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The user can now add separate filter lists per dimension. Towards add…
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…ressing #93.
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@stavrospapadopoulos
stavrospapadopoulos committed Mar 19, 2020
1 parent 44ff68b commit 2a0c514
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4 changes: 4 additions & 0 deletions HISTORY.md
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
## New features

* The user can now set separate coordinate buffers to the query. Also any subset of the dimensions is supported.
* The user can set separate filter lists per dimension, as well as the number of values per coordinate.

## Improvements

Expand All @@ -34,6 +35,9 @@

* Added C API function `tiledb_array_has_metadata_key` and C++ API function `Array::has_metadata_key` [#1439](https://github.com/TileDB-Inc/TileDB/pull/1439)
* Added C API functions `tiledb_array_schema_{set,get}_allows_dups` and C++ API functions `Array::set_allows_dups` and `Array::allows_dups`
* Added C API functions `tiledb_dimension_{set,get}_filter_list` and `tiledb_dimension_{set,get}_cell_val_num`
* Added C++ API functions `Dimension::set_cell_val_num` and `Dimension::cell_val_num`.
* Added C++ API functions `Dimension::set_filter_list` and `Dimension::filter_list`.

## API removals

Expand Down
241 changes: 213 additions & 28 deletions test/src/unit-capi-array_schema.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ struct ArraySchemaFx {
* If true, array schema is serialized before submission, to test the
* serialization paths.
*/
bool serialize_array_schema = false;
bool serialize_array_schema_ = false;

// TileDB context and vfs
tiledb_ctx_t* ctx_;
Expand Down Expand Up @@ -289,7 +289,7 @@ int ArraySchemaFx::array_create_wrapper(
return tiledb_array_create(ctx_, path.c_str(), array_schema);
#endif

if (!serialize_array_schema) {
if (!serialize_array_schema_) {
return tiledb_array_create(ctx_, path.c_str(), array_schema);
}

Expand Down Expand Up @@ -348,7 +348,7 @@ int ArraySchemaFx::array_schema_load_wrapper(
return tiledb_array_schema_load(ctx_, path.c_str(), array_schema);
#endif

if (!serialize_array_schema) {
if (!serialize_array_schema_) {
return tiledb_array_schema_load(ctx_, path.c_str(), array_schema);
}

Expand Down Expand Up @@ -408,7 +408,7 @@ int ArraySchemaFx::array_get_schema_wrapper(
return tiledb_array_get_schema(ctx_, array, array_schema);
#endif

if (!serialize_array_schema) {
if (!serialize_array_schema_) {
return tiledb_array_get_schema(ctx_, array, array_schema);
}

Expand Down Expand Up @@ -467,7 +467,7 @@ int ArraySchemaFx::array_schema_get_domain_wrapper(
return tiledb_array_schema_get_domain(ctx_, array_schema, domain);
#endif

if (!serialize_array_schema) {
if (!serialize_array_schema_) {
return tiledb_array_schema_get_domain(ctx_, array_schema, domain);
}

Expand Down Expand Up @@ -565,6 +565,32 @@ void ArraySchemaFx::create_array(const std::string& path) {
&d4);
REQUIRE(rc == TILEDB_ERR);

// Set up filters
tiledb_filter_t* filter;
rc = tiledb_filter_alloc(ctx_, TILEDB_FILTER_BZIP2, &filter);
REQUIRE(rc == TILEDB_OK);
int level = 5;
rc = tiledb_filter_set_option(ctx_, filter, TILEDB_COMPRESSION_LEVEL, &level);
REQUIRE(rc == TILEDB_OK);
tiledb_filter_list_t* filter_list;
rc = tiledb_filter_list_alloc(ctx_, &filter_list);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_filter_list_add_filter(ctx_, filter_list, filter);
REQUIRE(rc == TILEDB_OK);
tiledb_filter_free(&filter);
rc = tiledb_filter_alloc(ctx_, TILEDB_FILTER_BIT_WIDTH_REDUCTION, &filter);
REQUIRE(rc == TILEDB_OK);
int window = 1000;
rc = tiledb_filter_set_option(
ctx_, filter, TILEDB_BIT_WIDTH_MAX_WINDOW, &window);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_filter_list_add_filter(ctx_, filter_list, filter);
REQUIRE(rc == TILEDB_OK);

// Add filters to dimension
rc = tiledb_dimension_set_filter_list(ctx_, d2, filter_list);
REQUIRE(rc == TILEDB_OK);

