Merge pull request #9 from TileDB-Inc/dev

Release 0.6.0

.gitignore

@@ -1,4 +1,5 @@
 *.swp
+build/*
 core/bin/*
 core/obj/*
 core/lib/*

.travis.yml

@@ -10,8 +10,10 @@ env:
 install:
     # Install cmake, lcov, MPICH
     - sudo apt-get -y install cmake lcov mpich 
-    # Install zlib, OpenSSL, Gtest and LZ4
-    - sudo apt-get -y install zlib1g-dev libssl-dev libgtest-dev liblz4-dev
+    # Install zlib, bzip2 and LZ4
+    - sudo apt-get -y install zlib1g-dev libbz2-dev liblz4-dev
+    # Install OpenSSL and Gtest
+    - sudo apt-get -y install libssl-dev libgtest-dev
     # Install Zstandard
     - wget https://github.com/facebook/zstd/archive/v1.0.0.tar.gz
     - tar xf v1.0.0.tar.gz

CMakeLists.txt

@@ -79,6 +79,9 @@ set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} ${ZSTD_LIBRARIES})
 find_package(OpenSSL REQUIRED)
 include_directories(${OPENSSL_INCLUDE_DIR})
 set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} ${OPENSSL_LIBRARIES})
+find_package(Bzip2 REQUIRED)
+include_directories(${BZIP2_INCLUDE_DIR})
+set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} ${BZIP2_LIBRARIES})
 
 # Find optional library dependencies
 find_package(GTest)

README.md

@@ -1,10 +1,9 @@
 # TileDB
 
-[![Travis](https://img.shields.io/travis/Intel-HLS/TileDB.svg?maxAge=2592000)]
-(https://travis-ci.org/Intel-HLS/TileDB)
+[![Travis](https://travis-ci.org/TileDB-Inc/TileDB.svg?branch=master)](https://travis-ci.org/TileDB-Inc/TileDB)
 
 The installation guide for TileDB can be found at this [Github
-Wiki](https://github.com/Intel-HLS/TileDB/wiki).
+Wiki](https://github.com/TileDB-Inc/TileDB/wiki).
 
 The TileDB C API documentation and tutorials can be
-found at the [TileDB official website](http://istc-bigdata.org/tiledb).
+found at the [TileDB official website](http://www.tiledb.org).

cmake/Modules/FindBzip2.cmake

@@ -0,0 +1,64 @@
+#
+# FindBzip2.cmake
+#
+#
+# The MIT License
+#
+# 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.
+#
+# Finds the Bzip2 library. This module defines:
+#   - BZIP2_INCLUDE_DIR, directory containing headers
+#   - BZIP2_LIBRARIES, the Bzip2 library path
+#   - BZIP2_FOUND, whether Bzip2 has been found
+
+# Find header files  
+if(BZIP2_SEARCH_HEADER_PATHS)
+  find_path( 
+      BZIP2_INCLUDE_DIR bzip2.h 
+      PATHS ${BZIP2_SEARCH_HEADER_PATHS}   
+      NO_DEFAULT_PATH
+  )
+else()
+  find_path(BZIP2_INCLUDE_DIR bzlib.h)
+endif()
+
+# Find library
+if(BZIP2_SEARCH_LIB_PATH)
+  find_library(
+      BZIP2_LIBRARIES NAMES bz2
+      PATHS ${BZIP2_SEARCH_LIB_PATH}$
+      NO_DEFAULT_PATH
+  )
+else()
+  find_library(BZIP2_LIBRARIES NAMES bz2)
+endif()
+
+if(BZIP2_INCLUDE_DIR AND BZIP2_LIBRARIES)
+  message(STATUS "Found Bzip2: ${BZIP2_LIBRARIES}")
+  set(BZIP2_FOUND TRUE)
+else()
+  set(BZIP2_FOUND FALSE)
+endif()
+
+if(BZIP2_FIND_REQUIRED AND NOT BZIP2_FOUND)
+  message(FATAL_ERROR "Could not find the Bzip2 library.")
+endif()
+

core/include/array/array_schema.h

@@ -35,7 +35,6 @@
 
 #include "array_schema_c.h"
 #include "metadata_schema_c.h"
-#include "hilbert_curve.h"
 #include <limits>
 #include <string>
 #include <typeinfo>
@@ -416,7 +415,6 @@ class ArraySchema {
    * Sets the tile order. Supported tile orders. 
    *    - TILEDB_ROW_MAJOR
    *    - TILEDB_COL_MAJOR
-   *    - TILEDB_HILBSERT
    *
    * @param tile_order The tile order.
    * @return TILEDB_AS_OK for success, and TILEDB_AS_ERR for error.
@@ -432,12 +430,24 @@ class ArraySchema {
    *     - TILEDB_INT64
    *     - TILEDB_FLOAT32
    *     - TILEDB_FLOAT64
+   *     - TILEDB_INT8
+   *     - TILEDB_UINT8
+   *     - TILEDB_INT16
+   *     - TILEDB_UINT16
+   *     - TILEDB_UINT32
+   *     - TILEDB_UINT64
    *
    * The supported types for the coordinates are:
    *     - TILEDB_INT32
    *     - TILEDB_INT64
    *     - TILEDB_FLOAT32
    *     - TILEDB_FLOAT64
+   *     - TILEDB_INT8
+   *     - TILEDB_UINT8
+   *     - TILEDB_INT16
+   *     - TILEDB_UINT16
+   *     - TILEDB_UINT32
+   *     - TILEDB_UINT64
    *
    * @param types The types.
    * @return TILEDB_AS_OK for success, and TILEDB_AS_ERR for error.
@@ -609,16 +619,6 @@ class ArraySchema {
   template<class T>
   void get_tile_subarray(const T* tile_coords, T* tile_subarray) const;
 
