Source code for nvtabular.workflow.workflow

# Copyright (c) 2021, NVIDIA CORPORATION.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
import json
import logging
import sys
import time
import warnings
from typing import TYPE_CHECKING, Optional

import cloudpickle
import fsspec

    import cudf
except ImportError:
    cudf = None
import dask
import pandas as pd
from dask.core import flatten

import nvtabular
from merlin.core.dispatch import concat_columns, is_list_dtype, list_val_dtype
from merlin.core.utils import (
from merlin.dag import Graph
from import Dataset
from import clean_worker_cache
from merlin.schema import Schema
from nvtabular.ops import StatOperator
from nvtabular.workflow.node import WorkflowNode

LOG = logging.getLogger("nvtabular")

    import distributed

[docs]class Workflow: """ The Workflow class applies a graph of operations onto a dataset, letting you transform datasets to do feature engineering and preprocessing operations. This class follows an API similar to Transformers in sklearn: we first ``fit`` the workflow by calculating statistics on the dataset, and then once fit we can ``transform`` datasets by applying these statistics. Example usage:: # define a graph of operations cat_features = CAT_COLUMNS >> nvtabular.ops.Categorify() cont_features = CONT_COLUMNS >> nvtabular.ops.FillMissing() >> nvtabular.ops.Normalize() workflow = nvtabular.Workflow(cat_features + cont_features + "label") # calculate statistics on the training dataset # transform the training and validation datasets and write out as parquet workflow.transform( workflow.transform( Parameters ---------- output_node: WorkflowNode The last node in the graph of operators this workflow should apply """
[docs] def __init__(self, output_node: WorkflowNode, client: Optional["distributed.Client"] = None): # Deprecate `client` if client is not None: set_client_deprecated(client, "Workflow") self.graph = Graph(output_node)
[docs] def transform(self, dataset: Dataset) -> Dataset: """Transforms the dataset by applying the graph of operators to it. Requires the ``fit`` method to have already been called, or calculated statistics to be loaded from disk This method returns a Dataset object, with the transformations lazily loaded. None of the actual computation will happen until the produced Dataset is consumed, or written out to disk. Parameters ----------- dataset: Dataset Input dataset to transform Returns ------- Dataset Transformed Dataset with the workflow graph applied to it """ return self._transform_impl(dataset)
[docs] def fit_schema(self, input_schema: Schema): """Fits the schema onto the workflow, computing the Schema for each node in the Workflow Graph Parameters ---------- input_schema : Schema The input schema to use Returns ------- Workflow This workflow where each node in the graph has a fitted schema """ self.graph.construct_schema(input_schema) return self
@property def input_dtypes(self): return self.graph.input_dtypes @property def input_schema(self): return self.graph.input_schema @property def output_schema(self): return self.graph.output_schema @property def output_dtypes(self): return self.graph.output_dtypes @property def output_node(self): return self.graph.output_node def _input_columns(self): return self.graph._input_columns()
[docs] def remove_inputs(self, input_cols) -> "Workflow": """Removes input columns from the workflow. This is useful for the case of inference where you might need to remove label columns from the processed set. Parameters ---------- input_cols : list of str List of column names to Returns ------- Workflow This workflow with the input columns removed from it See Also -------- merlin.dag.Graph.remove_inputs """ self.graph.remove_inputs(input_cols) return self
[docs] def fit(self, dataset: Dataset) -> "Workflow": """Calculates statistics for this workflow on the input dataset Parameters ----------- dataset: Dataset The input dataset to calculate statistics for. If there is a train/test split this data should be the training dataset only. Returns ------- Workflow This Workflow with statistics calculated on it """ self._clear_worker_cache() self.clear_stats() if not self.graph.output_schema: self.graph.construct_schema(dataset.schema) ddf = dataset.to_ddf(columns=self._input_columns()) # Get a dictionary mapping all StatOperators we need to fit to a set of any dependent # StatOperators (having StatOperators that depend on the output of other StatOperators # means that will have multiple phases in the fit cycle here) stat_ops = { op: _get_stat_ops(op.parents_with_dependencies) for op in _get_stat_ops([self.graph.output_node]) } while stat_ops: # get all the StatOperators that we can currently call fit on (no outstanding # dependencies) current_phase = [op for op, dependencies in stat_ops.items() if not dependencies] if not current_phase: # this shouldn't happen, but lets not infinite loop just in case raise RuntimeError("failed to find dependency-free StatOperator to fit") stats, ops = [], [] for workflow_node in current_phase: # Check for additional input columns that aren't generated by parents addl_input_cols = set() if workflow_node.parents: upstream_output_cols = sum( [ upstream.output_columns for upstream in workflow_node.parents_with_dependencies ], nvtabular.ColumnSelector(), ) addl_input_cols = set(workflow_node.input_columns.names) - set( upstream_output_cols.names ) # apply transforms necessary for the inputs to the current column group, ignoring # the transforms from the statop itself transformed_ddf = ensure_optimize_dataframe_graph( ddf=_transform_ddf( ddf, workflow_node.parents_with_dependencies, additional_columns=addl_input_cols, capture_dtypes=True, ) ) op = workflow_node.op try: stats.append(, transformed_ddf)) ops.append(op) except Exception: LOG.exception("Failed to fit operator %s", workflow_node.op) raise dask_client = global_dask_client() if dask_client: results = [r.result() for r in dask_client.compute(stats)] else: results = dask.compute(stats, scheduler="synchronous")[0] for computed_stats, op in zip(results, ops): op.fit_finalize(computed_stats) # Remove all the operators we processed in this phase, and remove # from the dependencies of other ops too for stat_op in current_phase: stat_ops.pop(stat_op) for dependencies in stat_ops.values(): dependencies.difference_update(current_phase) # This captures the output dtypes of operators like LambdaOp where # the dtype can't be determined without running the transform self._transform_impl(dataset, capture_dtypes=True).sample_dtypes() self.graph.construct_schema(dataset.schema, preserve_dtypes=True) return self
[docs] def fit_transform(self, dataset: Dataset) -> Dataset: """Convenience method to both fit the workflow and transform the dataset in a single call. Equivalent to calling ```` followed by ``workflow.transform(dataset)`` Parameters ----------- dataset: Dataset Input dataset to calculate statistics on, and transform results Returns ------- Dataset Transformed Dataset with the workflow graph applied to it See Also -------- fit transform """ return self.transform(dataset)
def _transform_impl(self, dataset: Dataset, capture_dtypes=False): self._clear_worker_cache() if not self.graph.output_schema: self.graph.construct_schema(dataset.schema) ddf = dataset.to_ddf(columns=self._input_columns()) return Dataset( _transform_ddf( ddf, self.output_node, self.output_dtypes, capture_dtypes=capture_dtypes ), cpu=dataset.cpu, base_dataset=dataset.base_dataset, schema=self.output_schema, )
[docs] def save(self, path): """Save this workflow to disk Parameters ---------- path: str The path to save the workflow to """ # avoid a circular import getting the version from nvtabular import __version__ as nvt_version fs = fsspec.get_fs_token_paths(path)[0] fs.makedirs(path, exist_ok=True) # point all stat ops to store intermediate output (parquet etc) at the path # this lets us easily bundle for stat in _get_stat_ops([self.output_node]): stat.op.set_storage_path(path, copy=True) # generate a file of all versions used to generate this bundle lib = cudf if cudf else pd with[path, "metadata.json"]), "w") as o: json.dump( { "versions": { "nvtabular": nvt_version, lib.__name__: lib.__version__, "python": sys.version, }, "generated_timestamp": int(time.time()), }, o, ) # dump out the full workflow (graph/stats/operators etc) using cloudpickle with[path, "workflow.pkl"]), "wb") as o: cloudpickle.dump(self, o)
[docs] @classmethod def load(cls, path, client=None) -> "Workflow": """Load up a saved workflow object from disk Parameters ---------- path: str The path to load the workflow from client: distributed.Client, optional The Dask distributed client to use for multi-gpu processing and multi-node processing Returns ------- Workflow The Workflow loaded from disk """ # avoid a circular import getting the version from nvtabular import __version__ as nvt_version fs = fsspec.get_fs_token_paths(path)[0] # check version information from the metadata blob, and warn if we have a mismatch meta = json.load([path, "metadata.json"]))) def parse_version(version): return version.split(".")[:2] def check_version(stored, current, name): if parse_version(stored) != parse_version(current): warnings.warn( f"Loading workflow generated with {name} version {stored} " f"- but we are running {name} {current}. This might cause issues" ) # make sure we don't have any major/minor version conflicts between the stored worklflow # and the current environment lib = cudf if cudf else pd versions = meta["versions"] check_version(versions["nvtabular"], nvt_version, "nvtabular") check_version(versions["python"], sys.version, "python") if lib.__name__ in versions: check_version(versions[lib.__name__], lib.__version__, lib.__name__) else: expected = "GPU" if "cudf" in versions else "CPU" warnings.warn(f"Loading workflow generated on {expected}") # load up the workflow object di workflow = cloudpickle.load([path, "workflow.pkl"]), "rb")) workflow.client = client # we might have been copied since saving, update all the stat ops # with the new path to their storage locations for stat in _get_stat_ops([workflow.output_node]): stat.op.set_storage_path(path, copy=False) return workflow
def __getstate__(self): # dask client objects aren't picklable - exclude from saved representation return {k: v for k, v in self.__dict__.items() if k != "client"}
