multiple configuration for repository

README.md

@@ -0,0 +1,25 @@
+# Using dataverse repository with Argos
+
+The repository-deposit-dataverse module implements the [https://code-repo.d4science.org/MaDgiK-CITE/repository-deposit-base](https://) interface for the dataverse repository.
+
+## Setup
+
+After creating the jar from the project, environment variables should be set since they are used in the application.properties
+1) STORAGE_TMP_DATAVERSE - a temporary storage needed
+2) CONFIGURATION_DATAVERSE - path to json file which includes the configuration for the repository
+
+### JSON configuration file
+
+The following fields should be set:<br>
+**depositType** - an integer representing how the dmp user can deposit in the repository,<br>
+a. **0** stands for system deposition meaning the dmp is deposited using argos credentials to the repository,<br>
+b. **1** stands for user deposition in which the argos user specifies his/her own credentials to the repository,<br>
+c. **2** stands for both ways deposition if the repository allows the deposits of dmps to be made from both argos and users accounts<br>
+note: depositType should be set to **0** since dataverse does not provide oauth2 protocol but, instead, uses api tokens<br>
+**repositoryId** - unique identifier for the repository<br>
+**apiToken** - api token provided for the depositions<br>
+**repositoryUrl** - repository's api url e.g. "https://demo.dataverse.org/api/"<br>
+**repositoryRecordUrl** - repository's record url, this url is used to index dmps that are created e.g. "https://demo.dataverse.org/dataset.xhtml?persistentId=doi:"<br>
+**server** - repository's server url e.g. "https://demo.dataverse.org"<br>
+**parentDataverseAlias** - dataverse alias in which all dmps that are deposited will be resided, **note**: the dataverse alias used should be published before making any dmp deposit<br>
+**hasLogo** - if the repository has a logo<br>

pom.xml

@@ -58,7 +58,7 @@
         <dependency>
             <groupId>gr.cite.opendmp</groupId>
             <artifactId>repositorydepositbase</artifactId>
-            <version>1.0.0</version>
+            <version>1.0.4</version>
         </dependency>
 
         <dependency>
@@ -113,6 +113,7 @@
                                     <artifact>*:*</artifact>
                                     <excludes>
                                         <exclude>module-info.class</exclude>
+                                        <exclude>javax/**/*</exclude>
                                     </excludes>
                                 </filter>
 <!--                            </filters>-->

src/main/java/eu/eudat/depositinterface/dataverserepository/config/ConfigLoader.java

@@ -1,5 +1,8 @@
 package eu.eudat.depositinterface.dataverserepository.config;
 
+import java.util.List;
+
 public interface ConfigLoader {
-    DataverseConfig getDataverseConfig();
+    byte[] getLogo(String repositoryId);
+    List<DataverseConfig> getDataverseConfig();
 }

src/main/java/eu/eudat/depositinterface/dataverserepository/config/ConfigLoaderImpl.java

@@ -1,5 +1,6 @@
 package eu.eudat.depositinterface.dataverserepository.config;
 
+import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -11,27 +12,58 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
 
 @Service("dataverseConfigLoader")
 public class ConfigLoaderImpl implements ConfigLoader{
     private static final Logger logger = LoggerFactory.getLogger(ConfigLoaderImpl.class);
     private static final ObjectMapper mapper = new ObjectMapper();
 
-    private DataverseConfig dataverseConfig;
+    private List<DataverseConfig> dataverseConfigs = new ArrayList<>();
+
+    private final Environment environment;
 
     @Autowired
-    private Environment environment;
+    public ConfigLoaderImpl(Environment environment){
+        this.environment = environment;
+    }
 
