Merge branch 'develop' into 'master'

Develop

See merge request !22

.gitlab-ci.yml

@@ -5,7 +5,8 @@ variables:
   DOCKER_REGISTRY: registry.gitlab.bsc.es
   #any doubts regarind gitlab ci cd enviroment variables go to 
   #https://docs.gitlab.com/ee/ci/variables/predefined_variables.html
-  IMAGE_FULL_PATH: $DOCKER_REGISTRY/$CI_PROJECT_PATH:$CI_COMMIT_REF_NAME
+  #IMAGE_FULL_PATH: $DOCKER_REGISTRY/$CI_PROJECT_PATH:$CI_COMMIT_REF_NAME
+  IMAGE_FULL_PATH: $DOCKER_REGISTRY/$CI_PROJECT_PATH:latest_develop
 stages:
   - build
 build_docker_image:

pom.xml

@@ -21,7 +21,7 @@
 	<parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.1.6.RELEASE</version>
+        <version>2.5.0</version>
     </parent>
 
     <dependencies>
@@ -29,11 +29,46 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
         </dependency>
+        
+        
+        <dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-security</artifactId>
+		</dependency>
+      	
+      	
+      	
+      	 <!-- <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-oauth2-client</artifactId>
+        </dependency>  -->
+        
+        
+        
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-test</artifactId>
             <scope>test</scope>
         </dependency>
+        
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-devtools</artifactId>
+            <optional>true</optional>
+        </dependency>
+        
+        
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-oauth2-resource-server</artifactId>
+        </dependency>
+        
+        <dependency>
+   			<groupId>org.springframework.security</groupId>
+   			<artifactId>spring-security-oauth2-jose</artifactId>
+		</dependency> 
+        
+        
         <dependency>
 		    <groupId>com.fasterxml.jackson.core</groupId>
 		    <artifactId>jackson-databind</artifactId>
@@ -47,15 +82,16 @@
 			<artifactId>gson</artifactId>
 		</dependency>
 		<dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-devtools</artifactId>
-            <optional>true</optional>
-        </dependency>
-      	<dependency>
-			<groupId>org.springframework.boot</groupId>
-			<artifactId>spring-boot-starter-security</artifactId>
+		    <groupId>commons-io</groupId>
+		    <artifactId>commons-io</artifactId>
+		    <version>2.11.0</version>
 		</dependency>
-      	
+		<dependency>
+		    <groupId>org.apache.commons</groupId>
+		    <artifactId>commons-collections4</artifactId>
+		    <version>4.4</version>
+		</dependency>
+        
 <!--       	<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-security</artifactId>

src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java

@@ -20,7 +20,7 @@ import es.bsc.inb.ades.rest.api.services.DocumentService;
 
 
 @RestController
-@CrossOrigin()
+@CrossOrigin(origins="*")
 public class DocumentController {
 	
