Merge pull request #4 from apache/master

Syncing from original

c_glib/arrow-glib/Makefile.am

@@ -16,6 +16,7 @@
 # under the License.
 
 CLEANFILES =
+DISTCLEANFILES =
 
 EXTRA_DIST =					\
 	meson.build
@@ -169,6 +170,10 @@ BUILT_SOURCES =					\
 	stamp-enums.c				\
 	stamp-enums.h
 
+DISTCLEANFILES +=				\
+	stamp-enums.c				\
+	stamp-enums.h
+
 EXTRA_DIST +=					\
 	enums.c.template			\
 	enums.h.template
@@ -214,7 +219,7 @@ INTROSPECTION_SCANNER_ARGS =
 INTROSPECTION_SCANNER_ENV =
 if USE_ARROW_BUILD_DIR
 INTROSPECTION_SCANNER_ENV +=			\
-	LD_LIBRARY_PATH=$(ARROW_LIB_DIR):$${PKG_CONFIG_PATH}
+	LD_LIBRARY_PATH=$(ARROW_LIB_DIR):$${LD_LIBRARY_PATH}
 endif
 if OS_MACOS
 INTROSPECTION_SCANNER_ENV +=			\

cpp/apidoc/HDFS.md

@@ -50,6 +50,10 @@ export CLASSPATH=`$HADOOP_HOME/bin/hadoop classpath --glob`
 * `ARROW_LIBHDFS_DIR` (optional): explicit location of `libhdfs.so` if it is
 installed somewhere other than `$HADOOP_HOME/lib/native`.
 
+To accommodate distribution-specific nuances, the `JAVA_HOME` variable may be
+set to the root path for the Java SDK, the JRE path itself, or to the directory
+containing the `libjvm` library.
+
 ### Mac Specifics
 
 The installed location of Java on OS X can vary, however the following snippet

cpp/cmake_modules/FindParquet.cmake

@@ -60,8 +60,22 @@ if(PARQUET_HOME)
         PATHS ${PARQUET_HOME} NO_DEFAULT_PATH
         PATH_SUFFIXES "lib")
     get_filename_component(PARQUET_LIBS ${PARQUET_LIBRARIES} PATH )
-    set(PARQUET_ABI_VERSION "1.0.0")
-    set(PARQUET_SO_VERSION "1")
+
+    # Try to autodiscover the Parquet ABI version
+    get_filename_component(PARQUET_LIB_REALPATH ${PARQUET_LIBRARIES} REALPATH)
+    get_filename_component(PARQUET_EXT_REALPATH ${PARQUET_LIB_REALPATH} EXT)
+    string(REGEX MATCH ".([0-9]+.[0-9]+.[0-9]+)" HAS_ABI_VERSION ${PARQUET_EXT_REALPATH})
+    if (HAS_ABI_VERSION)
+      if (APPLE)
+        string(REGEX REPLACE ".([0-9]+.[0-9]+.[0-9]+).dylib" "\\1" PARQUET_ABI_VERSION ${PARQUET_EXT_REALPATH})
+      else()
+        string(REGEX REPLACE ".so.([0-9]+.[0-9]+.[0-9]+)" "\\1" PARQUET_ABI_VERSION ${PARQUET_EXT_REALPATH})
+      endif()
+      string(REGEX REPLACE "([0-9]+).[0-9]+.[0-9]+" "\\1" PARQUET_SO_VERSION ${PARQUET_ABI_VERSION})
+    else()
+      set(PARQUET_ABI_VERSION "1.0.0")
+      set(PARQUET_SO_VERSION "1")
+    endif()
 else()
     pkg_check_modules(PARQUET parquet)
     if (PARQUET_FOUND)

cpp/src/arrow/buffer-test.cc

@@ -194,4 +194,29 @@ TEST(TestBuffer, SliceMutableBuffer) {
   ASSERT_TRUE(slice->Equals(expected));
 }
 