// Set domain
tiledb_domain_t* domain;
rc = tiledb_domain_alloc(ctx_, &domain);
Expand Down Expand Up @@ -600,6 +626,8 @@ void ArraySchemaFx::create_array(const std::string& path) {
tiledb_attribute_t* attr;
rc = tiledb_attribute_alloc(ctx_, ATTR_NAME, ATTR_TYPE, &attr);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_attribute_set_filter_list(ctx_, attr, filter_list);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_array_schema_add_attribute(ctx_, array_schema, attr);
REQUIRE(rc == TILEDB_OK);

Expand All @@ -616,6 +644,8 @@ void ArraySchemaFx::create_array(const std::string& path) {
REQUIRE(rc == TILEDB_ERR);

// Clean up
tiledb_filter_free(&filter);
tiledb_filter_list_free(&filter_list);
tiledb_array_schema_free(&array_schema);
tiledb_attribute_free(&attr);
tiledb_dimension_free(&d1);
Expand Down Expand Up @@ -713,7 +743,7 @@ void ArraySchemaFx::load_and_check_array_schema(const std::string& path) {
rc = tiledb_attribute_get_filter_list(ctx_, attr, &attr_filters);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_filter_list_get_nfilters(ctx_, attr_filters, &nfilters);
CHECK(nfilters == 0);
CHECK(nfilters == 2);
tiledb_filter_list_free(&attr_filters);

unsigned int cell_val_num;
Expand Down Expand Up @@ -805,21 +835,23 @@ void ArraySchemaFx::load_and_check_array_schema(const std::string& path) {
"- Cell order: " + CELL_ORDER_STR + "\n" +
"- Tile order: " + TILE_ORDER_STR + "\n" + "- Capacity: " + CAPACITY_STR +
"\n"
"- Coordinates compressor: ZSTD\n" +
"- Coordinates compression level: -1\n\n" +
"=== Domain ===\n"
"- Dimensions type: " +
DIM_TYPE_STR + "\n\n" + "### Dimension ###\n" + "- Name: " + DIM1_NAME +
"\n" + "- Domain: " + DIM1_DOMAIN_STR + "\n" +
"- Tile extent: " + DIM1_TILE_EXTENT_STR + "\n" + "\n" +
"- Allows duplicates: " +
"false\n"
"- Coordinates filters: 1\n" +
" > ZSTD: COMPRESSION_LEVEL=-1\n" + "- Offsets filters: 1\n" +
" > ZSTD: COMPRESSION_LEVEL=-1\n\n" + "### Dimension ###\n" +
"- Name: " + DIM1_NAME + "\n" + "- Domain: " + DIM1_DOMAIN_STR + "\n" +
"- Tile extent: " + DIM1_TILE_EXTENT_STR + "\n" + "- Filters: 0\n\n" +
"### Dimension ###\n" + "- Name: " + DIM2_NAME + "\n" +
"- Domain: " + DIM2_DOMAIN_STR + "\n" +
"- Tile extent: " + DIM2_TILE_EXTENT_STR + "\n" + "\n" +
"- Tile extent: " + DIM2_TILE_EXTENT_STR + "\n" + "- Filters: 2\n" +
" > BZIP2: COMPRESSION_LEVEL=5\n" +
" > BitWidthReduction: BIT_WIDTH_MAX_WINDOW=1000\n\n" +
"### Attribute ###\n" + "- Name: " + ATTR_NAME + "\n" +
"- Type: " + ATTR_TYPE_STR + "\n" +
"- Compressor: " + ATTR_COMPRESSOR_STR + "\n" +
"- Compression level: " + ATTR_COMPRESSION_LEVEL_STR + "\n" +
"- Cell val num: " + CELL_VAL_NUM_STR + "\n";
"- Cell val num: " + CELL_VAL_NUM_STR + "\n" + "- Filters: 2\n" +
" > BZIP2: COMPRESSION_LEVEL=5\n" +
" > BitWidthReduction: BIT_WIDTH_MAX_WINDOW=1000\n";
FILE* gold_fout = fopen("gold_fout.txt", "w");
const char* dump = dump_str.c_str();
fwrite(dump, sizeof(char), strlen(dump), gold_fout);
Expand Down Expand Up @@ -852,12 +884,12 @@ std::string ArraySchemaFx::random_name(const std::string& prefix) {
TEST_CASE_METHOD(
ArraySchemaFx,
"C API: Test array schema creation and retrieval",
"[capi], [array-schema]") {
"[capi][array-schema]") {
SECTION("- No serialization") {
serialize_array_schema = false;
serialize_array_schema_ = false;
}
SECTION("- Serialization") {
serialize_array_schema = true;
serialize_array_schema_ = true;
}

