update to TileDB-2.17.3 and add support for Enum extend

Author: DimitrisStaratzis

build.gradle

@@ -9,7 +9,7 @@ plugins {
 }
 
 group 'io.tiledb'
-version '0.19.2-SNAPSHOT'
+version '0.19.3-SNAPSHOT'
 
 repositories {
     jcenter()

cmake/Modules/FindTileDB_EP.cmake

@@ -48,24 +48,24 @@ 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/2.17.2/tiledb-windows-x86_64-2.17.2-06a09ae.zip")
-          SET(DOWNLOAD_SHA1 "44120f41a4e6d625f2640f9201369c5cd5976e6c")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.3/tiledb-windows-x86_64-2.17.3-0c2de58.zip")
+          SET(DOWNLOAD_SHA1 "0eea09e813a7e748ec9cd66bf2a3b8430e8132c5")
         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/2.17.2/tiledb-macos-x86_64-2.17.2-06a09ae.tar.gz")
-            SET(DOWNLOAD_SHA1 "91de353b6f786e0b04557b3680065baab6650968")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.3/tiledb-macos-x86_64-2.17.3-0c2de58.tar.gz")
+            SET(DOWNLOAD_SHA1 "2132ff2544b80acbc37d71c317603225d20ddd76")
 
           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/2.17.2/tiledb-macos-arm64-2.17.2-06a09ae.tar.gz")
-            SET(DOWNLOAD_SHA1 "eb5962b75a32f86ab42cfbb920ecce59a276d8f4")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.3/tiledb-macos-arm64-2.17.3-0c2de58.tar.gz")
+            SET(DOWNLOAD_SHA1 "222bb66496b8619fd6a87436104f8422aa8c1a2b")
           endif()
 
         else() # Linux
-          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.2/tiledb-linux-x86_64-2.17.2-06a09ae.tar.gz")
-          SET(DOWNLOAD_SHA1 "456b0caa3c8fad936356d16e284431f1da56caba")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.3/tiledb-linux-x86_64-2.17.3-0c2de58.tar.gz")
+          SET(DOWNLOAD_SHA1 "34c93c11aae7677f2a085f8d2c78e64d554688fe")
         endif()
 
         ExternalProject_Add(ep_tiledb

gradle.properties

@@ -1,5 +1,5 @@
 TILEDB_GIT_REPOSITORY=https://github.com/TileDB-Inc/TileDB
-TILEDB_GIT_TAG=2.17.2
+TILEDB_GIT_TAG=2.17.3
 TILEDB_VERBOSE=ON
 TILEDB_S3=ON
 TILEDB_AZURE=OFF

src/main/c/generated/tiledb_wrap.cxx

@@ -12831,6 +12831,82 @@ SWIGEXPORT jlong JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1enumeration_
 }
 
