diff --git a/UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt b/UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt
deleted file mode 100644
index e4e16e47dc903d046dbfce53f951b392cdbfb57e..0000000000000000000000000000000000000000
--- a/UserselidrAppDataLocalTempA_study_of_the_safety_immunology_virolog-references.txt
+++ /dev/null
@@ -1 +0,0 @@
-"hahahahahahaha"
\ No newline at end of file
diff --git "a/UserselidrAppDataLocalTemp\302\263661.263675-references.txt" "b/UserselidrAppDataLocalTemp\302\263661.263675-references.txt"
deleted file mode 100644
index 83c274254ec158b2a4435fc682e24ae923bd65c3..0000000000000000000000000000000000000000
--- "a/UserselidrAppDataLocalTemp\302\263661.263675-references.txt"
+++ /dev/null
@@ -1 +0,0 @@
-"heeeeeeeeeeeeeeeeeeej"
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index dc68618947fdd6b25a373e0d3392cdbe078815fb..6f43c062409d9d282334047fe9f250288a3a61c2 100644
--- a/pom.xml
+++ b/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>
diff --git a/src/main/java/com/dre0059/articleprocessor/GrobidClient.java b/src/main/java/com/dre0059/articleprocessor/GrobidClient.java
index 4b52d743885498178c707895bd0d54918dee2100..7b58e41e4fb2e40d432509c7d20b60eb0c677cfc 100644
--- a/src/main/java/com/dre0059/articleprocessor/GrobidClient.java
+++ b/src/main/java/com/dre0059/articleprocessor/GrobidClient.java
@@ -1,5 +1,7 @@
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 bežà GROBID server
+ public GrobidClient(GrobidProperties grobidProperties) {
+
+ this.webClient = WebClient.builder()
+ .baseUrl(grobidProperties.getHost()) // URL kde bežà GROBID server
.build();
}
diff --git a/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java b/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java
index f520ae58f0bacb7e6daff7db441b37cb9a8da53d..fb4481081e0dd42f1e96d43d8e85244e1aaa42cb 100644
--- a/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java
+++ b/src/main/java/com/dre0059/articleprocessor/apacheTika/PDFbox.java
@@ -1,14 +1,11 @@
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 {
diff --git a/src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java b/src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java
index 279e40509468c80b466c0148cd09c62811cdc801..d02dafd2cf1b4fded61e144a79348c52f0204bb2 100644
--- a/src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java
+++ b/src/main/java/com/dre0059/articleprocessor/apacheTika/ReferencesScanner.java
@@ -1,15 +1,16 @@
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 {
diff --git a/src/main/java/com/dre0059/articleprocessor/controller/DocumentController.java b/src/main/java/com/dre0059/articleprocessor/controller/DocumentController.java
index 5529c3aa90eb357b528987733cc09945761cd61c..4bb5031f85bfb9f709ba063d045d750499b8b609 100644
--- a/src/main/java/com/dre0059/articleprocessor/controller/DocumentController.java
+++ b/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";
}
diff --git a/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java b/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
index b5e1d07c7139a5acd349123c7f15ffffc29ac987..42addb697ecc78f7f849abbd1b45b3b5e136419b 100644
--- a/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
+++ b/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
@@ -1,57 +1,53 @@
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();
diff --git a/src/main/java/com/dre0059/articleprocessor/dto/DocumentDto.java b/src/main/java/com/dre0059/articleprocessor/dto/DocumentDto.java
index 8f97cc0a80cb3e3ff89184df8b13b46fff9ee5d2..95d2875498e020efdc732fd52b475539b69c13d0 100644
--- a/src/main/java/com/dre0059/articleprocessor/dto/DocumentDto.java
+++ b/src/main/java/com/dre0059/articleprocessor/dto/DocumentDto.java
@@ -1,5 +1,10 @@
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;
- }
}
diff --git a/src/main/java/com/dre0059/articleprocessor/dto/SimpleDocumentDto.java b/src/main/java/com/dre0059/articleprocessor/dto/SimpleDocumentDto.java
index 9ed6b674f30bd38a295e87fe873303f1fc7dccbc..ea44d6b9b3e9a14e887084308020c13fea0ce3f7 100644
--- a/src/main/java/com/dre0059/articleprocessor/dto/SimpleDocumentDto.java
+++ b/src/main/java/com/dre0059/articleprocessor/dto/SimpleDocumentDto.java
@@ -1,26 +1,16 @@
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;
- }
}
diff --git a/src/main/java/com/dre0059/articleprocessor/mapper/DocumentMapper.java b/src/main/java/com/dre0059/articleprocessor/mapper/DocumentMapper.java
index 2a5516c35ff4603e90d1164743deff8f90224afe..854bab14f670c821492d945d9577e8668b971717 100644
--- a/src/main/java/com/dre0059/articleprocessor/mapper/DocumentMapper.java
+++ b/src/main/java/com/dre0059/articleprocessor/mapper/DocumentMapper.java
@@ -1,16 +1,31 @@
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);
+ }
+ }
+
}
diff --git a/src/main/java/com/dre0059/articleprocessor/model/Dokument.java b/src/main/java/com/dre0059/articleprocessor/model/Dokument.java
index 1e6e8dd456530be3d8f176a941997d87778aa1c7..0969142429d23a7effdef4880ac1e1390cead349 100644
--- a/src/main/java/com/dre0059/articleprocessor/model/Dokument.java
