            headerService.processHeader(header, categoryId, tmpFile);
+            //System.out.println("Header saved to database.");
 
-            headerService.processHeader(header, categoryOptional);
             referenceService.extractReferences(references);
-
-            //System.out.println(header);
-            //System.out.println(references);
-
-
+            //System.out.println("References extracted..");
 
             tmpFile.delete();
 

src/main/java/com/dre0059/articleprocessor/dto/DocumentDto.java

 package com.dre0059.articleprocessor.dto;
 
+import lombok.Getter;
+import lombok.Setter;
+
+@Getter
+@Setter
 public class DocumentDto {
   private Long id;
   private String title;
@@ -10,67 +15,5 @@ public class DocumentDto {
   private String publisher;
   private String target;
 
-  public Long getId() {
-    return id;
-  }
-
-  public void setId(Long id) {
-    this.id = id;
-  }
-
-  public String getTitle() {
-    return title;
-  }
-
-  public void setTitle(String title) {
-    this.title = title;
-  }
-
-  public Integer getPublicationYear() {
-    return publicationYear;
-  }
-
-  public void setPublicationYear(Integer publicationYear) {
-    this.publicationYear = publicationYear;
-  }
-
-  public String getDoi() {
-    return doi;
-  }
-
-  public void setDoi(String doi) {
-    this.doi = doi;
-  }
-
-  public String getAbstractText() {
-    return abstractText;
-  }
-
-  public void setAbstractText(String abstractText) {
-    this.abstractText = abstractText;
-  }
-
-  public String getStatus() {
-    return status;
-  }
-
-  public void setStatus(String status) {
-    this.status = status;
-  }
-
-  public String getPublisher() {
-    return publisher;
-  }
-
-  public void setPublisher(String publisher) {
-    this.publisher = publisher;
-  }
-
-  public String getTarget() {
-    return target;
-  }
 
-  public void setTarget(String target) {
-    this.target = target;
-  }
 }

src/main/java/com/dre0059/articleprocessor/dto/SimpleDocumentDto.java

 package com.dre0059.articleprocessor.dto;
 
+import lombok.Getter;
+import lombok.Setter;
+
+@Getter
+@Setter
 public class SimpleDocumentDto {
   private Long id;
   private String title;
+  private String status;
 
   public String getLink() {
     return "/api/document/"+getId();
   }
-
-  public Long getId() {
-    return id;
-  }
-
-  public void setId(Long id) {
-    this.id = id;
-  }
-
-  public String getTitle() {
-    return title;
-  }
-
-  public void setTitle(String title) {
-    this.title = title;
-  }
 }

src/main/java/com/dre0059/articleprocessor/mapper/DocumentMapper.java

 package com.dre0059.articleprocessor.mapper;
 
+import com.dre0059.articleprocessor.dto.DocumentContentDto;
 import com.dre0059.articleprocessor.dto.DocumentDto;
 import com.dre0059.articleprocessor.dto.SimpleDocumentDto;
 import com.dre0059.articleprocessor.model.Dokument;
 import java.util.List;
 import org.mapstruct.Mapper;
+import org.mapstruct.Mapping;
 
 @Mapper(componentModel = "spring")
 public interface DocumentMapper {
 
+  @Mapping(target = "publicationYear", source = "year")
   DocumentDto toDocumentDto(Dokument entity);
-  SimpleDocumentDto toSimpleDocument(Dokument entity);
+
+  DocumentContentDto toDocumentContentDto(Dokument entity);
+
+  SimpleDocumentDto toSimpleDocumentDto(Dokument entity);
 
   List<SimpleDocumentDto> toSimpleDocumentList(List<Dokument> entities);
+
+  default String toString(byte[] bytes) {
+    if (bytes == null) {
+      return null;
+    } else {
+      return new String(bytes);
+    }
+  }
+
 }

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

 package com.dre0059.articleprocessor.model;
 
-import jakarta.persistence.*;
-import org.hibernate.annotations.Cascade;
-
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.JoinTable;
+import jakarta.persistence.Lob;
+import jakarta.persistence.ManyToMany;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
 import java.util.ArrayList;
 import java.util.List;
 
