Context map for TileDB-backed SOMA objects
Super classes
tiledbsoma::MappingBase -> tiledbsoma::ScalarMap -> tiledbsoma::SOMAContextBase -> SOMATileDBContext
Methods
Method new()
Usage
SOMATileDBContext$new(config = NULL, cached = TRUE)Method to_tiledb_context()
Returns
A tiledb_ctx object, dynamically
constructed. Most useful for the constructor of this class.
Method context()
Returns
A tiledb_ctx object, which is
a stored (and long-lived) result from to_tiledb_context.
Examples
(ctx <- SOMATileDBContext$new())
#> <SOMATileDBContext>
#> config.env_var_prefix: TILEDB_
#> config.logging_format: DEFAULT
#> config.logging_level: 0
#> filestore.buffer_size: 104857600
#> profile_dir:
#> profile_name:
#> rest.capnp_traversal_limit: 2147483648
#> rest.curl.buffer_size: 524288
#> rest.curl.retry_errors: true
#> rest.curl.tcp_keepalive: true
#> rest.curl.verbose: false
#> rest.http_compressor: any
#> rest.load_enumerations_on_array_open: false
#> rest.load_enumerations_on_array_open_all_schemas: false
#> rest.load_metadata_on_array_open: true
#> rest.load_non_empty_domain_on_array_open: true
#> rest.payer_namespace:
#> rest.retry_count: 25
#> rest.retry_delay_factor: 1.25
#> rest.retry_http_codes: 503
#> rest.retry_initial_delay_ms: 500
#> rest.server_address: https://api.tiledb.com
#> rest.server_serialization_format: CAPNP
#> rest.use_refactored_array_open: true
#> rest.use_refactored_array_open_and_query_submit: true
#> sm.allow_separate_attribute_writes: false
#> sm.allow_updates_experimental: false
#> sm.check_coord_dups: true
#> sm.check_coord_oob: true
#> sm.check_global_order: true
#> sm.compute_concurrency_level: 4
#> sm.consolidation.amplification: 1.0
#> sm.consolidation.buffer_size: 50000000
#> sm.consolidation.max_fragment_size: 18446744073709551615
#> sm.consolidation.mode: fragments
#> sm.consolidation.purge_deleted_cells: false
#> sm.consolidation.step_max_frags: 4294967295
#> sm.consolidation.step_min_frags: 4294967295
#> sm.consolidation.step_size_ratio: 0.0
#> sm.consolidation.steps: 4294967295
#> sm.consolidation.timestamp_end: 18446744073709551615
#> sm.consolidation.timestamp_start: 0
#> sm.dedup_coords: false
#> sm.enable_signal_handlers: true
#> sm.encryption_key:
#> sm.encryption_type: NO_ENCRYPTION
#> sm.enumerations_max_size: 10485760
#> sm.enumerations_max_total_size: 52428800
#> sm.fragment_info.preload_mbrs: false
#> sm.group.timestamp_end: 18446744073709551615
#> sm.group.timestamp_start: 0
#> sm.io_concurrency_level: 4
#> sm.max_tile_overlap_size: 314572800
#> sm.mem.consolidation.buffers_weight: 1
#> sm.mem.consolidation.reader_weight: 3
#> sm.mem.consolidation.writer_weight: 2
#> sm.mem.malloc_trim: true
#> sm.mem.reader.sparse_global_order.ratio_array_data: 0.3
#> sm.mem.reader.sparse_global_order.ratio_coords: 0.5
#> sm.mem.reader.sparse_global_order.ratio_tile_ranges: 0.1
#> sm.mem.reader.sparse_unordered_with_dups.ratio_array_data: 0.1
#> sm.mem.reader.sparse_unordered_with_dups.ratio_coords: 0.5
#> sm.mem.reader.sparse_unordered_with_dups.ratio_tile_ranges: 0.1
#> sm.mem.tile_upper_memory_limit: 1073741824
#> sm.mem.total_budget: 10737418240
#> sm.memory_budget: 5368709120
