[WIP] implement dataverse repository deposit

dmp-backend/dataverseRepository/pom.xml

@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>org.springframework.boot</groupId>
+        <artifactId>spring-boot-starter-parent</artifactId>
+        <version>2.7.4</version>
+        <relativePath/>
+    </parent>
+    <groupId>eu.eudat.depositinterface</groupId>
+    <artifactId>dataverseRepository</artifactId>
+    <version>0.0.1-SNAPSHOT</version>
+    <name>dataverseRepository</name>
+
+    <properties>
+        <java.version>11</java.version>
+    </properties>
+
+    <repositories>
+        <repository>
+            <id>jitpack.io</id>
+            <url>https://jitpack.io</url>
+        </repository>
+    </repositories>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-web</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>eu.eudat</groupId>
+            <artifactId>depositinterface</artifactId>
+            <version>1.0-SNAPSHOT</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.github.IQSS</groupId>
+            <artifactId>dataverse-client-java</artifactId>
+            <version>master-dv14-12-compatible-ge2dc343-7</version>
+        </dependency>
+    </dependencies>
+
+</project>

dmp-backend/dataverseRepository/src/main/java/eu/eudat/depositinterface/dataverserepository/interfaces/DataverseDeposit.java

@@ -0,0 +1,159 @@
+package eu.eudat.depositinterface.dataverserepository.interfaces;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.researchspace.dataverse.api.v1.DataverseAPI;
+import com.researchspace.dataverse.api.v1.DataverseConfig;
+import com.researchspace.dataverse.entities.DataverseContacts;
+import com.researchspace.dataverse.entities.DataversePost;
+import com.researchspace.dataverse.entities.DataverseResponse;
+import com.researchspace.dataverse.entities.Identifier;
+import com.researchspace.dataverse.entities.facade.DatasetAuthor;
+import com.researchspace.dataverse.entities.facade.DatasetContact;
+import com.researchspace.dataverse.entities.facade.DatasetDescription;
+import com.researchspace.dataverse.entities.facade.DatasetFacade;
+import com.researchspace.dataverse.http.DataverseAPIImpl;
+import eu.eudat.depositinterface.models.DMPDepositModel;
+import eu.eudat.depositinterface.repository.RepositoryDeposit;
+import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.env.Environment;
+import org.springframework.http.*;
+import org.springframework.stereotype.Component;
+import org.springframework.util.LinkedMultiValueMap;
+import org.springframework.util.MultiValueMap;
+import org.springframework.web.client.RestTemplate;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.nio.file.Files;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+import static eu.eudat.depositinterface.repository.RepositoryDepositConfiguration.DepositAccountStatus.SystemDeposit;
+
+@Component
+public class DataverseDeposit implements RepositoryDeposit {
+    private static final Logger logger = LoggerFactory.getLogger(DataverseDeposit.class);
+    private static final ObjectMapper objectMapper = new ObjectMapper();
+
+    private static final String API_TOKEN = "";
+    private static final String SYSTEM_PARENT_DATAVERSE_ALIAS = "";
+    private static final String SERVER = "";
+    private static final String SYSTEM_EMAIL = "";
+
+    private DataverseAPI api;
+    private boolean isApiSet;
+
+    private Environment environment;
+
+    @Autowired
+    public DataverseDeposit(Environment environment){
+        this.environment = environment;
+        this.isApiSet = false;
+    }
+
+    private void setDataverseApi() throws MalformedURLException {
+        if(!this.isApiSet) {
+            this.api = new DataverseAPIImpl();
+            DataverseConfig config = new DataverseConfig(new URL(SERVER), API_TOKEN, SYSTEM_PARENT_DATAVERSE_ALIAS);
+            api.configure(config);
+            this.isApiSet = true;
+        }
+    }
+
+    @Override
+    public String deposit(DMPDepositModel dmpDepositModel, boolean update, String repositoryAccessToken) throws Exception {
+
+        if(!this.isApiSet)
+            this.setDataverseApi();
+
+        DataversePost entity = new DataversePost();
+        entity.setName(dmpDepositModel.getLabel());
