HDF5: Add cleaner way of handling object destruction (explicit Close() for file and dataset, all destructors have HDF5 TRY blocks)

writer/HDF5Objects.cpp

@@ -90,7 +90,12 @@ void HDF5DataSpace::SelectHyperslabWithStride(const std::vector<hsize_t> &start,
 }
 
 HDF5DataSpace::~HDF5DataSpace() {
-    if (id >= 0) H5Sclose(id);
+    if (id >= 0) {
+        H5E_BEGIN_TRY {
+            H5Sclose(id);
+        } H5E_END_TRY;
+        id = -1;
+    }
 }
 
 uint8_t HDF5DataSpace::GetNumOfDimensions() const {
@@ -204,7 +209,12 @@ HDF5DataType::HDF5DataType(const HDF5DataSet &data_set) :HDF5Id() {
 }
 
 HDF5DataType::~HDF5DataType() {
-    if (id >= 0) H5Tclose(id);
+    if (id >= 0) {
+        H5E_BEGIN_TRY {
+            H5Tclose(id);
+        } H5E_END_TRY;
+        id = -1;
+    }
 }
 
 size_t HDF5DataType::GetElemSize() const {
@@ -251,7 +261,12 @@ HDF5Dcpl::HDF5Dcpl(const HDF5DataSet &data_set) : HDF5Id() {
 }
 
 HDF5Dcpl::~HDF5Dcpl() {
-    if (id >= 0) H5Pclose(id);
+    if (id >= 0) {
+        H5E_BEGIN_TRY {
+            H5Pclose(id);
+        } H5E_END_TRY;
+        id = -1;
+    }
 }
 
 void HDF5Dcpl::SetChunking(const std::vector<hsize_t> &dims) {
@@ -308,7 +323,11 @@ HDF5Fapl::HDF5Fapl() : HDF5Id() {
 }
 
 HDF5Fapl::~HDF5Fapl() {
-    H5Pclose(id);
+    if (id >= 0) {
+        H5E_BEGIN_TRY {
+            H5Pclose(id);
+        } H5E_END_TRY;
+    }
 }
 
 void HDF5Fapl::SetVersionTo1p10orNewer() {
@@ -685,7 +704,12 @@ HDF5Group::HDF5Group(const HDF5Object& parent, const char *name) : HDF5Object()
 }
 
 HDF5Group::~HDF5Group() {
-    H5Gclose(id);
+    if (id >= 0) {
+        H5E_BEGIN_TRY {
+            H5Gclose(id);
+        } H5E_END_TRY;
+        id = -1;
+    }
 }
 
 HDF5File::HDF5File(const std::string& filename, bool v1_10) : HDF5Object() {
@@ -698,8 +722,27 @@ HDF5File::HDF5File(const std::string& filename, bool v1_10) : HDF5Object() {
         throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot open/create data HDF5 file " + filename);
 }
 
+void HDF5File::Close() {
+    if (id < 0)
+        return;
+
+    if (H5Fflush(id, H5F_SCOPE_GLOBAL) < 0)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Failed to flush HDF5 file");
+
+    hid_t tmp = id;
+    id = -1;
+
+    if (H5Fclose(tmp) < 0)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Failed to close HDF5 file");
+}
+
 HDF5File::~HDF5File() {
-    if (id >= 0) H5Fclose(id);
+    if (id >= 0) {
+        H5E_BEGIN_TRY {
+            H5Fclose(id);
+        } H5E_END_TRY;
+        id = -1;
+    }
 }
 
 void HDF5File::Delete(const std::string& path) {
@@ -799,8 +842,22 @@ std::string HDF5DataSet::ReadString() const {
     return buffer;
 }
 
+void HDF5DataSet::Close() {
+    if (id < 0)
+        return;
+    hid_t tmp = id;
+    id = -1;
+    if (H5Dclose(tmp) < 0)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot close HDF5 dataset");
+}
+
 HDF5DataSet::~HDF5DataSet() {
-    if (id >= 0) H5Dclose(id);
+    if (id >= 0) {
+        H5E_BEGIN_TRY {
+            H5Dclose(id);
+        } H5E_END_TRY;
+        id = -1;
+    }
 }
 
 void HDF5DataSet::ReadDirectChunk(std::vector<uint8_t> &val, const std::vector<hsize_t> &offset) {

writer/HDF5Objects.h

@@ -169,6 +169,7 @@ public:
     explicit HDF5File(const std::string& filename, bool v1_10 = false);
     ~HDF5File();
     void Delete(const std::string& path);
+    void Close();
 };
 
 class HDF5ReadOnlyFile : public HDF5Object {
@@ -321,6 +322,7 @@ public:
     }
 
     std::string ReadString() const;
+    void Close();
 };
 
 inline std::unique_ptr<HDF5DataSet> SaveScalar(const HDF5Object& parent, const std::string &name, const char* val) {