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eland/eland/etl.py
Bart Broere 75c57b0775
Support Pandas 2 (#742) 
* Fix test setup to match pandas 2.0 demands

* Use the now deprecated _append method

(Better solution might exist)

* Deal with numeric_only being removed in metrics test

* Skip mad metric for other pandas versions

* Account for differences between pandas versions in describe methods

* Run black

* Check Pandas version first

* Mirror behaviour of installed Pandas version when running value_counts

* Allow passing arguments to the individual asserters

* Fix for method _construct_axes_from_arguments no longer existing

* Skip mad metric if it does not exist

* Account for pandas 2.0 timestamp default behaviour

* Deal with empty vs other inferred data types

* Account for default datetime precision change

* Run Black

* Solution for differences in inferred_type only

* Fix csv and json issues

* Skip two doctests

* Passing a set as indexer is no longer allowed

* Don't validate output where it differs between Pandas versions in the environment

* Update test matrix and packaging metadata

* Update version of Python in the docs

* Update Python version in demo notebook

* Match noxfile

* Symmetry

* Fix trailing comma in JSON

* Revert some changes in setup.py to fix building the documentation

* Revert "Revert some changes in setup.py to fix building the documentation"

This reverts commit ea9879753129d8d8390b3cbbce57155a8b4fb346.

* Use PANDAS_VERSION from eland.common

* Still skip the doctest, but make the output pandas 2 instead of 1

* Still skip doctest, but switch to pandas 2 output

* Prepare for pandas 3

* Reference the right column

* Ignore output in tests but switch to pandas 2 output

* Add line comment about NBVAL_IGNORE_OUTPUT

* Restore missing line and add stderr cell

* Use non-private method instead

* Fix indentation and parameter issues

* If index is not specified, and pandas 1 is present, set it to True

From pandas 2 and upwards, index is set to None by default

* Run black

* Newer version of black might have different opinions?

* Add line comment

* Remove unused import

* Add reason for ignore statement

* Add reason for skip

---------

Co-authored-by: Quentin Pradet <quentin.pradet@elastic.co>
2025-02-04 17:43:43 +04:00