 
+SWIGEXPORT jlong JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1enumeration_1extend(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jlong jarg3, jobject jarg4, jlong jarg5, jobject jarg6, jlong jarg7) {
+  jlong jresult = 0 ;
+  tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+  tiledb_enumeration_t *arg2 = (tiledb_enumeration_t *) 0 ;
+  void *arg3 = (void *) 0 ;
+  uint64_t arg4 ;
+  void *arg5 = (void *) 0 ;
+  uint64_t arg6 ;
+  tiledb_enumeration_t **arg7 = (tiledb_enumeration_t **) 0 ;
+  SwigValueWrapper< capi_return_t > result;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(tiledb_ctx_t **)&jarg1; 
+  arg2 = *(tiledb_enumeration_t **)&jarg2; 
+  arg3 = *(void **)&jarg3; 
+  {
+    jclass clazz;
+    jmethodID mid;
+    jbyteArray ba;
+    jbyte* bae;
+    jsize sz;
+    int i;
+    
+    if (!jarg4) {
+      SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "BigInteger null");
+      return 0;
+    }
+    clazz = jenv->GetObjectClass(jarg4);
+    mid = jenv->GetMethodID(clazz, "toByteArray", "()[B");
+    ba = (jbyteArray)jenv->CallObjectMethod(jarg4, mid);
+    bae = jenv->GetByteArrayElements(ba, 0);
+    sz = jenv->GetArrayLength(ba);
+    arg4 = 0;
+    if (sz > 0) {
+      arg4 = (uint64_t)(signed char)bae[0];
+      for(i=1; i<sz; i++) {
+        arg4 = (arg4 << 8) | (uint64_t)(unsigned char)bae[i];
+      }
+    }
+    jenv->ReleaseByteArrayElements(ba, bae, 0);
+  }
+  arg5 = *(void **)&jarg5; 
+  {
+    jclass clazz;
+    jmethodID mid;
+    jbyteArray ba;
+    jbyte* bae;
+    jsize sz;
+    int i;
+    
+    if (!jarg6) {
+      SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "BigInteger null");
+      return 0;
+    }
+    clazz = jenv->GetObjectClass(jarg6);
+    mid = jenv->GetMethodID(clazz, "toByteArray", "()[B");
+    ba = (jbyteArray)jenv->CallObjectMethod(jarg6, mid);
+    bae = jenv->GetByteArrayElements(ba, 0);
+    sz = jenv->GetArrayLength(ba);
+    arg6 = 0;
+    if (sz > 0) {
+      arg6 = (uint64_t)(signed char)bae[0];
+      for(i=1; i<sz; i++) {
+        arg6 = (arg6 << 8) | (uint64_t)(unsigned char)bae[i];
+      }
+    }
+    jenv->ReleaseByteArrayElements(ba, bae, 0);
+  }
+  arg7 = *(tiledb_enumeration_t ***)&jarg7; 
+  result = tiledb_enumeration_extend(arg1,arg2,(void const *)arg3,arg4,(void const *)arg5,arg6,arg7);
+  *(capi_return_t **)&jresult = new capi_return_t((const capi_return_t &)result); 
+  return jresult;
+}
+
+
 SWIGEXPORT void JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1enumeration_1free(JNIEnv *jenv, jclass jcls, jlong jarg1) {
   tiledb_enumeration_t **arg1 = (tiledb_enumeration_t **) 0 ;
 
@@ -14379,6 +14455,24 @@ SWIGEXPORT jlong JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1array_1schem
 }
 
 
+SWIGEXPORT jlong JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1array_1schema_1evolution_1extend_1enumeration(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jlong jarg3) {
+  jlong jresult = 0 ;
+  tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+  tiledb_array_schema_evolution_t *arg2 = (tiledb_array_schema_evolution_t *) 0 ;
+  tiledb_enumeration_t *arg3 = (tiledb_enumeration_t *) 0 ;
+  SwigValueWrapper< capi_return_t > result;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(tiledb_ctx_t **)&jarg1; 
+  arg2 = *(tiledb_array_schema_evolution_t **)&jarg2; 
+  arg3 = *(tiledb_enumeration_t **)&jarg3; 
+  result = tiledb_array_schema_evolution_extend_enumeration(arg1,arg2,arg3);
+  *(capi_return_t **)&jresult = new capi_return_t((const capi_return_t &)result); 
+  return jresult;
+}
+
+
 SWIGEXPORT jlong JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1array_1schema_1evolution_1drop_1enumeration(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3) {
   jlong jresult = 0 ;
   tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;

src/main/java/io/tiledb/java/api/ArraySchemaEvolution.java

@@ -149,6 +149,18 @@ public void dropEnumeration(String name) throws TileDBError {
             ctx.getCtxp(), getEvolutionp(), name));
   }
 
+  /**
+   * Extends an Enumeration during array schema evolution.
+   *
+   * @param enumeration The Enumeration to extend.
+   * @throws TileDBError
+   */
+  public void extendEnumeration(Enumeration enumeration) throws TileDBError {
+    ctx.handleError(
+        tiledb.tiledb_array_schema_evolution_extend_enumeration(
+            ctx.getCtxp(), this.getEvolutionp(), enumeration.getEnumerationp()));
+  }
+
   /**
    * Evolves the schema of an array.
    *

src/main/java/io/tiledb/java/api/Enumeration.java

@@ -119,6 +119,34 @@ public boolean getOrdered() throws TileDBError {
     }
   }
 
