Add flush function for the IO and fix test build warnings for testHDF5IO

NeurodataWithoutBorders · Aug 9, 2024 · 6aff062 · 6aff062
1 parent bc4b68c
commit 6aff062
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Showing 4 changed files with 29 additions and 4 deletions.
diff --git a/src/BaseIO.hpp b/src/BaseIO.hpp
@@ -132,6 +132,12 @@ class BaseIO
    */
   virtual Status close() = 0;
 
+  /**
+   * @brief Flush data to disk
+   * @return The status of the flush operation.
+   */
+  virtual Status flush() = 0;
+
   /**
    * @brief Creates an attribute at a given location in the file.
    * @param type The base data type of the attribute.

diff --git a/src/hdf5/HDF5IO.cpp b/src/hdf5/HDF5IO.cpp
@@ -84,6 +84,12 @@ Status checkStatus(int status)
     return Status::Success;
 }
 
+Status HDF5IO::flush()
+{
+  int status =  H5Fflush(this->file->getId(), H5F_SCOPE_GLOBAL);
+  return checkStatus(status);
+}
+
 Status HDF5IO::createAttribute(const BaseDataType& type,
                                const void* data,
                                const std::string& path,
@@ -407,7 +413,7 @@ Status HDF5IO::stopRecording()
   if (!disableSWMRMode) {
     close();  // SWMR mode cannot be disabled so close the file
   } else {
-    H5Fflush(this->file->getId(), H5F_SCOPE_GLOBAL);  // flush all data to disk
+    this->flush();
   }
   return Status::Success;
 }

diff --git a/src/hdf5/HDF5IO.hpp b/src/hdf5/HDF5IO.hpp
@@ -74,6 +74,12 @@ class HDF5IO : public BaseIO
    */
   Status close() override;
 
+  /**
+   * @brief Flush data to disk
+   * @return The status of the flush operation.
+   */
+   Status flush() override;
+
   /**
    * @brief Creates an attribute at a given location in the file.
    * @param type The base data type of the attribute.

diff --git a/tests/testHDF5IO.cpp b/tests/testHDF5IO.cpp
@@ -90,6 +90,7 @@ TEST_CASE("writeDataset", "[hdf5io]")
                                    dataPath);
     Status status = dataset->writeDataBlock(
         dataShape, positionOffset, BaseDataType::I32, testData.data());
+    REQUIRE(status == Status::Success);
 
     // Read back the 1D data block from 3D dataset
     std::unique_ptr<BaseRecordingData> dataRead1D =
@@ -129,6 +130,7 @@ TEST_CASE("writeDataset", "[hdf5io]")
     // Write 2D data block
     Status status = dataset->writeDataBlock(
         dataShape, positionOffset, BaseDataType::I32, testData.data());
+    REQUIRE(status == Status::Success);
 
     // Read back the 2D data block
     std::unique_ptr<BaseRecordingData> dsetRead2D =
@@ -165,6 +167,7 @@ TEST_CASE("writeDataset", "[hdf5io]")
                                    dataPath);
     Status status = dataset->writeDataBlock(
         dataShape, positionOffset, BaseDataType::I32, testData.data());
+    REQUIRE(status == Status::Success);
 
     // Read back the 1D data block from 3D dataset
     std::unique_ptr<BaseRecordingData> dataRead1D =
@@ -201,6 +204,7 @@ TEST_CASE("writeDataset", "[hdf5io]")
                                    dataPath);
     Status status = dataset->writeDataBlock(
         dataShape, positionOffset, BaseDataType::I32, testData.data());
+    REQUIRE(status == Status::Success);
 
     // Read back the 2D data block from 3D dataset
     std::unique_ptr<BaseRecordingData> dataRead2D =
@@ -312,7 +316,7 @@ TEST_CASE("SWMRmode", "[hdf5io]")
         std::move(promise));
 
     // write to file
-    for (int b = 0; b <= numBlocks; b++) {
+    for (SizeType b = 0; b <= numBlocks; b++) {
       // write data block and flush to file
       std::vector<SizeType> dataShape = {numSamples};
       dataset->writeDataBlock(dataShape, BaseDataType::I32, &testData[0]);
@@ -336,6 +340,9 @@ TEST_CASE("SWMRmode", "[hdf5io]")
     REQUIRE(retSWMREnabled == 0);  // process should succeed if data was written
                                    // and read successfully
 
+    // test flush data to disk
+    REQUIRE(hdf5io->flush() == Status::Success);
+
     // stop recording, check that file is closed and recording cannot be
     // restarted
     status = hdf5io->stopRecording();
@@ -365,7 +372,7 @@ TEST_CASE("SWMRmode", "[hdf5io]")
     REQUIRE(hdf5io->canModifyObjects() == true);
 
     // write to file
-    for (int b = 0; b <= numBlocks; b++) {
+    for (SizeType b = 0; b <= numBlocks; b++) {
       // write data block and flush to file
       std::vector<SizeType> dataShape = {numSamples};
       dataset->writeDataBlock(dataShape, BaseDataType::I32, &testData[0]);
@@ -396,7 +403,7 @@ TEST_CASE("SWMRmode", "[hdf5io]")
                                    SizeArray {1},
                                    dataPathPostRestart);
 
-    for (int b = 0; b <= numBlocks; b++) {
+    for (SizeType b = 0; b <= numBlocks; b++) {
       // write data block and flush to file
       std::vector<SizeType> dataShape = {numSamples};
       datasetPostRestart->writeDataBlock(