Package io.tiledb.java.api

Class Array

  • All Implemented Interfaces:
    java.lang.AutoCloseable
    public class Array
extends java.lang.Object
implements java.lang.AutoCloseable
    Class representing a TileDB array object.

    An Array object represents array data in TileDB at some persisted location, e.g. on disk, in an S3 bucket, etc. Once an array has been opened for reading or writing, interact with the data through Query objects. 

    Example:
 
   // Create an ArraySchema, add attributes, domain, etc.
   Context ctx = new Context();
   ArraySchema schema = new ArraySchema(...);
   // Create empty array named "my_array" on persistent storage.
   Array.create("my_array", schema);

    • Constructor Summary

      Constructors 
      Constructor Description
      Array​(Context ctx, java.lang.String uri)
      Constructs an Array object opening the array for reading.
      Array​(Context ctx, java.lang.String uri, QueryType query_type)
      Constructs an Array object, opening the array for the given query type.
      Array​(Context ctx, java.lang.String uri, QueryType query_type, EncryptionType encryption_type, byte[] key)
      Constructs an Array object, opening the encrypted array for the given query type.
      Array​(Context ctx, java.lang.String uri, QueryType query_type, EncryptionType encryption_type, byte[] key, java.math.BigInteger timestamp)
      Constructs an Array object, opening the encrypted array for the given query type.
      Array​(Context ctx, java.lang.String uri, java.math.BigInteger timestamp)
      Constructs an Array object opening the array for reading at a user-given timestamp (time-travelling).

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Free's the native objects and closes the Array.
      static void consolidate​(Context ctx, java.lang.String uri)
      Consolidates the fragments of an array into a single fragment.
      static void consolidate​(Context ctx, java.lang.String uri, Config config)
      Consolidates the fragments of an array into a single fragment.
      static void consolidate​(Context ctx, java.lang.String uri, EncryptionType encryption_type, byte[] key)
      Consolidates the fragments of an array into a single fragment.
      static void consolidate​(Context ctx, java.lang.String uri, EncryptionType encryption_type, byte[] key, Config config)
      Consolidates the fragments of an array into a single fragment.
      static void create​(java.lang.String uri, ArraySchema schema)
      Creates a persisted TileDB array given an input ArraySchema
      static void create​(java.lang.String uri, ArraySchema schema, EncryptionType encryption_type, byte[] key)
      Creates an encrypted persisted TileDBArray given input ArraySchema and encryption key
      void deleteMetadata​(java.lang.String key)
      Deletes a metadata key-value item from an open array.
      static boolean exists​(Context ctx, java.lang.String uri)
      Checks if a given URI is an existing TileDB array object
      protected SWIGTYPE_p_tiledb_array_t getArrayp()  
      Context getCtx()  
      NativeArray getMetadata​(java.lang.String key)
      Get a metadata key-value item from an open array.
      NativeArray getMetadata​(java.lang.String key, Datatype nativeType)
      Get a metadata key-value item from an open array.
      Pair<java.lang.String,​NativeArray> getMetadataFromIndex​(long index)
      Gets a metadata item from an open array using an index.
      Pair<java.lang.String,​NativeArray> getMetadataFromIndex​(java.math.BigInteger index)
      Gets a metadata item from an open array using an index.
      java.util.Map<java.lang.String,​java.lang.Object> getMetadataMap()
      Returns a HashMap with all array metadata in a key-value manner.
      java.math.BigInteger getMetadataNum()
      Gets the number of metadata items in an open array.
      Pair getNonEmptyDomainFromIndex​(long index)
      Given a dimension's index, return the bounding coordinates for that dimension.
      Pair getNonEmptyDomainFromName​(java.lang.String name)
      Given a dimension's name, return the bounding coordinates for that dimension.
      Pair<java.lang.String,​java.lang.String> getNonEmptyDomainVarFromIndex​(long index)
      Retrieves the non-empty domain from an array for a given dimension index.
      Pair<java.lang.String,​java.lang.String> getNonEmptyDomainVarFromName​(java.lang.String name)
      Retrieves the non-empty domain from an array for a given dimension name.
      Pair<java.math.BigInteger,​java.math.BigInteger> getNonEmptyDomainVarSizeFromIndex​(long index)
      Retrieves the non-empty domain range sizes from an array for a given dimension index.
      Pair<java.math.BigInteger,​java.math.BigInteger> getNonEmptyDomainVarSizeFromName​(java.lang.String name)
      Retrieves the non-empty domain range sizes from an array for a given dimension name.
      QueryType getQueryType()  
      ArraySchema getSchema()  
      java.lang.String getUri()  
      java.lang.Boolean hasMetadataKey​(java.lang.String key)
      Checks if the key is present in the Array metadata.
      java.util.HashMap<java.lang.String,​Pair<java.lang.Long,​java.lang.Long>> maxBufferElements​(NativeArray subarray)
      Compute an upper bound on the buffer elements needed to read a subarray.
      java.util.HashMap<java.lang.String,​Pair> nonEmptyDomain()
      Get the non-empty domain of an array, returning the bounding coordinates for each dimension.
      void putMetadata​(java.lang.String key, NativeArray value)
      Puts a metadata key-value item to an open array.
      void putMetadata​(java.lang.String key, java.lang.Object buffer)
      Puts a metadata key-value item to an open array.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • Array

