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backend.py
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backend.py
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from typing import Mapping, List, Union, TypeVar, Tuple, Dict, Optional, Any, AbstractSet
import abc
import orjson
import pkg_resources
import zipfile
from hailtop.config.user_config import unchecked_configuration_of
from hailtop.fs.fs import FS
from ..builtin_references import BUILTIN_REFERENCE_RESOURCE_PATHS
from ..expr import Expression
from ..expr.types import HailType
from ..ir import BaseIR
from ..linalg.blockmatrix import BlockMatrix
from ..matrixtable import MatrixTable
from ..table import Table
from ..utils.java import FatalError
Dataset = TypeVar('Dataset', Table, MatrixTable, BlockMatrix)
def fatal_error_from_java_error_triplet(short_message, expanded_message, error_id):
from .. import __version__
if error_id != -1:
return FatalError(f'Error summary: {short_message}', error_id)
return FatalError(f'''{short_message}
Java stack trace:
{expanded_message}
Hail version: {__version__}
Error summary: {short_message}''',
error_id)
class Backend(abc.ABC):
# Must match knownFlags in HailFeatureFlags.py
_flags_env_vars_and_defaults: Dict[str, Tuple[str, Optional[str]]] = {
"no_whole_stage_codegen": ("HAIL_DEV_NO_WHOLE_STAGE_CODEGEN", None),
"no_ir_logging": ("HAIL_DEV_NO_IR_LOG", None),
"lower": ("HAIL_DEV_LOWER", None),
"lower_only": ("HAIL_DEV_LOWER_ONLY", None),
"lower_bm": ("HAIL_DEV_LOWER_BM", None),
"print_ir_on_worker": ("HAIL_DEV_PRINT_IR_ON_WORKER", None),
"print_inputs_on_worker": ("HAIL_DEV_PRINT_INPUTS_ON_WORKER", None),
"max_leader_scans": ("HAIL_DEV_MAX_LEADER_SCANS", "1000"),
"distributed_scan_comb_op": ("HAIL_DEV_DISTRIBUTED_SCAN_COMB_OP", None),
"jvm_bytecode_dump": ("HAIL_DEV_JVM_BYTECODE_DUMP", None),
"write_ir_files": ("HAIL_WRITE_IR_FILES", None),
"method_split_ir_limit": ("HAIL_DEV_METHOD_SPLIT_LIMIT", "16"),
"use_new_shuffle": ("HAIL_USE_NEW_SHUFFLE", None),
"shuffle_max_branch_factor": ("HAIL_SHUFFLE_MAX_BRANCH", "64"),
"shuffle_cutoff_to_local_sort": ("HAIL_SHUFFLE_CUTOFF", "512000000"), # This is in bytes
"grouped_aggregate_buffer_size": ("HAIL_GROUPED_AGGREGATE_BUFFER_SIZE", "50"),
"use_ssa_logs": ("HAIL_USE_SSA_LOGS", None),
"gcs_requester_pays_project": ("HAIL_GCS_REQUESTER_PAYS_PROJECT", None),
"gcs_requester_pays_buckets": ("HAIL_GCS_REQUESTER_PAYS_BUCKETS", None),
"index_branching_factor": ("HAIL_INDEX_BRANCHING_FACTOR", None),
"rng_nonce": ("HAIL_RNG_NONCE", "0x0"),
"profile": ("HAIL_PROFILE", None),
}
def _valid_flags(self) -> AbstractSet[str]:
return self._flags_env_vars_and_defaults.keys()
@abc.abstractmethod
def __init__(self):
self._persisted_locations = dict()
self._references = {}
@abc.abstractmethod
def stop(self):
pass
@abc.abstractmethod
def validate_file_scheme(self, url):
pass
@abc.abstractmethod
def execute(self, ir: BaseIR, timed: bool = False) -> Any:
pass
@abc.abstractmethod
async def _async_execute(self, ir, timed=False):
pass
@abc.abstractmethod
def value_type(self, ir):
pass
@abc.abstractmethod
def table_type(self, tir):
pass
@abc.abstractmethod
def matrix_type(self, mir):
pass
@abc.abstractmethod
def load_references_from_dataset(self, path):
pass
@abc.abstractmethod
def from_fasta_file(self, name, fasta_file, index_file, x_contigs, y_contigs, mt_contigs, par):
pass
def add_reference(self, rg):
self._references[rg.name] = rg
self._add_reference_to_scala_backend(rg)
def _add_reference_to_scala_backend(self, rg):
pass
def get_reference(self, name):
return self._references[name]
def initialize_references(self):
from hail.genetics.reference_genome import ReferenceGenome
jar_path = pkg_resources.resource_filename(__name__, 'hail-all-spark.jar')
for path_in_jar in BUILTIN_REFERENCE_RESOURCE_PATHS.values():
rg_config = orjson.loads(zipfile.ZipFile(jar_path).open(path_in_jar).read())
rg = ReferenceGenome._from_config(rg_config, _builtin=True)
self._references[rg.name] = rg
def remove_reference(self, name):
del self._references[name]
self._remove_reference_from_scala_backend(name)
def _remove_reference_from_scala_backend(self, name):
pass
@abc.abstractmethod
def add_sequence(self, name, fasta_file, index_file):
pass
@abc.abstractmethod
def remove_sequence(self, name):
pass
@abc.abstractmethod
def add_liftover(self, name, chain_file, dest_reference_genome):
pass
@abc.abstractmethod
def remove_liftover(self, name, dest_reference_genome):
pass
@abc.abstractmethod
def parse_vcf_metadata(self, path):
pass
@property
@abc.abstractmethod
def logger(self):
pass
@property
@abc.abstractmethod
def fs(self) -> FS:
pass
@abc.abstractmethod
def import_fam(self, path: str, quant_pheno: bool, delimiter: str, missing: str):
pass
def persist(self, dataset: Dataset) -> Dataset:
from hail.context import TemporaryFilename
tempfile = TemporaryFilename(prefix=f'persist_{type(dataset).__name__}')
persisted = dataset.checkpoint(tempfile.__enter__())
self._persisted_locations[persisted] = (tempfile, dataset)
return persisted
def unpersist(self, dataset: Dataset) -> Dataset:
tempfile, unpersisted = self._persisted_locations.pop(dataset, (None, None))
if tempfile is None:
return dataset
tempfile.__exit__(None, None, None)
return unpersisted
@abc.abstractmethod
def register_ir_function(self,
name: str,
type_parameters: Union[Tuple[HailType, ...], List[HailType]],
value_parameter_names: Union[Tuple[str, ...], List[str]],
value_parameter_types: Union[Tuple[HailType, ...], List[HailType]],
return_type: HailType,
body: Expression):
pass
@abc.abstractmethod
def _is_registered_ir_function_name(self, name: str) -> bool:
pass
@abc.abstractmethod
def persist_expression(self, expr: Expression) -> Expression:
pass
def _initialize_flags(self, initial_flags: Dict[str, str]) -> None:
self.set_flags(**{
k: unchecked_configuration_of('query', k, None, default, deprecated_envvar=deprecated_envvar)
for k, (deprecated_envvar, default) in Backend._flags_env_vars_and_defaults.items()
if k not in initial_flags
}, **initial_flags)
@abc.abstractmethod
def set_flags(self, **flags: Mapping[str, str]):
"""Set Hail flags."""
pass
@abc.abstractmethod
def get_flags(self, *flags) -> Mapping[str, str]:
"""Mapping of Hail flags."""
pass
@property
@abc.abstractmethod
def requires_lowering(self):
pass