     @Override
-    public DataverseConfig getDataverseConfig() {
-        if(dataverseConfig == null){
+    public List<DataverseConfig> getDataverseConfig() {
+        if(dataverseConfigs == null || dataverseConfigs.isEmpty()){
             try{
-                dataverseConfig = mapper.readValue(getStreamFromPath(environment.getProperty("configuration.dataverse")), DataverseConfig.class);
+                dataverseConfigs = mapper.readValue(getStreamFromPath(environment.getProperty("dataverse.plugin.configuration.dataverse")), new TypeReference<List<DataverseConfig>>() {});
             } catch (IOException e) {
                 logger.error(e.getLocalizedMessage(), e);
             }
         }
-        return dataverseConfig;
+        return dataverseConfigs;
+    }
+
+    @Override
+    public byte[] getLogo(String repositoryId) {
+        if (!dataverseConfigs.isEmpty()) {
+            DataverseConfig dataverseConfig = dataverseConfigs.stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
+            if (dataverseConfig != null) {
+                String logo = dataverseConfig.getLogo();
+                InputStream logoStream;
+                if (logo != null && !logo.isEmpty()) {
+                    logoStream = getStreamFromPath(logo);
+                }
+                else {
+                    logoStream = getClass().getClassLoader().getResourceAsStream("dataverse.png");
+                }
+                try {
+                    return (logoStream != null) ? logoStream.readAllBytes() : null;
+                }
+                catch (IOException e) {
+                    logger.error(e.getMessage(), e);
+                }
+            }
+            return null;
+        }
+        return null;
     }
 
     private InputStream getStreamFromPath(String filePath) {

src/main/java/eu/eudat/depositinterface/dataverserepository/config/DataverseConfig.java

@@ -45,6 +45,10 @@ public class DataverseConfig {
     private String server;
     @JsonProperty("parentDataverseAlias")
     private String parentDataverseAlias;
+    @JsonProperty("hasLogo")
+    private boolean hasLogo;
+    @JsonProperty("logo")
+    private String logo;
 
     public int getDepositType() {
         return depositType;
@@ -95,12 +99,27 @@ public class DataverseConfig {
         this.parentDataverseAlias = parentDataverseAlias;
     }
 
+    public boolean isHasLogo() {
+        return hasLogo;
+    }
+    public void setHasLogo(boolean hasLogo) {
+        this.hasLogo = hasLogo;
+    }
+
+    public String getLogo() {
+        return logo;
+    }
+    public void setLogo(String logo) {
+        this.logo = logo;
+    }
+
     public RepositoryDepositConfiguration toRepoConfig() {
         RepositoryDepositConfiguration config = new RepositoryDepositConfiguration();
         config.setDepositType(this.depositType);
         config.setRepositoryId(this.repositoryId);
         config.setRepositoryUrl(this.repositoryUrl);
         config.setRepositoryRecordUrl(this.repositoryRecordUrl);
+        config.setHasLogo(this.hasLogo);
         return config;
     }
 }

src/main/java/eu/eudat/depositinterface/dataverserepository/interfaces/DataverseDeposit.java

@@ -12,6 +12,7 @@ import com.researchspace.dataverse.entities.facade.DatasetFacade;
 import com.researchspace.dataverse.http.DataverseAPIImpl;
 import eu.eudat.depositinterface.dataverserepository.config.ConfigLoader;
 import eu.eudat.depositinterface.models.DMPDepositModel;
+import eu.eudat.depositinterface.models.FileEnvelope;
 import eu.eudat.depositinterface.repository.RepositoryDeposit;
 import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
 import org.json.JSONObject;
@@ -44,81 +45,85 @@ public class DataverseDeposit implements RepositoryDeposit {
     private static final Logger logger = LoggerFactory.getLogger(DataverseDeposit.class);
     private static final ObjectMapper objectMapper = new ObjectMapper();
 
-    private DataverseAPI api;
-    private boolean isApiSet;
-
-    private ConfigLoader configLoader;
-    private Environment environment;
+    private final ConfigLoader configLoader;
+    private final Environment environment;
 
     @Autowired
     public DataverseDeposit(ConfigLoader configLoader, Environment environment){
         this.configLoader = configLoader;
         this.environment = environment;
-        this.isApiSet = false;
-    }
-
-    private void setDataverseApi() throws MalformedURLException {
-        if(!this.isApiSet) {
-            this.api = new DataverseAPIImpl();
-            eu.eudat.depositinterface.dataverserepository.config.DataverseConfig jsonConfig = this.configLoader.getDataverseConfig();
-            DataverseConfig config = new DataverseConfig(new URL(jsonConfig.getServer()), jsonConfig.getApiToken(), jsonConfig.getParentDataverseAlias());
-            api.configure(config);
-            this.isApiSet = true;
-        }
     }
 