+        entity.setAlias(dmpDepositModel.getLabel().replace(" ", "_"));
+        entity.setDescription(dmpDepositModel.getDescription());
+        entity.setCreationDate(new Date());
+        entity.setDataverseContacts(Collections.singletonList(new DataverseContacts(SYSTEM_EMAIL)));
+        DataverseResponse<DataversePost> response = this.api.getDataverseOperations().createNewDataverse(SYSTEM_PARENT_DATAVERSE_ALIAS, entity);
+
+        DatasetFacade dataset = DatasetFacade.builder()
+                .title(dmpDepositModel.getLabel())
+                .authors(dmpDepositModel.getUsers().stream().map(x -> DatasetAuthor.builder().authorName(x.getUser().getName()).build()).collect(Collectors.toList()))
+                .contacts(dmpDepositModel.getUsers().stream().map(x -> DatasetContact.builder().datasetContactEmail(x.getUser().getEmail()).build()).collect(Collectors.toList()))
+                .subject("Other")
+                .description(DatasetDescription.builder().description(dmpDepositModel.getDescription()).build())
+                .languages(new ArrayList<>())
+                .depositor("")
+                .build();
+        Identifier id = this.api.getDataverseOperations().createDataset(dataset, entity.getAlias());
+
+        String doi = this.api.getDatasetOperations().getDataset(id).getDoiId().orElse(null);
+
+        this.uploadFile(dmpDepositModel.getPdfFileName(), dmpDepositModel.getPdfFile(), doi);
+
+        String contentDisposition = dmpDepositModel.getRdaJson().getHeaders().get("Content-Disposition").get(0);
+        String jsonFileName = contentDisposition.substring(contentDisposition.lastIndexOf('=')  + 1);
+        File rdaJson = new File(this.environment.getProperty("storage.temp") + jsonFileName);
+        OutputStream output = new FileOutputStream(rdaJson);
+        try {
+            output.write(Objects.requireNonNull(dmpDepositModel.getRdaJson().getBody()));
+            output.flush();
+            output.close();
+        } catch (IOException e) {
+            logger.error(e.getMessage(), e);
+        }
+        this.uploadFile(jsonFileName, rdaJson, doi);
+        Files.deleteIfExists(rdaJson.toPath());
+
+        return doi;
+
+    }
+
+    private void uploadFile(String filename, File file, String doi) throws IOException {
+        HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.MULTIPART_FORM_DATA);
+        headers.set("X-Dataverse-key", API_TOKEN);
+        MultiValueMap<String, String> fileMap = new LinkedMultiValueMap<>();
+        ContentDisposition contentDisposition = ContentDisposition
+                .builder("form-data")
+                .name("file")
+                .filename(filename)
+                .build();
+        fileMap.add(HttpHeaders.CONTENT_DISPOSITION, contentDisposition.toString());
+        HttpEntity<byte[]> fileEntity = new HttpEntity<>(Files.readAllBytes(file.toPath()), fileMap);
+        MultiValueMap<String, Object> body = new LinkedMultiValueMap<>();
+        body.add("file", fileEntity);
+        body.add("jsonData", "{\"restrict\":\"true\", \"tabIngest\":\"false\"}");
+        HttpEntity<MultiValueMap<String, Object>> requestEntity
+                = new HttpEntity<>(body, headers);
+
+        String serverUrl = SERVER + "/api/datasets/:persistentId/add?persistentId=doi:" + doi;
+
+        RestTemplate restTemplate = new RestTemplate();
+        ResponseEntity<Object> resp = restTemplate.postForEntity(serverUrl, requestEntity, Object.class);
+    }
+
+    @Override
+    public RepositoryDepositConfiguration getConfiguration() {
+        RepositoryDepositConfiguration conf = new RepositoryDepositConfiguration();
+        conf.setRepositoryId("Dataverse");
+        conf.setDepositAccountStatus(SystemDeposit.getValue());
+        conf.setAccessToken(API_TOKEN);
+        conf.setRepositoryUrl(SERVER + "/api/");
+        conf.setRepositoryRecordUrl(SERVER + "/dataverse/");
+        return conf;
+    }
+
+    @Override
+    public String authenticate(String code) {
+        return null;
+    }
+}

dmp-backend/dataverseRepository/src/main/resources/application.properties

@@ -0,0 +1 @@
+storage.temp=

dmp-backend/depositinterface/src/main/java/eu/eudat/depositinterface/models/UserInfoDepositModel.java

