This is a combination of 5 commits.

otter606 · otter606 · commit 22da346d8263 · 2022-11-27T10:40:32.000Z
add overloaded method to add input stream

fix tests

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

docs: javadocs

Update src/main/java/com/researchspace/dataverse/http/DataverseOperationsImplV1.java

remove obsolete comment
diff --git a/CHANGELOG.md b/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
 
diff --git a/src/integration-test/java/com/researchspace/dataverse/http/DatasetOperationsTest.java b/src/integration-test/java/com/researchspace/dataverse/http/DatasetOperationsTest.java
@@ -11,8 +11,10 @@
 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;
@@ -63,17 +65,51 @@ public void testPostSampleDataset() throws IOException, InterruptedException, UR
 	}
 
 	@Test
-	public void uploadFileToDataSetWithNativeApi() throws IOException, URISyntaxException {
-		DatasetFacade facade = createFacade();
-		Identifier datasetId = dataverseOps.createDataset(facade, dataverseAlias);
+	public void uploadFileToDataSetWithNativeApiBytes() throws IOException, URISyntaxException {
+		//arrange
+		Identifier datasetId = createADataset();
 		assertNotNull(datasetId.getId());
-		FileUploadMetadata meta = FileUploadMetadata.builder().description("My description.").categories(Arrays.asList(new String[]{"Data"}))
-				.directoryLabel("test/x").build();
-		DatasetFileList datasetFileList = datasetOps.uploadNativeFile(meta, datasetId, new byte[]{1, 2, 3, 4, 5}, "myFileName.dat");
+		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
diff --git a/src/main/java/com/researchspace/dataverse/api/v1/DatasetOperations.java b/src/main/java/com/researchspace/dataverse/api/v1/DatasetOperations.java
@@ -42,7 +42,6 @@ public interface DatasetOperations {
 	 */
 	DatasetVersion updateDataset(DatasetFacade facade, Identifier id);
 
-    
 	/**
 	 * Retrieves a {@link Dataset} based on its Id.
 	 * @param dsIdentifier
@@ -57,7 +56,27 @@ public interface DatasetOperations {
 	 */
 	List<DatasetVersion> getDatasetVersions(Identifier dsIdentifier);
 
-    DatasetFileList uploadNativeFile(FileUploadMetadata metadata, Identifier dsIdentifier, byte[] data, 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 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
diff --git a/src/main/java/com/researchspace/dataverse/entities/Checksum.java b/src/main/java/com/researchspace/dataverse/entities/Checksum.java
@@ -1,7 +1,12 @@
 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;
diff --git a/src/main/java/com/researchspace/dataverse/entities/DatasetFile.java b/src/main/java/com/researchspace/dataverse/entities/DatasetFile.java
@@ -1,9 +1,14 @@
 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;
diff --git a/src/main/java/com/researchspace/dataverse/entities/DatasetFileDetails.java b/src/main/java/com/researchspace/dataverse/entities/DatasetFileDetails.java
@@ -1,9 +1,14 @@
 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;
diff --git a/src/main/java/com/researchspace/dataverse/entities/DatasetFileList.java b/src/main/java/com/researchspace/dataverse/entities/DatasetFileList.java
@@ -3,6 +3,10 @@
 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;
diff --git a/src/main/java/com/researchspace/dataverse/entities/ObjectOrStringMessageDeserializer.java b/src/main/java/com/researchspace/dataverse/entities/ObjectOrStringMessageDeserializer.java
@@ -21,7 +21,7 @@ public String deserialize(JsonParser jp, DeserializationContext ctxt)
         } else if (node.isObject()){
             return node.get("message").toString();
         } else{
-            throw new IllegalArgumentException("expect a string or an object with a string property");
+            throw new IllegalArgumentException("expect a string or an object with a string property 'message'");
         }
 