+TEST(TestBufferBuilder, ResizeReserve) {
+  const std::string data = "some data";
+  auto data_ptr = data.c_str();
+
+  BufferBuilder builder;
+
+  ASSERT_OK(builder.Append(data_ptr, 9));
+  ASSERT_EQ(9, builder.length());
+
+  ASSERT_OK(builder.Resize(128));
+  ASSERT_EQ(128, builder.capacity());
+
+  // Do not shrink to fit
+  ASSERT_OK(builder.Resize(64, false));
+  ASSERT_EQ(128, builder.capacity());
+
+  // Shrink to fit
+  ASSERT_OK(builder.Resize(64));
+  ASSERT_EQ(64, builder.capacity());
+
+  // Reserve elements
+  ASSERT_OK(builder.Reserve(60));
+  ASSERT_EQ(128, builder.capacity());
+}
+
 }  // namespace arrow

cpp/src/arrow/buffer.h

@@ -25,20 +25,20 @@
 #include <string>
 #include <type_traits>
 
+#include "arrow/memory_pool.h"
 #include "arrow/status.h"
 #include "arrow/util/bit-util.h"
 #include "arrow/util/macros.h"
 #include "arrow/util/visibility.h"
 
 namespace arrow {
 
-class MemoryPool;
-
 // ----------------------------------------------------------------------
 // Buffer classes
 
-/// Immutable API for a chunk of bytes which may or may not be owned by the
-/// class instance.
+/// \class Buffer
+/// \brief Object containing a pointer to a piece of contiguous memory with a
+/// particular size. Base class does not own its memory
 ///
 /// Buffers have two related notions of length: size and capacity. Size is
 /// the number of bytes that might have valid data. Capacity is the number
@@ -133,7 +133,8 @@ ARROW_EXPORT
 std::shared_ptr<Buffer> SliceMutableBuffer(const std::shared_ptr<Buffer>& buffer,
                                            const int64_t offset, const int64_t length);
 
-/// A Buffer whose contents can be mutated. May or may not own its data.
+/// \class MutableBuffer
+/// \brief A Buffer whose contents can be mutated. May or may not own its data.
 class ARROW_EXPORT MutableBuffer : public Buffer {
  public:
   MutableBuffer(uint8_t* data, const int64_t size) : Buffer(data, size) {
@@ -148,6 +149,8 @@ class ARROW_EXPORT MutableBuffer : public Buffer {
   MutableBuffer() : Buffer(NULLPTR, 0) {}
 };
 
+/// \class ResizableBuffer
+/// \brief A mutable buffer that can be resized
 class ARROW_EXPORT ResizableBuffer : public MutableBuffer {
  public:
   /// Change buffer reported size to indicated size, allocating memory if
@@ -190,13 +193,22 @@ class ARROW_EXPORT PoolBuffer : public ResizableBuffer {
   MemoryPool* pool_;
 };
 
+/// \class BufferBuilder
+/// \brief A class for incrementally building a contiguous chunk of in-memory data
 class ARROW_EXPORT BufferBuilder {
  public:
-  explicit BufferBuilder(MemoryPool* pool)
+  explicit BufferBuilder(MemoryPool* pool ARROW_MEMORY_POOL_DEFAULT)
       : pool_(pool), data_(NULLPTR), capacity_(0), size_(0) {}
 
-  /// Resizes the buffer to the nearest multiple of 64 bytes per Layout.md
-  Status Resize(const int64_t elements) {
+  /// \brief Resizes the buffer to the nearest multiple of 64 bytes
+  ///
+  /// \param elements the new capacity of the of the builder. Will be rounded
+  /// up to a multiple of 64 bytes for padding
+  /// \param shrink_to_fit if new capacity smaller than existing size,
+  /// reallocate internal buffer. Set to false to avoid reallocations when
+  /// shrinking the builder
+  /// \return Status
+  Status Resize(const int64_t elements, bool shrink_to_fit = true) {
     // Resize(0) is a no-op
     if (elements == 0) {
       return Status::OK();
@@ -205,7 +217,7 @@ class ARROW_EXPORT BufferBuilder {
       buffer_ = std::make_shared<PoolBuffer>(pool_);
     }
     int64_t old_capacity = capacity_;
-    RETURN_NOT_OK(buffer_->Resize(elements));
+    RETURN_NOT_OK(buffer_->Resize(elements, shrink_to_fit));
     capacity_ = buffer_->capacity();
     data_ = buffer_->mutable_data();
     if (capacity_ > old_capacity) {
@@ -214,7 +226,14 @@ class ARROW_EXPORT BufferBuilder {
     return Status::OK();
   }
 
