mirror of
https://github.com/elastic/eland.git
synced 2025-07-11 00:02:14 +08:00
Checkpoint code before attempting major investigation into using modin
This commit is contained in:
Stephen Dodson
parent
30df901fce
commit
5e10b2e818
@ -1,7 +1,7 @@
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from .utils import *
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from .client import *
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from .ndframe import *
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from .index import *
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from .mappings import *
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from .dataframe import *
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from .series import *
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from .dataframe import *
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from .utils import *
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@ -1,4 +1,5 @@
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from elasticsearch import Elasticsearch
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from elasticsearch import helpers
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class Client():
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"""
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@ -17,7 +18,13 @@ class Client():
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def indices(self):
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return self.es.indices
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def bulk(self, actions, refresh=False):
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return helpers.bulk(self.es, actions, refresh=refresh)
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def scan(self, **kwargs):
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return helpers.scan(self.es, **kwargs)
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def search(self, **kwargs):
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return self.es.search(**kwargs)
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@ -32,9 +32,14 @@ from pandas.io.formats.printing import pprint_thing
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from pandas.compat import StringIO
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from pandas.io.common import _expand_user, _stringify_path
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from pandas.io.formats import console
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from pandas.core import common as com
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from eland import NDFrame
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from eland import Index
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from eland import Series
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class DataFrame(NDFrame):
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@ -217,10 +222,6 @@ class DataFrame(NDFrame):
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return num_rows, num_columns
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@property
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def columns(self):
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return super()._columns
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def set_index(self, index_field):
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copy = self.copy()
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copy._index = Index(index_field)
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@ -265,7 +266,6 @@ class DataFrame(NDFrame):
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def __getitem__(self, key):
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# NOTE: there is a difference between pandas here.
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# e.g. df['a'] returns pd.Series, df[['a','b']] return pd.DataFrame
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# we always return DataFrame - TODO maybe create eland.Series at some point...
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# Implementation mainly copied from pandas v0.24.2
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# (https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html)
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@ -291,10 +291,12 @@ class DataFrame(NDFrame):
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# We are left with two options: a single key, and a collection of keys,
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columns = []
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is_single_key = False
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if isinstance(key, str):
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if not self._mappings.is_source_field(key):
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raise TypeError('Column does not exist: [{0}]'.format(key))
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columns.append(key)
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is_single_key = True
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elif isinstance(key, list):
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columns.extend(key)
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else:
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@ -303,7 +305,18 @@ class DataFrame(NDFrame):
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mappings = self._filter_mappings(columns)
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# Return new eland.DataFrame with modified mappings
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return DataFrame(self._client, self._index_pattern, mappings=mappings)
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if is_single_key:
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return Series(self._client, self._index_pattern, mappings=mappings)
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else:
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return DataFrame(self._client, self._index_pattern, mappings=mappings)
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def __getattr__(self, name):
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# Note: obj.x will always call obj.__getattribute__('x') prior to
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# calling obj.__getattr__('x').
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mappings = self._filter_mappings([name])
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return Series(self._client, self._index_pattern, mappings=mappings)
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def copy(self):
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# TODO - test and validate...may need deep copying
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@ -373,7 +386,8 @@ class DataFrame(NDFrame):
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result = _buf.getvalue()
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return result
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def to_pandas(selfs):
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return super()._to_pandas()
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# From pandas.DataFrame
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def _put_str(s, space):
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@ -2,6 +2,7 @@ import warnings
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import pandas as pd
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from pandas.core.dtypes.common import (is_float_dtype, is_bool_dtype, is_integer_dtype, is_datetime_or_timedelta_dtype, is_string_dtype)
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class Mappings():
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"""
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@ -217,6 +218,7 @@ class Mappings():
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return capability_matrix_df.sort_index()
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@staticmethod
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def _es_dtype_to_pd_dtype(es_dtype):
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"""
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Mapping Elasticsearch types to pandas dtypes
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@ -259,6 +261,84 @@ class Mappings():
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# Return 'object' for all unsupported TODO - investigate how different types could be supported
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return 'object'
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@staticmethod
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def _pd_dtype_to_es_dtype(pd_dtype):
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"""
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Mapping pandas dtypes to Elasticsearch dtype
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--------------------------------------------
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```
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Pandas dtype Python type NumPy type Usage
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object str string_, unicode_ Text
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int64 int int_, int8, int16, int32, int64, uint8, uint16, uint32, uint64 Integer numbers
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float64 float float_, float16, float32, float64 Floating point numbers
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bool bool bool_ True/False values
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datetime64 NA datetime64[ns] Date and time values
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timedelta[ns] NA NA Differences between two datetimes
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category NA NA Finite list of text values
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```
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"""
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es_dtype = None
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# Map all to 64-bit - TODO map to specifics: int32 -> int etc.