+++ b/src/main/java/com/dre0059/articleprocessor/model/Dokument.java
@@ -1,12 +1,27 @@
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;}
}
diff --git a/src/main/java/com/dre0059/articleprocessor/repository/AuthorRepository.java b/src/main/java/com/dre0059/articleprocessor/repository/AuthorRepository.java
index 913ab5bf0255c1e28efb934c50072a3d73559eb7..348dde743fdc0be9f9a15adb06a0e61abe765ba3 100644
--- a/src/main/java/com/dre0059/articleprocessor/repository/AuthorRepository.java
+++ b/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")
diff --git a/src/main/java/com/dre0059/articleprocessor/repository/DocumentRepository.java b/src/main/java/com/dre0059/articleprocessor/repository/DocumentRepository.java
index 306c37f2d428a4eb84f14ddc52f719cc470a7271..84557ad5e69a9fe722093d3490d910eb819878a4 100644
--- a/src/main/java/com/dre0059/articleprocessor/repository/DocumentRepository.java
+++ b/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);
}
diff --git a/src/main/java/com/dre0059/articleprocessor/service/DocumentService.java b/src/main/java/com/dre0059/articleprocessor/service/DocumentService.java
index e32a09ddf7c885df6017be9c2024432a0da92f2f..fb9a2606c6f9e4dce1e3264847ad2c147a269c28 100644
--- a/src/main/java/com/dre0059/articleprocessor/service/DocumentService.java
+++ b/src/main/java/com/dre0059/articleprocessor/service/DocumentService.java
@@ -1,14 +1,17 @@
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);
+
+ // PouĹľitie 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());
}
+
}
diff --git a/src/main/java/com/dre0059/articleprocessor/service/HeaderService.java b/src/main/java/com/dre0059/articleprocessor/service/HeaderService.java
index 30fea4d56f6c13168c7d65ed11496cae487daac0..0a317b2f7686125bbb27483ed41b10e8dd9f4d66 100644
--- a/src/main/java/com/dre0059/articleprocessor/service/HeaderService.java
+++ b/src/main/java/com/dre0059/articleprocessor/service/HeaderService.java
@@ -1,18 +1,24 @@
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
diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
index c1d0451d1f56081349e5f3f6817f189c022c577d..d2bd1712b948c3ac1f70b9254133413108b9300f 100644
--- a/src/main/resources/application.properties
+++ b/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
diff --git a/src/main/resources/templates/upload.html b/src/main/resources/templates/upload.html
index 6855121c27740746406aab1f1240ed6beed42271..dc4370fbc0f1b92fa0aa005a7290cf343e489f9d 100644
--- a/src/main/resources/templates/upload.html
+++ b/src/main/resources/templates/upload.html
@@ -1,93 +1,94 @@
<!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(); // ZĂskanie vybranej kategĂłrie
+ // AJAX for sending a file
+ $('#uploadForm').submit(function(event) {
+ event.preventDefault();
+ const fileInput = $('#fileInput')[0].files[0];
+ const category = $('#category').val(); // ZĂskanie vybranej kategĂłrie
- 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 kategĂłriu
+ const formData = new FormData();
+ formData.append("file", fileInput);
+ formData.append("categoryId", category); // Posielame aj kategĂłriu
- $.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>
diff --git a/src/main/resources/templates/view-all.html b/src/main/resources/templates/view-all.html
index 8715ea9fbcbd92d5e5368ec5f8a55e28e952785a..f19cadadef38dedc1f7166f172c7ca443c72043f 100644
--- a/src/main/resources/templates/view-all.html
+++ b/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="${doc.status}"></td>
</tr>
</tbody>
</table>
diff --git a/src/main/resources/templates/view-pdf.html b/src/main/resources/templates/view-pdf.html
index 8715ea9fbcbd92d5e5368ec5f8a55e28e952785a..175b5e68d3894a2a3d8fa716f168248769786dfa 100644
--- a/src/main/resources/templates/view-pdf.html
+++ b/src/main/resources/templates/view-pdf.html
@@ -3,42 +3,87 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Upload PDF</title>
- <script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
+ <title>View single PDF</title>
+ <!-- Bootstrap CSS -->
+ <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet">
+ <link rel="stylesheet" href="/style.css">
+
<style>
- #pdf-preview {
- width: 500px;
- height: 600px;
- border: 1px solid #ddd;
- margin-top: 10px;
+ body {
+ margin: 25px;
+ background: linear-gradient(black, black, gray);
+ color: white;
+ }
+
+ a{
+ text-decoration: none;
+ }
+
+ /* RodiÄŤovskĂ˝ kontajner pre flexbox */
+ #container {
+ display: flex;
+ justify-content: space-between; /* Rozdelenie priestoru medzi textom a PDF */
+ align-items: flex-start; /* Zarovnanie na vrchnĂş ÄŤasĹĄ */
+ gap: 20px; /* Medzera medzi textom a PDF */
+ }
+
+ /* Pre textové informácie a referencie */
+ #text-container {
+ flex: 1; /* Text a referencie zabĂrajĂş všetok voÄľnĂ˝ priestor */
+ padding : 20px; /* Trochu medzery medzi textom a PDF */
+ }
+
+ /* Pre PDF kontajner */
+ #pdf-container {
+ width: 960px; /* Ĺ Ărka PDF kontajnera */
+ height: 1500px; /* Výška PDF kontajnera */
}
</style>
</head>
<body>
-<h1>PDF files</h1>
+<h1><a href="/view">All PDF files</a></h1>
+<h2>Title : <span th:text="${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>