 	@Autowired

src/main/java/es/bsc/inb/ades/rest/api/controllers/FileController.java

+
+package es.bsc.inb.ades.rest.api.controllers;
+
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.Resource;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.multipart.MultipartFile;
+import org.springframework.web.servlet.mvc.method.annotation.MvcUriComponentsBuilder;
+
+import es.bsc.inb.ades.rest.api.model.FileMessage;
+import es.bsc.inb.ades.rest.api.model.FileModel;
+import es.bsc.inb.ades.rest.api.services.FileService;
+
+@Controller
+@CrossOrigin("*")
+public class FileController {
+	@Autowired
+    FileService fileService;
+
+    @PostMapping("/upload")
+    public ResponseEntity<List<String>> uploadFiles(@RequestParam("files")MultipartFile[] files, @RequestParam("allow_duplicates")Boolean allow_duplicates){
+        try{
+            List<String> fileNames = new ArrayList<>();
+            List<String> errors = fileService.validate(files, allow_duplicates);
+            if(errors.size()==0) {
+            	Arrays.asList(files).stream().forEach(file->{
+                    fileService.save(file);
+                    fileNames.add(file.getOriginalFilename());
+                });
+            }else {
+            	errors.add("Validation fail, no document was uploaded.");
+            	return ResponseEntity.status(HttpStatus.EXPECTATION_FAILED).body(errors);
+            }
+            List<String> messages = new ArrayList<String>();
+            messages.add("The documents with their annotations were uploaded correctly.");
+            return ResponseEntity.status(HttpStatus.OK).body(messages);
+        }catch (Exception e){
+        	e.printStackTrace();
+        	List<String> messages = new ArrayList<String>();
+        	messages.add("An error occurred while uploading documents.");
+            return ResponseEntity.status(HttpStatus.EXPECTATION_FAILED).body(messages);
+        }
+    }
+
+    @GetMapping("/files")
+    public ResponseEntity<List<FileModel>> getFiles(){
+        List<FileModel> fileInfos = fileService.loadAll().map(path -> {
+          String filename = path.getFileName().toString();
+          String url = MvcUriComponentsBuilder.fromMethodName(FileController.class, "getFile",
+                  path.getFileName().toString()).build().toString();
+          return new FileModel(filename, url);
+        }).collect(Collectors.toList());
+
+        return ResponseEntity.status(HttpStatus.OK).body(fileInfos);
+    }
+
+
+    @GetMapping("/files/{filename:.+}")
+    public ResponseEntity<Resource> getFile(@PathVariable String filename){
+        Resource file = fileService.load(filename);
+        return ResponseEntity.ok().header(HttpHeaders.CONTENT_DISPOSITION,
+                "attachment; filename=\""+file.getFilename() + "\"").body(file);
+    }
+
+    @GetMapping("/delete/{filename:.+}")
+    public ResponseEntity<FileMessage> deleteFile(@PathVariable String filename) {
+        String message = "";
+        try {
+            message = fileService.deleteFile(filename);
+            return ResponseEntity.status(HttpStatus.OK).body(new FileMessage(message));
+        } catch (Exception e) {
+
+            return ResponseEntity.status(HttpStatus.EXPECTATION_FAILED).body(new FileMessage(message));
+        }
+    }
+
+}

src/main/java/es/bsc/inb/ades/rest/api/controllers/LivenessController.java

+package es.bsc.inb.ades.rest.api.controllers;
+
+import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+@CrossOrigin("*")
+@RestController
+public class LivenessController {
+
+  @GetMapping(path = "/liveness")
+  public String liveness() {
+      return "true";
+  }
+  
+  @GetMapping(path = "/readiness")
+  public String readeness() {
+      return "true";
+  }
+  
+  @GetMapping(path = "/hello")
+  public String hello() {
+      return "holita";
+  }
+}

src/main/java/es/bsc/inb/ades/rest/api/model/FileMessage.java

+package es.bsc.inb.ades.rest.api.model;
+
+
+public class FileMessage {
+    private String message;
+
+    public FileMessage(String message) {
+        this.message = message;
+    }
+
+    public String getMessage() {
+        return message;
+    }
+
+    public void setMessage(String message) {
+        this.message = message;
+    }
+}

src/main/java/es/bsc/inb/ades/rest/api/model/FileModel.java

+package es.bsc.inb.ades.rest.api.model;
+
+/**
+ * File model
+ * @author javi
+ *
+ */
+public class FileModel {
+
+    private String name;
+    private String url;
+
+    public FileModel() {
+    }
+
+    public FileModel(String name, String url) {
+        this.name = name;
+        this.url = url;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getUrl() {
+        return url;
+    }
+
+    public void setUrl(String url) {
+        this.url = url;
+    }
+}

src/main/java/es/bsc/inb/ades/rest/api/repository/DocumentRepository.java

@@ -13,7 +13,7 @@ public interface DocumentRepository extends DocumentRepositoryCustom, MongoRepos
 	
 	Document findBy_id(ObjectId _id);
 	
-	Document findByName(String name);
+	List<Document> findByName(String name);
 	
 	Document findByDocumentId(Long id);
 		

src/main/java/es/bsc/inb/ades/rest/api/repository/DocumentRepositoryImpl.java

@@ -33,8 +33,8 @@ public class DocumentRepositoryImpl implements DocumentRepositoryCustom{
 		query.fields().include("name");
 		query.fields().include("processDate");
 		query.fields().include("status");
-		Sort sort = new Sort(Sort.Direction.ASC, "name");
-		query.with(sort);
+		//Sort sort = new Sort(Sort.Direction.ASC, "name");
+		//query.with(sort);
 		List<Document> documents = mongoTemplate.find(query,  Document.class);
 		return documents;
 	}

src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java

@@ -7,15 +7,19 @@ import org.springframework.security.config.annotation.authentication.builders.Au
 import org.springframework.security.config.annotation.web.builders.HttpSecurity;
 import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
 