     }
diff --git a/src/main/java/com/researchspace/dataverse/http/DataverseOperationsImplV1.java b/src/main/java/com/researchspace/dataverse/http/DataverseOperationsImplV1.java
@@ -16,6 +16,9 @@
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.core.ParameterizedTypeReference;
+import org.springframework.core.io.AbstractResource;
+import org.springframework.core.io.ByteArrayResource;
+import org.springframework.core.io.InputStreamResource;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpMethod;
@@ -192,17 +195,43 @@ public List<DatasetVersion> getDatasetVersions (Identifier dsIdentifier) {
 	}
 
 	@Override
-	public DatasetFileList uploadNativeFile( FileUploadMetadata metadata, Identifier dsIdentifier, byte[] data, String fileName){
+	public DatasetFileList uploadNativeFile( byte[] data, FileUploadMetadata metadata, Identifier dsIdentifier,  String fileName){
+		ByteArrayResource resource = new ByteArrayResource(data){
+			@Override
+			public String getFilename(){
+				return fileName;
+			}
+		};
+		return getDatasetFileList(metadata, dsIdentifier, resource);
+	}
+	@Override
+	public DatasetFileList uploadNativeFile(InputStream data, long contentLength, FileUploadMetadata metadata, Identifier dsIdentifier,  String fileName) {
+		InputStreamResource resource = new InputStreamResource(data) {
+			@Override
+			public String getFilename(){
+				return fileName;
+			}
+
+			@Override
+			public long contentLength() throws IOException {
+				return contentLength;
+			}
+		};
+		return getDatasetFileList(metadata, dsIdentifier,  resource);
+
+	}
+
+	private DatasetFileList getDatasetFileList(FileUploadMetadata metadata, Identifier dsIdentifier, AbstractResource resource) {
 		String url = createV1Url("datasets", ":persistentId", "add") + "?persistentId=" + dsIdentifier.getPersistentId();
 		ParameterizedTypeReference<DataverseResponse<DatasetFileList>> type =
 				new ParameterizedTypeReference<DataverseResponse<DatasetFileList>>() {};
-		HttpEntity<MultiValueMap<String, Object>> entity = new NativeFileUploader().uploadFile(metadata, apiKey, data, fileName);
+		HttpEntity<MultiValueMap<String, Object>> entity = new NativeFileUploader().createFileUploadEntity(metadata, apiKey, resource);
 		ResponseEntity<DataverseResponse<DatasetFileList>> resp = template.exchange(url, HttpMethod.POST, entity, type);
 		log.debug("{}", resp.getBody());
 		handleError(resp);
 		return resp.getBody().getData();
 	}
-	
+
 	/* (non-Javadoc)
 	 * @see com.researchspace.dataverse.http.DataverseAPI#uploadFile(java.lang.String, java.io.File)
 	 */
diff --git a/src/main/java/com/researchspace/dataverse/http/FileUploadMetadata.java b/src/main/java/com/researchspace/dataverse/http/FileUploadMetadata.java
@@ -10,7 +10,6 @@
  */
 @Data
 @Builder
-
 public class FileUploadMetadata {
     private String description;
     private String directoryLabel;
diff --git a/src/main/java/com/researchspace/dataverse/http/NativeFileUploader.java b/src/main/java/com/researchspace/dataverse/http/NativeFileUploader.java
@@ -1,31 +1,28 @@
 package com.researchspace.dataverse.http;
 
-import org.springframework.core.io.ByteArrayResource;
-import org.springframework.http.*;
+import org.springframework.core.io.AbstractResource;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
 import org.springframework.util.LinkedMultiValueMap;
 import org.springframework.util.MultiValueMap;
-import org.springframework.web.client.RestTemplate;
 
+/**
+ * NativeFileUploader is  helper class that performs upload of files using native API
+ */
 public class NativeFileUploader {
 
