diff --git a/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java b/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
index 78fa9a561db0c001a9a3855e0ca7219ca04ceea1..af0c62efdcfc42665ce83b50de5c9898f95baa0d 100644
--- a/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
+++ b/src/main/java/com/dre0059/articleprocessor/controller/FileUploadController.java
@@ -3,6 +3,7 @@ package com.dre0059.articleprocessor.controller;
import com.dre0059.articleprocessor.GrobidClient;
import com.dre0059.articleprocessor.service.HeaderService;
+import com.dre0059.articleprocessor.service.ReferenceService;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
@@ -18,18 +19,12 @@ import java.io.IOException;
public class FileUploadController {
private final GrobidClient grobidClient;
private final HeaderService headerService;
+ private final ReferenceService referenceService;
- //private final DocumentRepository metadataRepository;
- //private final ReferenceRepository referenceRepository;
- //private final MetadataParser metadataParser;
- //private static final Logger logger = LoggerFactory.getLogger(FileUploadController.class);
-
- public FileUploadController(GrobidClient grobidClient, HeaderService headerService/*, DocumentRepository metadataRepository, ReferenceRepository referenceRepository, MetadataParser metadataParser*/) {
+ public FileUploadController(GrobidClient grobidClient, HeaderService headerService, ReferenceService referenceService) {
this.grobidClient = grobidClient;
this.headerService = headerService;
- // this.metadataRepository = metadataRepository;
- //this.referenceRepository = referenceRepository;
- //this.metadataParser = metadataParser;
+ this.referenceService = referenceService;
}
@GetMapping("/upload")
@@ -61,9 +56,10 @@ public class FileUploadController {
String references = grobidClient.processReferences(tmpFile);
headerService.processHeader(header);
+ referenceService.extractReferences(references);
System.out.println(header);
- //System.out.println(references);
+ System.out.println(references);
tmpFile.delete();
diff --git a/src/main/java/com/dre0059/articleprocessor/service/HeaderService.java b/src/main/java/com/dre0059/articleprocessor/service/HeaderService.java
index a4e9ace833784f699fb0b8df98a9da2e910458ad..9b24e5907805fc5f953156f057862371f054c96e 100644
--- a/src/main/java/com/dre0059/articleprocessor/service/HeaderService.java
+++ b/src/main/java/com/dre0059/articleprocessor/service/HeaderService.java
@@ -22,6 +22,7 @@ public class HeaderService {
private final DocumentRepository documentRepository;
private final AuthorRepository authorRepository;
+ private final ReferenceService referenceService;
//public Dokument(String title, Integer year, String doi, String abstractText, Integer pages, String publisher) {
@@ -36,9 +37,10 @@ public class HeaderService {
private String author;
@Autowired
- public HeaderService(DocumentRepository documentRepository, AuthorRepository authorRepository) {
+ public HeaderService(DocumentRepository documentRepository, AuthorRepository authorRepository, ReferenceService referenceService) {
this.documentRepository = documentRepository;
this.authorRepository = authorRepository;
+ this.referenceService = referenceService;
}
public void processHeader(String header){
@@ -85,6 +87,10 @@ public class HeaderService {
dokument.setAuthors(savedAuthors);
this.documentRepository.save(dokument);
+
+ // set the document, which has the list of references
+ referenceService.setFromDocument(dokument);
+
}
private String parseHeaderFields(String header, String field){
diff --git a/src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java b/src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java
index 836614114263c7adfd35239d4399afc3203c9b81..03a20e4b4f92a287f4c2701b982d490f368021e8 100644
--- a/src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java
+++ b/src/main/java/com/dre0059/articleprocessor/service/ReferenceService.java
@@ -5,14 +5,140 @@ import com.dre0059.articleprocessor.repository.*;
import jakarta.transaction.Transactional;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpressionException;
+import javax.xml.xpath.XPathFactory;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+// TODO :
+// 1. uloĹľiĹĄ prepojenie toDocument a fromDocument do tabuÄľky referencie
+// 2. vytiahnuť orderNumber z referencie (toto riešiť cez GROBID)
+// 3. aktuálne sa mi toDocument ukladá vždy ako nový.. ja ho potrebujem vyhľadať a na základe toho uložiť alebo prepojiť
@Service
public class ReferenceService {
+
+ private final DocumentRepository documentRepository;
+ private final AuthorRepository authorRepository;
+
+ //private String title;
+ private Integer year;
+ private String doi;
+ private String abstractText;
+ private Integer pages;
+ private String publisher;
+
+ private String author;