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# Licensed to Elasticsearch B.V. under one or more contributor
# license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright
# ownership. Elasticsearch B.V. licenses this file to you 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 csv
import warnings
from collections import deque
from typing import Any, Dict, Generator, List, Mapping, Optional, Tuple, Union
import pandas as pd # type: ignore
from elasticsearch import Elasticsearch
from elasticsearch.helpers import parallel_bulk
from eland import DataFrame
from eland.common import DEFAULT_CHUNK_SIZE, PANDAS_VERSION, ensure_es_client
from eland.field_mappings import FieldMappings, verify_mapping_compatibility
try:
from pandas.io.parsers import _c_parser_defaults # type: ignore
except ImportError:
from pandas.io.parsers.readers import _c_parser_defaults # type: ignore
_DEFAULT_LOW_MEMORY: bool = _c_parser_defaults["low_memory"]
def pandas_to_eland(
pd_df: pd.DataFrame,
es_client: Union[str, List[str], Tuple[str, ...], Elasticsearch],
es_dest_index: str,
es_if_exists: str = "fail",
es_refresh: bool = False,
es_dropna: bool = False,
es_type_overrides: Optional[Mapping[str, str]] = None,
es_verify_mapping_compatibility: bool = True,
thread_count: int = 4,
chunksize: Optional[int] = None,
use_pandas_index_for_es_ids: bool = True,
) -> DataFrame:
"""
Append a pandas DataFrame to an Elasticsearch index.
Mainly used in testing.
Modifies the elasticsearch destination index
Parameters
----------
es_client: Elasticsearch client argument(s)
- elasticsearch-py parameters or
- elasticsearch-py instance
es_dest_index: str
Name of Elasticsearch index to be appended to
es_if_exists : {'fail', 'replace', 'append'}, default 'fail'
How to behave if the index already exists.
- fail: Raise a ValueError.
- replace: Delete the index before inserting new values.
- append: Insert new values to the existing index. Create if does not exist.
es_refresh: bool, default 'False'
Refresh es_dest_index after bulk index
es_dropna: bool, default 'False'
* True: Remove missing values (see pandas.Series.dropna)
* False: Include missing values - may cause bulk to fail
es_type_overrides: dict, default None
Dict of field_name: es_data_type that overrides default es data types
es_verify_mapping_compatibility: bool, default 'True'
* True: Verify that the dataframe schema matches the Elasticsearch index schema
* False: Do not verify schema
thread_count: int
number of the threads to use for the bulk requests
chunksize: int, default None
Number of pandas.DataFrame rows to read before bulk index into Elasticsearch
use_pandas_index_for_es_ids: bool, default 'True'
* True: pandas.DataFrame.index fields will be used to populate Elasticsearch '_id' fields.
* False: Ignore pandas.DataFrame.index when indexing into Elasticsearch
Returns
-------
eland.Dataframe
eland.DataFrame referencing data in destination_index
Examples
--------
>>> pd_df = pd.DataFrame(data={'A': 3.141,
... 'B': 1,
... 'C': 'foo',
... 'D': pd.Timestamp('20190102'),
... 'E': [1.0, 2.0, 3.0],
... 'F': False,
... 'G': [1, 2, 3],
... 'H': 'Long text - to be indexed as es type text'},
... index=['0', '1', '2'])
>>> type(pd_df)
<class 'pandas.core.frame.DataFrame'>
>>> pd_df
A B ... G H
0 3.141 1 ... 1 Long text - to be indexed as es type text
1 3.141 1 ... 2 Long text - to be indexed as es type text
2 3.141 1 ... 3 Long text - to be indexed as es type text
<BLANKLINE>
[3 rows x 8 columns]
>>> pd_df.dtypes # doctest skip required for pandas < 2 # doctest: +SKIP
A float64
B int64
C object
D datetime64[s]
E float64
F bool
G int64
H object
dtype: object
Convert `pandas.DataFrame` to `eland.DataFrame` - this creates an Elasticsearch index called `pandas_to_eland`.
Overwrite existing Elasticsearch index if it exists `if_exists="replace"`, and sync index so it is
readable on return `refresh=True`
>>> ed_df = ed.pandas_to_eland(pd_df,
... 'http://localhost:9200',
... 'pandas_to_eland',
... es_if_exists="replace",
... es_refresh=True,
... es_type_overrides={'H':'text'}) # index field 'H' as text not keyword
>>> type(ed_df)
<class 'eland.dataframe.DataFrame'>
>>> ed_df
