Fix 127 Refactor writeStringDataBlock to overload writeDataBlock (#140)

NeurodataWithoutBorders · Jan 15, 2025 · c2ee9e6 · c2ee9e6
1 parent 7c69ed1
commit c2ee9e6
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Showing 8 changed files with 26 additions and 28 deletions.
diff --git a/src/io/BaseIO.hpp b/src/io/BaseIO.hpp
@@ -552,11 +552,10 @@ class BaseRecordingData
    * @param data Vector with the string data
    * @return The status of the write operation.
    */
-  virtual Status writeStringDataBlock(
-      const std::vector<SizeType>& dataShape,
-      const std::vector<SizeType>& positionOffset,
-      const BaseDataType& type,
-      const std::vector<std::string>& data) = 0;
+  virtual Status writeDataBlock(const std::vector<SizeType>& dataShape,
+                                const std::vector<SizeType>& positionOffset,
+                                const BaseDataType& type,
+                                const std::vector<std::string>& data) = 0;
 
 protected:
   /**

diff --git a/src/io/hdf5/HDF5IO.cpp b/src/io/hdf5/HDF5IO.cpp
@@ -923,10 +923,10 @@ Status HDF5IO::createStringDataSet(const std::string& path,
   dataset = std::unique_ptr<IO::BaseRecordingData>(createArrayDataSet(
       IO::BaseDataType::V_STR, SizeArray {values.size()}, SizeArray {1}, path));
 
-  dataset->writeStringDataBlock(std::vector<SizeType> {1},
-                                std::vector<SizeType> {0},
-                                IO::BaseDataType::V_STR,
-                                values);
+  dataset->writeDataBlock(std::vector<SizeType> {1},
+                          std::vector<SizeType> {0},
+                          IO::BaseDataType::V_STR,
+                          values);
 
   return Status::Success;
 }

diff --git a/src/io/hdf5/HDF5RecordingData.cpp b/src/io/hdf5/HDF5RecordingData.cpp
@@ -94,7 +94,7 @@ Status HDF5RecordingData::writeDataBlock(
   return Status::Success;
 }
 
-Status HDF5RecordingData::writeStringDataBlock(
+Status HDF5RecordingData::writeDataBlock(
     const std::vector<SizeType>& dataShape,
     const std::vector<SizeType>& positionOffset,
     const AQNWB::IO::BaseDataType& type,
@@ -208,4 +208,4 @@ Status HDF5RecordingData::writeDataBlockHelper(
   fSpace.selectHyperslab(H5S_SELECT_SET, dataDims.data(), offset.data());
 
   return Status::Success;
-}
+}
diff --git a/src/io/hdf5/HDF5RecordingData.hpp b/src/io/hdf5/HDF5RecordingData.hpp
@@ -64,10 +64,10 @@ class HDF5RecordingData : public AQNWB::IO::BaseRecordingData
    * @param data Vector with the string data
    * @return The status of the write operation.
    */
-  Status writeStringDataBlock(const std::vector<SizeType>& dataShape,
-                              const std::vector<SizeType>& positionOffset,
-                              const AQNWB::IO::BaseDataType& type,
-                              const std::vector<std::string>& data);
+  Status writeDataBlock(const std::vector<SizeType>& dataShape,
+                        const std::vector<SizeType>& positionOffset,
+                        const AQNWB::IO::BaseDataType& type,
+                        const std::vector<std::string>& data);
 
   /**
    * @brief Gets a const pointer to the HDF5 dataset.

diff --git a/src/nwb/base/TimeSeries.cpp b/src/nwb/base/TimeSeries.cpp
@@ -146,11 +146,10 @@ void TimeSeries::initialize(const IO::BaseDataType& dataType,
             controlDescriptionShape,
             controlDescriptionChunkSize,
             AQNWB::mergePaths(m_path, "control_description")));
-    this->control_description->writeStringDataBlock(
-        controlDescriptionShape,
-        controlDescriptionPositionOffset,
-        controlDesriptionType,
-        controlDescription);
+    this->control_description->writeDataBlock(controlDescriptionShape,
+                                              controlDescriptionPositionOffset,
+                                              controlDesriptionType,
+                                              controlDescription);
   } else {
     this->control = nullptr;
     this->control_description = nullptr;

diff --git a/src/nwb/hdmf/table/DynamicTable.cpp b/src/nwb/hdmf/table/DynamicTable.cpp
@@ -38,7 +38,7 @@ void DynamicTable::addColumn(std::unique_ptr<VectorData>& vectorData,
   } else {
     // write in loop because variable length string
     for (SizeType i = 0; i < values.size(); i++)
-      vectorData->m_dataset->writeStringDataBlock(
+      vectorData->m_dataset->writeDataBlock(
           std::vector<SizeType> {1},
           std::vector<SizeType> {i},
           IO::BaseDataType::STR(values[i].size() + 1),

diff --git a/tests/testHDF5IO.cpp b/tests/testHDF5IO.cpp
@@ -1364,7 +1364,7 @@ TEST_CASE("HDF5IO; read dataset", "[hdf5io]")
     // Write fixed-length string data block
     std::vector<SizeType> strDataShape = {3};
     std::vector<SizeType> strPositionOffset = {0};
-    writeStatus = strDataset->writeStringDataBlock(
+    writeStatus = strDataset->writeDataBlock(
         strDataShape, strPositionOffset, strType, testDataStr);
     REQUIRE(writeStatus == Status::Success);
 
@@ -1391,10 +1391,10 @@ TEST_CASE("HDF5IO; read dataset", "[hdf5io]")
     std::vector<SizeType> vstrDataShape = {3};
     std::vector<SizeType> vstrPositionOffset = {0};
     writeStatus =
-        vstrDataset->writeStringDataBlock(vstrDataShape,
-                                          vstrPositionOffset,
-                                          vstrType,  // Pass the vstrType object
-                                          testDataVStr);
+        vstrDataset->writeDataBlock(vstrDataShape,
+                                    vstrPositionOffset,
+                                    vstrType,  // Pass the vstrType object
+                                    testDataVStr);
     REQUIRE(writeStatus == Status::Success);
 
     // Confirm reading the variable-length string data is correct
@@ -1547,4 +1547,4 @@ TEST_CASE("HDF5IO; read dataset subset", "[hdf5io]")
 
     hdf5io->close();
   }
-}
+}
diff --git a/tests/testVectorData.cpp b/tests/testVectorData.cpp
@@ -177,7 +177,7 @@ TEST_CASE("VectorData", "[base]")
     columnVectorData.initialize(std::move(columnDataset), description);
 
     // Write data to file
-    Status writeStatus = columnVectorData.m_dataset->writeStringDataBlock(
+    Status writeStatus = columnVectorData.m_dataset->writeDataBlock(
         dataShape, positionOffset, dataType, data);
     REQUIRE(writeStatus == Status::Success);
     io->flush();