+import lombok.Getter;
+import lombok.Setter;
+import org.hibernate.annotations.Cascade;
 
+@Setter
+@Getter
 @Entity
 @Table(name = "documents")
 public class Dokument {
@@ -26,14 +41,19 @@ public class Dokument {
     @JoinColumn(name = "category_id")
     private Category category;
 
-    // @Lob for huge text
-    //@Column(name = "abstractText", columnDefinition = "TEXT")
-    //private String abstractText;
+    @Lob
+    @Column
+    private byte[] abstractText;
+
+    @Lob
+    @Column
+    private byte[] content;
 
     private String status; // if the value is PDF - the whole document was uploaded, otherwise the document was just mentioned in references
     private String publisher;
     private String target; // http link
 
+
     @OneToMany(mappedBy = "fromDocument", cascade = CascadeType.ALL)
     private List<Reference> references = new ArrayList<>();
 
@@ -57,34 +77,7 @@ public class Dokument {
         this.status = status;
     }
 
-    public Long getId() { return id; }
-    public String getTitle() { return title; }
-    public Integer getYear() { return publicationYear; }
-    public String getDoi() { return doi; }
-    //public String getAbstractText() { return abstractText; }
-    public String getStatus() { return status; }
-    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; }
-    public void setTitle(String title) { this.title = title; }
-    public void setTarget(String target) { this.target = target; }
-    public void setPublicationYear(Integer publicationYear) {
-        this.publicationYear = publicationYear;
-    }
-    public void setDoi(String doi) {
-        this.doi = doi;
-    }
-    public void setStatus(String status) {
-        this.status = status;
-    }
-    public void setPublisher(String publisher) {
-        this.publisher = publisher;
-    }
-    public void setReferences(List<Reference> references) {
-        this.references = references;
+    public Integer getYear(){
+        return publicationYear;
     }
-    public void setCategory(Category category) { this.category = category;}
 }

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

@@ -2,12 +2,8 @@ package com.dre0059.articleprocessor.repository;
 
 import com.dre0059.articleprocessor.model.Author;
 import org.springframework.data.jpa.repository.JpaRepository;
-import org.springframework.data.jpa.repository.Query;
-import org.springframework.data.repository.query.Param;
 import org.springframework.stereotype.Repository;
 
-import java.util.Optional;
-
 @Repository
 public interface AuthorRepository extends JpaRepository<Author, Long> {
     /*@Query("SELECT CASE WHEN COUNT(a) > 0 THEN true ELSE false END FROM Author a WHERE a.lastName = :lastName AND a.firstName = :firstName")

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

@@ -40,7 +40,7 @@ public interface DocumentRepository extends JpaRepository<Dokument, Long> {
         WHERE d.id = :id
         """
     )
-    List<Dokument> getReferencedDocumentsById(@Param("id") Long id);
+    List<Dokument> getReferencedDocumentsById(@Param("id") Long fromDocumentId);
 
 }
 

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

 package com.dre0059.articleprocessor.service;
 
+import com.dre0059.articleprocessor.dto.DocumentContentDto;
 import com.dre0059.articleprocessor.dto.DocumentDto;
 import com.dre0059.articleprocessor.dto.SimpleDocumentDto;
 import com.dre0059.articleprocessor.mapper.DocumentMapper;
-import com.dre0059.articleprocessor.repository.*;
-import com.dre0059.articleprocessor.model.*;
-
+import com.dre0059.articleprocessor.model.Author;
+import com.dre0059.articleprocessor.model.Category;
+import com.dre0059.articleprocessor.model.Dokument;
+import com.dre0059.articleprocessor.repository.AuthorRepository;
+import com.dre0059.articleprocessor.repository.CategoryRepository;
+import com.dre0059.articleprocessor.repository.DocumentRepository;
 import jakarta.transaction.Transactional;
 import java.util.List;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 @Service
@@ -17,32 +20,40 @@ public class DocumentService {
   private final DocumentMapper documentMapper;
   private final DocumentRepository documentRepository;
   private final AuthorRepository authorRepository;
+  private final CategoryRepository categoryRepository;
 
   public DocumentService(DocumentMapper documentMapper, DocumentRepository documentRepository,
-      AuthorRepository authorRepository) {
+      AuthorRepository authorRepository, CategoryRepository categoryRepository) {
     this.documentMapper = documentMapper;
     this.documentRepository = documentRepository;
     this.authorRepository = authorRepository;
+    this.categoryRepository = categoryRepository;
   }
 