A B ... G H
0 3.141 1 ... 1 Long text - to be indexed as es type text
1 3.141 1 ... 2 Long text - to be indexed as es type text
2 3.141 1 ... 3 Long text - to be indexed as es type text
<BLANKLINE>
[3 rows x 8 columns]
>>> ed_df.dtypes
A float64
B int64
C object
D datetime64[ns]
E float64
F bool
G int64
H object
dtype: object
See Also
--------
eland.eland_to_pandas: Create a pandas.Dataframe from eland.DataFrame
"""
if chunksize is None:
chunksize = DEFAULT_CHUNK_SIZE
mapping = FieldMappings._generate_es_mappings(pd_df, es_type_overrides)
es_client = ensure_es_client(es_client)
# If table exists, check if_exists parameter
if es_client.indices.exists(index=es_dest_index):
if es_if_exists == "fail":
raise ValueError(
f"Could not create the index [{es_dest_index}] because it "
f"already exists. "
f"Change the 'es_if_exists' parameter to "
f"'append' or 'replace' data."
)
elif es_if_exists == "replace":
es_client.indices.delete(index=es_dest_index)
es_client.indices.create(index=es_dest_index, mappings=mapping["mappings"])
elif es_if_exists == "append" and es_verify_mapping_compatibility:
dest_mapping = es_client.indices.get_mapping(index=es_dest_index)[
es_dest_index
]
verify_mapping_compatibility(
ed_mapping=mapping,
es_mapping=dest_mapping,
es_type_overrides=es_type_overrides,
)
else:
es_client.indices.create(index=es_dest_index, mappings=mapping["mappings"])
def action_generator(
pd_df: pd.DataFrame,
es_dropna: bool,
use_pandas_index_for_es_ids: bool,
es_dest_index: str,
) -> Generator[Dict[str, Any], None, None]:
for row in pd_df.iterrows():
if es_dropna:
values = row[1].dropna().to_dict()
else:
values = row[1].to_dict()
if use_pandas_index_for_es_ids:
# Use index as _id
id = row[0]
action = {"_index": es_dest_index, "_source": values, "_id": str(id)}
else:
action = {"_index": es_dest_index, "_source": values}
yield action
# parallel_bulk is lazy generator so use deque to consume them immediately
# maxlen = 0 because don't need results of parallel_bulk
deque(
parallel_bulk(
client=es_client,
actions=action_generator(
pd_df, es_dropna, use_pandas_index_for_es_ids, es_dest_index
),
thread_count=thread_count,
chunk_size=int(chunksize / thread_count),
),
maxlen=0,
)
if es_refresh:
es_client.indices.refresh(index=es_dest_index)
return DataFrame(es_client, es_dest_index)
def eland_to_pandas(ed_df: DataFrame, show_progress: bool = False) -> pd.DataFrame:
"""
Convert an eland.Dataframe to a pandas.DataFrame
**Note: this loads the entire Elasticsearch index into in core pandas.DataFrame structures. For large
indices this can create significant load on the Elasticsearch cluster and require signficant memory**
Parameters
----------
ed_df: eland.DataFrame
The source eland.Dataframe referencing the Elasticsearch index
show_progress: bool
Output progress of option to stdout? By default False.
Returns
-------
pandas.Dataframe
pandas.DataFrame contains all rows and columns in eland.DataFrame
Examples
--------
>>> ed_df = ed.DataFrame('http://localhost:9200', 'flights').head()
>>> type(ed_df)
<class 'eland.dataframe.DataFrame'>
>>> ed_df
AvgTicketPrice Cancelled ... dayOfWeek timestamp
0 841.265642 False ... 0 2018-01-01 00:00:00
1 882.982662 False ... 0 2018-01-01 18:27:00
2 190.636904 False ... 0 2018-01-01 17:11:14
3 181.694216 True ... 0 2018-01-01 10:33:28
4 730.041778 False ... 0 2018-01-01 05:13:00
<BLANKLINE>
[5 rows x 28 columns]
Convert `eland.DataFrame` to `pandas.DataFrame` (Note: this loads entire Elasticsearch index into core memory)
>>> pd_df = ed.eland_to_pandas(ed_df)
>>> type(pd_df)
<class 'pandas.core.frame.DataFrame'>
>>> pd_df
AvgTicketPrice Cancelled ... dayOfWeek timestamp
0 841.265642 False ... 0 2018-01-01 00:00:00
1 882.982662 False ... 0 2018-01-01 18:27:00
2 190.636904 False ... 0 2018-01-01 17:11:14
3 181.694216 True ... 0 2018-01-01 10:33:28
4 730.041778 False ... 0 2018-01-01 05:13:00
<BLANKLINE>
[5 rows x 28 columns]
Convert `eland.DataFrame` to `pandas.DataFrame` and show progress every 10000 rows
>>> pd_df = ed.eland_to_pandas(ed.DataFrame('http://localhost:9200', 'flights'), show_progress=True) # doctest: +SKIP
2020-01-29 12:43:36.572395: read 10000 rows