-@Configuration
+//@Configuration
 public class SecurityConfig extends WebSecurityConfigurerAdapter {
 	@Override
 	protected void configure(HttpSecurity http) throws Exception {
 		        http.cors().and().csrf().disable().
 		        //http.csrf().disable().
-
-				authorizeRequests().antMatchers(HttpMethod.OPTIONS, "/**").permitAll().anyRequest().authenticated()
+		        
+				authorizeRequests().
+				antMatchers(HttpMethod.OPTIONS, "/**").permitAll().
+				antMatchers(HttpMethod.GET, "/liveness").permitAll().
+				antMatchers(HttpMethod.GET, "/readiness").permitAll().anyRequest().authenticated()
 				.and().httpBasic();
+		        
 	}
 
 	@Autowired

src/main/java/es/bsc/inb/ades/rest/api/security/pkce/SecurityConfig.java

+package es.bsc.inb.ades.rest.api.security.pkce;
+
+
+
+import org.springframework.context.annotation.Configuration;
+import org.springframework.http.HttpMethod;
+import org.springframework.security.config.annotation.web.builders.HttpSecurity;
+import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
+import org.springframework.security.config.http.SessionCreationPolicy;
+
+@Configuration
+public class SecurityConfig extends WebSecurityConfigurerAdapter {
+
+    @Override
+    public void configure(HttpSecurity httpSecurity) throws Exception {
+
+    	httpSecurity.headers().frameOptions().sameOrigin();
+    	httpSecurity
+                .authorizeRequests()
+                .antMatchers(HttpMethod.GET, "/liveness").permitAll()
+				.antMatchers(HttpMethod.GET, "/readiness").permitAll()
+				.anyRequest().authenticated()
+                .and()
+                .sessionManagement()
+                .sessionCreationPolicy(SessionCreationPolicy.STATELESS)
+                .and()
+                .cors()
+                .and()
+                .csrf()
+                .disable()
+                .oauth2ResourceServer()
+                .jwt();
+
+    }
+}

src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java

@@ -16,6 +16,8 @@ public interface DocumentService  {
 
 	Document findByDocumentId2(Long id);
 	
+	List<Document> findByDocumentsName(String name);
+	
 	//String findTextSnippetByDocumentIdAndFindingId2(Long id, Integer findingId);
 	
 	String findFindingEvidenceByDocumentIdAndFindingId(Long id, Integer findingId);

src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java

@@ -87,24 +87,9 @@ public class DocumentServiceImpl implements DocumentService {
 		return documentRepository.findByDocumentId(id);
 	}
 
-	
-//	@Override
-//	public String findTextSnippetByDocumentIdAndFindingId2(Long id, Integer findingId) {
-//		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
-//		Document document = this.findByDocumentId(id);
-//		Finding findingSelected = null;
-//		for (Finding finding : documentAnnotations.getFindings()) {
-//			if(finding.getFindingId().equals(findingId)) {
-//					findingSelected = finding;
-//					break;
-//				}
-//		}
-//		
-//		if(findingSelected!=null) {
-//			return this.generateFindingSnippet2(document.getText(), findingSelected);
-//		}
-//		return "";
-//	}
+	public List<Document> findByDocumentsName(String name) {
+		return documentRepository.findByName(name);
+	}
 	
 	@Override
 	public Boolean setFindingValidation(Long id, Integer findingId, String status) {
@@ -251,10 +236,12 @@ public class DocumentServiceImpl implements DocumentService {
 	public String findFindingEvidenceByDocumentIdAndFindingId(Long id, Integer findingId) {
 		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Finding findingSelected = null;
+		Annotation sentenceRelevantText = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
 			for (Finding finding : annotation.getFindings()) {
 				if(finding.getFindingId().equals(findingId)) {
 					findingSelected = finding;
+					sentenceRelevantText = annotation;
 					break;
 				}
 			}
@@ -276,7 +263,10 @@ public class DocumentServiceImpl implements DocumentService {
 //			annotation.setStartOffset(start_off + Constants.POINTS_INT);
 //			annotation.setEndOffset(start_off + Constants.POINTS_INT + text_size);
 //			return this.generateFindingSnippet3(subtext, findingSelected, start_annotation_aux);
-			Annotation annotation = findingSelected.getRelevant_text();
+			
+			//I removed relevant text as atribute so ...
+			//Annotation annotation = findingSelected.getRelevant_text();
+			Annotation annotation = sentenceRelevantText;
 			int text_size = annotation.getEndOffset() - annotation.getStartOffset();
 			int start_ = 0;
 			int start_off = 0;

