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relay: more tests and bug fixes for hdf5 i/o
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@cyrush
cyrush committed Apr 22, 2016
1 parent bc50a02 commit b40332c
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Showing 2 changed files with 184 additions and 83 deletions.
8 changes: 3 additions & 5 deletions src/libs/relay/relay_hdf5.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -655,10 +655,6 @@ write_conduit_leaf_to_hdf5_dataset(const Node &node,
CONDUIT_CHECK_HDF5_ERROR(h5_status,
"Failed to write to HDF5 Dataset " << hdf5_dset_id);

// close our dataset
CONDUIT_CHECK_HDF5_ERROR(H5Dclose(hdf5_dset_id),
"Failed to close HDF5 Dataset " << hdf5_dset_id);

}

//---------------------------------------------------------------------------//
Expand Down Expand Up @@ -707,7 +703,9 @@ write_conduit_leaf_to_hdf5_group(const Node &node,
// write the data
write_conduit_leaf_to_hdf5_dataset(node,
h5_child_id);


CONDUIT_CHECK_HDF5_ERROR(H5Dclose(h5_child_id),
"Failed to close HDF5 Dataset: " << h5_child_id);
}

//---------------------------------------------------------------------------//
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259 changes: 181 additions & 78 deletions src/tests/relay/t_relay_io_hdf5.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -122,80 +122,6 @@ TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_by_file_name)

}

//-----------------------------------------------------------------------------
// This variant tests when a caller code has already opened a HDF5 file
// and has a handle ready.
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_by_file_handle)
{
uint32 a_val = 20;
uint32 b_val = 8;
uint32 c_val = 13;

Node n;
n["a"] = a_val;
n["b"] = b_val;
n["c"] = c_val;

EXPECT_EQ(n["a"].as_uint32(), a_val);
EXPECT_EQ(n["b"].as_uint32(), b_val);
EXPECT_EQ(n["c"].as_uint32(), c_val);

std::string test_file_name = "tout_hdf5_write_read_by_file_handle.hdf5";

// Set up hdf5 file and group that caller code would already have.
hid_t h5_file_id = H5Fcreate(test_file_name.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);

// Prepare group that caller code wants conduit to save it's tree to that
// group. (could also specify group name for conduit to create via
// hdf5_path argument to write call.
hid_t h5_group_id = H5Gcreate(h5_file_id,
"sample_group_name",
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);

io::hdf5_write(n,h5_group_id);
hid_t status = H5Gclose(h5_group_id);

// Another variant of this - caller code has a pre-existing group they
// want to write into, but they want to use the 'group name' arg to do it
// Relay should be able to write into existing group.
h5_group_id = H5Gcreate(h5_file_id,
"sample_group_name2",
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);
io::hdf5_write(n,h5_file_id, "sample_group_name2");

status = H5Gclose(h5_group_id);

status = H5Fclose(h5_file_id);

h5_file_id = H5Fopen(test_file_name.c_str(),
H5F_ACC_RDONLY,
H5P_DEFAULT);

// Caller code switches to group it wants to read in. (could also
// specify group name for conduit to read out via hdf5_path arg to read
// call)
h5_group_id = H5Gopen(h5_file_id, "sample_group_name", 0);

Node n_load;

io::hdf5_read(h5_group_id, n_load);

status = H5Gclose(h5_group_id);
status = H5Fclose(h5_file_id);

EXPECT_EQ(n_load["a"].as_uint32(), a_val);
EXPECT_EQ(n_load["b"].as_uint32(), b_val);
EXPECT_EQ(n_load["c"].as_uint32(), c_val);

}

//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_special_paths)
{
Expand Down Expand Up @@ -294,18 +220,195 @@ TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_array)
}

}


//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, write_and_read_conduit_leaf_to_hdf5_dataset_handle)
{
std::string ofname = "tout_hdf5_wr_conduit_leaf_to_hdf5_dataset_handle.hdf5";

hid_t h5_file_id = H5Fcreate(ofname.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);

// create a dataset for a 16-bit signed integer array with 2 elements


hid_t h5_dtype = H5T_NATIVE_SHORT;

hsize_t num_eles = 2;

hid_t h5_dspace_id = H5Screate_simple(1,
&num_eles,
NULL);

// create new dataset
hid_t h5_dset_id = H5Dcreate(h5_file_id,
"mydata",
h5_dtype,
h5_dspace_id,
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);

