#
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# 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
try:
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 (
ensure_optimize_dataframe_graph,
global_dask_client,
set_client_deprecated,
)
from merlin.dag import Graph
from merlin.io import Dataset
from merlin.io.worker import clean_worker_cache
from merlin.schema import Schema
from nvtabular.ops import StatOperator
from nvtabular.workflow.node import WorkflowNode
LOG = logging.getLogger("nvtabular")
if TYPE_CHECKING:
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
workflow.fit(merlin.io.Dataset(TRAIN_PATH))
# transform the training and validation datasets and write out as parquet
workflow.transform(merlin.io.Dataset(TRAIN_PATH)).to_parquet(output_path=TRAIN_OUT_PATH)
workflow.transform(merlin.io.Dataset(VALID_PATH)).to_parquet(output_path=VALID_OUT_PATH)
Parameters
----------
output_node: WorkflowNode
The last node in the graph of operators this workflow should apply
"""
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 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 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(op.fit(workflow_node.input_columns, 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
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 fs.open(fs.sep.join([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 fs.open(fs.sep.join([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(fs.open(fs.sep.join([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(fs.open(fs.sep.join([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:
dask_client.run(clean_worker_cache)
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