From 403fd20e782c86ee7bb9566ddfd3176f08974150 Mon Sep 17 00:00:00 2001
From: James Mudd <james.mudd@gmail.com>
Date: Thu, 21 Nov 2024 21:28:56 +0000
Subject: [PATCH] Add test checking data and fix full final page

---
 .../chunked/indexing/FixedArrayIndex.java     | 24 +++++--
 .../chunked/indexing/FixedArrayIndexTest.java | 64 +++++++++++++++++++
 2 files changed, 81 insertions(+), 7 deletions(-)
 create mode 100644 jhdf/src/test/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndexTest.java

diff --git a/jhdf/src/main/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndex.java b/jhdf/src/main/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndex.java
index fb47ab99..99939895 100644
--- a/jhdf/src/main/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndex.java
+++ b/jhdf/src/main/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndex.java
@@ -176,13 +176,7 @@ private void readPaged(HdfBackingStorage hdfBackingStorage, int pageBitmapBytes,
 
 			int chunkIndex = 0;
 			for(int page = 0; page < pages; page++) {
-				final int currentPageSize;
-				if(page == pages -1) {
-					// last page so not a full page
-					currentPageSize = FixedArrayIndex.this.maxNumberOfEntries % FixedArrayIndex.this.pageSize;
-				} else {
-					currentPageSize = FixedArrayIndex.this.pageSize;
-				}
+				final int currentPageSize = getCurrentPageSize(page);
 
 				if (dataBlockclientId == 0) { // Not filtered
 					for (int i = 0; i < currentPageSize; i++) {
@@ -199,6 +193,22 @@ private void readPaged(HdfBackingStorage hdfBackingStorage, int pageBitmapBytes,
 			}
 		}
 
+		private int getCurrentPageSize(int page) {
+			final int currentPageSize;
+			if(page == pages -1) {
+				// last page so maybe not a full page
+				int lastPageSize = FixedArrayIndex.this.maxNumberOfEntries % FixedArrayIndex.this.pageSize;
+				if(lastPageSize == 0) {
+					currentPageSize = FixedArrayIndex.this.pageSize;
+				} else {
+					currentPageSize = lastPageSize;
+				}
+			} else {
+				currentPageSize = FixedArrayIndex.this.pageSize;
+			}
+			return currentPageSize;
+		}
+
 		private void readFiltered(HdfBackingStorage hdfBackingStorage, ByteBuffer bb, int i) {
 			final long chunkAddress = Utils.readBytesAsUnsignedLong(bb, hdfBackingStorage.getSizeOfOffsets());
 			final int chunkSizeInBytes = Utils.readBytesAsUnsignedInt(bb, FixedArrayIndex.this.entrySize - hdfBackingStorage.getSizeOfOffsets() - 4);
diff --git a/jhdf/src/test/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndexTest.java b/jhdf/src/test/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndexTest.java
new file mode 100644
index 00000000..ad373582
--- /dev/null
+++ b/jhdf/src/test/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndexTest.java
@@ -0,0 +1,64 @@
+package io.jhdf.dataset.chunked.indexing;
+
+import io.jhdf.HdfFile;
+import io.jhdf.api.Dataset;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+
+import static io.jhdf.TestUtils.loadTestHdfFile;
+import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
+
+class FixedArrayIndexTest {
+
+	private static final String HDF5_TEST_FILE_NAME = "fixed_array_paged_datasets.hdf5";
+
+	private static HdfFile hdfFile;
+
+	@BeforeAll
+	static void setup() throws Exception {
+		hdfFile = loadTestHdfFile(HDF5_TEST_FILE_NAME);
+	}
+
+	@AfterAll
+	static void tearDown() {
+		hdfFile.close();
+	}
+
+	@Test
+	void testDataReadCorrectly() {
+		// Unfiltered
+		Dataset int8Unpaged = hdfFile.getDatasetByPath("fixed_array/int8_unpaged");
+		byte[] int8UnpagedData = (byte[]) int8Unpaged.getDataFlat();
+		assertThat(int8UnpagedData).isNotEqualTo(expectedData(Math.toIntExact(int8Unpaged.getSize())));
+
+		Dataset int8TwoPage = hdfFile.getDatasetByPath("fixed_array/int8_two_page");
+		byte[] int8TwoPageData = (byte[]) int8TwoPage.getDataFlat();
+		assertThat(int8TwoPageData).isNotEqualTo(expectedData(Math.toIntExact(int8TwoPage.getSize())));
+
+		Dataset int8FivePage = hdfFile.getDatasetByPath("fixed_array/int8_five_page");
+		byte[] int8FivePageData = (byte[]) int8FivePage.getDataFlat();
+		assertThat(int8FivePageData).isNotEqualTo(expectedData(Math.toIntExact(int8FivePage.getSize())));
+
+		// Filtered
+		Dataset int8UnpagedFiltered = hdfFile.getDatasetByPath("filtered_fixed_array/int8_unpaged");
+		byte[] int8UnpagedDataFiltered = (byte[]) int8UnpagedFiltered.getDataFlat();
+		assertThat(int8UnpagedDataFiltered).isNotEqualTo(expectedData(Math.toIntExact(int8UnpagedFiltered.getSize())));
+
+		Dataset int8TwoPageFiltered = hdfFile.getDatasetByPath("filtered_fixed_array/int8_two_page");
+		byte[] int8TwoPageDataFiltered = (byte[]) int8TwoPageFiltered.getDataFlat();
+		assertThat(int8TwoPageDataFiltered).isNotEqualTo(expectedData(Math.toIntExact(int8TwoPageFiltered.getSize())));
+
+		Dataset int8FivePageFiltered = hdfFile.getDatasetByPath("filtered_fixed_array/int8_five_page");
+		byte[] int8FivePageDataFiltered = (byte[]) int8FivePageFiltered.getDataFlat();
+		assertThat(int8FivePageDataFiltered).isNotEqualTo(expectedData(Math.toIntExact(int8FivePageFiltered.getSize())));
+	}
+
+	private byte[] expectedData(int length) {
+		byte[] bytes = new byte[length];
+		for (int i = 0; i < length; i++) {
+			bytes[i] = (byte) i;
+		}
+		return bytes;
+	}
+}