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Created May 7, 2020 19:34
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tiledb-df-demo.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Introduction\n",
"\n",
"This notebook presents several examples of TileDB usage. First, we import a CSV dataset as a 1D dense array, with automatic TileDB schema creation based on inferred CSV column types (loading to/from a Pandas DataFrame in the process). Next, we build a multi-dimensional sparse array with heterogeneous columns manually, and demonstrate slicing along different axes.\n",
" \n",
"\n",
"# Setup\n",
"\n",
"- install tiledb:\n",
"```\n",
"pip install tiledb\n",
"```\n",
"\n",
"- download data from UCI ML Repository\n",
" https://archive.ics.uci.edu/ml/datasets/Bank+Marketing\n",
"- unzip to usable path\n",
" ```\n",
" unzip bank.zip\n",
" ```\n",
"- update `csv_path` below if necessary"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"# imports\n",
"import tiledb\n",
"import numpy as np\n",
"import pandas as pd\n",
"\n",
"array_uri1 = \"/tmp/tiledb_demo1\"\n",
"array_uri2 = \"/tmp/tiledb_demo2\""
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"csv_path = \"bank-full.csv\"\n",
"\n",
"# note that this array URI could also be an `s3://` URI with\n",
"# no extra dependencies:\n",
"array_uri = \"/tmp/tiledb_demo1\"\n",
"\n",
"tiledb.from_csv(array_uri, csv_path, sep=';')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"# the dataset was saved with column types preserved, and can\n",
"# be re-loaded as a dataframe\n",
"df = tiledb.open_dataframe(array_uri)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"pandas.core.frame.DataFrame"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# it is a dataframe!\n",
"type(df)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
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" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>age</th>\n",
" <th>job</th>\n",
" <th>marital</th>\n",
" <th>education</th>\n",
" <th>default</th>\n",
" <th>balance</th>\n",
" <th>housing</th>\n",
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" <td>entrepreneur</td>\n",
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" <td>blue-collar</td>\n",
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" <td>5</td>\n",
" <td>may</td>\n",
" <td>198</td>\n",
" <td>1</td>\n",
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" <td>unknown</td>\n",
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" </tr>\n",
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" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
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" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45206</th>\n",
" <td>51</td>\n",
" <td>technician</td>\n",
" <td>married</td>\n",
" <td>tertiary</td>\n",
" <td>no</td>\n",
" <td>825</td>\n",
" <td>no</td>\n",
" <td>no</td>\n",
" <td>cellular</td>\n",
" <td>17</td>\n",
" <td>nov</td>\n",
" <td>977</td>\n",
" <td>3</td>\n",
" <td>-1</td>\n",
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" <td>unknown</td>\n",
" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45207</th>\n",
" <td>71</td>\n",
" <td>retired</td>\n",
" <td>divorced</td>\n",
" <td>primary</td>\n",
" <td>no</td>\n",
" <td>1729</td>\n",
" <td>no</td>\n",
" <td>no</td>\n",
" <td>cellular</td>\n",
" <td>17</td>\n",
" <td>nov</td>\n",
" <td>456</td>\n",
" <td>2</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" <td>unknown</td>\n",
" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45208</th>\n",
" <td>72</td>\n",
" <td>retired</td>\n",
" <td>married</td>\n",
" <td>secondary</td>\n",
" <td>no</td>\n",
" <td>5715</td>\n",
" <td>no</td>\n",
" <td>no</td>\n",
" <td>cellular</td>\n",
" <td>17</td>\n",
" <td>nov</td>\n",
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" <td>5</td>\n",
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" <tr>\n",
" <th>45209</th>\n",
" <td>57</td>\n",
" <td>blue-collar</td>\n",
" <td>married</td>\n",
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" <td>668</td>\n",
" <td>no</td>\n",
" <td>no</td>\n",
" <td>telephone</td>\n",
" <td>17</td>\n",
" <td>nov</td>\n",
" <td>508</td>\n",
" <td>4</td>\n",
" <td>-1</td>\n",
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" <td>unknown</td>\n",
" <td>no</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45210</th>\n",