src/main/java/es/bsc/inb/ades/rest/api/services/FileService.java

+package es.bsc.inb.ades.rest.api.services;
+
+import org.springframework.core.io.Resource;
+import org.springframework.web.multipart.MultipartFile;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.stream.Stream;
+
+public interface FileService {
+
+    /*
+    Metodo para crear la carpeta donde vamos a guardar los archivos
+     */
+    public void init();
+
+    /*
+    Metodo para guardar los archivos
+     */
+    public void save(MultipartFile file);
+
+    /*
+    Metodo para cargar un archivo
+     */
+    public Resource load(String filename);
+
+    /*
+    Metodo para borrar todos los archivos cada vez que se inicie el servidor
+     */
+    public void deleteAll();
+
+    /*
+    Metodo para Cargar todos los archivos
+     */
+    public Stream<Path> loadAll();
+
+    /*
+    Metodo para Borrar un archivo
+     */
+    public String deleteFile(String filename);
+    /**
+     * 
+     * @param files
+     * @return
+     */
+	public List<String> validate(MultipartFile[] files, Boolean allow_duplicates);
+}

src/main/java/es/bsc/inb/ades/rest/api/services/FileServiceImp.java

+package es.bsc.inb.ades.rest.api.services;
+
+
+
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.bson.Document;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.Resource;
+import org.springframework.core.io.UrlResource;
+import org.springframework.data.mongodb.core.MongoTemplate;
+import org.springframework.stereotype.Service;
+import org.springframework.util.FileSystemUtils;
+import org.springframework.web.multipart.MultipartFile;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.mongodb.client.MongoCollection;
+import com.mongodb.client.MongoDatabase;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Stream;
+
+@Service
+public class FileServiceImp implements FileService {
+  	//Nombre de la carpeta donde vamos a almacenar los archivos
+    //Se crea a nivel de raiz la carpeta
+    private final Path root = Paths.get("uploads");
+    
+    @Autowired
+    MongoTemplate mongoTemplate;
+    
+    @Autowired
+    DocumentService documentService;
+    
+    @Override
+    public void init() {
+        try {
+            Files.createDirectory(root);
+        } catch (IOException e) {
+            throw new RuntimeException("No se puede inicializar la carpeta uploads");
+        }
+    }
+    
+    /**
+	 * Execute process in a document
+	 * @param file
+	 * @param outputGATEFile
+	 * @throws ResourceInstantiationException
+	 * @throws IOException 
+	 * @throws JsonGenerationException 
+	 * @throws InvalidOffsetException
+	 */
+	public void save(MultipartFile file){
+		try {
+			String collectionName = "annotations";
+			if(file.getOriginalFilename().endsWith("documents.json")) {
+				collectionName = "documents";
+			}
+			ByteArrayInputStream stream = new   ByteArrayInputStream(file.getBytes());
+			String jsonString = IOUtils.toString(stream, "UTF-8");
+			Document doc = Document.parse(jsonString);
+			mongoTemplate.save(doc, collectionName);
+			doc.clear();
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+	}
+	/**
+	 * return if document id exist in database.
+	 * @param doc
+	 */
+    private Boolean documentIdExist(Document doc) {
+		Long documentId = doc.getLong("id");
+		es.bsc.inb.ades.rest.api.model.Document  document = documentService.findByDocumentId(documentId);
+		if(document!=null) {
+			return true;
+		}
+		return false;
+	}
+
+    /**
+	 * Return if document name already exist in database.
+	 * @param doc
+	 */
+    private Boolean documentNameExist(Document doc) {
+		String name = doc.getString("name");
+		List<es.bsc.inb.ades.rest.api.model.Document>  documents = documentService.findByDocumentsName(name);
+		if(documents!=null && documents.size()>0) {
+			return true;
+		}
+		return false;
+	}
+    
+	@Override
+    public Resource load(String filename) {
+        try {
+            Path file = root.resolve(filename);
+            Resource resource = new UrlResource(file.toUri());
+
+            if(resource.exists() || resource.isReadable()){
+                return resource;
+            }else{
+                throw new RuntimeException("No se puede leer el archivo ");
+            }
+