update to TileDB-2.26.0 (#371)

* update to TileDB-2.26.0

* implement dump methods as ```toString()``` Overrides

Author: DimitrisStaratzis

build.gradle

@@ -9,7 +9,7 @@ plugins {
 }
 
 group 'io.tiledb'
-version '0.27.0-SNAPSHOT'
+version '0.28.0-SNAPSHOT'
 
 repositories {
     mavenCentral()

cmake/Modules/FindTileDB_EP.cmake

@@ -48,30 +48,30 @@ if (NOT TILEDB_FOUND)
     # Try to download prebuilt artifacts unless the user specifies to build from source
     if(DOWNLOAD_TILEDB_PREBUILT)
         if (WIN32) # Windows
-          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.25.0/tiledb-windows-x86_64-2.25.0-bbcbd3f.zip")
-          SET(DOWNLOAD_SHA1 "b2b8cdfefbcbb07296c86e52cb9a2979ef455d2a")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.26.0/tiledb-windows-x86_64-2.26.0-983b716.zip")
+          SET(DOWNLOAD_SHA1 "ee66c3f86d32aa1c88e233c25455141d764eff47")
         elseif(APPLE) # macOS
 
           if (CMAKE_OSX_ARCHITECTURES STREQUAL x86_64 OR CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)")
             message(STATUS "Building for intel mac")
 
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.25.0/tiledb-macos-x86_64-2.25.0-bbcbd3f.tar.gz")
-            SET(DOWNLOAD_SHA1 "9c799d7de64e78d9e95cfa7db95b569cd3d3c8b0")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.26.0/tiledb-macos-x86_64-2.26.0-983b716.tar.gz")
+            SET(DOWNLOAD_SHA1 "e218ef0c5c6bc7ce55e423f6ad63ca8dd0b7719e")
 
           elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64 OR CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm")
             message(STATUS "Building for apple silicon mac")
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.25.0/tiledb-macos-arm64-2.25.0-bbcbd3f.tar.gz")
-            SET(DOWNLOAD_SHA1 "c6a1ab5213c36e53dd8e6da87c18b8bc695c532d")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.26.0/tiledb-macos-arm64-2.26.0-983b716.tar.gz")
+            SET(DOWNLOAD_SHA1 "9372924a4e8945bdfddb5c9b1741233aa8ff504e")
           endif()
         else() # Linux
           if (USE_AVX2)
             message(STATUS "Using Linux binaries with AVX2")
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.25.0/tiledb-linux-x86_64-2.25.0-bbcbd3f.tar.gz")
-            SET(DOWNLOAD_SHA1 "1d789af5d88ce09edf60d16ea3988631e780252a")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.26.0/tiledb-linux-x86_64-2.26.0-983b716.tar.gz")
+            SET(DOWNLOAD_SHA1 "b2abfc91285653050a4cb743a71d7c2f2f9a89c4")
           else()
             message(STATUS "Using Linux binaries without AVX2")
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.25.0/tiledb-linux-x86_64-noavx2-2.25.0-bbcbd3f.tar.gz")
-            SET(DOWNLOAD_SHA1 "02f3b9951e5d21614ea0d577190161aed2b04240")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.26.0/tiledb-linux-x86_64-noavx2-2.26.0-983b716.tar.gz")
+            SET(DOWNLOAD_SHA1 "337da10f222afe3727166d92de66e480304179bb")
           endif()
         endif()
 

generate_tiledb_jni

@@ -97,13 +97,13 @@ fi
 
 # define the necessary macro constants
 # (removed during preprocessor macro expansion)
-g++ -dM -I ${prefix_dir}/include -x c++-header -E ${tiledb_header} ${tiledb_experimental_header} | grep "#define TILEDB" > swig/tiledb_generated.h ||
-  die "could not write ./swig/tiledb_generated.h tmp file"
-
-## remove system headers
-awk '!/#\s*include/ || /tiledb_/ || /tiledb\/api/ {print}' ${tiledb_header} ${tiledb_experimental_header} |
-   g++ -E -P -nostdinc++  -I "${prefix_dir}/include/tiledb" -I "${prefix_dir}/include/" -x c++ - >> swig/tiledb_generated.h ||
-   die "error generating temp combined swig/tiledb_generated.h header for swig generation"
+#g++ -dM -I ${prefix_dir}/include -x c++-header -E ${tiledb_header} ${tiledb_experimental_header} | grep "#define TILEDB" > swig/tiledb_generated.h ||
+#  die "could not write ./swig/tiledb_generated.h tmp file"
+#
+### remove system headers
+#awk '!/#\s*include/ || /tiledb_/ || /tiledb\/api/ {print}' ${tiledb_header} ${tiledb_experimental_header} |
+#   g++ -E -P -nostdinc++  -I "${prefix_dir}/include/tiledb" -I "${prefix_dir}/include/" -x c++ - >> swig/tiledb_generated.h ||
+#   die "error generating temp combined swig/tiledb_generated.h header for swig generation"
 
 # if existing libtiledb generated source exists, delete it
 cleanup_java() {

gradle.properties

@@ -1,5 +1,5 @@
 TILEDB_GIT_REPOSITORY=https://github.com/TileDB-Inc/TileDB
-TILEDB_GIT_TAG=2.25.0
+TILEDB_GIT_TAG=2.26.0
 TILEDB_VERBOSE=ON
 TILEDB_S3=ON
 TILEDB_AZURE=OFF

src/main/c/README.md

@@ -10,4 +10,4 @@ The `tiledb_wrap.cxx` file under this directory contains the auto-generated JNI
 The `tiledb_custom.cxx` file under this directory contains custom methods defined by the developer that are  not
 auto-generated. Any custom method that needs to be added should be put in this file. Also, the signature of the
 new custom method should be also put in the `tiledb.i` file under the `TileDB-Java/swig` dir. For implementation details,
-all `*_nio` methods (e.g. `tiledb_query_set_subarray_nio`) are good examples.
+all `*_nio` methods (e.g. `tiledb_query_set_offsets_buffer_nio`) are good examples.

src/main/c/custom/tiledb_custom.cxx

@@ -1110,25 +1110,6 @@ extern "C" {
     return jresult;
   }
 
-  SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1subarray_1nio(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jobject jarg3) {
-    void* buffer = (void *)jenv->GetDirectBufferAddress(jarg3);
-
-    jint jresult = 0 ;
-    tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
-    tiledb_query_t *arg2 = (tiledb_query_t *) 0 ;
-    void *arg3 = (void *) 0 ;
-    int32_t result;
-
-    (void)jenv;
-    (void)jcls;
-    arg1 = *(tiledb_ctx_t **)&jarg1;
-    arg2 = *(tiledb_query_t **)&jarg2;
-    arg3 = *(void **)&jarg3;
-    result = (int32_t)tiledb_query_set_subarray(arg1,arg2,buffer);
-    jresult = (jint)result;
-    return jresult;
-  }
-
   SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1data_1buffer_1nio(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3, jobject jarg4, jlong jarg5) {
     void* buffer = (void *)jenv->GetDirectBufferAddress(jarg4);