Victorgiannakouris/ch1879/support variable length ranges

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

@@ -521,7 +521,6 @@ public Pair getNonEmptyDomainFromIndex(long index) throws TileDBError {
    */
   public Pair getNonEmptyDomainFromName(String name) throws TileDBError {
     checkIsOpen();
-    HashMap<String, Pair> ret = new HashMap<String, Pair>();
     try (Domain domain = schema.getDomain();
         NativeArray domainArray =
             new NativeArray(ctx, 2 * (int) domain.getRank(), domain.getType())) {

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

@@ -161,6 +161,8 @@ public Class javaClass() throws TileDBError {
         return String.class;
       case TILEDB_STRING_UCS4:
         return String.class;
+      case TILEDB_STRING_ASCII:
+        return String.class;
       case TILEDB_ANY:
       default:
         throw new TileDBError("No such enum value" + this.name());

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

@@ -96,23 +96,31 @@ public Dimension(Context ctx, String name, Datatype type, Pair<T, T> domain, T e
   private void createImpl(Context ctx, String name, Datatype dimType, Pair<T, T> domain, T extent)
       throws TileDBError {
     SWIGTYPE_p_p_tiledb_dimension_t dimensionpp = tiledb.new_tiledb_dimension_tpp();
-    try (NativeArray domainBuffer = new NativeArray(ctx, 2, dimType);
-        NativeArray tileExtent = new NativeArray(ctx, 1, dimType)) {
-      domainBuffer.setItem(0, domain.getFirst());
-      domainBuffer.setItem(1, domain.getSecond());
-      tileExtent.setItem(0, extent);
+
+    if (dimType.equals(Datatype.TILEDB_STRING_ASCII)) {
       ctx.handleError(
           tiledb.tiledb_dimension_alloc(
-              ctx.getCtxp(),
-              name,
-              dimType.toSwigEnum(),
-              domainBuffer.toVoidPointer(),
-              tileExtent.toVoidPointer(),
-              dimensionpp));
-    } catch (Exception err) {
-      tiledb.delete_tiledb_dimension_tpp(dimensionpp);
-      throw err;
+              ctx.getCtxp(), name, dimType.toSwigEnum(), null, null, dimensionpp));
+    } else {
+      try (NativeArray domainBuffer = new NativeArray(ctx, 2, dimType);
+          NativeArray tileExtent = new NativeArray(ctx, 1, dimType)) {
+        domainBuffer.setItem(0, domain.getFirst());
+        domainBuffer.setItem(1, domain.getSecond());
+        tileExtent.setItem(0, extent);
+        ctx.handleError(
+            tiledb.tiledb_dimension_alloc(
+                ctx.getCtxp(),
+                name,
+                dimType.toSwigEnum(),
+                domainBuffer.toVoidPointer(),
+                tileExtent.toVoidPointer(),
+                dimensionpp));
+      } catch (Exception err) {
+        tiledb.delete_tiledb_dimension_tpp(dimensionpp);
+        throw err;
+      }
     }
+
     this.ctx = ctx;
     this.name = name;
     this.domain = domain;

