Add arbitrary fill value support

HISTORY.md

@@ -6,6 +6,8 @@
 
 ## Breaking behavior
 
+* Empty dense arrays now return cells with fill values.
+
 ## New features
 
 ## Improvements
@@ -14,8 +16,18 @@
 
 ## Bug fixes
 
+* Fixed bug in setting a fill value for var-sized attributes.
+
 ## API additions
 
+### C API
+
+* Added functions `tiledb_attribute_{set,get}_fill_value` to get/set default fill values
+
+### C++ API
+
+* Added functions `Attribute::{set,get}_fill_value` to get/set default fill values
+
 # TileDB v2.0.2 Release Notes
 
 ## Bug fixes

doc/source/c-api.rst

@@ -335,6 +335,10 @@ Attribute
     :project: TileDB-C
 .. doxygenfunction:: tiledb_attribute_dump
     :project: TileDB-C
+.. doxygenfunction:: tiledb_attribute_set_fill_value
+    :project: TileDB-C
+.. doxygenfunction:: tiledb_attribute_get_fill_value
+    :project: TileDB-C
 
 Domain
 ------

format_spec/array_schema.md

@@ -67,4 +67,6 @@ The attribute has internal format:
 | Attribute datatype | `uint8_t` | Datatype of the attribute values |
 | Cell val num | `uint32_t` | Number of attribute values per cell. For variable-length attributes, this is `std::numeric_limits<uint32_t>::max()` |
 | Filters | [Filter Pipeline](./filter_pipeline.md) | The filter pipeline used on attribute value tiles |
+| Fill value size | `uint64_t` | The size in bytes of the fill value |
+| Fill value | `uint8_t[]` | The fill value |
 

test/CMakeLists.txt

@@ -61,6 +61,7 @@ set(TILEDB_TEST_SOURCES
   src/unit-capi-empty-var-length.cc
   src/unit-capi-enum_values.cc
   src/unit-capi-error.cc
+  src/unit-capi-fill_values.cc
   src/unit-capi-filter.cc
   src/unit-capi-incomplete.cc
   src/unit-capi-incomplete-2.cc
@@ -119,6 +120,7 @@ if (TILEDB_CPP_API)
     src/unit-cppapi-consolidation.cc
     src/unit-cppapi-consolidation-sparse.cc
     src/unit-cppapi-datetimes.cc
+    src/unit-cppapi-fill_values.cc
     src/unit-cppapi-filter.cc
     src/unit-cppapi-metadata.cc
     src/unit-cppapi-query.cc

test/src/unit-capi-array.cc

@@ -939,7 +939,7 @@ TEST_CASE_METHOD(
   tiledb_query_free(&query);
 
   // Check correctness
-  int buffer_read_c[] = {1, 2, 3, 4, 50, 60, 70, 8, 9, 10};
+  int32_t buffer_read_c[] = {1, 2, 3, 4, 50, 60, 70, 8, 9, 10};
   CHECK(!std::memcmp(buffer_read, buffer_read_c, sizeof(buffer_read_c)));
   CHECK(buffer_read_size == sizeof(buffer_read_c));
 
@@ -987,7 +987,8 @@ TEST_CASE_METHOD(
   tiledb_query_free(&query);
 
   // Check correctness
-  CHECK(buffer_read_size == 0);  // Empty array
+  // Empty array still returns fill values
+  CHECK(buffer_read_size == 10 * sizeof(int32_t));
 
   // ---- READ AT TIMESTAMP BEFORE UPDATE ----
   buffer_read_size = sizeof(buffer_read);
@@ -1241,7 +1242,8 @@ TEST_CASE_METHOD(
   tiledb_query_free(&query);
 
   // Check correctness
-  CHECK(buffer_read_size == 0);  // Empty array
+  // Empty array still returns fill values
+  CHECK(buffer_read_size == 10 * sizeof(int32_t));
 
   // ---- READ AT THE WRITTEN TIMESTAMP ----
   buffer_read_size = sizeof(buffer_read);

test/src/unit-capi-array_schema.cc

@@ -979,7 +979,8 @@ void ArraySchemaFx::load_and_check_array_schema(const std::string& path) {
       "- Type: " + ATTR_TYPE_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";
+      "  > BitWidthReduction: BIT_WIDTH_MAX_WINDOW=1000\n" +
+      "- Fill value: -2147483648\n";
   FILE* gold_fout = fopen("gold_fout.txt", "w");
   const char* dump = dump_str.c_str();
   fwrite(dump, sizeof(char), strlen(dump), gold_fout);

test/src/unit-capi-consolidation.cc

@@ -4103,7 +4103,7 @@ TEST_CASE_METHOD(
   CHECK(status == TILEDB_COMPLETED);
 
   // Check buffers
-  CHECK(a_size == 0);
+  CHECK(a_size == 410 * sizeof(int32_t));
 