-  Status Append(const uint8_t* data, int64_t length) {
+  /// \brief Ensure that builder can accommodate the additional number of bytes
+  /// without the need to perform allocations
+  ///
+  /// \param size number of additional bytes to make space for
+  /// \return Status
+  Status Reserve(const int64_t size) { return Resize(size_ + size, false); }
+
+  Status Append(const void* data, int64_t length) {
     if (capacity_ < length + size_) {
       int64_t new_capacity = BitUtil::NextPower2(length + size_);
       RETURN_NOT_OK(Resize(new_capacity));
@@ -248,7 +267,7 @@ class ARROW_EXPORT BufferBuilder {
   }
 
   // Unsafe methods don't check existing size
-  void UnsafeAppend(const uint8_t* data, int64_t length) {
+  void UnsafeAppend(const void* data, int64_t length) {
     memcpy(data_ + size_, data, static_cast<size_t>(length));
     size_ += length;
   }

cpp/src/arrow/io/hdfs-internal.cc

@@ -147,7 +147,7 @@ static std::vector<fs::path> get_potential_libjvm_paths() {
   file_name = "jvm.dll";
 #elif __APPLE__
   search_prefixes = {""};
-  search_suffixes = {"", "/jre/lib/server"};
+  search_suffixes = {"", "/jre/lib/server", "/lib/server"};
   file_name = "libjvm.dylib";
 
 // SFrame uses /usr/libexec/java_home to find JAVA_HOME; for now we are
@@ -175,7 +175,7 @@ static std::vector<fs::path> get_potential_libjvm_paths() {
       "/usr/lib/jvm/default",                     // alt centos
       "/usr/java/latest",                         // alt centos
   };
-  search_suffixes = {"/jre/lib/amd64/server"};
+  search_suffixes = {"", "/jre/lib/amd64/server", "/lib/amd64/server"};
   file_name = "libjvm.so";
 #endif
   // From direct environment variable

dev/docker-compose.yml

@@ -17,7 +17,7 @@
 version: '3'
 services:
   gen_apidocs:
-    build: 
+    build:
       context: gen_apidocs
     volumes:
      - ../..:/apache-arrow
@@ -29,7 +29,7 @@ services:
     volumes:
      - ../..:/apache-arrow
   dask_integration:
-    build: 
+    build:
       context: dask_integration
     volumes:
      - ../..:/apache-arrow

dev/gen_apidocs/Dockerfile

@@ -14,19 +14,24 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-FROM ubuntu:14.04
-# Prerequsites for apt-add-repository
-RUN apt-get update && apt-get install -y \
-    software-properties-common python-software-properties
+FROM ubuntu:16.04
+
 # Basic OS dependencies
-RUN apt-add-repository -y ppa:ubuntu-toolchain-r/test && \
-    apt-get update && apt-get install -y \
+RUN apt-get update && apt-get install -y \
         wget \
         rsync \
         git \
         gcc-4.9 \
         g++-4.9 \
-        build-essential
+        build-essential \
+        software-properties-common
+
+# Java build fails with default JDK8
+RUN add-apt-repository ppa:openjdk-r/ppa &&\
+    apt-get update &&\
+    apt-get install -y openjdk-7-jdk &&\
+    update-java-alternatives -s java-1.7.0-openjdk-amd64
+
 # This will install conda in /home/ubuntu/miniconda
 RUN wget -O /tmp/miniconda.sh \
     https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
@@ -73,6 +78,7 @@ RUN /home/ubuntu/miniconda/bin/conda create -y -q -n pyarrow-dev \
         doxygen \
         maven \
         -c conda-forge
+
 ADD . /apache-arrow
 WORKDIR /apache-arrow
 CMD arrow/dev/gen_apidocs/create_documents.sh

dev/gen_apidocs/create_documents.sh

@@ -27,6 +27,7 @@ export ARROW_HOME=$(pwd)/dist
 export PARQUET_HOME=$(pwd)/dist
 CONDA_BASE=/home/ubuntu/miniconda
 export LD_LIBRARY_PATH=$(pwd)/dist/lib:${CONDA_BASE}/lib:${LD_LIBRARY_PATH}
+export PKG_CONFIG_PATH=$(pwd)/dist/lib/pkgconfig:${PKG_CONFIG_PATH}
 export PATH=${CONDA_BASE}/bin:${PATH}
 