     @Override
-    public String deposit(DMPDepositModel dmpDepositModel, String repositoryAccessToken) throws Exception {
+    public String deposit(String repositoryId, DMPDepositModel dmpDepositModel, String repositoryAccessToken) throws Exception {
 
-        if(!this.isApiSet)
-            this.setDataverseApi();
+        eu.eudat.depositinterface.dataverserepository.config.DataverseConfig jsonConfig = this.configLoader.getDataverseConfig().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
 
-        String doi;
-        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();
 
-        if(dmpDepositModel.getPreviousDOI() == null || dmpDepositModel.getPreviousDOI().isEmpty()){
-            Identifier id = this.api.getDataverseOperations().createDataset(dataset, this.configLoader.getDataverseConfig().getParentDataverseAlias());
+        if(jsonConfig != null) {
 
-            doi = this.api.getDatasetOperations().getDataset(id).getDoiId().orElse(null);
+            DataverseAPI api = new DataverseAPIImpl();
+            DataverseConfig config = new DataverseConfig(new URL(jsonConfig.getServer()), jsonConfig.getApiToken(), jsonConfig.getParentDataverseAlias());
+            api.configure(config);
 
-            this.uploadFiles(dmpDepositModel, doi);
 
-            this.api.getDatasetOperations().publishDataset(id, MAJOR);
-        }
-        else{
-            Map<String, Object> datasetJson = this.getDatasetIdentifier(dmpDepositModel.getPreviousDOI());
-            Identifier id = new Identifier();
-            id.setId(((Integer) datasetJson.get("id")).longValue());
-            JsonNode jsonNode = this.objectMapper.readTree(new JSONObject(datasetJson).toString());
-            List<JsonNode> files = jsonNode.findValues("dataFile");
-            for(JsonNode file: files){
-                int fileId = file.get("id").asInt();
-                this.deleteFile(fileId);
+            String dmpDescription = dmpDepositModel.getDescription();
+            if (dmpDescription == null || dmpDescription.isEmpty()) {
+                dmpDescription = "-";
             }
 
-            this.uploadFiles(dmpDepositModel, dmpDepositModel.getPreviousDOI());
+            String doi;
+            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(dmpDescription).build())
+                    .languages(new ArrayList<>())
+                    .depositor("")
+                    .build();
+
+            if (dmpDepositModel.getPreviousDOI() == null || dmpDepositModel.getPreviousDOI().isEmpty()) {
+                Identifier id = api.getDataverseOperations().createDataset(dataset, jsonConfig.getParentDataverseAlias());
+
+                doi = api.getDatasetOperations().getDataset(id).getDoiId().orElse(null);
+
+                this.uploadFiles(jsonConfig, dmpDepositModel, doi);
+
+                api.getDatasetOperations().publishDataset(id, MAJOR);
+            } else {
+                Map<String, Object> datasetJson = this.getDatasetIdentifier(jsonConfig, dmpDepositModel.getPreviousDOI());
+                Identifier id = new Identifier();
+                id.setId(((Integer) datasetJson.get("id")).longValue());
+                JsonNode jsonNode = objectMapper.convertValue(datasetJson, JsonNode.class);
+                JsonNode latestVersion = jsonNode.get("latestVersion");
+                JsonNode files = latestVersion.get("files");
+                if (files.isArray()) {
+                    for (JsonNode file : files) {
+                        int fileId = file.get("dataFile").get("id").asInt();
+                        this.deleteFile(jsonConfig, fileId);
+                    }
+                }
+
+                this.uploadFiles(jsonConfig, dmpDepositModel, dmpDepositModel.getPreviousDOI());
+
+                api.getDatasetOperations().updateDataset(dataset, id);
+                DataverseResponse<PublishedDataset> publishedDataset = api.getDatasetOperations().publishDataset(id, MAJOR);
+                doi = publishedDataset.getData().getAuthority() + "/" + publishedDataset.getData().getIdentifier();
+            }
+
+
+            return doi;
 