+  /**
+   * Extend an Enumeration.
+   *
+   * @param data A pointer to the enumeration value data to add.
+   * @param dataSize The length of the data buffer provided.
+   * @param offsets A pointer to the offsets buffer if enumeration is var sized.
+   * @param offsetsSize The length of the offsets buffer, zero if no offsets.
+   */
+  public Enumeration extend(
+      NativeArray data, BigInteger dataSize, NativeArray offsets, BigInteger offsetsSize) {
+    SWIGTYPE_p_p_tiledb_enumeration_t enumeration_t = tiledb.new_tiledb_enumeration_tpp();
+
+    try {
+      ctx.handleError(
+          tiledb.tiledb_enumeration_extend(
+              ctx.getCtxp(),
+              this.getEnumerationp(),
+              data.toVoidPointer(),
+              dataSize,
+              offsets.toVoidPointer(),
+              offsetsSize,
+              enumeration_t));
+    } catch (TileDBError e) {
+      tiledb.delete_tiledb_enumeration_tpp(enumeration_t);
+    }
+    return new Enumeration(ctx, enumeration_t);
+  }
+
   /**
    * Return the datatype of the enumeration values
    *

src/main/java/io/tiledb/libtiledb/tiledb.java

@@ -4663,6 +4663,26 @@ public static capi_return_t tiledb_enumeration_alloc(
         true);
   }
 
+  public static capi_return_t tiledb_enumeration_extend(
+      SWIGTYPE_p_tiledb_ctx_t ctx,
+      SWIGTYPE_p_tiledb_enumeration_t old_enumeration,
+      SWIGTYPE_p_void data,
+      java.math.BigInteger data_size,
+      SWIGTYPE_p_void offsets,
+      java.math.BigInteger offsets_size,
+      SWIGTYPE_p_p_tiledb_enumeration_t new_enumeration) {
+    return new capi_return_t(
+        tiledbJNI.tiledb_enumeration_extend(
+            SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx),
+            SWIGTYPE_p_tiledb_enumeration_t.getCPtr(old_enumeration),
+            SWIGTYPE_p_void.getCPtr(data),
+            data_size,
+            SWIGTYPE_p_void.getCPtr(offsets),
+            offsets_size,
+            SWIGTYPE_p_p_tiledb_enumeration_t.getCPtr(new_enumeration)),
+        true);
+  }
+
   public static void tiledb_enumeration_free(SWIGTYPE_p_p_tiledb_enumeration_t enumeration) {
     tiledbJNI.tiledb_enumeration_free(SWIGTYPE_p_p_tiledb_enumeration_t.getCPtr(enumeration));
   }
@@ -5469,6 +5489,18 @@ public static capi_return_t tiledb_array_schema_evolution_add_enumeration(
         true);
   }
 
+  public static capi_return_t tiledb_array_schema_evolution_extend_enumeration(
+      SWIGTYPE_p_tiledb_ctx_t ctx,
+      SWIGTYPE_p_tiledb_array_schema_evolution_t array_schema_evolution,
+      SWIGTYPE_p_tiledb_enumeration_t enumeration) {
+    return new capi_return_t(
+        tiledbJNI.tiledb_array_schema_evolution_extend_enumeration(
+            SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx),
+            SWIGTYPE_p_tiledb_array_schema_evolution_t.getCPtr(array_schema_evolution),
+            SWIGTYPE_p_tiledb_enumeration_t.getCPtr(enumeration)),
+        true);
+  }
+
   public static capi_return_t tiledb_array_schema_evolution_drop_enumeration(
       SWIGTYPE_p_tiledb_ctx_t ctx,
       SWIGTYPE_p_tiledb_array_schema_evolution_t array_schema_evolution,