Node n;
n.set(DataType::c_short(2));
short_array vals = n.value();

vals[0] = -16;
vals[1] = -16;

// this should succeed
io::hdf5_write(n,h5_dset_id);


// this should also succeed
vals[1] = 16;

io::hdf5_write(n,h5_dset_id);

n.set(DataType::uint16(10));
// this should fail
EXPECT_THROW(io::hdf5_write(n,h5_dset_id),Error);

Node n_read;
io::hdf5_read(h5_dset_id,n_read);

// check values of data
short_array read_vals = n_read.value();
EXPECT_EQ(-16,read_vals[0]);
EXPECT_EQ(16,read_vals[1]);

H5Sclose(h5_dspace_id);
H5Dclose(h5_dset_id);
H5Fclose(h5_file_id);


}

//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_read_dataset_from_handle)
TEST(conduit_relay_io_hdf5, write_conduit_object_to_hdf5_group_handle)
{
EXPECT_TRUE(false);
std::string ofname = "tout_hdf5_wr_conduit_object_to_hdf5_group_handle.hdf5";

hid_t h5_file_id = H5Fcreate(ofname.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);

hid_t h5_group_id = H5Gcreate(h5_file_id,
"mygroup",
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);


Node n;
n["a/b"].set(DataType::int16(2));
int16_array vals = n["a/b"].value();
vals[0] =-16;
vals[1] =-16;

// this should succeed
io::hdf5_write(n,h5_group_id);

n["a/c"] = "mystring";

// this should also succeed
vals[1] = 16;

io::hdf5_write(n,h5_group_id);

n["a/b"].set(DataType::uint16(10));
// this should fail
EXPECT_THROW(io::hdf5_write(n,h5_group_id),Error);

Node n_read;
io::hdf5_read(h5_group_id,n_read);

// check values of data
int16_array read_vals = n_read["a/b"].value();
EXPECT_EQ(-16,read_vals[0]);
EXPECT_EQ(16,read_vals[1]);
EXPECT_EQ("mystring",n_read["a/c"].as_string());

H5Gclose(h5_group_id);
H5Fclose(h5_file_id);
}

//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_read_group_from_handle)
// This variant tests when a caller code has already opened a HDF5 file
// and has a handle ready.
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_by_file_handle)
{
EXPECT_TRUE(false);
uint32 a_val = 20;
uint32 b_val = 8;
uint32 c_val = 13;

Node n;
n["a"] = a_val;
n["b"] = b_val;
n["c"] = c_val;

EXPECT_EQ(n["a"].as_uint32(), a_val);
EXPECT_EQ(n["b"].as_uint32(), b_val);
EXPECT_EQ(n["c"].as_uint32(), c_val);

std::string test_file_name = "tout_hdf5_write_read_by_file_handle.hdf5";

// Set up hdf5 file and group that caller code would already have.
hid_t h5_file_id = H5Fcreate(test_file_name.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);

// Prepare group that caller code wants conduit to save it's tree to that
// group. (could also specify group name for conduit to create via
// hdf5_path argument to write call.
hid_t h5_group_id = H5Gcreate(h5_file_id,
"sample_group_name",
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);

io::hdf5_write(n,h5_group_id);
hid_t status = H5Gclose(h5_group_id);

// Another variant of this - caller code has a pre-existing group they
// want to write into, but they want to use the 'group name' arg to do it
// Relay should be able to write into existing group.
h5_group_id = H5Gcreate(h5_file_id,
"sample_group_name2",
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);
io::hdf5_write(n,h5_file_id, "sample_group_name2");

status = H5Gclose(h5_group_id);

status = H5Fclose(h5_file_id);

h5_file_id = H5Fopen(test_file_name.c_str(),
H5F_ACC_RDONLY,
H5P_DEFAULT);

// Caller code switches to group it wants to read in. (could also
// specify group name for conduit to read out via hdf5_path arg to read
// call)
h5_group_id = H5Gopen(h5_file_id, "sample_group_name", 0);

Node n_load;

io::hdf5_read(h5_group_id, n_load);

status = H5Gclose(h5_group_id);
status = H5Fclose(h5_file_id);

EXPECT_EQ(n_load["a"].as_uint32(), a_val);
EXPECT_EQ(n_load["b"].as_uint32(), b_val);
EXPECT_EQ(n_load["c"].as_uint32(), c_val);

}


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