add additional tests and refactor io functions

NeurodataWithoutBorders · Aug 7, 2024 · 51d4c52 · 51d4c52
1 parent 3a9aa90
commit 51d4c52
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Showing 3 changed files with 41 additions and 19 deletions.
diff --git a/src/hdf5/HDF5IO.cpp b/src/hdf5/HDF5IO.cpp
@@ -67,8 +67,11 @@ Status HDF5IO::open(bool newfile)
 
 Status HDF5IO::close()
 {
-  file = nullptr;
-  opened = false;
+  if (this->file != nullptr && opened) {
+    this->file->close();
+    this->file = nullptr;
+    this->opened = false;
+  }
 
   return Status::Success;
 }
@@ -403,10 +406,8 @@ Status HDF5IO::stopRecording()
   // if SWMR mode is disabled, stopping the recording will leave the file open
   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
+  } else {
+    H5Fflush(this->file->getId(), H5F_SCOPE_GLOBAL);  // flush all data to disk
   }
   return Status::Success;
 }
@@ -416,21 +417,18 @@ bool HDF5IO::canModifyObjects()
   if (!opened)
     return false;
 
-  // Get the file access intent
+  // Check if we are in SWMR mode
+  bool inSWMRMode = false;
   unsigned int intent;
   herr_t status = H5Fget_intent(this->file->getId(), &intent);
-  if (status < 0) {
-    return false;  // We could not access the file so modifying objects is not
-                   // going to work
+  bool statusOK = (status >= 0);
+  if (statusOK) {
+    inSWMRMode = (intent & (H5F_ACC_SWMR_READ | H5F_ACC_SWMR_WRITE));
   }
 
-  // Check if SWMR mode is enabled
-  if (intent & (H5F_ACC_SWMR_READ | H5F_ACC_SWMR_WRITE)) {
-    return false;  // File is in SWMR mode
-  } else {
-    return true;  // File is not in SWMR mode
-  }
-  return true;
+  // if the file is opened and we are not in swmr mode then we can modify
+  // objects
+  return statusOK && !inSWMRMode;
 }
 
 std::unique_ptr<AQNWB::BaseRecordingData> HDF5IO::getDataSet(

diff --git a/src/hdf5/HDF5IO.hpp b/src/hdf5/HDF5IO.hpp
@@ -252,7 +252,8 @@ class HDF5IO : public BaseIO
 
 private:
   std::unique_ptr<H5::H5File> file;
-  bool disableSWMRMode;   // when set do not use SWMR mode when opening the HDF5 file
+  bool disableSWMRMode;  // when set do not use SWMR mode when opening the HDF5
+                         // file
 };
 
 /**

diff --git a/tests/testHDF5IO.cpp b/tests/testHDF5IO.cpp
@@ -383,6 +383,29 @@ TEST_CASE("SWMRmode", "[hdf5io]")
     // restarted
     status = hdf5io->stopRecording();
     REQUIRE(hdf5io->isOpen() == true);
-    REQUIRE(hdf5io->startRecording() == Status::Success);
+
+    // restart recording and write to a dataset
+    Status statusRestart = hdf5io->startRecording();
+    REQUIRE(statusRestart == Status::Success);
+
+    std::string dataPathPostRestart = "/dataPostRestart/data";
+    hdf5io->createGroup("/dataPostRestart");
+    std::unique_ptr<BaseRecordingData> datasetPostRestart =
+        hdf5io->createArrayDataSet(BaseDataType::I32,
+                                   SizeArray {0},
+                                   SizeArray {1},
+                                   dataPathPostRestart);
+
+    for (int b = 0; b <= numBlocks; b++) {
+      // write data block and flush to file
+      std::vector<SizeType> dataShape = {numSamples};
+      datasetPostRestart->writeDataBlock(
+          dataShape, BaseDataType::I32, &testData[0]);
+      H5Dflush(static_cast<HDF5::HDF5RecordingData*>(datasetPostRestart.get())
+                   ->getDataSet()
+                   ->getId());
+    }
+
+    hdf5io->close();
   }
 }