        public Array​(Context ctx,
             java.lang.String uri)
      throws TileDBError
        Constructs an Array object opening the array for reading. 
        Example:
 
   Context ctx = new Context();
   Array array new Array(ctx, "s3://bucket-name/array-name");
        Parameters:
        ctx - TileDB context
        uri - The array URI
        Throws:
        TileDBError - A TileDB exception

      • Array

        public Array​(Context ctx,
             java.lang.String uri,
             java.math.BigInteger timestamp)
      throws TileDBError
        Constructs an Array object opening the array for reading at a user-given timestamp (time-travelling). 
        Example:
 
   Context ctx = new Context();
   Array array new Array(ctx, "s3://bucket-name/array-name");
        Parameters:
        ctx - TileDB context
        uri - The array URI
        timestamp - The timestamp
        Throws:
        TileDBError - A TileDB exception

      • Array

        public Array​(Context ctx,
             java.lang.String uri,
             QueryType query_type)
      throws TileDBError
        Constructs an Array object, opening the array for the given query type. 
        Example:
 
 Context ctx = new Context();
 Array array new Array(ctx, "s3://bucket-name/array-name", TILEDB_READ);
        Parameters:
        ctx - TileDB context
        uri - The array URI
        query_type - Query type to open the array for.
        Throws:
        TileDBError - A TileDB exception

      • Array

        public Array​(Context ctx,
             java.lang.String uri,
             QueryType query_type,
             EncryptionType encryption_type,
             byte[] key)
      throws TileDBError
        Constructs an Array object, opening the encrypted array for the given query type. 
        Example:
 
 Context ctx = new Context();
 String key = "0123456789abcdeF0123456789abcdeF";
 Array array new Array(ctx, "s3://bucket-name/array-name",
                       TILEDB_READ,
                       TILEDB_AES_256_GCM,
                       key.getBytes(StandardCharsets.UTF_8));
        Parameters:
        ctx - TileDB context
        uri - The array URI
        query_type - Query type to open the array for
        encryption_type - The encryption type to use
        key - The encryption key to use
        Throws:
        TileDBError - A TileDB exception

      • Array

        public Array​(Context ctx,
             java.lang.String uri,
             QueryType query_type,
             EncryptionType encryption_type,
             byte[] key,
             java.math.BigInteger timestamp)
      throws TileDBError
        Constructs an Array object, opening the encrypted array for the given query type. 
        Example:
 
 Context ctx = new Context();
 String key = "0123456789abcdeF0123456789abcdeF";
 Array array new Array(ctx, "s3://bucket-name/array-name",
                       TILEDB_READ,
                       TILEDB_AES_256_GCM,
                       key.getBytes(StandardCharsets.UTF_8));
        Parameters:
        ctx - TileDB context
        uri - The array URI
        query_type - Query type to open the array for
        encryption_type - The encryption type to use
        key - The encryption key to use
        timestamp - The timestamp
        Throws:
        TileDBError - A TileDB exception

    • Method Detail

      • consolidate

        public static void consolidate​(Context ctx,
                               java.lang.String uri)
                        throws TileDBError
        Consolidates the fragments of an array into a single fragment.