   // Close array
   rc = tiledb_array_close(ctx_, array);

test/src/unit-capi-error.cc

@@ -36,7 +36,7 @@
 
 #include <iostream>
 
-TEST_CASE("C API: Test error and error message", "[capi], [error]") {
+TEST_CASE("C API: Test error and error message", "[capi][error]") {
   tiledb_ctx_t* ctx;
   int rc = tiledb_ctx_alloc(nullptr, &ctx);
   CHECK(rc == TILEDB_OK);

test/src/unit-capi-fill_values.cc

@@ -0,0 +1,187 @@
+/**
+ * @file   unit-capi-fill_values.cc
+ *
+ * @section LICENSE
+ *
+ * The MIT License
+ *
+ * @copyright Copyright (c) 2017-2020 TileDB Inc.
+ * @copyright Copyright (c) 2016 MIT and Intel Corporation
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ *
+ * @section DESCRIPTION
+ *
+ * Tests the attribute fill values with the C API.
+ */
+
+#include "catch.hpp"
+#include "tiledb/sm/c_api/tiledb.h"
+
+#include <iostream>
+
+void check_dump(
+    tiledb_ctx_t* ctx, tiledb_attribute_t* a, const std::string& gold_out) {
+  FILE* gold_fout = fopen("gold_fout.txt", "w");
+  fwrite(gold_out.c_str(), sizeof(char), gold_out.size(), gold_fout);
+  fclose(gold_fout);
+  FILE* fout = fopen("fout.txt", "w");
+  tiledb_attribute_dump(ctx, a, fout);
+  fclose(fout);
+#ifdef _WIN32
+  CHECK(!system("FC gold_fout.txt fout.txt > nul"));
+#else
+  CHECK(!system("diff gold_fout.txt fout.txt"));
+#endif
+
+  // Clean up
+  tiledb_vfs_t* vfs;
+  tiledb_vfs_alloc(ctx, nullptr, &vfs);
+  CHECK(tiledb_vfs_remove_file(ctx, vfs, "gold_fout.txt") == TILEDB_OK);
+  CHECK(tiledb_vfs_remove_file(ctx, vfs, "fout.txt") == TILEDB_OK);
+  tiledb_vfs_free(&vfs);
+}
+
+TEST_CASE(
+    "C API: Test fill values, basic errors", "[capi][fill-values][basic]") {
+  int32_t value = 5;
+  uint64_t value_size = sizeof(int32_t);
+
+  tiledb_ctx_t* ctx;
+  int32_t rc = tiledb_ctx_alloc(nullptr, &ctx);
+  CHECK(rc == TILEDB_OK);
+
+  // Fixed-sized
+  tiledb_attribute_t* a;
+  rc = tiledb_attribute_alloc(ctx, "a", TILEDB_INT32, &a);
+  CHECK(rc == TILEDB_OK);
+
+  // Null value
+  rc = tiledb_attribute_set_fill_value(ctx, a, NULL, value_size);
+  CHECK(rc == TILEDB_ERR);
+
+  // Zero size
+  rc = tiledb_attribute_set_fill_value(ctx, a, &value, 0);
+  CHECK(rc == TILEDB_ERR);
+
+  // Wrong size
+  rc = tiledb_attribute_set_fill_value(ctx, a, &value, 100);
+  CHECK(rc == TILEDB_ERR);
+
+  // Get default
+  const void* value_ptr;
+  rc = tiledb_attribute_get_fill_value(ctx, a, &value_ptr, &value_size);
+  CHECK(rc == TILEDB_OK);
+  CHECK(*(const int32_t*)value_ptr == -2147483648);
+  CHECK(value_size == sizeof(int32_t));
+
+  // Check dump
+  std::string dump = std::string("### Attribute ###\n") + "- Name: a\n" +
+                     "- Type: INT32\n" + "- Cell val num: 1\n" +
+                     "- Filters: 0\n" + "- Fill value: -2147483648\n";
+  check_dump(ctx, a, dump);
+
+  // Correct setter
+  rc = tiledb_attribute_set_fill_value(ctx, a, &value, value_size);
+  CHECK(rc == TILEDB_OK);
+
+  // Get the set value
+  rc = tiledb_attribute_get_fill_value(ctx, a, &value_ptr, &value_size);
+  CHECK(rc == TILEDB_OK);
+  CHECK(*(const int32_t*)value_ptr == 5);
+  CHECK(value_size == sizeof(int32_t));
+
+  // Check dump
+  dump = std::string("### Attribute ###\n") + "- Name: a\n" +
+         "- Type: INT32\n" + "- Cell val num: 1\n" + "- Filters: 0\n" +
+         "- Fill value: 5\n";
+  check_dump(ctx, a, dump);
+
+  // Setting the cell val num, also sets the fill value to a new default