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if is_float_dtype(pd_dtype):
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es_dtype = 'double'
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elif is_integer_dtype(pd_dtype):
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es_dtype = 'long'
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elif is_bool_dtype(pd_dtype):
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es_dtype = 'boolean'
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elif is_string_dtype(pd_dtype):
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es_dtype = 'keyword'
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elif is_datetime_or_timedelta_dtype(pd_dtype):
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es_dtype = 'date'
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else:
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warnings.warn('No mapping for pd_dtype: [{0}], using default mapping'.format(pd_dtype))
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return es_dtype
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@staticmethod
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def _generate_es_mappings(dataframe):
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"""Given a pandas dataframe, generate the associated Elasticsearch mapping
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Parameters
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----------
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dataframe : pandas.DataFrame
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pandas.DataFrame to create schema from
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Returns
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-------
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mapping : str
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"""
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"""
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"mappings" : {
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"properties" : {
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"AvgTicketPrice" : {
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"type" : "float"
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},
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"Cancelled" : {
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"type" : "boolean"
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},
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"Carrier" : {
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"type" : "keyword"
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},
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"Dest" : {
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"type" : "keyword"
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}
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}
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}
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"""
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mappings = {}
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mappings['properties'] = {}
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for column_name, dtype in dataframe.dtypes.iteritems():
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es_dtype = Mappings._pd_dtype_to_es_dtype(dtype)
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mappings['properties'][column_name] = {}
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mappings['properties'][column_name]['type'] = es_dtype
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return {"mappings": mappings}
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def all_fields(self):
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"""
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Returns
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@ -379,3 +459,14 @@ class Mappings():
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"""
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return pd.Series(self._mappings_capabilities[self._mappings_capabilities._source == True].groupby('pd_dtype')[
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'_source'].count().to_dict())
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def to_pandas(self):
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"""
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Returns
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-------
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df : pd.DataFrame
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pandas DaraFrame representing this index
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"""
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@ -23,10 +23,14 @@ only Elasticsearch aggregatable fields can be aggregated or grouped.
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"""
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import pandas as pd
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import functools
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from elasticsearch_dsl import Search
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import eland as ed
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from pandas.core.generic import NDFrame as pd_NDFrame
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from pandas._libs import Timestamp, iNaT, properties
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class NDFrame():
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"""
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@ -44,7 +48,6 @@ class NDFrame():
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--------
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"""
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def __init__(self,
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client,
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index_pattern,
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@ -191,7 +194,12 @@ class NDFrame():
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rows = []
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index = []
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for hit in results['hits']['hits']:
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if isinstance(results, dict):
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iterator = results['hits']['hits']
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else:
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iterator = results
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for hit in iterator:
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row = hit['_source']
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# get index value - can be _id or can be field value in source
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@ -255,6 +263,23 @@ class NDFrame():
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# reverse order (index ascending)
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return df.sort_index()
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def _to_pandas(self):
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"""
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Protected method that returns all data as pandas.DataFrame.