        All queries to the array before consolidation must be finalized before consolidation can begin. Consolidation temporarily aquires an exclusive lock on the array when finalizing the resulting merged fragment. 

        Example:
 
   Context ctx = new Context();
   Array.consolidate(ctx, "s3://bucket-name/array-name");
        Parameters:
        ctx - TileDB context object
        uri - TileDB URI string
        Throws:
        TileDBError - A TileDB exception

      • consolidate

        public static void consolidate​(Context ctx,
                               java.lang.String uri,
                               Config config)
                        throws TileDBError
        Consolidates the fragments of an array into a single fragment.

        All queries to the array before consolidation must be finalized before consolidation can begin. Consolidation temporarily aquires an exclusive lock on the array when finalizing the resulting merged fragment. 

        Example:
 
   Context ctx = new Context();
   Array.consolidate(ctx, "s3://bucket-name/array-name");
        Parameters:
        ctx - TileDB context object
        uri - TileDB URI string
        config - A TileDB config object with configuration parameters for the consolidation
        Throws:
        TileDBError - A TileDB exception

      • consolidate

        public static void consolidate​(Context ctx,
                               java.lang.String uri,
                               EncryptionType encryption_type,
                               byte[] key)
                        throws TileDBError
        Consolidates the fragments of an array into a single fragment.

        All queries to the array before consolidation must be finalized before consolidation can begin. Consolidation temporarily aquires an exclusive lock on the array when finalizing the resulting merged fragment. 

        Example:
 
   Context ctx = new Context();
   String key = "0123456789abcdeF0123456789abcdeF";
   Array.consolidate(ctx, "s3://bucket-name/array-name",
                     TILEDB_AES_256_GCM,
                     key.getBytes(StandardCharsets.UTF_8));
        Parameters:
        ctx - A TileDB Context
        uri - URI string to TileDB array
        encryption_type - Encryption type the array is encrypted with
        key - A byte array key to decrypt array
        Throws:
        TileDBError

      • consolidate

        public static void consolidate​(Context ctx,
                               java.lang.String uri,
                               EncryptionType encryption_type,
                               byte[] key,
                               Config config)
                        throws TileDBError
        Consolidates the fragments of an array into a single fragment.

        All queries to the array before consolidation must be finalized before consolidation can begin. Consolidation temporarily aquires an exclusive lock on the array when finalizing the resulting merged fragment. 

        Example:
 
   Context ctx = new Context();
   String key = "0123456789abcdeF0123456789abcdeF";
   Array.consolidate(ctx, "s3://bucket-name/array-name",
                     TILEDB_AES_256_GCM,
                     key.getBytes(StandardCharsets.UTF_8));
        Parameters:
        ctx - A TileDB Context
        uri - URI string to TileDB array
        encryption_type - Encryption type the array is encrypted with
        key - A byte array key to decrypt array
        config - A TileDB config object with configuration parameters for the consolidation
        Throws:
        TileDBError

      • exists

        public static boolean exists​(Context ctx,
                             java.lang.String uri)
                      throws TileDBError
        Checks if a given URI is an existing TileDB array object
        Parameters:
        ctx - TileDB context object
        uri - TileDB URI array string
        Returns:
        true if the uri is an array object, false otherwise
        Throws:
        TileDBError

      • create

        public static void create​(java.lang.String uri,
                          ArraySchema schema)
                   throws TileDBError
        Creates a persisted TileDB array given an input ArraySchema 
        Example:
 
   Array.create("my_array", schema);
        Parameters:
        uri - The array URI string
        schema - The TileDB ArraySchema
        Throws:
        TileDBError - A TileDB exception

      • create

        public static void create​(java.lang.String uri,
                          ArraySchema schema,
                          EncryptionType encryption_type,
                          byte[] key)
                   throws TileDBError
        Creates an encrypted persisted TileDBArray given input ArraySchema and encryption key 
        Example:
 
