Merge pull request #642 from jamesmudd/issue-641

Fix for Issue 641
jamesmudd · Oct 28, 2024 · cebec09 · cebec09
2 parents 68c03d7 + 26c6216
commit cebec09
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diff --git a/jhdf/src/main/java/io/jhdf/object/datatype/StringData.java b/jhdf/src/main/java/io/jhdf/object/datatype/StringData.java
@@ -252,9 +252,14 @@ private void encodeDataInternal(Object data, int[] dims, ByteBuffer buffer) {
 				encodeDataInternal(newArray, stripLeadingIndex(dims), buffer);
 			}
 		} else {
-			for (String str : (String[]) data) {
-				buffer.put(this.charset.encode(str)).put(NULL);
-			}
+			final int offset = buffer.position();
+            String[] strings = (String[]) data;
+            for (int i = 0; i < strings.length; i++) {
+                String str = strings[i];
+                buffer.put(this.charset.encode(str))
+                        .put(NULL)
+                        .position(offset + (i + 1) * getSize());
+            }
 		}
 	}
 

diff --git a/jhdf/src/test/java/io/jhdf/writing/StringWritingTest.java b/jhdf/src/test/java/io/jhdf/writing/StringWritingTest.java
@@ -13,12 +13,14 @@
 import io.jhdf.HdfFile;
 import io.jhdf.TestUtils;
 import io.jhdf.WritableHdfFile;
+import io.jhdf.api.Dataset;
 import io.jhdf.api.Node;
 import io.jhdf.api.WritiableDataset;
 import io.jhdf.examples.TestAllFilesBase;
 import io.jhdf.h5dump.EnabledIfH5DumpAvailable;
 import io.jhdf.h5dump.H5Dump;
 import io.jhdf.h5dump.HDF5FileXml;
+import org.apache.commons.lang3.RandomStringUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.junit.jupiter.api.MethodOrderer;
 import org.junit.jupiter.api.Order;
@@ -96,7 +98,8 @@ void writeStrings() throws Exception {
 			{"element 2,1", "element 2,2", "element 2,3", "element 2,4", "element 2,5"}
 		});
 
-		writableHdfFile.putDataset("prose", StringUtils.split(prose));
+		WritiableDataset proseDataset = writableHdfFile.putDataset("prose", StringUtils.split(prose));
+		proseDataset.putAttribute("prose_attr", StringUtils.split(prose));
 
 		// Actually flush and write everything
 		writableHdfFile.close();
@@ -131,4 +134,62 @@ void readStringDatasetsWithH5Dump() throws Exception {
 			H5Dump.assetXmlAndHdfFileMatch(hdf5FileXml, hdfFile);
 		}
 	}
+
+	@Test
+	@Order(3)
+	// https://github.com/jamesmudd/jhdf/issues/641
+	void writeVarStringAttributes() throws Exception {
+		Path tempFile = Files.createTempFile(this.getClass().getSimpleName(), ".hdf5");
+		WritableHdfFile writableHdfFile = HdfFile.write(tempFile);
+
+		// Write a dataset with string attributes
+		WritiableDataset writiableDataset = writableHdfFile.putDataset("dataset", new String[] {"vv", "xx", "abcdef"});
+		writiableDataset.putAttribute("labels", new String[] {"vv", "xx", "abcdef"});
+		writiableDataset.putAttribute("units", new String[] {"", "1", "mm2"});
+		writableHdfFile.close();
+
+		// Now read it back
+		try (HdfFile hdfFile = new HdfFile(tempFile)) {
+			Dataset dataset = hdfFile.getDatasetByPath("dataset");
+			assertThat(dataset.getData()).isEqualTo(new String[] {"vv", "xx", "abcdef"});
+
+			// Expected :["vv", "xx", "abcdef"]
+			// Actual   :["vv", "cdedf", ""]
+			assertThat(dataset.getAttribute("labels").getData()).isEqualTo(new String[] {"vv", "xx", "abcdef"});
+
+			// Expected :["", "1", "mm2"]
+			// Actual   :["", "m2", ""]
+			assertThat(dataset.getAttribute("units").getData()).isEqualTo(new String[] {"", "1", "mm2"});
+		} finally {
+			tempFile.toFile().delete();
+		}
+	}
+
+	@Test()
+	@Order(4)
+	void writeReallyLongStrings() throws Exception {
+		Path tempFile = Files.createTempFile(this.getClass().getSimpleName(), ".hdf5");
+		WritableHdfFile writableHdfFile = HdfFile.write(tempFile);
+
+		// Write a dataset with string attributes
+		String[] randomLongStringData = {
+			RandomStringUtils.insecure().nextAlphanumeric(234, 456),
+			RandomStringUtils.insecure().nextAlphanumeric(234, 456),
+			RandomStringUtils.insecure().nextAlphanumeric(234, 456),
+			RandomStringUtils.insecure().nextAlphanumeric(234, 456),
+			RandomStringUtils.insecure().nextAlphanumeric(234, 456),
+		};
+		WritiableDataset writiableDataset = writableHdfFile.putDataset("dataset", randomLongStringData);
+		writiableDataset.putAttribute("attr", randomLongStringData);
+		writableHdfFile.close();
+
+		// Now read it back
+		try (HdfFile hdfFile = new HdfFile(tempFile)) {
+			Dataset dataset = hdfFile.getDatasetByPath("dataset");
+			assertThat(dataset.getData()).isEqualTo(randomLongStringData);
+			assertThat(dataset.getAttribute("attr").getData()).isEqualTo(randomLongStringData);
+		} finally {
+			tempFile.toFile().delete();
+		}
+	}
 }