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Returns
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-------
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df
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pandas.DataFrame of all values
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"""
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sort_params = self._index.sort_field + ":asc"
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results = self._client.scan(index=self._index_pattern)
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# We sort here rather than in scan - once everything is in core this
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# should be faster
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return self._es_results_to_pandas(results)
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def _describe(self):
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numeric_source_fields = self._mappings.numeric_source_fields()
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@ -294,6 +319,10 @@ class NDFrame():
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return mappings
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@property
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def columns(self):
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return self._columns
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@property
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def index(self):
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return self._index
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@ -309,7 +338,6 @@ class NDFrame():
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def get_dtype_counts(self):
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return self._mappings.get_dtype_counts()
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def _index_count(self):
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"""
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Returns
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@ -72,14 +72,17 @@ class Series(NDFrame):
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def __init__(self,
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client,
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index_pattern,
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field_name,
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field_name=None,
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mappings=None,
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index_field=None):
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# python 3 syntax
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super().__init__(client, index_pattern, mappings=mappings, index_field=index_field)
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# now select column (field_name)
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self._mappings = self._filter_mappings([field_name])
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if field_name is not None:
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self._mappings = self._filter_mappings([field_name])
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elif len(self._mappings.source_fields()) != 1:
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raise TypeError('Series must have 1 field: [{0}]'.format(len(self._mappings.source_fields())))
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def head(self, n=5):
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return self._df_to_series(super()._head(n))
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@ -199,6 +202,10 @@ class Series(NDFrame):
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fmt.buffer_put_lines(buf, lines)
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@property
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def name(self):
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return list(self._mappings.source_fields())[0]
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@property
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def shape(self):
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"""
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@ -257,7 +264,7 @@ class Series(NDFrame):
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return super()._describe()
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def _df_to_series(self, df):
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return df.iloc[:, 0]
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return df[self.name]
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# ----------------------------------------------------------------------
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# Rendering Methods
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@ -269,8 +276,8 @@ class Series(NDFrame):
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max_rows = pd.get_option("display.max_rows")
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self.to_string(buf=buf, na_rep='NaN', float_format=None, header=True, index=True, length=False,
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dtype=False, name=False, max_rows=max_rows)
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self.to_string(buf=buf, na_rep='NaN', float_format=None, header=True, index=True, length=True,
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dtype=True, name=True, max_rows=max_rows)
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return buf.getvalue()
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@ -279,7 +286,7 @@ class Series(NDFrame):
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index=True, length=True, dtype=True,
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name=True, max_rows=None):
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"""
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From pandas
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From pandas 0.24.2
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Render a string representation of the Series.
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@ -343,7 +350,6 @@ class Series(NDFrame):
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"""
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A hacked overridden version of pandas.io.formats.SeriesFormatter that writes correct length
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"""
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def __init__(self, series, series_length, buf=None, length=True, header=True, index=True,
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na_rep='NaN', name=False, float_format=None, dtype=True,
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max_rows=None):
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@ -1,5 +1,6 @@
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# File called _pytest for PyCharm compatability
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import numpy as np
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from pandas.util.testing import (
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assert_series_equal, assert_frame_equal)
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@ -88,3 +89,36 @@ class TestMapping(TestData):
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assert 'object' == field_capabilities['pd_dtype']
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assert True == field_capabilities['searchable']
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assert True == field_capabilities['aggregatable']
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def test_generate_es_mappings(self):
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df = pd.DataFrame(data={'A': np.random.rand(3),
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'B': 1,
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'C': 'foo',
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'D': pd.Timestamp('20190102'),
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'E': [1.0, 2.0, 3.0],
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'F': False,
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'G': [1, 2, 3]},
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index=['0','1','2'])
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expected_mappings = {'mappings': {
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'properties': {'A': {'type': 'double'},