@@ -2,6 +2,7 @@ package eu.eudat.depositinterface.models;
 
 public class UserInfoDepositModel {
     private String name;
+    private String email;
 
     public String getName() {
         return name;
@@ -9,4 +10,11 @@ public class UserInfoDepositModel {
     public void setName(String name) {
         this.name = name;
     }
+
+    public String getEmail() {
+        return email;
+    }
+    public void setEmail(String email) {
+        this.email = email;
+    }
 }

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java

@@ -2115,14 +2115,9 @@ public class DataManagementPlanManager {
             throw new Exception("DMP already has a DOI");*/
 
         FileEnvelope file = getWordDocument(depositRequest.getDmpId(), principal, configLoader);
-        String name = file.getFilename().substring(0, file.getFilename().length() - 5);
+        String name = file.getFilename().substring(0, file.getFilename().length() - 5).replace(" ", "_").replace(",", "_");
-        //File pdfFile = PDFUtils.convertToPDF(file, environment);
+        File pdfFile = PDFUtils.convertToPDF(file, environment);
-        String uuid = UUID.randomUUID().toString();
-        File pdfFile = new File(environment.getProperty("temp.temp") + uuid + ".pdf");
-        FileOutputStream output = new FileOutputStream(pdfFile);
-        IOUtils.write("testing".getBytes(StandardCharsets.UTF_8), output);
         String fileName = name + ".pdf";
-        output.close();
         ResponseEntity<byte[]> jsonFile;
         try {
             jsonFile = getRDAJsonDocument(depositRequest.getDmpId(), principal);

dmp-backend/web/src/main/java/eu/eudat/logic/security/repositorydeposit/mapper/DMPToDepositMapper.java

@@ -40,6 +40,7 @@ public class DMPToDepositMapper {
     private static UserInfoDepositModel fromUserInfo(UserInfo entity){
         UserInfoDepositModel deposit = new UserInfoDepositModel();
         deposit.setName(entity.getName());
+        deposit.setEmail(entity.getEmail());
         return deposit;
     }
 

dmp-backend/zenodoRepository/src/main/java/eu/eudat/depositinterface/dummyrepository/TestDummy.java

@@ -1,29 +0,0 @@
-package eu.eudat.depositinterface.dummyrepository;
-
-import eu.eudat.depositinterface.models.DMPDepositModel;
-import eu.eudat.depositinterface.repository.RepositoryDeposit;
-import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
-import org.springframework.stereotype.Component;
-
-import static eu.eudat.depositinterface.repository.RepositoryDepositConfiguration.DepositAccountStatus.BothWaysDeposit;
-
-@Component
-public class TestDummy implements RepositoryDeposit {
-    @Override
-    public String deposit(DMPDepositModel dmpDepositModel, boolean update, String repositoryAccessToken) throws Exception {
-        return "test2";
-    }
-
-    @Override
-    public RepositoryDepositConfiguration getConfiguration() {
-        RepositoryDepositConfiguration conf = new RepositoryDepositConfiguration();
-        conf.setRepositoryId("Dummy");
-        conf.setDepositAccountStatus(BothWaysDeposit.getValue());
-        return conf;
-    }
-
-    @Override
-    public String authenticate(String code) {
-        return "accessToken";
-    }
-}

dmp-frontend/src/app/ui/dmp/editor/dmp-deposit-dialog/dmp-deposit-dialog.component.ts

@@ -93,6 +93,18 @@ export class DmpDepositDialogComponent extends BaseComponent implements OnInit {
 		  });
 
     }
+    else if(repo.depositAccountStatus == DepositConfigurationStatus.System){
+      this.depositRepositoriesService.createDoi(repo.repositoryId, this.dmp.id, null)
+        .pipe(takeUntil(this._destroyed))
+        .subscribe(doi =>{
+          this.onDOICallbackSuccess();
+          this.outputRepos.push(doi);
+          this.inputRepos = this.inputRepos.filter(function(x) { return x.repositoryId !== repo.repositoryId; });
+          if(this.inputRepos.length == 0){
+            this.close();
+          }
+        }, error => this.onDOICallbackError(error));
+    }
   }
 
   onDOICallbackSuccess(): void {