Compare commits
No commits in common. 'e848367378b6cc907f45abe97a3aa0a0202c40f9' and 'c872ba8cc2a0c629da212ed09c402d2e970e7b51' have entirely different histories.
e848367378
...
c872ba8cc2
@ -1,149 +0,0 @@
|
|||||||
{
|
|
||||||
"cells": [
|
|
||||||
{
|
|
||||||
"cell_type": "markdown",
|
|
||||||
"metadata": {},
|
|
||||||
"source": [
|
|
||||||
"#### Writing data-transport plugins\n",
|
|
||||||
"\n",
|
|
||||||
"The data-transport plugins are designed to automate pre/post processing i.e\n",
|
|
||||||
"\n",
|
|
||||||
" - Read -> Post processing\n",
|
|
||||||
" - Write-> Pre processing\n",
|
|
||||||
" \n",
|
|
||||||
"In this example we will assume, data and write both pre/post processing to any supported infrastructure. We will equally show how to specify the plugins within a configuration file"
|
|
||||||
]
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"cell_type": "code",
|
|
||||||
"execution_count": 1,
|
|
||||||
"metadata": {},
|
|
||||||
"outputs": [],
|
|
||||||
"source": [
|
|
||||||
"#\n",
|
|
||||||
"# Writing to Google Bigquery database\n",
|
|
||||||
"#\n",
|
|
||||||
"import transport\n",
|
|
||||||
"from transport import providers\n",
|
|
||||||
"import pandas as pd\n",
|
|
||||||
"import os\n",
|
|
||||||
"import shutil\n",
|
|
||||||
"#\n",
|
|
||||||
"#\n",
|
|
||||||
"\n",
|
|
||||||
"DATABASE = '/home/steve/tmp/demo.db3'\n",
|
|
||||||
"if os.path.exists(DATABASE) :\n",
|
|
||||||
" os.remove(DATABASE)\n",
|
|
||||||
"#\n",
|
|
||||||
"# \n",
|
|
||||||
"_data = pd.DataFrame({\"name\":['James Bond','Steve Rogers','Steve Nyemba'],'age':[55,150,44]})\n",
|
|
||||||
"litew = transport.get.writer(provider=providers.SQLITE,database=DATABASE)\n",
|
|
||||||
"litew.write(_data,table='friends')"
|
|
||||||
]
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"cell_type": "markdown",
|
|
||||||
"metadata": {},
|
|
||||||
"source": [
|
|
||||||
"#### Reading from SQLite\n",
|
|
||||||
"\n",
|
|
||||||
"The cell below reads the data that has been written by the cell above and computes the average age from a plugin function we will write. \n",
|
|
||||||
"\n",
|
|
||||||
"- Basic read of the designated table (friends) created above\n",
|
|
||||||
"- Read with pipeline functions defined in code\n",
|
|
||||||
"\n",
|
|
||||||
"**NOTE**\n",
|
|
||||||
"\n",
|
|
||||||
"It is possible to use **transport.factory.instance** or **transport.instance** or **transport.get.<[reader|writer]>** they are the same. It allows the maintainers to know that we used a factory design pattern."
|
|
||||||
]
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"cell_type": "code",
|
|
||||||
"execution_count": 4,
|
|
||||||
"metadata": {},
|
|
||||||
"outputs": [
|
|
||||||
{
|
|
||||||
"name": "stdout",
|
|
||||||
"output_type": "stream",
|
|
||||||
"text": [
|
|
||||||
" name age\n",
|
|
||||||
"0 James Bond 55\n",
|
|
||||||
"1 Steve Rogers 150\n",
|
|
||||||
"2 Steve Nyemba 44\n",
|
|
||||||
"\n",
|
|
||||||
"\n",
|
|
||||||
" name age autoinc\n",
|
|
||||||
"0 James Bond 5.5 0\n",
|
|
||||||
"1 Steve Rogers 15.0 1\n",
|
|
||||||
"2 Steve Nyemba 4.4 2\n"
|
|
||||||
]
|
|
||||||
}
|
|
||||||
],
|
|
||||||
"source": [
|
|
||||||
"\n",
|
|
||||||
"import transport\n",
|
|
||||||
"from transport import providers\n",
|
|
||||||
"import os\n",
|
|
||||||
"import numpy as np\n",
|
|
||||||
"def _autoincrement (_data,**kwargs) :\n",
|
|
||||||
" \"\"\"\n",
|
|
||||||
" This function will add an autoincrement field to the table\n",
|
|
||||||
" \"\"\"\n",
|
|
||||||
" _data['autoinc'] = np.arange(_data.shape[0])\n",
|
|
||||||
" \n",
|
|
||||||
" return _data\n",
|
|
||||||
"def reduce(_data,**_args) :\n",
|
|
||||||
" \"\"\"\n",
|
|
||||||
" This function will reduce the age of the data frame\n",
|
|
||||||
" \"\"\"\n",
|
|
||||||
" _data.age /= 10\n",
|
|
||||||
" return _data\n",
|
|
||||||
"reader = transport.get.reader(provider=providers.SQLITE,database=DATABASE,table='friends')\n",
|
|
||||||
"#\n",
|
|
||||||
"# basic read of the data created in the first cell\n",
|
|
||||||
"_df = reader.read()\n",
|
|
||||||
"print (_df)\n",
|
|
||||||
"print ()\n",
|
|
||||||
"print()\n",
|
|
||||||
"#\n",
|
|
||||||
"# read of the data with pipeline function provided to alter the database\n",
|
|
||||||
"print (reader.read(pipeline=[_autoincrement,reduce]))"
|
|
||||||
]
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"cell_type": "markdown",
|
|
||||||
"metadata": {},
|
|
||||||
"source": [
|
|
||||||
"The parameters for instianciating a transport object (reader or writer) can be found at [data-transport home](https://healthcareio.the-phi.com/data-transport)\n"
|
|
||||||
]
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"cell_type": "code",
|
|
||||||
"execution_count": null,
|
|
||||||
"metadata": {},
|
|
||||||
"outputs": [],
|
|
||||||
"source": []
|
|
||||||
}
|
|
||||||
],
|
|
||||||
"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": "3.9.7"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"nbformat": 4,
|
|
||||||
"nbformat_minor": 2
|
|
||||||
}
|
|
@ -1,19 +0,0 @@
|
|||||||
"""
|
|
||||||
This file will be intended to handle duckdb database
|
|
||||||
"""
|
|
||||||
|
|
||||||
import duckdb
|
|
||||||
from transport.common import Reader,Writer
|
|
||||||
|
|
||||||
class Duck(Reader):
|
|
||||||
def __init__(self,**_args):
|
|
||||||
super().__init__(**_args)
|
|
||||||
self._path = None if 'path' not in _args else _args['path']
|
|
||||||
self._handler = duckdb.connect() if not self._path else duckdb.connect(self._path)
|
|
||||||
|
|
||||||
|
|
||||||
class DuckReader(Duck) :
|
|
||||||
def __init__(self,**_args):
|
|
||||||
super().__init__(**_args)
|
|
||||||
def read(self,**_args) :
|
|
||||||
pass
|
|
Loading…
Reference in new issue