2020-01-29 12:43:37.309031: read 13059 rows
See Also
--------
eland.pandas_to_eland: Create an eland.Dataframe from pandas.DataFrame
"""
return ed_df.to_pandas(show_progress=show_progress)
def csv_to_eland( # type: ignore
filepath_or_buffer,
es_client: Union[str, List[str], Tuple[str, ...], Elasticsearch],
es_dest_index: str,
es_if_exists: str = "fail",
es_refresh: bool = False,
es_dropna: bool = False,
es_type_overrides: Optional[Mapping[str, str]] = None,
sep=",",
delimiter=None,
# Column and Index Locations and Names
header="infer",
names=None,
index_col=None,
usecols=None,
squeeze=None,
prefix=None,
mangle_dupe_cols=None,
# General Parsing Configuration
dtype=None,
engine=None,
converters=None,
true_values=None,
false_values=None,
skipinitialspace=False,
skiprows=None,
skipfooter=0,
nrows=None,
# Iteration
# iterator=False,
chunksize=None,
# NA and Missing Data Handling
na_values=None,
keep_default_na=True,
na_filter=True,
verbose=False,
skip_blank_lines=True,
# Datetime Handling
parse_dates=False,
infer_datetime_format=False,
keep_date_col=False,
date_parser=None,
dayfirst=False,
cache_dates=True,
# Quoting, Compression, and File Format
compression="infer",
thousands=None,
decimal=b".",
lineterminator=None,
quotechar='"',
quoting=csv.QUOTE_MINIMAL,
doublequote=True,
escapechar=None,
comment=None,
encoding=None,
dialect=None,
# Error Handling
warn_bad_lines: bool = True,
error_bad_lines: bool = True,
on_bad_lines: str = "error",
# Internal
delim_whitespace=False,
low_memory: bool = _DEFAULT_LOW_MEMORY,
memory_map=False,
float_precision=None,
**extra_kwargs,
) -> "DataFrame":
"""
Read a comma-separated values (csv) file into eland.DataFrame (i.e. an Elasticsearch index).
**Modifies an Elasticsearch index**
**Note pandas iteration options not supported**
Parameters
----------
es_client: Elasticsearch client argument(s)
- elasticsearch-py parameters or
- elasticsearch-py instance
es_dest_index: str
Name of Elasticsearch index to be appended to
es_if_exists : {'fail', 'replace', 'append'}, default 'fail'
How to behave if the index already exists.
- fail: Raise a ValueError.
- replace: Delete the index before inserting new values.
- append: Insert new values to the existing index. Create if does not exist.
es_dropna: bool, default 'False'
* True: Remove missing values (see pandas.Series.dropna)
* False: Include missing values - may cause bulk to fail
es_type_overrides: dict, default None
Dict of columns: es_type to override default es datatype mappings
chunksize
number of csv rows to read before bulk index into Elasticsearch
Other Parameters
----------------
Parameters derived from :pandas_api_docs:`pandas.read_csv`.
See Also
--------
:pandas_api_docs:`pandas.read_csv`
Notes
-----
iterator not supported
Examples
--------
See if 'churn' index exists in Elasticsearch
>>> from elasticsearch import Elasticsearch # doctest: +SKIP
>>> es = Elasticsearch() # doctest: +SKIP
>>> es.indices.exists(index="churn") # doctest: +SKIP
False
Read 'churn.csv' and use first column as _id (and eland.DataFrame index)
::
# churn.csv
,state,account length,area code,phone number,international plan,voice mail plan,number vmail messages,total day minutes,total day calls,total day charge,total eve minutes,total eve calls,total eve charge,total night minutes,total night calls,total night charge,total intl minutes,total intl calls,total intl charge,customer service calls,churn
0,KS,128,415,382-4657,no,yes,25,265.1,110,45.07,197.4,99,16.78,244.7,91,11.01,10.0,3,2.7,1,0
1,OH,107,415,371-7191,no,yes,26,161.6,123,27.47,195.5,103,16.62,254.4,103,11.45,13.7,3,3.7,1,0
...
>>> ed.csv_to_eland(
... "churn.csv",
... es_client='http://localhost:9200',
... es_dest_index='churn',
... es_refresh=True,
... index_col=0
... ) # doctest: +SKIP
account length area code churn customer service calls ... total night calls total night charge total night minutes voice mail plan
0 128 415 0 1 ... 91 11.01 244.7 yes
1 107 415 0 1 ... 103 11.45 254.4 yes
2 137 415 0 0 ... 104 7.32 162.6 no
3 84 408 0 2 ... 89 8.86 196.9 no
4 75 415 0 3 ... 121 8.41 186.9 no
... ... ... ... ... ... ... ... ... ...
3328 192 415 0 2 ... 83 12.56 279.1 yes