std::string array_name;
Expand Down Expand Up @@ -1069,10 +1101,10 @@ TEST_CASE_METHOD(
"C API: Test array schema offsets/coords filter lists",
"[capi], [array-schema], [filter]") {
SECTION("- No serialization") {
serialize_array_schema = false;
serialize_array_schema_ = false;
}
SECTION("- Serialization") {
serialize_array_schema = true;
serialize_array_schema_ = true;
}

// Create array schema
Expand Down Expand Up @@ -1210,10 +1242,10 @@ TEST_CASE_METHOD(
"C API: Test array schema load error condition",
"[capi], [array-schema]") {
SECTION("- No serialization") {
serialize_array_schema = false;
serialize_array_schema_ = false;
}
SECTION("- Serialization") {
serialize_array_schema = true;
serialize_array_schema_ = true;
}

// Create array schema
Expand Down Expand Up @@ -1300,10 +1332,10 @@ TEST_CASE_METHOD(
"C API: Test array schema datetimes",
"[capi][array-schema][datetime]") {
SECTION("- No serialization") {
serialize_array_schema = false;
serialize_array_schema_ = false;
}
SECTION("- Serialization") {
serialize_array_schema = true;
serialize_array_schema_ = true;
}

// Create array schema
Expand Down Expand Up @@ -1359,10 +1391,10 @@ TEST_CASE_METHOD(
"C API: Test array schema setter/getter for allows_dups",
"[capi][array-schema][allows-dups]") {
SECTION("- No serialization") {
serialize_array_schema = false;
serialize_array_schema_ = false;
}
SECTION("- Serialization") {
serialize_array_schema = true;
serialize_array_schema_ = true;
}

// --- Test dense (should error out on allowing duplicates) ---
Expand Down Expand Up @@ -1435,3 +1467,156 @@ TEST_CASE_METHOD(
delete_array(array_name);
remove_temp_dir(FILE_URI_PREFIX + FILE_TEMP_DIR);
}

TEST_CASE_METHOD(
ArraySchemaFx,
"C API: Test array schema setter/getter for dimension filters and cell val "
"num",
"[capi][array-schema][dimension]") {
SECTION("- No serialization") {
serialize_array_schema_ = false;
}
SECTION("- Serialization") {
serialize_array_schema_ = true;
}

// Allocate array schema
tiledb_array_schema_t* array_schema;
int rc = tiledb_array_schema_alloc(ctx_, TILEDB_SPARSE, &array_schema);
REQUIRE(rc == TILEDB_OK);

// Set up filter list
tiledb_filter_t* filter;
rc = tiledb_filter_alloc(ctx_, TILEDB_FILTER_BZIP2, &filter);
REQUIRE(rc == TILEDB_OK);
int level = 5;
rc = tiledb_filter_set_option(ctx_, filter, TILEDB_COMPRESSION_LEVEL, &level);
REQUIRE(rc == TILEDB_OK);
tiledb_filter_list_t* filter_list;
rc = tiledb_filter_list_alloc(ctx_, &filter_list);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_filter_list_add_filter(ctx_, filter_list, filter);
REQUIRE(rc == TILEDB_OK);

// Create dimension
tiledb_dimension_t* d;
rc = tiledb_dimension_alloc(
ctx_, "d", TILEDB_INT64, &DIM_DOMAIN[0], &TILE_EXTENTS[0], &d);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_dimension_set_cell_val_num(ctx_, d, 3);
CHECK(rc == TILEDB_ERR);
rc = tiledb_dimension_set_cell_val_num(ctx_, d, 1);
CHECK(rc == TILEDB_OK);
rc = tiledb_dimension_set_filter_list(ctx_, d, filter_list);
CHECK(rc == TILEDB_OK);

// Set domain
tiledb_domain_t* domain;
rc = tiledb_domain_alloc(ctx_, &domain);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_domain_add_dimension(ctx_, domain, d);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_array_schema_set_domain(ctx_, array_schema, domain);
REQUIRE(rc == TILEDB_OK);