" <td>37</td>\n",
" <td>entrepreneur</td>\n",
" <td>married</td>\n",
" <td>secondary</td>\n",
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" <td>2971</td>\n",
" <td>no</td>\n",
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" <td>17</td>\n",
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" <td>361</td>\n",
" <td>2</td>\n",
" <td>188</td>\n",
" <td>11</td>\n",
" <td>other</td>\n",
" <td>no</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>45211 rows × 17 columns</p>\n",
"</div>"
],
"text/plain": [
" age job marital education default balance housing loan \\\n",
"0 58 management married tertiary no 2143 yes no \n",
"1 44 technician single secondary no 29 yes no \n",
"2 33 entrepreneur married secondary no 2 yes yes \n",
"3 47 blue-collar married unknown no 1506 yes no \n",
"4 33 unknown single unknown no 1 no no \n",
"... ... ... ... ... ... ... ... ... \n",
"45206 51 technician married tertiary no 825 no no \n",
"45207 71 retired divorced primary no 1729 no no \n",
"45208 72 retired married secondary no 5715 no no \n",
"45209 57 blue-collar married secondary no 668 no no \n",
"45210 37 entrepreneur married secondary no 2971 no no \n",
"\n",
" contact day month duration campaign pdays previous poutcome y \n",
"0 unknown 5 may 261 1 -1 0 unknown no \n",
"1 unknown 5 may 151 1 -1 0 unknown no \n",
"2 unknown 5 may 76 1 -1 0 unknown no \n",
"3 unknown 5 may 92 1 -1 0 unknown no \n",
"4 unknown 5 may 198 1 -1 0 unknown no \n",
"... ... ... ... ... ... ... ... ... ... \n",
"45206 cellular 17 nov 977 3 -1 0 unknown yes \n",
"45207 cellular 17 nov 456 2 -1 0 unknown yes \n",
"45208 cellular 17 nov 1127 5 184 3 success yes \n",
"45209 telephone 17 nov 508 4 -1 0 unknown no \n",
"45210 cellular 17 nov 361 2 188 11 other no \n",
"\n",
"[45211 rows x 17 columns]"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# we can preview the data as usual in the notebook display\n",
"df"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
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" vertical-align: top;\n",
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" <tr>\n",
" <th>...</th>\n",
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" <tr>\n",
" <th>45204</th>\n",
" <td>73</td>\n",
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" <td>40</td>\n",
" <td>8</td>\n",
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" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45206</th>\n",
" <td>51</td>\n",
" <td>technician</td>\n",
" <td>married</td>\n",
" <td>tertiary</td>\n",
" <td>no</td>\n",
" <td>825</td>\n",
" <td>no</td>\n",
" <td>no</td>\n",
" <td>cellular</td>\n",
" <td>17</td>\n",
" <td>nov</td>\n",
" <td>977</td>\n",
" <td>3</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" <td>unknown</td>\n",
" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45207</th>\n",
" <td>71</td>\n",
" <td>retired</td>\n",
" <td>divorced</td>\n",
" <td>primary</td>\n",
" <td>no</td>\n",
" <td>1729</td>\n",
" <td>no</td>\n",
" <td>no</td>\n",
" <td>cellular</td>\n",
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" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45208</th>\n",
" <td>72</td>\n",
" <td>retired</td>\n",
" <td>married</td>\n",
" <td>secondary</td>\n",
" <td>no</td>\n",
" <td>5715</td>\n",
" <td>no</td>\n",
" <td>no</td>\n",
" <td>cellular</td>\n",
" <td>17</td>\n",
" <td>nov</td>\n",
" <td>1127</td>\n",
" <td>5</td>\n",
" <td>184</td>\n",
" <td>3</td>\n",
" <td>success</td>\n",
" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45209</th>\n",
" <td>57</td>\n",
" <td>blue-collar</td>\n",
" <td>married</td>\n",
" <td>secondary</td>\n",
" <td>no</td>\n",
" <td>668</td>\n",
" <td>no</td>\n",
" <td>no</td>\n",
" <td>telephone</td>\n",
" <td>17</td>\n",
" <td>nov</td>\n",
" <td>508</td>\n",
" <td>4</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" <td>unknown</td>\n",
" <td>no</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>9255 rows × 17 columns</p>\n",
"</div>"
],
"text/plain": [
" age job marital education default balance housing loan \\\n",
"0 58 management married tertiary no 2143 yes no \n",
"8 58 retired married primary no 121 yes no \n",
"12 53 technician married secondary no 6 yes no \n",
"13 58 technician married unknown no 71 yes no \n",
"14 57 services married secondary no 162 yes no \n",
"... ... ... ... ... ... ... ... ... \n",