 # Prepare the asf-site before copying api docs
@@ -38,16 +39,38 @@ git clone --branch=asf-site \
     https://git-wip-us.apache.org/repos/asf/arrow-site.git asf-site
 popd
 
+# Make Java documentation
+export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
+wget http://mirrors.gigenet.com/apache/maven/maven-3/3.5.2/binaries/apache-maven-3.5.2-bin.tar.gz
+tar xvf apache-maven-3.5.2-bin.tar.gz
+export PATH=$(pwd)/apache-maven-3.5.2/bin:$PATH
+
+pushd arrow/java
+rm -rf target/site/apidocs/*
+mvn -Drat.skip=true install
+mvn -Drat.skip=true site
+mkdir -p ../site/asf-site/docs/java/
+rsync -r target/site/apidocs/ ../site/asf-site/docs/java/
+popd
+
 # Make Python documentation (Depends on C++ )
 # Build Arrow C++
 source activate pyarrow-dev
 
 export ARROW_BUILD_TOOLCHAIN=$CONDA_PREFIX
+export BOOST_ROOT=$CONDA_PREFIX
 export PARQUET_BUILD_TOOLCHAIN=$CONDA_PREFIX
+export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:${LD_LIBRARY_PATH}
+export PKG_CONFIG_PATH=$CONDA_PREFIX/lib/pkgconfig:${PKG_CONFIG_PATH}
+
+export CC=gcc-4.9
+export CXX=g++-4.9
 
-rm -rf arrow/cpp/build_docs
-mkdir arrow/cpp/build_docs
-pushd arrow/cpp/build_docs
+CPP_BUILD_DIR=$(pwd)/arrow/cpp/build_docs
+
+rm -rf $CPP_BUILD_DIR
+mkdir $CPP_BUILD_DIR
+pushd $CPP_BUILD_DIR
 cmake -DCMAKE_BUILD_TYPE=$ARROW_BUILD_TYPE \
       -DCMAKE_INSTALL_PREFIX=$ARROW_HOME \
       -DARROW_PYTHON=on \
@@ -58,6 +81,28 @@ make -j4
 make install
 popd
 
+# Build c_glib documentation
+pushd arrow/c_glib
+if [ -f Makefile ]; then
+    # Ensure updating to prevent auto re-configure
+    touch configure **/Makefile
+    make distclean
+    # Work around for 'make distclean' removes doc/reference/xml/
+    git checkout doc/reference/xml
+fi
+./autogen.sh
+rm -rf build_docs
+mkdir build_docs
+pushd build_docs
+../configure \
+    --prefix=${AROW_HOME} \
+    --enable-gtk-doc
+make -j4 GTK_DOC_V_XREF=": "
+mkdir -p ../../site/asf-site/docs/c_glib
+rsync -r doc/reference/html/ ../../site/asf-site/docs/c_glib
+popd
+popd
+
 # Build Parquet C++
 rm -rf parquet-cpp/build_docs
 mkdir parquet-cpp/build_docs
@@ -83,32 +128,10 @@ mkdir -p ../site/asf-site/docs/python
 rsync -r doc/_build/html/ ../site/asf-site/docs/python
 popd
 
-# Build c_glib documentation
-pushd arrow/c_glib
-rm -rf doc/reference/html/*
-./autogen.sh
-./configure \
-    --with-arrow-cpp-build-dir=$(pwd)/../cpp/build \
-    --with-arrow-cpp-build-type=$ARROW_BUILD_TYPE \
-    --enable-gtk-doc
-LD_LIBRARY_PATH=$(pwd)/../cpp/build/$ARROW_BUILD_TYPE make GTK_DOC_V_XREF=": "
-mkdir -p ../site/asf-site/docs/c_glib
-rsync -r doc/reference/html/ ../site/asf-site/docs/c_glib
-popd
-
 # Make C++ documentation
 pushd arrow/cpp/apidoc
 rm -rf html/*
 doxygen Doxyfile
 mkdir -p ../../site/asf-site/docs/cpp
 rsync -r html/ ../../site/asf-site/docs/cpp
 popd
-
-# Make Java documentation
-pushd arrow/java
-rm -rf target/site/apidocs/*
-mvn -Drat.skip=true install
-mvn -Drat.skip=true site
-mkdir -p ../site/asf-site/docs/java/
-rsync -r target/site/apidocs/ ../site/asf-site/docs/java/
-popd