#> sm.memory_budget_var: 10737418240
#> sm.merge_overlapping_ranges_experimental: true
#> sm.partial_tile_offsets_loading: false
#> sm.query.condition_evaluator: ast
#> sm.query.dense.qc_coords_mode: false
#> sm.query.dense.reader: refactored
#> sm.query.sparse_global_order.preprocess_tile_merge: 32768
#> sm.query.sparse_global_order.reader: refactored
#> sm.query.sparse_unordered_with_dups.reader: refactored
#> sm.read_range_oob: warn
#> sm.skip_checksum_validation: false
#> sm.skip_est_size_partitioning: false
#> sm.skip_unary_partitioning_budget_check: false
#> sm.vacuum.mode: fragments
#> sm.var_offsets.bitsize: 64
#> sm.var_offsets.extra_element: false
#> sm.var_offsets.mode: bytes
#> ssl.ca_file:
#> ssl.ca_path:
#> ssl.verify: true
#> vfs.azure.blob_endpoint:
#> vfs.azure.block_list_block_size: 5242880
#> vfs.azure.is_data_lake_endpoint:
#> vfs.azure.max_parallel_ops: 4
#> vfs.azure.max_retries: 5
#> vfs.azure.max_retry_delay_ms: 60000
#> vfs.azure.retry_delay_ms: 800
#> vfs.azure.storage_account_key:
#> vfs.azure.storage_account_name:
#> vfs.azure.storage_sas_token:
#> vfs.azure.use_block_list_upload: true
#> vfs.file.posix_directory_permissions: 755
#> vfs.file.posix_file_permissions: 644
#> vfs.gcs.endpoint:
#> vfs.gcs.impersonate_service_account:
#> vfs.gcs.max_direct_upload_size: 10737418240
#> vfs.gcs.max_parallel_ops: 4
#> vfs.gcs.multi_part_size: 5242880
#> vfs.gcs.project_id:
#> vfs.gcs.request_timeout_ms: 3000
#> vfs.gcs.service_account_key:
#> vfs.gcs.use_multi_part_upload: true
#> vfs.gcs.workload_identity_configuration:
#> vfs.log_operations: false
#> vfs.max_batch_size: 104857600
#> vfs.min_batch_gap: 512000
#> vfs.min_batch_size: 20971520
#> vfs.min_parallel_size: 10485760
#> vfs.read_ahead_cache_size: 10485760
#> vfs.read_ahead_size: 102400
#> vfs.read_logging_mode:
#> vfs.s3.aws_access_key_id:
#> vfs.s3.aws_external_id:
#> vfs.s3.aws_load_frequency:
#> vfs.s3.aws_role_arn:
#> vfs.s3.aws_secret_access_key:
#> vfs.s3.aws_session_name:
#> vfs.s3.aws_session_token:
#> vfs.s3.bucket_canned_acl: NOT_SET
#> vfs.s3.ca_file:
#> vfs.s3.ca_path:
#> vfs.s3.config_source: auto
#> vfs.s3.connect_max_tries: 5
#> vfs.s3.connect_scale_factor: 25
#> vfs.s3.connect_timeout_ms: 10800
#> vfs.s3.endpoint_override:
#> vfs.s3.install_sigpipe_handler: true
#> vfs.s3.logging_level: Off
#> vfs.s3.max_parallel_ops: 4
#> vfs.s3.multipart_part_size: 5242880
#> vfs.s3.no_sign_request: false
#> vfs.s3.object_canned_acl: NOT_SET
#> vfs.s3.proxy_host:
#> vfs.s3.proxy_password:
#> vfs.s3.proxy_port: 0
#> vfs.s3.proxy_scheme: http
#> vfs.s3.proxy_username:
#> vfs.s3.region:
#> vfs.s3.request_timeout_ms: 3000
#> vfs.s3.requester_pays: false
#> vfs.s3.scheme: https
#> vfs.s3.skip_init: false
#> vfs.s3.sse:
#> vfs.s3.sse_kms_key_id:
#> vfs.s3.storage_class: NOT_SET
#> vfs.s3.use_multipart_upload: true
#> vfs.s3.use_virtual_addressing: true
#> vfs.s3.verify_ssl: true
ctx$get("sm.mem.reader.sparse_global_order.ratio_array_data")
#> sm.mem.reader.sparse_global_order.ratio_array_data
#> "0.3"
ctx$to_tiledb_context()
#> An object of class "tiledb_ctx"
#> Slot "ptr":
#> <pointer: 0x55e684180d00>
#>