-  /** 
-   * Returns the Hilbert id of the input coordinates. 
-   *
-   * @tparam T The coordinates type.
-   * @param coords The coordinates for which the Hilbert id is computed.
-   * @return The computed Hilbert id.
-   */
-  template<class T>
-  int64_t hilbert_id(const T* coords) const;
-
   /**
    * Checks the order of the input coordinates. First the tile order is checked
    * (which, in case of non-regular tiles, is always the same), breaking the
@@ -695,7 +695,6 @@ class ArraySchema {
    * The cell order. It can be one of the following:
    *    - TILEDB_ROW_MAJOR
    *    - TILEDB_COL_MAJOR
-   *    - TILEDB_HILBERT. 
    */
   int cell_order_;
   /** Stores the size of every attribute (plus coordinates in the end). */
@@ -721,10 +720,9 @@ class ArraySchema {
    *    - TILEDB_BLOSC_ZLIB 
    *    - TILEDB_BLOSC_ZSTD 
    *    - TILEDB_RLE 
+   *    - TILEDB_BZIP2 
    */
   std::vector<int> compression_;
-  /** Auxiliary variable used when calculating Hilbert ids. */
-  int* coords_for_hilbert_;
   /** The size (in bytes) of the coordinates. */
   size_t coords_size_;
   /** 
@@ -742,13 +740,6 @@ class ArraySchema {
    * type.
    */
   void* domain_;
-  /** 
-   * Number of bits used for the calculation of cell ids with the 
-   * Hilbert curve. 
-   */
-  int hilbert_bits_;
-  /** A Hilbert curve object for finding cell ids. */
-  HilbertCurve* hilbert_curve_;
   /**  
    * The array domain. It should contain one [lower, upper] pair per dimension. 
    * The type of the values stored in this buffer should match the coordinates
@@ -775,7 +766,7 @@ class ArraySchema {
   /** 
    * The tile order. It can be one of the following:
    *    - TILEDB_ROW_MAJOR
-   *    - TILEDB_COL_MAJOR. 
+   *    - TILEDB_COL_MAJOR 
    */
   int tile_order_;
   /** 
@@ -786,12 +777,24 @@ class ArraySchema {
    *    - TILEDB_FLOAT32
    *    - TILEDB_FLOAT64
    *    - TILEDB_CHAR 
+   *    - TILEDB_INT8
+   *    - TILEDB_UINT8
+   *    - TILEDB_INT16
+   *    - TILEDB_UINT16
+   *    - TILEDB_UINT32
+   *    - TILEDB_UINT64
    *
    * The coordinate type can be one of the following: 
    *    - TILEDB_INT32
    *    - TILEDB_INT64
    *    - TILEDB_FLOAT32
    *    - TILEDB_FLOAT64
+   *    - TILEDB_INT8
+   *    - TILEDB_UINT8
+   *    - TILEDB_INT16
+   *    - TILEDB_UINT16
+   *    - TILEDB_UINT32
+   *    - TILEDB_UINT64
    */
   std::vector<int> types_;
   /** Stores the size of every attribute type (plus coordinates in the end). */
@@ -831,15 +834,6 @@ class ArraySchema {
   /** Computes and returns the size of an attribute (or coordinates). */
   size_t compute_cell_size(int attribute_id) const;
 
-  /** 
-   * Computes the number of bits per dimension required by the Hilbert curve. 
-   *
-   * @tparam T The domain type.
-   * @return void
-   */
-  template<class T>
-  void compute_hilbert_bits();
-
   /**
    * Computes the tile domain. Applicable only to arrays with regular tiles. 
    *

