Native file upload #16

CHANGELOG.md

@@ -1,5 +1,10 @@
 Significant changes since 0.1.0
 
+1.1.0 In progress
+
+- feature: Support upload of files to a dataset using native API. #16
+- feature: After creating a Dataset, the persistent ID is stored in the Identifier object. #22
+
 1.0.0 2022-11-21
 
 Increasing major version due to major updates to dependencies. However, there are no
@@ -8,7 +13,7 @@ breaking API changes in this library.
 - dependencies: Major dependency updates to Spring 5.3, Lombok 18.24. 
 - build: fix integration tests
 - build: enable integration test running through Github actions
-- build: test build and test on Java 8, 11, and 17
+- build: test build and test on Java 8, 11, and 17.
 
 0.2.0 2022-11-20
 

src/integration-test/java/com/researchspace/dataverse/http/DatasetOperationsTest.java

@@ -11,9 +11,12 @@
 import org.junit.Ignore;
 import org.junit.Test;
 
+import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.IOException;
+import java.net.MalformedURLException;
 import java.net.URISyntaxException;
+import java.util.Arrays;
 import java.util.List;
 
 import static com.researchspace.dataverse.entities.facade.DatasetTestFactory.createFacade;
@@ -59,7 +62,54 @@ public void testPostSampleDataset() throws IOException, InterruptedException, UR
 		String toPost = FileUtils.readFileToString(exampleDatasetJson);
 		Identifier datasetId = dataverseOps.createDataset(toPost, dataverseAlias);
 		assertNotNull(datasetId.getId());
+	}
+
+	@Test
+	public void uploadFileToDataSetWithNativeApiBytes() throws IOException, URISyntaxException {
+		//arrange
+		Identifier datasetId = createADataset();
+		assertNotNull(datasetId.getId());
+		FileUploadMetadata meta = getUploadMetadata();
+
+		//act
+		DatasetFileList datasetFileList = datasetOps.uploadNativeFile(new byte[]{1, 2, 3, 4, 5}, meta, datasetId,  "myFileName.dat");
+
+		//assert
+		assertNotNull(datasetFileList);
+		assertEquals(1, datasetFileList.getFiles().size());
+		assertTrue(datasetFileList.getFiles().get(0).getCategories().contains("Data"));
+		assertTrue(datasetFileList.getFiles().get(0).getDescription().equals(("My description.")));
+		assertEquals(5 ,datasetFileList.getFiles().get(0).getDataFile().getFilesize());
+	}
+
+	@Test
+	public void uploadFileToDataSetWithNativeApiInputStream() throws IOException, URISyntaxException {
+		// arrange
+		Identifier datasetId = createADataset();
+		assertNotNull(datasetId.getId());
+		FileUploadMetadata meta = getUploadMetadata();
+
+		//act
+		DatasetFileList datasetFileList = datasetOps.uploadNativeFile(new ByteArrayInputStream(new byte[]{1, 2, 3, 4, 5,6}), 6, meta, datasetId,  "myFileName.dat");
+
+		//assert
+		assertNotNull(datasetFileList);
+		assertEquals(1, datasetFileList.getFiles().size());
+		DatasetFile uploadedFile = datasetFileList.getFiles().get(0);
+		assertTrue(uploadedFile.getCategories().contains("Data"));
+		assertTrue(uploadedFile.getDescription().equals(("My description.")));
+		assertEquals(6 ,uploadedFile.getDataFile().getFilesize());
+	}
+
+	private Identifier createADataset() throws MalformedURLException, URISyntaxException {
+		DatasetFacade facade = createFacade();
+		Identifier datasetId = dataverseOps.createDataset(facade, dataverseAlias);
+		return datasetId;
+	}
 
+	private FileUploadMetadata getUploadMetadata() {
+		return FileUploadMetadata.builder().description("My description.").categories(Arrays.asList(new String[]{"Data"}))
+				.directoryLabel("test/x").build();
 	}
 
 	@Test

src/main/java/com/researchspace/dataverse/api/v1/DatasetOperations.java

@@ -3,19 +3,13 @@
  */
 package com.researchspace.dataverse.api.v1;
 