   @Transactional
-  public DocumentDto getDocumentById(Long id) {
-    return documentMapper.toDocumentDto(documentRepository.findById(id).orElse(null));
+  public DocumentDto getDocumentById(Long documentId) {
+    Dokument dokument = documentRepository.findById(documentId).orElse(null);
+
+    // Použitie mappera na konverziu dokumentu do DTO
+    DocumentDto documentDto = documentMapper.toDocumentDto(dokument);
+
+    return documentDto;
   }
 
+
   @Transactional
-  public List<SimpleDocumentDto> getDocumentReferences(Long id) {
-    return documentMapper.toSimpleDocumentList(documentRepository.getReferencedDocumentsById(id));
+  public DocumentContentDto getDocumentContentById(Long documentId) {
+    return documentMapper.toDocumentContentDto(documentRepository.findById(documentId).orElse(null));
   }
 
   @Transactional
-  public List<SimpleDocumentDto> getAllReferences() {
-    return documentMapper.toSimpleDocumentList(documentRepository.findAll());
+  public List<SimpleDocumentDto> getReferencedDocumentsById(Long documentId) {
+    return documentMapper.toSimpleDocumentList(documentRepository.getReferencedDocumentsById(documentId));
   }
 
   @Transactional
-  public Dokument saveDocument(Dokument document) {
-    Dokument dok = new Dokument();
-    return dok;
+  public List<SimpleDocumentDto> getAllDocuments() {
+    return documentMapper.toSimpleDocumentList(documentRepository.findAll());
   }
+
 }

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

 package com.dre0059.articleprocessor.service;
 
+import com.dre0059.articleprocessor.dto.CategoryDto;
 import com.dre0059.articleprocessor.model.Author;
 import com.dre0059.articleprocessor.model.Category;
 import com.dre0059.articleprocessor.model.Dokument;
 import com.dre0059.articleprocessor.repository.AuthorRepository;
 import com.dre0059.articleprocessor.repository.CategoryRepository;
 import com.dre0059.articleprocessor.repository.DocumentRepository;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
-
-import javax.swing.text.html.Option;
-import java.util.*;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import org.apache.commons.io.FileUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
 
 // TODO :
 //  1. VALIDATE author based on surname and first INITIAL of the firstName.
@@ -39,7 +45,6 @@ public class HeaderService {
     private List<Author> authorList = new ArrayList<>();
 
     private String author;
-    private Category category;
 
     @Autowired
     public HeaderService(DocumentRepository documentRepository, AuthorRepository authorRepository, ReferenceService referenceService, CategoryRepository categoryRepository) {
@@ -49,7 +54,7 @@ public class HeaderService {
         this.categoryRepository = categoryRepository;
     }
 
-    public void processHeader(String header, Optional<Category> category) {
+    public void processHeader(String header, String categoryId, File pdfFile) {
         this.title = this.parseHeaderFields(header, "title");
 
         if(!this.parseHeaderFields(header, "doi").equals("Not found")){
@@ -79,22 +84,26 @@ public class HeaderService {
         System.out.println("Author list before checking duplicity: " + authorList);
         System.out.println("Author last names before checking duplicity: " + authorLastNames);
 
-        boolean headerDuplicity = documentRepository.existsByTitleAndAuthorsIn(title, authorLastNames);
-
         // check duplicity of the document
-        if(headerDuplicity){
+        if(documentRepository.existsByTitleAndAuthorsIn(title, authorLastNames)){
             System.out.println("Document with this title and authors already exist");
             return;
         }
 
         List<Author> savedAuthors = authorRepository.saveAll(authorList);
         Dokument dokument = new Dokument(title, year, doi, publisher, "PDF");
+        Category category = categoryRepository.getReferenceById(categoryId);
 
-        //dokument.setCategory(category.get());
         dokument.setAuthors(savedAuthors);
 
