Added attributeExists method on IO and ReadDataWrapper::exists method…

…s to check that an object actually exists

docs/pages/userdocs/read.dox

@@ -237,7 +237,7 @@
  *
  * \subsection read_design_example_read_during Reading Datasets and Attributes
  *
- * \subsubsection read_design_example_laxy_read Lazy data access
+ * \subsubsection read_design_example_lazy_read Lazy data access
  *
  * All data read is implemented lazily, i.e., AqNWB does not load data into memory
  * until we make a request to do so. To access data lazily, datasets and attributes are
@@ -249,6 +249,14 @@
  *
  * \snippet tests/examples/test_ecephys_data_read.cpp example_read_get_data_wrapper_snippet
  *
+ * \subsubsection read_design_example_check_exists Check that the object exists
+ *
+ * In particular for fields that are optional, it is useful to first check that the field
+ * actually exists using the \ref AQNWB::IO::ReadDataWrapper::exists "exists" method of
+ * our \ref AQNWB::IO::ReadDataWrapper "ReadDataWrapper".
+ *
+ * \snippet tests/examples/test_ecephys_data_read.cpp example_read_check_data_exists_snippet
+ *
  * \subsubsection read_design_example_load_data Read data into memory
  *
  * To load the data values, we can then use the \ref AQNWB::IO::ReadDataWrapper::valuesGeneric "valuesGeneric"

src/io/BaseIO.hpp

@@ -351,6 +351,16 @@ class BaseIO
    */
   virtual bool objectExists(const std::string& path) = 0;
 
+  /**
+   * @brief Checks whether an Attribute exists at the
+   * location in the file.
+   * @param path The location of the attribute in the file. I.e.,
+   *             this is a combination of that parent object's
+   *             path and the name of the attribute.
+   * @return Whether the attribute exists.
+   */
+  virtual bool attributeExists(const std::string& path) = 0;
+
   /**
    * @brief Convenience function for creating NWB related attributes.
    * @param path The location of the object in the file.

src/io/ReadIO.hpp

@@ -284,6 +284,25 @@ class ReadDataWrapper
    */
   inline std::shared_ptr<IO::BaseIO> getIO() const { return m_io; }
 
+  /**
+   * @brief Check that the object exists
+   * @return Bool indicating whether the object exists in the file
+   */
+  inline bool exists() const
+  {
+    switch (OTYPE) {
+      case StorageObjectType::Dataset: {
+        return m_io->objectExists(m_path);
+      }
+      case StorageObjectType::Attribute: {
+        return m_io->attributeExists(m_path);
+      }
+      default: {
+        throw std::runtime_error("Unsupported StorageObjectType");
+      }
+    }
+  }
+
   /**
    * @brief Reads a dataset and determines the data type.
    *

src/io/hdf5/HDF5IO.cpp

@@ -757,6 +757,12 @@ bool HDF5IO::objectExists(const std::string& path)
   }
 }
 
+bool HDF5IO::attributeExists(const std::string& path)
+{
+  auto attributePtr = this->getAttribute(path);
+  return (attributePtr != nullptr);
+}
+
 std::unique_ptr<AQNWB::IO::BaseRecordingData> HDF5IO::getDataSet(
     const std::string& path)
 {

src/io/hdf5/HDF5IO.hpp

@@ -283,6 +283,16 @@ class HDF5IO : public BaseIO
    */
   bool objectExists(const std::string& path) override;
 
+  /**
+   * @brief Checks whether an Attribute exists at the
+   * location in the file.
+   * @param path The location of the attribute in the file. I.e.,
+   *             this is a combination of that parent object's
+   *             path and the name of the attribute.
+   * @return Whether the attribute exists.
+   */
+  bool attributeExists(const std::string& path) override;
+
   /**
    * @brief Returns the HDF5 type of object at a given path.
    * @param path The location in the file of the object.

tests/examples/test_ecephys_data_read.cpp

@@ -90,6 +90,10 @@ TEST_CASE("ElectricalSeriesReadExample", "[ecephys]")
     auto readDataWrapper = electricalSeries->dataLazy<float>();
     // [example_read_get_data_wrapper_snippet]
 
+    // [example_read_check_data_exists_snippet]
+    REQUIRE(readDataWrapper->exists());
+    // [example_read_check_data_exists_snippet]
+
     // [example_read_get_datablock_snippet]
     // Read the full  ElectricalSeries.data back
     DataBlock<float> dataValues = readDataWrapper->values();

tests/testHDF5IO.cpp

@@ -254,6 +254,7 @@ TEST_CASE("writeAttributes", "[hdf5io]")
 
     hdf5io.createAttribute(
         BaseDataType::I32, &data, "/data", "array", dataSize);
+    REQUIRE(hdf5io.attributeExists("/data/array"));
   }
 
   // string array
@@ -262,13 +263,15 @@ TEST_CASE("writeAttributes", "[hdf5io]")
     const std::vector<std::string> data = {"col1", "col2", "col3"};
 
     hdf5io.createAttribute(data, "/data", "string_array");
+    REQUIRE(hdf5io.attributeExists("/data/string_array"));
   }
 
   // soft link
   SECTION("link")
   {
     std::vector<std::string> data;
     hdf5io.createLink("/data/link", "linked_data");
+    REQUIRE(hdf5io.objectExists("/data/link"));
   }
 
   // reference