-    public HttpEntity<MultiValueMap<String, Object>> uploadFile(FileUploadMetadata metadata, String apiKey, byte[] data, String fName){
-        RestTemplate restTemplate = new RestTemplate();
+    public HttpEntity<MultiValueMap<String, Object>> createFileUploadEntity(FileUploadMetadata metadata, String apiKey, AbstractResource resource){
+
         MultiValueMap<String,Object> multipartRequest = new LinkedMultiValueMap<>();
 
         HttpHeaders requestHeaders = new HttpHeaders();
         requestHeaders.add(AbstractOpsImplV1.apiHeader, apiKey);
         requestHeaders.setContentType(MediaType.MULTIPART_FORM_DATA);//Main request's headers
 
         HttpHeaders requestHeadersAttachment = new HttpHeaders();
-        //requestHeadersAttachment.setContentType(MediaType.APPLICATION_OCTET_STREAM);// extract mediatype from file extensionHttpEntity<ByteArrayResource> attachmentPart;
-        ByteArrayResource fileAsResource = new ByteArrayResource(data){
-            @Override
-            public String getFilename(){
-                return fName;
-            }
-        };
-        HttpEntity attachmentPart = new HttpEntity<>(fileAsResource,requestHeadersAttachment);
 
+        HttpEntity attachmentPart = new HttpEntity<>(resource,requestHeadersAttachment);
         multipartRequest.set("file",attachmentPart);
 
         HttpHeaders requestHeadersJSON = new HttpHeaders();
diff --git a/src/test/java/com/researchspace/dataverse/http/DatasetFilePostMockServerTest.java b/src/test/java/com/researchspace/dataverse/http/DatasetFilePostMockServerTest.java
@@ -8,8 +8,6 @@
 import com.researchspace.dataverse.entities.Identifier;
 import com.researchspace.dataverse.search.entities.SearchConfig;
 import com.researchspace.dataverse.testutils.TestFileUtils;
-import org.junit.After;
-import org.junit.Before;
 import org.junit.Test;
 import org.springframework.http.HttpMethod;
 import org.springframework.test.web.client.ExpectedCount;
@@ -43,27 +41,22 @@
 </pre>
 */
 public class DatasetFilePostMockServerTest {
-		
-	@Before
-	public void setUp() throws Exception {
-	}
 
-	@After
-	public void tearDown() throws Exception {
-	}
 
 	@Test
 	public void testNativeFilePost() throws MalformedURLException {
 		RestTemplate template = new RestTemplate();
 		DataverseOperationsImplV1 tss = setupDataverseOps(template);
-		setUpServerResponse(template, "http://anyDataverse.com/api/v1/datasets/:persistentId/add?persistentId=1234",
+		final String persistentid = "doi://dsfh.dsdsd.sds";
+		setUpServerResponse(template, "http://anyDataverse.com/api/v1/datasets/:persistentId/add?persistentId="+persistentid,
 				getDataSetFileUploadResults() );
 		
 		DataverseConfig cfg = new DataverseConfig(new URL("http://anyDataverse.com"), "any", "alias");
 		tss.configure(cfg);
 		Identifier id = new Identifier();
 		id.setId(1234L);
-		DatasetFileList resp = tss.uploadNativeFile( FileUploadMetadata.builder().build(), id, null, null);
+		id.setPersistentId(persistentid);
+		DatasetFileList resp = tss.uploadNativeFile(new byte []{}, FileUploadMetadata.builder().build(), id,  "any");
 		assertNotNull(resp.getFiles());
 		assertEquals(1, resp.getFiles().size());
 	}

Original file line number	Diff line number	Diff line change
`@@ -21,7 +21,7 @@ public String deserialize(JsonParser jp, DeserializationContext ctxt)`
`21`	`21`	`} else if (node.isObject()){`
`22`	`22`	`return node.get("message").toString();`
`23`	`23`	`} else{`
`24`		`- throw new IllegalArgumentException("expect a string or an object with a string property");`
	`24`	`+ throw new IllegalArgumentException("expect a string or an object with a string property 'message'");`
`25`	`25`	`}`
`26`	`26`
`27`	`27`	`}`