-            this.api.getDatasetOperations().updateDataset(dataset, id);
-            DataverseResponse<PublishedDataset> publishedDataset = this.api.getDatasetOperations().publishDataset(id, MAJOR);
-            doi = publishedDataset.getData().getAuthority() + "/" + publishedDataset.getData().getIdentifier();
         }
 
-
-        return doi;
+        return null;
 
     }
 
-    private void deleteFile(int fileId){
-        HttpHeaders headers = this.createBasicAuthHeaders(this.configLoader.getDataverseConfig().getApiToken(), "");
-        String serverUrl = this.configLoader.getDataverseConfig().getServer() + "/dvn/api/data-deposit/v1.1/swordv2/edit-media/file/" + fileId;
+    private void deleteFile(eu.eudat.depositinterface.dataverserepository.config.DataverseConfig jsonConfig, int fileId){
+        HttpHeaders headers = this.createBasicAuthHeaders(jsonConfig.getApiToken(), "");
+        String serverUrl = jsonConfig.getServer() + "/dvn/api/data-deposit/v1.1/swordv2/edit-media/file/" + fileId;
         RestTemplate restTemplate = new RestTemplate();
         restTemplate.exchange(serverUrl, HttpMethod.DELETE, new HttpEntity<>(headers), Object.class);
     }
@@ -133,40 +138,52 @@ public class DataverseDeposit implements RepositoryDeposit {
         }};
     }
 
-    private void uploadFiles(DMPDepositModel dmpDepositModel, String doi) throws IOException {
-        this.uploadFile(dmpDepositModel.getPdfFileName(), dmpDepositModel.getPdfFile(), doi);
+    private void uploadFiles(eu.eudat.depositinterface.dataverserepository.config.DataverseConfig jsonConfig, DMPDepositModel dmpDepositModel, String doi) throws IOException {
+        this.uploadFile(jsonConfig, dmpDepositModel.getPdfFile().getFilename(), dmpDepositModel.getPdfFile().getFile(), doi);
 
-        String contentDisposition = dmpDepositModel.getRdaJson().getHeaders().get("Content-Disposition").get(0);
+        FileEnvelope rdaJsonEnvelope = dmpDepositModel.getRdaJsonFile();
+        HttpHeaders responseHeaders = new HttpHeaders();
+        responseHeaders.setContentLength(rdaJsonEnvelope.getFile().length());
+        responseHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM);
+        responseHeaders.set("Content-Disposition", "attachment;filename=" + rdaJsonEnvelope.getFilename());
+        responseHeaders.set("Access-Control-Expose-Headers", "Content-Disposition");
+        responseHeaders.get("Access-Control-Expose-Headers").add("Content-Type");
+
+        byte[] content = Files.readAllBytes(rdaJsonEnvelope.getFile().toPath());
+
+        ResponseEntity<byte[]> jsonFile = new ResponseEntity<>(content, responseHeaders, HttpStatus.OK);
+
+        String contentDisposition = jsonFile.getHeaders().get("Content-Disposition").get(0);
         String jsonFileName = contentDisposition.substring(contentDisposition.lastIndexOf('=')  + 1);
-        File rdaJson = new File(this.environment.getProperty("storage.temp") + jsonFileName);
+        File rdaJson = new File(this.environment.getProperty("dataverse_plugin.storage.temp") + jsonFileName);
         OutputStream output = new FileOutputStream(rdaJson);
         try {
-            output.write(Objects.requireNonNull(dmpDepositModel.getRdaJson().getBody()));
+            output.write(Objects.requireNonNull(jsonFile.getBody()));
             output.flush();
             output.close();
         } catch (IOException e) {
             logger.error(e.getMessage(), e);
         }
-        this.uploadFile(jsonFileName, rdaJson, doi);
+        this.uploadFile(jsonConfig, jsonFileName, rdaJson, doi);
         Files.deleteIfExists(rdaJson.toPath());
 
         if(dmpDepositModel.getSupportingFilesZip() != null) {
-            this.uploadFile(dmpDepositModel.getSupportingFilesZip().getName(), dmpDepositModel.getSupportingFilesZip(), doi);
+            this.uploadFile(jsonConfig, dmpDepositModel.getSupportingFilesZip().getName(), dmpDepositModel.getSupportingFilesZip(), doi);
         }
     }
 