+ private List<Author> authorList = new ArrayList<>();
+
+ private Dokument fromDocument;
+ private Dokument toDocument;
+
+
@Autowired
- private ReferenceRepository referenceRepository;
+ public ReferenceService(DocumentRepository documentRepository, AuthorRepository authorRepository) {
+ this.documentRepository = documentRepository;
+ this.authorRepository = authorRepository;
+ }
+
+ public void setFromDocument(Dokument fromDocument) {
+ this.fromDocument = fromDocument;
+ }
+
+ public void extractReferences(String xmlTeiReferences) {
+ List<Author> databaseAuthors = this.authorRepository.findAll();
+ Map<String, Author> authorMap = new HashMap<>();
+
+ for (Author author : databaseAuthors) {
+ String key = author.getLastname().toLowerCase() + "," + author.getFirstname().toLowerCase();
+ authorMap.put(key, author);
+ }
+
+ try {
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ factory.setNamespaceAware(true);
+ DocumentBuilder builder = factory.newDocumentBuilder();
+
+ InputSource inputSource = new InputSource(new StringReader(xmlTeiReferences));
+ Document doc = builder.parse(inputSource);
+
+ XPathFactory xpathFactory = XPathFactory.newInstance();
+ XPath xpath = xpathFactory.newXPath();
+ xpath.setNamespaceContext(new TEINamespaceContext());
- @Transactional
- public Reference saveReference(Reference reference) {
- return referenceRepository.save(reference);
+ NodeList biblNodes = (NodeList) xpath.evaluate("//tei:biblStruct", doc, XPathConstants.NODESET);
+
+ for (int i = 0; i < biblNodes.getLength(); i++) {
+ Node biblNode = biblNodes.item(i);
+ Dokument toDokument = new Dokument();
+
+ // Extract title - toDocument
+ String title = xpath.evaluate(".//tei:title[@level='m' or @level='a']", biblNode);
+ toDokument.setTitle(title);
+
+ // Extract authors
+ NodeList authorNodes = (NodeList) xpath.evaluate(".//tei:author/tei:persName", biblNode, XPathConstants.NODESET);
+ List<Author> authors = new ArrayList<>();
+
+ for (int j = 0; j < authorNodes.getLength(); j++) {
+ Node authorNode = authorNodes.item(j);
+
+ String firstName = xpath.evaluate(".//tei:forename", authorNode);
+ String lastName = xpath.evaluate(".//tei:surname", authorNode);
+
+ String authorKey = lastName.toLowerCase() + "," + firstName.toLowerCase();
+
+ if (authorMap.containsKey(authorKey)) {
+ authors.add(authorMap.get(authorKey));
+ System.out.println("Author: " + authorMap.get(authorKey) + " already exists in database.");
+ } else {
+ Author newAuthor = new Author(firstName, lastName);
+ authors.add(newAuthor);
+ authorMap.put(authorKey, newAuthor);
+ }
+
+ toDokument.setAuthors(authors);
+
+ // Extract year of publication
+ String yearStr = xpath.evaluate(".//tei:date[@type='published']/@when", biblNode);
+ if (yearStr != null && !yearStr.isEmpty()) {
+ try {
+ toDokument.setPublicationYear(Integer.valueOf(yearStr));
+ } catch (NumberFormatException e) {
+ System.out.println("Error during converting year." + yearStr);
+ }
+ }
+
+ // Extract publisher
+ String publisher = xpath.evaluate(".//tei:publisher", biblNode);
+ toDokument.setPublisher(publisher);
+
+ this.documentRepository.save(toDokument);
+ this.authorRepository.saveAll(authors);
+
+ }
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
}
-}
+
+
diff --git a/src/main/java/com/dre0059/articleprocessor/service/TEINamespaceContext.java b/src/main/java/com/dre0059/articleprocessor/service/TEINamespaceContext.java
new file mode 100644
index 0000000000000000000000000000000000000000..4902424f6b2d816643fcb6ed191499336dbcc971
--- /dev/null
+++ b/src/main/java/com/dre0059/articleprocessor/service/TEINamespaceContext.java
@@ -0,0 +1,19 @@
+package com.dre0059.articleprocessor.service;
+
+import javax.xml.namespace.NamespaceContext;
+import java.util.Iterator;
+
+public class TEINamespaceContext implements NamespaceContext {
+ @Override
+ public String getNamespaceURI(String prefix) {
+ if ("tei".equals(prefix)) {
+ return "http://www.tei-c.org/ns/1.0";
+ }
+ return null;
+ }
+
+ @Override
+ public String getPrefix(String namespaceURI) { return null; }
+ @Override
+ public Iterator<String> getPrefixes(String namespaceURI) { return null; }
+}
diff --git a/src/main/java/com/dre0059/articleprocessor/service/TEIparser.java b/src/main/java/com/dre0059/articleprocessor/service/TEIparser.java
index dbe9378219094cd9786e6aa26c2f0b3ea58c3a06..8e631c7f785bca156ad2ed4317430ea607033129 100644
--- a/src/main/java/com/dre0059/articleprocessor/service/TEIparser.java
+++ b/src/main/java/com/dre0059/articleprocessor/service/TEIparser.java
@@ -1,4 +1,4 @@
-package com.dre0059.articleprocessor.service;
+/*package com.dre0059.articleprocessor.service;
import com.dre0059.articleprocessor.model.Author;
import com.dre0059.articleprocessor.model.Dokument;
@@ -60,4 +60,6 @@ public class TEIparser {
}
}
-}
\ No newline at end of file
+}
+
+ */
\ No newline at end of file