+import com.researchspace.dataverse.entities.*;
+import com.researchspace.dataverse.entities.facade.DatasetFacade;
+import com.researchspace.dataverse.http.FileUploadMetadata;
+
 import java.io.File;
 import java.io.InputStream;
 import java.util.List;
-
-import com.researchspace.dataverse.entities.DataSetMetadataBlock;
-import com.researchspace.dataverse.entities.Dataset;
-import com.researchspace.dataverse.entities.DatasetVersion;
-import com.researchspace.dataverse.entities.DataverseResponse;
-import com.researchspace.dataverse.entities.DvMessage;
-import com.researchspace.dataverse.entities.Identifier;
-import com.researchspace.dataverse.entities.PublishedDataset;
-import com.researchspace.dataverse.entities.Version;
-import com.researchspace.dataverse.entities.facade.DatasetFacade;
 /**
 <pre>
   Copyright 2016 ResearchSpace
@@ -48,7 +42,6 @@ public interface DatasetOperations {
 	 */
 	DatasetVersion updateDataset(DatasetFacade facade, Identifier id);
 
-
 	/**
 	 * Retrieves a {@link Dataset} based on its Id.
 	 * @param dsIdentifier
@@ -64,6 +57,28 @@ public interface DatasetOperations {
 	List<DatasetVersion> getDatasetVersions(Identifier dsIdentifier);
 
 	/**
+	 * Upload a file to a dataset using Dataverse's native API (not Sword)
+	 * @param metadata Metadata to attach to the file upload
+	 * @param dsIdentifier The persistent identifier of the dataset
+	 * @param data bytes of data to upload
+	 * @param fileName The name of the file to be created on Dataverse
+	 * @return DatasetFileList information about the uploaded file.
+	 */
+    DatasetFileList uploadNativeFile( byte[] data, FileUploadMetadata metadata, Identifier dsIdentifier, String fileName);
+
+	/**
+	 * Upload a file to a dataset using Dataverse's native API (not Sword).
+	 * @param metadata Metadata to attach to the file upload
+	 * @param contentLength The length of the stream
+	 * @param dsIdentifier The persistent identifier of the dataset
+	 * @param data bytes of data to upload
+	 * @param fileName The name of the file to be created on Dataverse
+	 * @return DatasetFileList information about the uploaded file.
+	 */
+	DatasetFileList uploadNativeFile(InputStream data, long contentLength, FileUploadMetadata metadata,
+									 Identifier dsIdentifier,  String fileName);
+
+    /**
 	 * Uploads a file to a dataset
 	 * @param doi The DOI of the  Dataset
 	 * @param file The file to add to the DataSet

src/main/java/com/researchspace/dataverse/entities/Checksum.java

@@ -0,0 +1,14 @@
+package com.researchspace.dataverse.entities;
+
+import com.researchspace.dataverse.http.FileUploadMetadata;
+import lombok.Data;
+
+/**
+ * Checksum is part of the response from
+ * {@link com.researchspace.dataverse.api.v1.DatasetOperations#uploadNativeFile(byte[], FileUploadMetadata, Identifier, String)}
+ */
+@Data
+public class Checksum {
+    private  String type;
+    private  String value;
+}

src/main/java/com/researchspace/dataverse/entities/DatasetFile.java

@@ -0,0 +1,23 @@
+package com.researchspace.dataverse.entities;
+
+import com.researchspace.dataverse.http.FileUploadMetadata;
+import lombok.Data;
+
+import java.util.List;
+
+/**
+ * DatasetFile is part of the response from
+ * {@link com.researchspace.dataverse.api.v1.DatasetOperations#uploadNativeFile(byte[], FileUploadMetadata, Identifier, String)}
+ */
+@Data
+public class DatasetFile {
+    private  String description;
+    private  String label;
+    private  String directoryLabel;
+    private  String datasetVersionId;
+    private List<String> categories;
+    private  boolean restricted;
+    private  int version;
+    private DatasetFileDetails dataFile;
+
+}