+  rc = tiledb_attribute_set_cell_val_num(ctx, a, 2);
+  CHECK(rc == TILEDB_OK);
+  rc = tiledb_attribute_get_fill_value(ctx, a, &value_ptr, &value_size);
+  CHECK(rc == TILEDB_OK);
+  CHECK(((const int32_t*)value_ptr)[0] == -2147483648);
+  CHECK(((const int32_t*)value_ptr)[1] == -2147483648);
+  CHECK(value_size == 2 * sizeof(int32_t));
+
+  // Check dump
+  dump = std::string("### Attribute ###\n") + "- Name: a\n" +
+         "- Type: INT32\n" + "- Cell val num: 2\n" + "- Filters: 0\n" +
+         "- Fill value: -2147483648, -2147483648\n";
+  check_dump(ctx, a, dump);
+
+  // Set a fill value that is comprised of two integers
+  int32_t value_2[2] = {1, 2};
+  rc = tiledb_attribute_set_fill_value(ctx, a, value_2, sizeof(value_2));
+  CHECK(rc == TILEDB_OK);
+
+  // Get the new value back
+  rc = tiledb_attribute_get_fill_value(ctx, a, &value_ptr, &value_size);
+  CHECK(rc == TILEDB_OK);
+  CHECK(((const int32_t*)value_ptr)[0] == 1);
+  CHECK(((const int32_t*)value_ptr)[1] == 2);
+  CHECK(value_size == 2 * sizeof(int32_t));
+
+  // Check dump
+  dump = std::string("### Attribute ###\n") + "- Name: a\n" +
+         "- Type: INT32\n" + "- Cell val num: 2\n" + "- Filters: 0\n" +
+         "- Fill value: 1, 2\n";
+  check_dump(ctx, a, dump);
+
+  // Make the attribute var-sized
+  rc = tiledb_attribute_set_cell_val_num(ctx, a, TILEDB_VAR_NUM);
+  CHECK(rc == TILEDB_OK);
+
+  // Check dump
+  dump = std::string("### Attribute ###\n") + "- Name: a\n" +
+         "- Type: INT32\n" + "- Cell val num: var\n" + "- Filters: 0\n" +
+         "- Fill value: -2147483648\n";
+  check_dump(ctx, a, dump);
+
+  // Get the default var-sized fill value
+  rc = tiledb_attribute_get_fill_value(ctx, a, &value_ptr, &value_size);
+  CHECK(rc == TILEDB_OK);
+  CHECK(*(const int32_t*)value_ptr == -2147483648);
+  CHECK(value_size == sizeof(int32_t));
+
+  // Set a new fill value for the var-sized attribute
+  int32_t value_3[3] = {1, 2, 3};
+  rc = tiledb_attribute_set_fill_value(ctx, a, value_3, sizeof(value_3));
+  CHECK(rc == TILEDB_OK);
+
+  // Get the new fill value
+  rc = tiledb_attribute_get_fill_value(ctx, a, &value_ptr, &value_size);
+  CHECK(rc == TILEDB_OK);
+  CHECK(((const int32_t*)value_ptr)[0] == 1);
+  CHECK(((const int32_t*)value_ptr)[1] == 2);
+  CHECK(((const int32_t*)value_ptr)[2] == 3);
+  CHECK(value_size == 3 * sizeof(int32_t));
+
+  // Check dump
+  dump = std::string("### Attribute ###\n") + "- Name: a\n" +
+         "- Type: INT32\n" + "- Cell val num: var\n" + "- Filters: 0\n" +
+         "- Fill value: 1, 2, 3\n";
+  check_dump(ctx, a, dump);
+
+  // Clean up
+  tiledb_ctx_free(&ctx);
+  tiledb_attribute_free(&a);
+}

test/src/unit-cppapi-array.cc

@@ -783,7 +783,7 @@ TEST_CASE("C++ API: Open array at", "[cppapi][open-array-at]") {
   query_r_at_0.submit();
   array_r_at_0.close();
   auto result = query_r_at_0.result_buffer_elements();
-  CHECK(result["a"].second == 0);
+  CHECK(result["a"].second == 4);  // Empty arrays return fill values
   CHECK(!std::equal(a_r_at_0.begin(), a_r_at_0.end(), a_w.begin()));
 
   // Read from later timestamp
@@ -885,7 +885,7 @@ TEST_CASE(
   query_r_at_0.submit();
   array_r_at_0.close();
   auto result = query_r_at_0.result_buffer_elements();
-  CHECK(result["a"].second == 0);
+  CHECK(result["a"].second == 4);  // Empty arrays return fill values
   CHECK(!std::equal(a_r_at_0.begin(), a_r_at_0.end(), a_w.begin()));
 
   // Read from later timestamp