[docs] def clear_stats(self): """Removes calculated statistics from each node in the workflow graph See Also -------- nvtabular.ops.stat_operator.StatOperator.clear """ for stat in _get_stat_ops([self.output_node]): stat.op.clear()
def _clear_worker_cache(self): # Clear worker caches to be "safe" dask_client = global_dask_client() if dask_client: else: clean_worker_cache()
def _transform_ddf(ddf, workflow_nodes, meta=None, additional_columns=None, capture_dtypes=False): # Check if we are only selecting columns (no transforms). # If so, we should perform column selection at the ddf level. # Otherwise, Dask will not push the column selection into the # IO function. if not workflow_nodes: return ddf[_get_unique(additional_columns)] if additional_columns else ddf if isinstance(workflow_nodes, WorkflowNode): workflow_nodes = [workflow_nodes] columns = list(flatten(wfn.output_columns.names for wfn in workflow_nodes)) columns += additional_columns if additional_columns else [] if isinstance(meta, dict) and isinstance(ddf._meta, pd.DataFrame): dtypes = meta meta = type(ddf._meta)({k: [] for k in columns}) for column, dtype in dtypes.items(): meta[column] = meta[column].astype(dtype) elif not meta: # TODO: constructing meta like this loses dtype information on the ddf # and sets it all to 'float64'. We should propagate dtype information along # with column names in the columngroup graph. This currently only # happesn during intermediate 'fit' transforms, so as long as statoperators # don't require dtype information on the DDF this doesn't matter all that much meta = type(ddf._meta)({k: [] for k in columns}) return ddf.map_partitions( _transform_partition, workflow_nodes, additional_columns=additional_columns, capture_dtypes=capture_dtypes, meta=meta, enforce_metadata=False, ) def _get_stat_ops(nodes): return Graph.get_nodes_by_op_type(nodes, StatOperator) def _get_unique(cols): # Need to preserve order in unique-column list return list({x: x for x in cols}.keys()) def _transform_partition(root_df, workflow_nodes, additional_columns=None, capture_dtypes=False): """Transforms a single partition by appyling all operators in a WorkflowNode""" output = None for node in workflow_nodes: node_input_cols = _get_unique(node.input_schema.column_names) node_output_cols = _get_unique(node.output_schema.column_names) addl_input_cols = set(node.dependency_columns.names) # Build input dataframe if node.parents_with_dependencies: # If there are parents, collect their outputs # to build the current node's input input_df = None seen_columns = None for parent in node.parents_with_dependencies: parent_output_cols = _get_unique(parent.output_schema.column_names) parent_df = _transform_partition(root_df, [parent], capture_dtypes=capture_dtypes) if input_df is None or not len(input_df): input_df = parent_df[parent_output_cols] seen_columns = set(parent_output_cols) else: new_columns = set(parent_output_cols) - seen_columns input_df = concat_columns([input_df, parent_df[list(new_columns)]]) seen_columns.update(new_columns) # Check for additional input columns that aren't generated by parents # and fetch them from the root dataframe unseen_columns = set(node.input_schema.column_names) - seen_columns addl_input_cols = addl_input_cols.union(unseen_columns) # TODO: Find a better way to remove dupes addl_input_cols = addl_input_cols - set(input_df.columns) if addl_input_cols: input_df = concat_columns([input_df, root_df[list(addl_input_cols)]]) else: # If there are no parents, this is an input node, # so pull columns directly from root df input_df = root_df[node_input_cols + list(addl_input_cols)] # Compute the node's output if node.op: try: # use input_columns to ensure correct grouping (subgroups) selection = node.input_columns.resolve(node.input_schema) output_df = node.op.transform(selection, input_df) # Update or validate output_df dtypes for col_name, output_col_schema in node.output_schema.column_schemas.items(): col_series = output_df[col_name] col_dtype = col_series.dtype is_list = is_list_dtype(col_series) if is_list: col_dtype = list_val_dtype(col_series) output_df_schema = output_col_schema.with_dtype( col_dtype, is_list=is_list, is_ragged=is_list ) if capture_dtypes: node.output_schema.column_schemas[col_name] = output_df_schema elif len(output_df): if output_col_schema.dtype != output_df_schema.dtype: raise TypeError( f"Dtype discrepancy detected for column {col_name}: " f"operator {node.op.label} reported dtype " f"`{output_col_schema.dtype}` but returned dtype " f"`{output_df_schema.dtype}`." ) except Exception: LOG.exception("Failed to transform operator %s", node.op) raise if output_df is None: raise RuntimeError("Operator %s didn't return a value during transform" % node.op) else: output_df = input_df # Combine output across node loop iterations # dask needs output to be in the same order defined as meta, reorder partitions here # this also selects columns (handling the case of removing columns from the output using # "-" overload) if output is None: output = output_df[node_output_cols] else: output = concat_columns([output, output_df[node_output_cols]]) if additional_columns: output = concat_columns([output, root_df[_get_unique(additional_columns)]]) return output