src/main/java/com/researchspace/dataverse/entities/DatasetFileDetails.java

@@ -0,0 +1,26 @@
+package com.researchspace.dataverse.entities;
+
+import com.researchspace.dataverse.http.FileUploadMetadata;
+import lombok.Data;
+
+import java.util.Date;
+
+/**
+ * DatasetFileDetails is a subsection of the response from
+ * {@link com.researchspace.dataverse.api.v1.DatasetOperations#uploadNativeFile(byte[], FileUploadMetadata, Identifier, String)}
+ */
+@Data
+public class DatasetFileDetails {
+    private int id;
+    private int filesize;
+    private String persistentId;
+    private String pidURL;
+    private String filename;
+    private String contentType;
+    private String description;
+    private String storageIdentifier;
+    private String rootDataFileId;
+    private String md5;
+    private Checksum checksum;
+    private Date creationDate;
+}

src/main/java/com/researchspace/dataverse/entities/DatasetFileList.java

@@ -0,0 +1,14 @@
+package com.researchspace.dataverse.entities;
+
+import lombok.Data;
+
+import java.util.List;
+
+/**
+ * DatasetFileList is the response from uploading a file using the native API
+ */
+@Data
+public class DatasetFileList {
+    List<DatasetFile> files;
+}
+

src/main/java/com/researchspace/dataverse/entities/DataverseResponse.java

@@ -3,6 +3,7 @@
  */
 package com.researchspace.dataverse.entities;
 
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import lombok.Data;
 /**
  *  <pre>
@@ -30,6 +31,7 @@ public class DataverseResponse <T> {
 
 	private String status;
 	private T data;
+	@JsonDeserialize(using = ObjectOrStringMessageDeserializer.class )
 	private String message;
 
 }

src/main/java/com/researchspace/dataverse/entities/ObjectOrStringMessageDeserializer.java

@@ -0,0 +1,28 @@
+package com.researchspace.dataverse.entities;
+
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
+import com.fasterxml.jackson.databind.JsonNode;
+
+import java.io.IOException;
+
+/**
+ * 'message' property can be a string or an object with property 'message'; this handles both
+ */
+public class ObjectOrStringMessageDeserializer extends JsonDeserializer<String> {
+    @Override
+    public String deserialize(JsonParser jp, DeserializationContext ctxt)
+            throws IOException {
+
+        JsonNode node =  jp.getCodec().readTree((jp));
+        if (node.isTextual()){
+            return node.toString();
+        } else if (node.isObject()){
+            return node.get("message").toString();
+        } else{
+            throw new IllegalArgumentException("expect a string or an object with a string property 'message'");
+        }
+
+    }
+}

src/main/java/com/researchspace/dataverse/http/AbstractOpsImplV1.java

@@ -3,21 +3,19 @@
  */
 package com.researchspace.dataverse.http;
 
-import java.util.Arrays;
-
+import com.researchspace.dataverse.api.v1.DataverseConfig;
+import com.researchspace.dataverse.entities.DataverseResponse;
+import com.researchspace.springrest.ext.LoggingResponseErrorHandler;
+import com.researchspace.springrest.ext.RestUtil;
+import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.lang.StringUtils;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.client.RestClientException;
 import org.springframework.web.client.RestTemplate;
 
-import com.researchspace.dataverse.api.v1.DataverseConfig;
-import com.researchspace.dataverse.entities.DataverseResponse;
-import com.researchspace.springrest.ext.LoggingResponseErrorHandler;
-import com.researchspace.springrest.ext.RestUtil;
-
-import lombok.extern.slf4j.Slf4j;
+import java.util.Arrays;
 
 /** <pre>
 Copyright 2016 ResearchSpace
@@ -101,8 +99,12 @@ HttpHeaders addAPIKeyToHeader() {
 		HttpHeaders headers = new HttpHeaders();
 		headers.setContentType(MediaType.APPLICATION_JSON);
 		headers.setAccept(Arrays.asList(MediaType.APPLICATION_JSON));
-		headers.add(apiHeader, apiKey);
+		addApiKey(headers);
 		return headers;
 	}
 
+	 void addApiKey(HttpHeaders headers) {
+		headers.add(apiHeader, apiKey);
+	}
+
 }