   String key = "0123456789abcdeF0123456789abcdeF";
   Array.create("my_array", schema,
                TILEDB_AES_256_GCM,
                key.getBytes(StandardCharsets.UTF_8));
        Parameters:
        uri - The array URI string
        schema - The TileDB ArraySchema
        encryption_type - The encryption type to use
        key - The encryption key to use
        Throws:
        TileDBError - A TileDB exception

      • nonEmptyDomain

        public java.util.HashMap<java.lang.String,​Pair> nonEmptyDomain()
                                                              throws TileDBError
        Get the non-empty domain of an array, returning the bounding coordinates for each dimension.
        Returns:
        A HashMap of dimension names and (lower, upper) inclusive bounding coordinate range pair. Empty HashMap if the array has no data.
        Throws:
        TileDBError - A TileDB exception

      • getNonEmptyDomainFromIndex

        public Pair getNonEmptyDomainFromIndex​(long index)
                                throws TileDBError
        Given a dimension's index, return the bounding coordinates for that dimension. The method checks if the dimension is var-sized or not, and it works for both cases.
        Parameters:
        index - THe dimension's index
        Returns:
        A Pair that contains the dimension's bounds
        Throws:
        TileDBError - A TileDB exception

      • getNonEmptyDomainFromName

        public Pair getNonEmptyDomainFromName​(java.lang.String name)
                               throws TileDBError
        Given a dimension's name, return the bounding coordinates for that dimension. The method checks if the dimension is var-sized or not, and it works for both cases.
        Parameters:
        name - THe dimension's name
        Returns:
        A Pair that contains the dimension's bounds
        Throws:
        TileDBError - A TileDB exception

      • getNonEmptyDomainVarSizeFromIndex

        public Pair<java.math.BigInteger,​java.math.BigInteger> getNonEmptyDomainVarSizeFromIndex​(long index)
                                                                                        throws TileDBError
        Retrieves the non-empty domain range sizes from an array for a given dimension index. This is the union of the non-empty domains of the array fragments on the given dimension. Applicable only to var-sized dimensions.
        Parameters:
        index - The dimension index
        Returns:
        The non-empty domain range sizes
        Throws:
        TileDBError - A TileDB exception

      • getNonEmptyDomainVarSizeFromName

        public Pair<java.math.BigInteger,​java.math.BigInteger> getNonEmptyDomainVarSizeFromName​(java.lang.String name)
                                                                                       throws TileDBError
        Retrieves the non-empty domain range sizes from an array for a given dimension name. This is the union of the non-empty domains of the array fragments on the given dimension. Applicable only to var-sized dimensions.
        Parameters:
        name - The dimension name
        Returns:
        The non-empty domain range sizes
        Throws:
        TileDBError - A TileDB exception

      • getNonEmptyDomainVarFromIndex

        public Pair<java.lang.String,​java.lang.String> getNonEmptyDomainVarFromIndex​(long index)
                                                                            throws TileDBError
        Retrieves the non-empty domain from an array for a given dimension index. This is the union of the non-empty domains of the array fragments on the given dimension. Applicable only to var-sized dimensions.
        Parameters:
        index - The dimension index
        Returns:
        The non-empty domain
        Throws:
        TileDBError - A TileDB exception

      • getNonEmptyDomainVarFromName

        public Pair<java.lang.String,​java.lang.String> getNonEmptyDomainVarFromName​(java.lang.String name)
                                                                           throws TileDBError
        Retrieves the non-empty domain from an array for a given dimension name. This is the union of the non-empty domains of the array fragments on the given dimension. Applicable only to var-sized dimensions.
        Parameters:
        name - The dimension name
        Returns:
        The non-empty domain
        Throws:
        TileDBError - A TileDB exception

      • maxBufferElements

        public java.util.HashMap<java.lang.String,​Pair<java.lang.Long,​java.lang.Long>> maxBufferElements​(NativeArray subarray)
                                                                                                      throws TileDBError
        Compute an upper bound on the buffer elements needed to read a subarray.
        Parameters:
        subarray - Domain subarray
        Returns:
        The maximum number of elements for each array attribute. If the Array is sparse, max number of coordinates are also returned. Note that two numbers are returned per attribute. The first is the maximum number of elements in the offset buffer (0 for fixed-sized attributes and coordinates), the second is the maximum number of elements of the value buffer.
        Throws:
        TileDBError - A TileDB exception