"45204 73 retired married secondary no 2850 no no \n",
"45206 51 technician married tertiary no 825 no no \n",
"45207 71 retired divorced primary no 1729 no no \n",
"45208 72 retired married secondary no 5715 no no \n",
"45209 57 blue-collar married secondary no 668 no no \n",
"\n",
" contact day month duration campaign pdays previous poutcome y \n",
"0 unknown 5 may 261 1 -1 0 unknown no \n",
"8 unknown 5 may 50 1 -1 0 unknown no \n",
"12 unknown 5 may 517 1 -1 0 unknown no \n",
"13 unknown 5 may 71 1 -1 0 unknown no \n",
"14 unknown 5 may 174 1 -1 0 unknown no \n",
"... ... ... ... ... ... ... ... ... ... \n",
"45204 cellular 17 nov 300 1 40 8 failure yes \n",
"45206 cellular 17 nov 977 3 -1 0 unknown yes \n",
"45207 cellular 17 nov 456 2 -1 0 unknown yes \n",
"45208 cellular 17 nov 1127 5 184 3 success yes \n",
"45209 telephone 17 nov 508 4 -1 0 unknown no \n",
"\n",
"[9255 rows x 17 columns]"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# this dataset easily fits in memory, and of course we can slice with\n",
"# normal pandas operators:\n",
"df[df.age>50]"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"ArraySchema(\n",
" domain=Domain(*[\n",
" Dim(name='rows', domain=(0, 45210), tile=11, dtype='uint64'),\n",
" ]),\n",
" attrs=[\n",
" Attr(name='age', dtype='int64'),\n",
" Attr(name='job', dtype='<U0'),\n",
" Attr(name='marital', dtype='<U0'),\n",
" Attr(name='education', dtype='<U0'),\n",
" Attr(name='default', dtype='<U0'),\n",
" Attr(name='balance', dtype='int64'),\n",
" Attr(name='housing', dtype='<U0'),\n",
" Attr(name='loan', dtype='<U0'),\n",
" Attr(name='contact', dtype='<U0'),\n",
" Attr(name='day', dtype='int64'),\n",
" Attr(name='month', dtype='<U0'),\n",
" Attr(name='duration', dtype='int64'),\n",
" Attr(name='campaign', dtype='int64'),\n",
" Attr(name='pdays', dtype='int64'),\n",
" Attr(name='previous', dtype='int64'),\n",
" Attr(name='poutcome', dtype='<U0'),\n",
" Attr(name='y', dtype='<U0'),\n",
" ],\n",
" cell_order='row-major',\n",
" tile_order='row-major', sparse=False)\n",
"# note: filters omitted"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# now we can look directly at the underlying TileDB array\n",
"# and see that each column is a TileDB \"attribute\" with a\n",
"# specific type.\n",
"\n",
"a = tiledb.open(array_uri)\n",
"a.schema"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Building a sparse array from scratch\n",
"\n",
"Now, let's use some of the data above and build a sparse TileDB array\n",
"manually, in order to demonstrate TileDB's new heterogeneous dimensions and string-typed column slicing features.\n",
"\n",
"We use `id` and `job` below, but you can choose any other subset of columns as dimensions -- column choice should be determined by those you wish to slice mostly efficiently."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"# first we need to create an array schema\n",
"# we keep the first column as the row id, but use the\n",
"# `job` description as the second column:\n",
"\n",
"# note that the \"domain\" of a string-typed dimension is\n",
"# formed automatically as the data is written.\n",
"\n",
"from tiledb import *\n",
"\n",
"schema = ArraySchema(\n",
" domain=Domain(*[\n",
" Dim(name='id', domain=(0, 45211), tile=11, dtype='uint64'),\n",
" Dim(name='job', domain=(None,None), tile=None, dtype=np.bytes_),\n",
" ]),\n",
" attrs=[\n",
" Attr(name='age', dtype='int64'),\n",
" Attr(name='marital', dtype='<U0'),\n",
" Attr(name='education', dtype='<U0'),\n",
" Attr(name='default', dtype='<U0'),\n",
" Attr(name='balance', dtype='int64'),\n",
" Attr(name='housing', dtype='<U0'),\n",
" Attr(name='loan', dtype='<U0'),\n",
" Attr(name='contact', dtype='<U0'),\n",
" Attr(name='day', dtype='int64'),\n",
" Attr(name='month', dtype='<U0'),\n",
" Attr(name='duration', dtype='int64'),\n",
" Attr(name='campaign', dtype='int64'),\n",
" Attr(name='pdays', dtype='int64'),\n",
" Attr(name='previous', dtype='int64'),\n",
" Attr(name='poutcome', dtype='<U0'),\n",
" Attr(name='y', dtype='<U0'),\n",
" ],\n",
" cell_order='row-major',\n",
" tile_order='row-major', sparse=True)\n",
"# note: filters omitted"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"# write the array schema\n",
"tiledb.SparseArray.create(array_uri2, schema)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"# write the data to disk\n",