src/main/java/io/tiledb/libtiledb/tiledbConstants.java

@@ -17,5 +17,5 @@ public interface tiledbConstants {
   public static final int TILEDB_OOM = (-2);
   public static final int TILEDB_VERSION_MAJOR = 2;
   public static final int TILEDB_VERSION_MINOR = 17;
-  public static final int TILEDB_VERSION_PATCH = 0;
+  public static final int TILEDB_VERSION_PATCH = 3;
 }

src/main/java/io/tiledb/libtiledb/tiledbJNI.java

@@ -1586,6 +1586,15 @@ public static final native long tiledb_enumeration_alloc(
       java.math.BigInteger jarg9,
       long jarg10);
 
+  public static final native long tiledb_enumeration_extend(
+      long jarg1,
+      long jarg2,
+      long jarg3,
+      java.math.BigInteger jarg4,
+      long jarg5,
+      java.math.BigInteger jarg6,
+      long jarg7);
+
   public static final native void tiledb_enumeration_free(long jarg1);
 
   public static final native long tiledb_enumeration_get_name(long jarg1, long jarg2, long jarg3);
@@ -1775,6 +1784,9 @@ public static final native int tiledb_array_schema_evolution_drop_attribute(
   public static final native long tiledb_array_schema_evolution_add_enumeration(
       long jarg1, long jarg2, long jarg3);
 
+  public static final native long tiledb_array_schema_evolution_extend_enumeration(
+      long jarg1, long jarg2, long jarg3);
+
   public static final native long tiledb_array_schema_evolution_drop_enumeration(
       long jarg1, long jarg2, String jarg3);
 

src/test/java/io/tiledb/java/api/DatatypeTest.java

@@ -147,6 +147,7 @@ public void testEnumeratedDatatype() throws Exception {
     NativeArray enumsOffsets =
         new NativeArray(ctx, new long[] {0, 2, 4, 6}, Datatype.TILEDB_UINT64);
     NativeArray enums = new NativeArray(ctx, "aabbccdd", Datatype.TILEDB_STRING_ASCII);
+    NativeArray enums2 = new NativeArray(ctx, "eeffgghh", Datatype.TILEDB_STRING_ASCII);
 
     Enumeration en =
         new Enumeration(
@@ -294,7 +295,7 @@ public void testEnumeratedDatatype() throws Exception {
             ctx,
             "test_enum2",
             TILEDB_VAR_NUM,
-            Datatype.TILEDB_INT32,
+            Datatype.TILEDB_STRING_ASCII,
             false,
             enums,
             BigInteger.valueOf(enums.getSize() * Datatype.TILEDB_STRING_ASCII.getNativeSize()),
@@ -303,10 +304,24 @@ public void testEnumeratedDatatype() throws Exception {
     evolution.addEnumeration(en2);
     evolution.evolveArray(arrayURI);
 
-    // reopen array
+    // test extend
     array = new Array(ctx, arrayURI);
     e = array.getEnumeration("test_enum2");
     Assert.assertEquals(e.getName(), "test_enum2");
+    Enumeration newEnum =
+        e.extend(
+            enums2,
+            BigInteger.valueOf(enums.getSize() * Datatype.TILEDB_STRING_ASCII.getNativeSize()),
+            enumsOffsets,
+            BigInteger.valueOf(enumsOffsets.getSize() * Datatype.TILEDB_UINT64.getNativeSize()));
+    ArraySchemaEvolution extendEvolution = new ArraySchemaEvolution(ctx);
+    extendEvolution.extendEnumeration(newEnum);
+    extendEvolution.evolveArray(arrayURI);
+
+    // reopen array
+    array = new Array(ctx, arrayURI);
+    Enumeration extendedEnum = array.getEnumeration("test_enum2");
+    Assert.assertEquals("aabbccddeeffgghh", new String((byte[]) extendedEnum.getData()));
   }
 
   public void arrayCreate() throws Exception {