         System.out.println("Category: " + category);
-        category.ifPresent(dokument::setCategory);
+        dokument.setCategory(category);
+
+        try {
+            dokument.setContent(FileUtils.readFileToByteArray(pdfFile));
+        } catch (IOException e) {
+          System.err.println("Nepodarilo sa ulozit obsah suboru");
+        }
 
         this.documentRepository.save(dokument); // output : Optional.empty
 

src/main/resources/application.properties

@@ -23,7 +23,7 @@ spring.application.name=articleProcessor
 #spring.jpa.show-sql=true
 
 #spring.datasource.url=jdbc:h2:mem:testdb
-spring.datasource.url=jdbc:h2:file:/data/demo 
+spring.datasource.url=jdbc:h2:file:./data/demo
 spring.datasource.driverClassName=org.h2.Driver
 spring.datasource.username=sa
 spring.datasource.password=password
@@ -42,3 +42,5 @@ spring.thymeleaf.suffix=.html
 # Spring MVC for uploading PDF files
 spring.servlet.multipart.max-file-size=5MB
 spring.servlet.multipart.max-request-size=5MB
+
+grobid.host=http://158.196.98.65:8080
\ No newline at end of file

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>
+<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>
+    <link rel="stylesheet" th:href="@{/style.css}">
 
-    <body>
-        <h1>Upload your PDF</h1>
+    <style>
+        #pdf-preview {
+            width: 500px;
+            height: 600px;
+            border: 1px solid #ddd;
+            margin-top: 10px;
+        }
+    </style>
+</head>
 
-        <!-- 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">
+<body>
+<h1>Upload your PDF</h1>
 
-            <label for="category">Select Category:</label>
+<!-- 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">
 
-            <select id="category" name="category" >
-                <option th:each="c : ${categories}" th:value="${c.getId()}" th:text ="${c.getId() + ' ' + c.getName()}"></option>
-            </select>
+    <label for="category">Select Category:</label>
+    <select id="category" name="category">
+        <option th:each="c: ${categories}" th:value="${c.getId()}" th:text="${c.getName()}"></option>
+    </select>
 
-            <button type = "submit">Upload & Process the PDF</button>
-        </form>
+    <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>
+<!-- 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>
+<!-- JSON výstup -->
+<div id = "response-containter" style="display: none;">
+    <h3>Response : </h3>
+    <pre id = "json-output"></pre>
+</div>
 
-        <!--<a href="/api/document/22">click here</a> -->
+<!--<a href="/api/document/22">click here</a> -->
 
-        <!-- .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.');
-               }
-            });
+<!-- .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];
-                const category = $('#category').val(); // Získanie vybranej kategórie
+    // AJAX for sending a file
+    $('#uploadForm').submit(function(event) {
+        event.preventDefault();
+        const fileInput = $('#fileInput')[0].files[0];
+        const category = $('#category').val(); // Získanie vybranej kategórie
 
-                if(!fileInput){
-                    alert("Please select a PDF file first.");
-                    return;
-                }
+        if(!fileInput){
+            alert("Please select a PDF file first.");
+            return;
+        }
 
-                const formData = new FormData();
-                formData.append("file", fileInput);
-                formData.append("category", category); // Posielame aj kategóriu
+        const formData = new FormData();
+        formData.append("file", fileInput);
+        formData.append("categoryId", category); // Posielame aj kategóriu
 
-                $.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>
+        $.ajax({
+            url: "/api/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/main/resources/templates/view-all.html

@@ -3,39 +3,37 @@
 <head>
   <meta charset="UTF-8">
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  <title>Upload PDF</title>
+  <title>Article processor</title>
+  <link rel="stylesheet" th:href="@{/style.css}">
+
   <script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
   <style>
     #pdf-preview {
       width: 500px;
       height: 600px;
-      border: 1px solid #ddd;
+      border: none;
       margin-top: 10px;
     }
   </style>
 </head>
 
 <body>
-<h1>PDF files</h1>
+<h1>Article processor</h1>
 
-<!-- zobrazenie PDF -->
-<div id="pdf-container">
-  <iframe id="pdf-preview" src="" style="display: none;"></iframe>
-</div>
 