"# we must provide coordinates for each item written\n",
"\n",
"with tiledb.open(array_uri2, 'w') as A:\n",
" df_dict = {k: v.values for k,v in df.items()}\n",
" c_id = df.index.values\n",
" c_job = df_dict.pop('job')\n",
" A[c_id, c_job] = df_dict"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"A = tiledb.open(array_uri2)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"OrderedDict([('age', array([35, 28, 58])),\n",
" ('balance', array([231, 447, 121])),\n",
" ('campaign', array([1, 1, 1])),\n",
" ('contact',\n",
" array(['unknown', 'unknown', 'unknown'], dtype=object)),\n",
" ('day', array([5, 5, 5])),\n",
" ('default', array(['no', 'no', 'no'], dtype=object)),\n",
" ('duration', array([139, 217, 50])),\n",
" ('education',\n",
" array(['tertiary', 'tertiary', 'primary'], dtype=object)),\n",
" ('housing', array(['yes', 'yes', 'yes'], dtype=object)),\n",
" ('id', array([5, 6, 8], dtype=uint64)),\n",
" ('job',\n",
" array([b'management', b'management', b'retired'], dtype=object)),\n",
" ('loan', array(['no', 'yes', 'no'], dtype=object)),\n",
" ('marital',\n",
" array(['married', 'single', 'married'], dtype=object)),\n",
" ('month', array(['may', 'may', 'may'], dtype=object)),\n",
" ('pdays', array([-1, -1, -1])),\n",
" ('poutcome',\n",
" array(['unknown', 'unknown', 'unknown'], dtype=object)),\n",
" ('previous', array([0, 0, 0])),\n",
" ('y', array(['no', 'no', 'no'], dtype=object))])"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# we can slice on each dimension separately, returning a dictionary:\n",
"\n",
"# note that if the data was huge or stored on S3, we would efficiently pull\n",
"# only tiles matching the requested subset, and end with `val` in-memory locally:\n",
"\n",
"val = A.multi_index[1:10, ['retired', 'management']]\n",
"\n",
"val"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>age</th>\n",
" <th>balance</th>\n",
" <th>campaign</th>\n",
" <th>contact</th>\n",
" <th>day</th>\n",
" <th>default</th>\n",
" <th>duration</th>\n",
" <th>education</th>\n",
" <th>housing</th>\n",
" <th>id</th>\n",
" <th>job</th>\n",
" <th>loan</th>\n",
" <th>marital</th>\n",
" <th>month</th>\n",
" <th>pdays</th>\n",
" <th>poutcome</th>\n",
" <th>previous</th>\n",
" <th>y</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>35</td>\n",
" <td>231</td>\n",
" <td>1</td>\n",
" <td>unknown</td>\n",
" <td>5</td>\n",
" <td>no</td>\n",
" <td>139</td>\n",
" <td>tertiary</td>\n",
" <td>yes</td>\n",
" <td>5</td>\n",
" <td>b'management'</td>\n",
" <td>no</td>\n",
" <td>married</td>\n",
" <td>may</td>\n",
" <td>-1</td>\n",
" <td>unknown</td>\n",
" <td>0</td>\n",
" <td>no</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>28</td>\n",
" <td>447</td>\n",
" <td>1</td>\n",
" <td>unknown</td>\n",
" <td>5</td>\n",
" <td>no</td>\n",
" <td>217</td>\n",
" <td>tertiary</td>\n",
" <td>yes</td>\n",
" <td>6</td>\n",
" <td>b'management'</td>\n",
" <td>yes</td>\n",
" <td>single</td>\n",
" <td>may</td>\n",
" <td>-1</td>\n",
" <td>unknown</td>\n",
" <td>0</td>\n",
" <td>no</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>58</td>\n",
" <td>121</td>\n",
" <td>1</td>\n",
" <td>unknown</td>\n",
" <td>5</td>\n",
" <td>no</td>\n",
" <td>50</td>\n",
" <td>primary</td>\n",
" <td>yes</td>\n",
" <td>8</td>\n",
" <td>b'retired'</td>\n",
" <td>no</td>\n",
" <td>married</td>\n",
" <td>may</td>\n",
" <td>-1</td>\n",
" <td>unknown</td>\n",
" <td>0</td>\n",
" <td>no</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" age balance campaign contact day default duration education housing \\\n",
"0 35 231 1 unknown 5 no 139 tertiary yes \n",
"1 28 447 1 unknown 5 no 217 tertiary yes \n",
"2 58 121 1 unknown 5 no 50 primary yes \n",
"\n",
" id job loan marital month pdays poutcome previous y \n",
"0 5 b'management' no married may -1 unknown 0 no \n",
"1 6 b'management' yes single may -1 unknown 0 no \n",
"2 8 b'retired' no married may -1 unknown 0 no "
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# we can also view the slice result as a dataframe\n",
"\n",
"pd.DataFrame(val)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"# clean up steps if necessary\n",
"if False:\n",
" if tiledb.VFS().is_dir(array_uri1):\n",
" tiledb.VFS().remove_dir(array_uri1)\n",
" if tiledb.VFS().is_dir(array_uri2):\n",
" tiledb.VFS().remove_dir(array_uri2)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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