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

@@ -196,6 +196,7 @@ private int getSize(Object buffer) throws TileDBError {
         {
           return ((long[]) buffer).length;
         }
+      case TILEDB_STRING_ASCII:
       case TILEDB_CHAR:
         {
           return stringToBytes(buffer).length;
@@ -275,6 +276,7 @@ private void createNativeArrayFromBuffer(Object buffer) throws TileDBError {
           uint64_tArray = Utils.newInt64_tArray((long[]) buffer);
           break;
         }
+      case TILEDB_STRING_ASCII:
       case TILEDB_CHAR:
         {
           byte[] bytes = stringToBytes(buffer);
@@ -357,6 +359,7 @@ private void allocateEmptyArray() throws TileDBError {
           uint64_tArray = new int64_tArray(size);
           break;
         }
+      case TILEDB_STRING_ASCII:
       case TILEDB_CHAR:
         {
           int8_tArray = new int8_tArray(size);
@@ -438,6 +441,7 @@ public Object getItem(int index) throws ArrayIndexOutOfBoundsException, TileDBEr
         {
           return uint64_tArray.getitem(index);
         }
+      case TILEDB_STRING_ASCII:
       case TILEDB_CHAR:
         {
           return int8_tArray.getitem(index);
@@ -527,6 +531,7 @@ public void setItem(int index, Object value) throws ArrayIndexOutOfBoundsExcepti
           uint64_tArray.setitem(index, (long) value);
           break;
         }
+      case TILEDB_STRING_ASCII:
       case TILEDB_CHAR:
         {
           for (byte b : stringToBytes(value)) {
@@ -601,6 +606,7 @@ public SWIGTYPE_p_void toVoidPointer() throws TileDBError {
         {
           return PointerUtils.toVoid(uint64_tArray);
         }
+      case TILEDB_STRING_ASCII:
       case TILEDB_CHAR:
         {
           return PointerUtils.toVoid(int8_tArray);
@@ -771,6 +777,7 @@ public Object toJavaArray(int position, int elements) throws TileDBError {
         {
           return Utils.int64ArrayGet(uint64_tArray, position, elements);
         }
+      case TILEDB_STRING_ASCII:
       case TILEDB_CHAR:
         {
           return Utils.int8ArrayGet(int8_tArray, position, elements);

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

@@ -201,6 +201,104 @@ public synchronized Query addRange(int dimIdx, Object start, Object end) throws
     return this;
   }
 