-    private Map<String, Object> getDatasetIdentifier(String previousDOI) {
+    private Map<String, Object> getDatasetIdentifier(eu.eudat.depositinterface.dataverserepository.config.DataverseConfig jsonConfig, String previousDOI) {
         HttpHeaders headers = new HttpHeaders();
-        headers.set("X-Dataverse-key", this.configLoader.getDataverseConfig().getApiToken());
-        String serverUrl = this.configLoader.getDataverseConfig().getServer() + "/api/datasets/:persistentId?persistentId=doi:" + previousDOI;
+        headers.set("X-Dataverse-key", jsonConfig.getApiToken());
+        String serverUrl = jsonConfig.getServer() + "/api/datasets/:persistentId?persistentId=doi:" + previousDOI;
         RestTemplate restTemplate = new RestTemplate();
         return (Map<String, Object>) restTemplate.exchange(serverUrl, HttpMethod.GET, new HttpEntity<>(headers), Map.class).getBody().get("data");
     }
 
-    private void uploadFile(String filename, File file, String doi) throws IOException {
+    private void uploadFile(eu.eudat.depositinterface.dataverserepository.config.DataverseConfig jsonConfig, String filename, File file, String doi) throws IOException {
         HttpHeaders headers = new HttpHeaders();
         headers.setContentType(MediaType.MULTIPART_FORM_DATA);
-        headers.set("X-Dataverse-key", this.configLoader.getDataverseConfig().getApiToken());
+        headers.set("X-Dataverse-key", jsonConfig.getApiToken());
         MultiValueMap<String, String> fileMap = new LinkedMultiValueMap<>();
         ContentDisposition contentDisposition = ContentDisposition
                 .builder("form-data")
@@ -181,20 +198,32 @@ public class DataverseDeposit implements RepositoryDeposit {
         HttpEntity<MultiValueMap<String, Object>> requestEntity
                 = new HttpEntity<>(body, headers);
 
-        String serverUrl = this.configLoader.getDataverseConfig().getServer() + "/api/datasets/:persistentId/add?persistentId=doi:" + doi;
+        String serverUrl = jsonConfig.getServer() + "/api/datasets/:persistentId/add?persistentId=doi:" + doi;
 
         RestTemplate restTemplate = new RestTemplate();
         ResponseEntity<Object> resp = restTemplate.postForEntity(serverUrl, requestEntity, Object.class);
     }
 
     @Override
-    public RepositoryDepositConfiguration getConfiguration() {
-        eu.eudat.depositinterface.dataverserepository.config.DataverseConfig dataverseConfig = this.configLoader.getDataverseConfig();
-        return dataverseConfig.toRepoConfig();
+    public List<RepositoryDepositConfiguration> getConfiguration() {
+        List<eu.eudat.depositinterface.dataverserepository.config.DataverseConfig> dataverseConfigs = this.configLoader.getDataverseConfig();
+        return dataverseConfigs.stream().map(eu.eudat.depositinterface.dataverserepository.config.DataverseConfig::toRepoConfig).collect(Collectors.toList());
     }
 
     @Override
-    public String authenticate(String code) {
+    public String authenticate(String repositoryId, String code) {
+        return null;
+    }
+
+    @Override
+    public String getLogo(String repositoryId) {
+        RepositoryDepositConfiguration conf = this.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
+        if(conf != null) {
+            if (conf.isHasLogo()) {
+                byte[] logo = this.configLoader.getLogo(repositoryId);
+                return (logo != null && logo.length != 0) ? Base64.getEncoder().encodeToString(logo) : null;
+            }
+        }
         return null;
     }
 }

src/main/resources/application.properties

@@ -1,2 +1,2 @@
-storage.temp=${STORAGE_TMP_DATAVERSE}
-configuration.dataverse=${CONFIGURATION_DATAVERSE}
+dataverse_plugin.storage.temp=${STORAGE_TMP_DATAVERSE}
+dataverse.plugin.configuration.dataverse=${CONFIGURATION_DATAVERSE}