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'B': {'type': 'long'},
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'C': {'type': 'keyword'},
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'D': {'type': 'date'},
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'E': {'type': 'double'},
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'F': {'type': 'boolean'},
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'G': {'type': 'long'}}}}
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mappings = ed.Mappings._generate_es_mappings(df)
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assert expected_mappings == mappings
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# Now create index
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index_name = 'eland_test_generate_es_mappings'
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ed.pandas_to_es(df, ELASTICSEARCH_HOST, index_name, if_exists="replace", refresh=True)
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ed_df = ed.DataFrame(ELASTICSEARCH_HOST, index_name)
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ed_df_head = ed_df.head()
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assert_frame_equal(df, ed_df_head)
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@ -153,3 +153,7 @@ class TestDataFrameBasics(TestData):
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ed_flights_timestamp.info()
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ed_flights.info()
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def test_to_pandas(self):
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ed_ecommerce_pd_df = self.ed_ecommerce().to_pandas()
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assert_frame_equal(self.pd_ecommerce(), ed_ecommerce_pd_df)
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@ -15,7 +15,7 @@ class TestDataFrameGetItem(TestData):
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ed_carrier = self.ed_flights()['Carrier']
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# pandas returns a Series here
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assert_frame_equal(pd.DataFrame(pd_carrier.head(100)), ed_carrier.head(100))
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assert_series_equal(pd_carrier.head(100), ed_carrier.head(100))
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pd_3_items = self.pd_flights()[['Dest','Carrier','FlightDelay']]
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ed_3_items = self.ed_flights()[['Dest','Carrier','FlightDelay']]
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@ -36,28 +36,12 @@ class TestDataFrameGetItem(TestData):
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def test_getattr_basic(self):
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# Test 1 attribute
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pd_carrier = self.pd_flights().Carrier
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#ed_carrier = self.ed_flights().Carrier
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ed_carrier = self.ed_flights().Carrier
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print(type(pd_carrier))
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print(pd_carrier)
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assert_series_equal(pd_carrier.head(100), ed_carrier.head(100))
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def test_boolean(self):
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# Test 1 attribute
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pd_carrier = self.pd_flights()['Carrier == "Kibana Airlines"']
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#ed_carrier = self.ed_flights().Carrier
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pd_avgticketprice = self.pd_flights().AvgTicketPrice
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ed_avgticketprice = self.ed_flights().AvgTicketPrice
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print(type(pd_carrier))
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print(pd_carrier)
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def test_loc(self):
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pd = self.pd_flights().loc[10:15, ['Dest', 'Carrier']]
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print(type(pd))
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print(pd)
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pd = self.pd_flights().loc[10]
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print(type(pd))
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print(pd)
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assert_series_equal(pd_avgticketprice.head(100), ed_avgticketprice.head(100))
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@ -1,4 +1,73 @@
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import eland as ed
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from eland import Client
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from eland import DataFrame
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from eland import Mappings
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def read_es(es_params, index_pattern):
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return ed.DataFrame(client=es_params, index_pattern=index_pattern)
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return DataFrame(client=es_params, index_pattern=index_pattern)
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def pandas_to_es(df, es_params, destination_index, if_exists='fail', chunk_size=10000, refresh=False):
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"""
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Append a pandas DataFrame to an Elasticsearch index.
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Mainly used in testing.
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Parameters
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----------
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es_params : Elasticsearch client argument
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elasticsearch-py parameters or
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elasticsearch-py instance or
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eland.Client instance
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destination_index : str
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Name of Elasticsearch index to be written
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if_exists : str, default 'fail'
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Behavior when the destination index exists. Value can be one of:
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``'fail'``
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If table exists, do nothing.
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``'replace'``
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If table exists, drop it, recreate it, and insert data.
|
||||
``'append'``
|
||||
If table exists, insert data. Create if does not exist.
|
||||
"""
|
||||
client = Client(es_params)
|
||||
|
||||
mapping = Mappings._generate_es_mappings(df)
|
||||
|
||||
# If table exists, check if_exists parameter
|
||||
if client.indices().exists(destination_index):
|
||||
if if_exists == "fail":
|
||||
raise ValueError(
|
||||
"Could not create the index [{0}] because it "
|
||||
"already exists. "
|
||||
"Change the if_exists parameter to "
|
||||
"'append' or 'replace' data.".format(destination_index)
|
||||
)
|
||||
elif if_exists == "replace":
|
||||
client.indices().delete(destination_index)
|
||||
client.indices().create(destination_index, mapping)
|
||||
#elif if_exists == "append":
|
||||
# TODO validate mapping is compatible
|
||||
else:
|
||||
client.indices().create(destination_index, mapping)
|
||||
|
||||
# Now add data
|
||||
actions = []
|
||||
n = 0
|
||||
for row in df.iterrows():
|
||||
# Use index as _id
|
||||
id = row[0]
|
||||
values = row[1].to_dict()
|
||||
|
||||
# Use integer as id field for repeatable results
|
||||
action = {'_index': destination_index, '_source': values, '_id': str(id)}
|
||||
|
||||
actions.append(action)
|
||||
|
||||
n = n + 1
|
||||
|
||||
if n % chunk_size == 0:
|
||||
client.bulk(actions, refresh=refresh)
|
||||
actions = []
|
||||
|
||||
client.bulk(actions, refresh=refresh)
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user