+  /**
+   * Adds a 1D variable-sized range along a subarray dimension, which is in the form (start, end).
+   * Applicable only to variable-sized dimensions.
+   *
+   * @param dimIdx The index of the dimension to add the range to
+   * @param start The range start
+   * @param end The range end
+   * @return This query
+   * @throws TileDBError A TileDB exception
+   */
+  public synchronized Query addRangeVar(int dimIdx, String start, String end) throws TileDBError {
+    Datatype dimType;
+    try (ArraySchema schema = array.getSchema();
+        Domain domain = schema.getDomain()) {
+      dimType = domain.getType();
+    }
+
+    Types.javaTypeCheck(start.getClass(), dimType.javaClass());
+    Types.javaTypeCheck(end.getClass(), dimType.javaClass());
+
+    try (NativeArray startArr = new NativeArray(ctx, 1, dimType);
+        NativeArray endArr = new NativeArray(ctx, 1, dimType)) {
+      startArr.setItem(0, start);
+      endArr.setItem(0, end);
+
+      ctx.handleError(
+          tiledb.tiledb_query_add_range_var(
+              ctx.getCtxp(),
+              queryp,
+              dimIdx,
+              startArr.toVoidPointer(),
+              BigInteger.valueOf(start.length()),
+              endArr.toVoidPointer(),
+              BigInteger.valueOf(end.length())));
+    }
+
+    return this;
+  }
+
+  /**
+   * Retrieves a range's start and end size for a given variable-length dimensions at a given range
+   * index.
+   *
+   * @param dimIdx The index of the dimension to add the range to
+   * @return This query
+   * @throws TileDBError A TileDB exception
+   */
+  public synchronized Pair<Long, Long> getRangeVarSize(int dimIdx, BigInteger rangeIdx)
+      throws TileDBError {
+    SWIGTYPE_p_unsigned_long_long startSize = tiledb.new_ullp();
+    SWIGTYPE_p_unsigned_long_long endSize = tiledb.new_ullp();
+    try {
+      ctx.handleError(
+          tiledb.tiledb_query_get_range_var_size(
+              ctx.getCtxp(), queryp, dimIdx, rangeIdx, startSize, endSize));
+
+      return new Pair(
+          tiledb.ullp_value(startSize).longValue(), tiledb.ullp_value(endSize).longValue());
+    } catch (TileDBError error) {
+      throw error;
+    }
+  }
+
+  /**
+   * Retrieves a specific range of the query subarray along a given variable-length dimension.
+   *
+   * @param dimIdx The index of the dimension to add the range to
+   * @return This query
+   * @throws TileDBError A TileDB exception
+   */
+  public synchronized Pair<String, String> getRangeVar(int dimIdx, BigInteger rangeIdx)
+      throws TileDBError {
+    Datatype dimType;
+    try (ArraySchema schema = array.getSchema();
+        Domain domain = schema.getDomain()) {
+      dimType = domain.getType();
+    }
+
+    Pair<Long, Long> size = this.getRangeVarSize(dimIdx, rangeIdx);
+
+    try (NativeArray startArr = new NativeArray(ctx, size.getFirst().intValue(), dimType);
+        NativeArray endArr = new NativeArray(ctx, size.getSecond().intValue(), dimType)) {
+
+      ctx.handleError(
+          tiledb.tiledb_query_get_range_var(
+              ctx.getCtxp(),
+              queryp,
+              dimIdx,
+              rangeIdx,
+              startArr.toVoidPointer(),
+              endArr.toVoidPointer()));
+
+      Object start = new String((byte[]) startArr.toJavaArray());
+      Object end = new String((byte[]) endArr.toJavaArray());
+      return new Pair(start, end);
+    }
+  }
+
   /**
    * Retrieves the number of ranges of the query subarray along a given dimension.
    *
@@ -272,7 +370,7 @@ public synchronized Query setBuffer(String attr, NativeArray buffer) throws Tile
         if (attr.equals(tiledb.tiledb_coords())) {
           Types.typeCheck(domain.getType(), buffer.getNativeType());
         } else if (domain.hasDimension(attr)) {
-          Types.typeCheck(domain.getType(), buffer.getNativeType());
+          Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
         } else {
           try (Attribute attribute = schema.getAttribute(attr)) {
             Types.typeCheck(attribute.getType(), buffer.getNativeType());
@@ -333,7 +431,7 @@ public synchronized Query setBuffer(String attr, NativeArray buffer, long buffer
         if (attr.equals(tiledb.tiledb_coords())) {
           Types.typeCheck(domain.getType(), buffer.getNativeType());
         } else if (domain.hasDimension(attr)) {
-          Types.typeCheck(domain.getType(), buffer.getNativeType());
+          Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
         } else {
           try (Attribute attribute = schema.getAttribute(attr)) {
             Types.typeCheck(attribute.getType(), buffer.getNativeType());
@@ -391,9 +489,18 @@ public synchronized Query setBuffer(String attr, NativeArray offsets, NativeArra
     }
 
     // Type check the buffer native type matches the schema attribute type
-    try (ArraySchema schema = array.getSchema();
-        Attribute attribute = schema.getAttribute(attr)) {
-      Types.typeCheck(attribute.getType(), buffer.getNativeType());
+    try (ArraySchema schema = array.getSchema()) {
+      try (Domain domain = schema.getDomain()) {
+        if (attr.equals(tiledb.tiledb_coords())) {
+          Types.typeCheck(domain.getType(), buffer.getNativeType());
+        } else if (domain.hasDimension(attr)) {
+          Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
+        } else {
+          try (Attribute attribute = schema.getAttribute(attr)) {
+            Types.typeCheck(attribute.getType(), buffer.getNativeType());
+          }
+        }
+      }
     }
 
     uint64_tArray offsets_array = PointerUtils.uint64_tArrayFromVoid(offsets.toVoidPointer());

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

@@ -111,6 +111,7 @@ public static Class getJavaType(Datatype type) throws TileDBError {
         {
           return Long.class;
         }
+      case TILEDB_STRING_ASCII:
       case TILEDB_CHAR:
         {
           return String.class;