 <table>
   <thead>
   <tr>
     <th>ID</th>
     <th>Title</th>
-    <th>Link</th>
+    <th>Status</th>
   </tr>
   </thead>
   <tbody>
-    <tr th:each="ref: ${references}">
-      <td th:text="${ref.id}"></td>
-      <td th:text="${ref.title}"></td>
-      <td><a th:href="@{'/api/document/' + ${ref.id}}" th:text="${ref.title}"></a></td>
+    <tr th:each="doc: ${documents}">
+      <td th:text="${doc.id}"></td>
+      <td><a th:href="@{'/view/' + ${doc.id}}" th:text="${doc.title}"></a></td>
+      <td th:text="${doc.status}"></td>
     </tr>
   </tbody>
 </table>

src/main/resources/templates/view-pdf.html

@@ -3,42 +3,87 @@
 <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>
+  <title>View single PDF</title>
+  <!-- Bootstrap CSS -->
+  <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet">
+  <link rel="stylesheet" href="/style.css">
+
   <style>
-    #pdf-preview {
-      width: 500px;
-      height: 600px;
-      border: 1px solid #ddd;
-      margin-top: 10px;
+    body {
+      margin: 25px;
+      background: linear-gradient(black, black, gray);
+      color: white;
+    }
+
+    a{
+      text-decoration: none;
+    }
+
+    /* Rodičovský kontajner pre flexbox */
+    #container {
+      display: flex;
+      justify-content: space-between; /* Rozdelenie priestoru medzi textom a PDF */
+      align-items: flex-start; /* Zarovnanie na vrchnú časť */
+      gap: 20px; /* Medzera medzi textom a PDF */
+    }
+
+    /* Pre textové informácie a referencie */
+    #text-container {
+      flex: 1; /* Text a referencie zabírajú všetok voľný priestor */
+      padding : 20px; /* Trochu medzery medzi textom a PDF */
+    }
+
+    /* Pre PDF kontajner */
+    #pdf-container {
+      width: 960px; /* Šírka PDF kontajnera */
+      height: 1500px; /* Výška PDF kontajnera */
     }
   </style>
 </head>
 
 <body>
-<h1>PDF files</h1>
+<h1><a href="/view">All PDF files</a></h1>
+<h2>Title : <span th:text="${docTitle}"></span> </h2> <!-- title aktuálneho dokumentu -->
 
-<!-- zobrazenie PDF -->
-<div id="pdf-container">
-  <iframe id="pdf-preview" src="" style="display: none;"></iframe>
-</div>
+<div id="container">
+  <!-- Textová sekcia -->
+  <div id="text-container">
+
+    <h3>Information about document </h3>
+    Category : <span> </span><br>
+    Author : <span> </span><br><br>
+
+    Title : <span th:text="${docTitle}"></span><br>
+    Publication year : <span th:text="${year}"></span><br>
+    DOI : <span th:text="${doi}"></span><br>
+    Link : <span th:text="${link}"></span><br><br>
 
-<table>
-  <thead>
-  <tr>
-    <th>ID</th>
-    <th>Title</th>
-    <th>Link</th>
-  </tr>
-  </thead>
-  <tbody>
-    <tr th:each="ref: ${references}">
-      <td th:text="${ref.id}"></td>
-      <td th:text="${ref.title}"></td>
-      <td><a th:href="@{'/api/document/' + ${ref.id}}" th:text="${ref.title}"></a></td>
-    </tr>
-  </tbody>
-</table>
+    <h2>References : </h2>
+
+    <table>
+      <thead>
+      <tr>
+        <th>ID</th>
+        <th>Title</th>
+        <th>Status</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr th:each="ref: ${references}">
+        <td th:text="${ref.id}"></td>
+        <!--<td th:text="${ref.title}"></td>-->
+        <td><a th:href="@{'/view/' + ${ref.id}}" th:text="${ref.title}"></a></td>
+        <td></td>
+      </tr>
+      </tbody>
+    </table>
+  </div>
+
+  <!-- PDF sekcia -->
+  <div id="pdf-container">
+    <embed th:src="@{'/api/documents/' + ${documentId} + '/content'}" type="application/pdf" width="960px" height="70%"/>
+  </div>
+</div>
 
 </body>
 </html>