      • getMetadata

        public NativeArray getMetadata​(java.lang.String key)
                        throws TileDBError
        Get a metadata key-value item from an open array. The array must be opened in READ mode, otherwise the function will error out.
        Parameters:
        key - a key to retrieve from the metadata key-value
        Returns:
        NativeArray which contains the metadata
        Throws:
        TileDBError - A TileDB exception

      • getMetadata

        public NativeArray getMetadata​(java.lang.String key,
                               Datatype nativeType)
                        throws TileDBError
        Get a metadata key-value item from an open array. The array must be opened in READ mode, otherwise the function will error out.
        Parameters:
        key - a key to retrieve from the metadata key-value
        nativeType - The Datatype
        Returns:
        NativeArray which contains the metadata
        Throws:
        TileDBError - A TileDB exception

      • deleteMetadata

        public void deleteMetadata​(java.lang.String key)
                    throws TileDBError
        Deletes a metadata key-value item from an open array. The array must be opened in WRITE mode, otherwise the function will error out.
        Parameters:
        key - a key to delete from the metadata key-value
        Throws:
        TileDBError - A TileDB exception

      • getMetadataNum

        public java.math.BigInteger getMetadataNum()
                                    throws TileDBError
        Gets the number of metadata items in an open array. The array must be opened in READ mode, otherwise the function will error out.
        Returns:
        the number of metadata items
        Throws:
        TileDBError - A TileDB exception

      • getMetadataFromIndex

        public Pair<java.lang.String,​NativeArray> getMetadataFromIndex​(long index)
                                                              throws TileDBError
        Gets a metadata item from an open array using an index. The array must be opened in READ mode, otherwise the function will error out.
        Parameters:
        index - index to retrieve metadata from
        Returns:
        a pair, key and the metadata
        Throws:
        TileDBError - A TileDB exception

      • getMetadataFromIndex

        public Pair<java.lang.String,​NativeArray> getMetadataFromIndex​(java.math.BigInteger index)
                                                              throws TileDBError
        Gets a metadata item from an open array using an index. The array must be opened in READ mode, otherwise the function will error out.
        Parameters:
        index - index to retrieve metadata from
        Returns:
        a pair, key and the metadata
        Throws:
        TileDBError - A TileDB exception

      • getMetadataMap

        public java.util.Map<java.lang.String,​java.lang.Object> getMetadataMap()
                                                                      throws TileDBError
        Returns a HashMap with all array metadata in a key-value manner.
        Returns:
        The metadata
        Throws:
        TileDBError

      • hasMetadataKey

        public java.lang.Boolean hasMetadataKey​(java.lang.String key)
                                 throws TileDBError
        Checks if the key is present in the Array metadata. The array must be opened in READ mode, otherwise the function will error out.
        Parameters:
        key - a key to retrieve from the metadata key-value
        Returns:
        true if the key is present in the metadata, false if it is not
        Throws:
        TileDBError - A TileDB exception

      • putMetadata

        public void putMetadata​(java.lang.String key,
                        java.lang.Object buffer)
                 throws TileDBError
        Puts a metadata key-value item to an open array. The array must be opened in WRITE mode, otherwise the function will error out.
        Parameters:
        key - a key to assign to the input value
        buffer - the metadata to put into the Array metadata
        Throws:
        TileDBError - A TileDB exception

      • putMetadata

        public void putMetadata​(java.lang.String key,
                        NativeArray value)
                 throws TileDBError
        Puts a metadata key-value item to an open array. The array must be opened in WRITE mode, otherwise the function will error out.
        Parameters:
        key - a key to assign to the input value
        value - the metadata to put into the Array metadata
        Throws:
        TileDBError - A TileDB exception

      • getCtx

        public Context getCtx()
        Returns:
        The TileDB Context object associated with the Array instance.

      • getUri

        public java.lang.String getUri()
        Returns:
        The URI string of the array

      • getQueryType

        public QueryType getQueryType()
        Returns:
        The TileDB QueryType enum value that the Array instance.

      • close

        public void close()
        Free's the native objects and closes the Array.
        Specified by:
        close in interface java.lang.AutoCloseable