3329 68 415 0 3 ... 123 8.61 191.3 no
3330 28 510 0 2 ... 91 8.64 191.9 no
3331 184 510 0 2 ... 137 6.26 139.2 no
3332 74 415 0 0 ... 77 10.86 241.4 yes
<BLANKLINE>
[3333 rows x 21 columns]
Validate data now exists in 'churn' index:
>>> es.search(index="churn", size=1) # doctest: +SKIP
{'took': 1, 'timed_out': False, '_shards': {'total': 1, 'successful': 1, 'skipped': 0, 'failed': 0}, 'hits': {'total': {'value': 3333, 'relation': 'eq'}, 'max_score': 1.0, 'hits': [{'_index': 'churn', '_id': '0', '_score': 1.0, '_source': {'state': 'KS', 'account length': 128, 'area code': 415, 'phone number': '382-4657', 'international plan': 'no', 'voice mail plan': 'yes', 'number vmail messages': 25, 'total day minutes': 265.1, 'total day calls': 110, 'total day charge': 45.07, 'total eve minutes': 197.4, 'total eve calls': 99, 'total eve charge': 16.78, 'total night minutes': 244.7, 'total night calls': 91, 'total night charge': 11.01, 'total intl minutes': 10.0, 'total intl calls': 3, 'total intl charge': 2.7, 'customer service calls': 1, 'churn': 0}}]}}
TODO - currently the eland.DataFrame may not retain the order of the data in the csv.
"""
kwargs: Dict[str, Any] = {
"sep": sep,
"delimiter": delimiter,
"engine": engine,
"dialect": dialect,
"compression": compression,
# "engine_specified": engine_specified,
"doublequote": doublequote,
"escapechar": escapechar,
"quotechar": quotechar,
"quoting": quoting,
"skipinitialspace": skipinitialspace,
"lineterminator": lineterminator,
"header": header,
"index_col": index_col,
"names": names,
"prefix": prefix,
"skiprows": skiprows,
"skipfooter": skipfooter,
"na_values": na_values,
"true_values": true_values,
"false_values": false_values,
"keep_default_na": keep_default_na,
"thousands": thousands,
"comment": comment,
"decimal": decimal,
"parse_dates": parse_dates,
"keep_date_col": keep_date_col,
"dayfirst": dayfirst,
"date_parser": date_parser,
"cache_dates": cache_dates,
"nrows": nrows,
# "iterator": iterator,
"chunksize": chunksize,
"converters": converters,
"dtype": dtype,
"usecols": usecols,
"verbose": verbose,
"encoding": encoding,
"memory_map": memory_map,
"float_precision": float_precision,
"na_filter": na_filter,
"delim_whitespace": delim_whitespace,
"warn_bad_lines": warn_bad_lines,
"error_bad_lines": error_bad_lines,
"on_bad_lines": on_bad_lines,
"low_memory": low_memory,
"infer_datetime_format": infer_datetime_format,
"skip_blank_lines": skip_blank_lines,
**extra_kwargs,
}
if chunksize is None:
kwargs["chunksize"] = DEFAULT_CHUNK_SIZE
if PANDAS_VERSION >= (1, 3):
# Bug in Pandas v1.3.0
# If names and prefix both passed as None, it's considering them as specified values and throwing ValueError
# Ref: https://github.com/pandas-dev/pandas/issues/42387
if kwargs["names"] is None and kwargs["prefix"] is None:
kwargs.pop("prefix")
if kwargs["warn_bad_lines"] is True:
kwargs["on_bad_lines"] = "warn"
if kwargs["error_bad_lines"] is True:
kwargs["on_bad_lines"] = "error"
kwargs.pop("warn_bad_lines")
kwargs.pop("error_bad_lines")
else:
if on_bad_lines == "warn":
kwargs["warn_bad_lines"] = True
if on_bad_lines == "error":
kwargs["error_bad_lines"] = True
kwargs.pop("on_bad_lines")
if "squeeze" in kwargs:
kwargs.pop("squeeze")
warnings.warn(
"This argument no longer works, use .squeeze('columns') on your DataFrame instead"
)
if "mangle_dupe_cols" in kwargs:
kwargs.pop("mangle_dupe_cols")
warnings.warn(
"The mangle_dupe_cols argument no longer works. Furthermore, "
"duplicate columns will automatically get a number suffix."
)
# read csv in chunks to pandas DataFrame and dump to eland DataFrame (and Elasticsearch)
reader = pd.read_csv(filepath_or_buffer, **kwargs)
first_write = True
for chunk in reader:
pandas_to_eland(
chunk,
es_client,
es_dest_index,
chunksize=chunksize,
es_refresh=es_refresh,
es_dropna=es_dropna,
es_type_overrides=es_type_overrides,
# es_if_exists should be 'append' except on the first call to pandas_to_eland()
es_if_exists=(es_if_exists if first_write else "append"),
)
first_write = False
# Now create an eland.DataFrame that references the new index
return DataFrame(es_client, es_index_pattern=es_dest_index)
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