// Set attribute
tiledb_attribute_t* a;
rc = tiledb_attribute_alloc(ctx_, "a", ATTR_TYPE, &a);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_array_schema_add_attribute(ctx_, array_schema, a);
REQUIRE(rc == TILEDB_OK);

// Create array
std::string array_name = FILE_URI_PREFIX + FILE_TEMP_DIR + "dimension";
create_temp_dir(FILE_URI_PREFIX + FILE_TEMP_DIR);
rc = array_create_wrapper(array_name, array_schema);
REQUIRE(rc == TILEDB_OK);

// Clean up
tiledb_filter_free(&filter);
tiledb_filter_list_free(&filter_list);
tiledb_attribute_free(&a);
tiledb_dimension_free(&d);
tiledb_domain_free(&domain);
tiledb_array_schema_free(&array_schema);

// Load array schema
rc = array_schema_load_wrapper(array_name.c_str(), &array_schema);
REQUIRE(rc == TILEDB_OK);

// Get dimension
rc = tiledb_array_schema_get_domain(ctx_, array_schema, &domain);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_domain_get_dimension_from_index(ctx_, domain, 0, &d);
REQUIRE(rc == TILEDB_OK);

// Check cell val num
unsigned num;
rc = tiledb_dimension_get_cell_val_num(ctx_, d, &num);
REQUIRE(rc == TILEDB_OK);
CHECK(num == 1);

// Check filter list
rc = tiledb_dimension_get_filter_list(ctx_, d, &filter_list);
REQUIRE(rc == TILEDB_OK);
uint32_t nfilters;
rc = tiledb_filter_list_get_nfilters(ctx_, filter_list, &nfilters);
CHECK(nfilters == 1);
rc = tiledb_filter_list_get_filter_from_index(ctx_, filter_list, 0, &filter);
REQUIRE(rc == TILEDB_OK);
tiledb_filter_type_t type;
rc = tiledb_filter_get_type(ctx_, filter, &type);
REQUIRE(rc == TILEDB_OK);
REQUIRE(type == TILEDB_FILTER_BZIP2);
int read_level;
rc = tiledb_filter_get_option(
ctx_, filter, TILEDB_COMPRESSION_LEVEL, &read_level);
REQUIRE(rc == TILEDB_OK);
REQUIRE(read_level == level);

// Clean up
tiledb_filter_free(&filter);
tiledb_filter_list_free(&filter_list);
tiledb_dimension_free(&d);
tiledb_domain_free(&domain);
tiledb_array_schema_free(&array_schema);
delete_array(array_name);
remove_temp_dir(FILE_URI_PREFIX + FILE_TEMP_DIR);
}

TEST_CASE_METHOD(
ArraySchemaFx,
"C API: Test array schema, set filter errors",
"[capi][array-schema][filter-error]") {
// Set up filter list
tiledb_filter_t* filter;
int rc = tiledb_filter_alloc(ctx_, TILEDB_FILTER_DOUBLE_DELTA, &filter);
REQUIRE(rc == TILEDB_OK);
tiledb_filter_list_t* filter_list;
rc = tiledb_filter_list_alloc(ctx_, &filter_list);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_filter_list_add_filter(ctx_, filter_list, filter);
REQUIRE(rc == TILEDB_OK);

// Create real dimension and test double delta
tiledb_dimension_t* d;
float domain[] = {1.0f, 2.0f};
float extent = .5f;
rc = tiledb_dimension_alloc(ctx_, "d", TILEDB_FLOAT32, domain, &extent, &d);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_dimension_set_filter_list(ctx_, d, filter_list);
CHECK(rc == TILEDB_ERR);

// Create real attribute and test double delta
tiledb_attribute_t* a;
rc = tiledb_attribute_alloc(ctx_, "a", TILEDB_FLOAT64, &a);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_attribute_set_filter_list(ctx_, a, filter_list);
CHECK(rc == TILEDB_ERR);

// Clean up
tiledb_filter_free(&filter);
tiledb_filter_list_free(&filter_list);
tiledb_attribute_free(&a);
tiledb_dimension_free(&d);
}
2 changes: 1 addition & 1 deletion test/src/unit-capi-dense_array.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -3355,7 +3355,7 @@ TEST_CASE_METHOD(
TEST_CASE_METHOD(
DenseArrayFx,
"C API: Test dense array, simultaneous writes",
"[capi], [dense], [dense-simultaneous-writes]") {
"[capi][dense][dense-simultaneous-writes]") {
SECTION("- No serialization") {
serialize_query_ = false;
}
Expand Down
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