core/include/array/array_schema_c.h

@@ -55,7 +55,6 @@ typedef struct ArraySchemaC {
    * The cell order. It can be one of the following:
    *    - TILEDB_ROW_MAJOR
    *    - TILEDB_COL_MAJOR
-   *    - TILEDB_HILBERT. 
    */
   int cell_order_;
   /**
@@ -79,6 +78,7 @@ typedef struct ArraySchemaC {
    *    - TILEDB_BLOSC_ZLIB 
    *    - TILEDB_BLOSC_ZSTD 
    *    - TILEDB_RLE 
+   *    - TILEDB_BZIP2 
    */
   int* compression_;
   /** 
@@ -117,12 +117,24 @@ typedef struct ArraySchemaC {
    *    - TILEDB_FLOAT32
    *    - TILEDB_FLOAT64
    *    - TILEDB_CHAR 
+   *    - TILEDB_INT8
+   *    - TILEDB_UINT8
+   *    - TILEDB_INT16
+   *    - TILEDB_UINT16
+   *    - TILEDB_UINT32
+   *    - TILEDB_UINT64
    *
    * The coordinate type can be one of the following: 
    *    - TILEDB_INT32
    *    - TILEDB_INT64
    *    - TILEDB_FLOAT32
    *    - TILEDB_FLOAT64
+   *    - TILEDB_INT8
+   *    - TILEDB_UINT8
+   *    - TILEDB_INT16
+   *    - TILEDB_UINT16
+   *    - TILEDB_UINT32
+   *    - TILEDB_UINT64
    */
   int* types_;
 } ArraySchemaC;

core/include/array/array_sorted_write_state.h

@@ -643,8 +643,8 @@ class ArraySortedWriteState {
 
   /**
    * Fills the **a single** cell in a variable-sized buffer of the current copy 
-   * tile slab with the input id with an empty value, based on the template t
-   * ype. Applicable only to variable-sized attributes.
+   * tile slab with the input id with an empty value, based on the template 
+   * type. Applicable only to variable-sized attributes.
    *
    * @tparam T The attribute type.
    * @param bid The buffer id corresponding to the targeted attribute.

core/include/c_api/tiledb.h

@@ -222,7 +222,6 @@ typedef struct TileDB_ArraySchema {
    * The cell order. It can be one of the following:
    *    - TILEDB_ROW_MAJOR
    *    - TILEDB_COL_MAJOR
-   *    - TILEDB_HILBERT. 
    */
   int cell_order_;
   /**
@@ -246,6 +245,7 @@ typedef struct TileDB_ArraySchema {
    *    - TILEDB_BLOSC_ZLIB 
    *    - TILEDB_BLOSC_ZSTD 
    *    - TILEDB_RLE
+   *    - TILEDB_BZIP2
    *
    * If it is *NULL*, then the default TILEDB_NO_COMPRESSION is used for all
    * attributes.
@@ -286,12 +286,24 @@ typedef struct TileDB_ArraySchema {
    *    - TILEDB_FLOAT32
    *    - TILEDB_FLOAT64
    *    - TILEDB_CHAR 
+   *    - TILEDB_INT8
+   *    - TILEDB_UINT8
+   *    - TILEDB_INT16
+   *    - TILEDB_UINT16
+   *    - TILEDB_UINT32
+   *    - TILEDB_UINT64
    *
    * The coordinate type can be one of the following: 
    *    - TILEDB_INT32
    *    - TILEDB_INT64
    *    - TILEDB_FLOAT32
    *    - TILEDB_FLOAT64
+   *    - TILEDB_INT8
+   *    - TILEDB_UINT8
+   *    - TILEDB_INT16
+   *    - TILEDB_UINT16
+   *    - TILEDB_UINT32
+   *    - TILEDB_UINT64
    */
   int* types_;
 } TileDB_ArraySchema;
@@ -759,6 +771,7 @@ typedef struct TileDB_MetadataSchema {
    *    - TILEDB_BLOSC_ZLIB 
    *    - TILEDB_BLOSC_ZSTD 
    *    - TILEDB_RLE
+   *    - TILEDB_BZIP2
    *
    * If it is *NULL*, then the default TILEDB_NO_COMPRESSION is used for all
    * attributes.
@@ -771,7 +784,13 @@ typedef struct TileDB_MetadataSchema {
    *    - TILEDB_INT64
    *    - TILEDB_FLOAT32
    *    - TILEDB_FLOAT64
-   *    - TILEDB_CHAR. 
+   *    - TILEDB_CHAR 
+   *    - TILEDB_INT8
+   *    - TILEDB_UINT8
+   *    - TILEDB_INT16
+   *    - TILEDB_UINT16
+   *    - TILEDB_UINT32
+   *    - TILEDB_UINT64
    */
   int* types_;
 } TileDB_MetadataSchema;
@@ -1084,6 +1103,22 @@ TILEDB_EXPORT int tiledb_metadata_iterator_finalize(
 /*       DIRECTORY MANAGEMENT        */
 /* ********************************* */
 
+/**
+ * Returns the type of the input directory. 
+ *
+ * @param tiledb_ctx The TileDB context.
+ * @param dir The input directory.
+ * @return It can be one of the following:
+ *    - TILEDB_WORKSPACE
+ *    - TILEDB_GROUP
+ *    - TILEDB_ARRAY
+ *    - TILEDB_METADATA
+ *    - -1 (none of the above) 
+ */
+TILEDB_EXPORT int tiledb_dir_type(
+    const TileDB_CTX* tiledb_ctx,
+    const char* dir);
+
 /**
  * Clears a TileDB directory. The corresponding TileDB object (workspace,
  * group, array, or metadata) will still exist after the execution of the