Pandas but without bringing the data into memory
Project description
Pandas-DB
A lightweight object for analyzing data directly from a Database without having to load anything onto memory
You can get the package directly from PyPI
pip install pandasdb2
Why use Pandas-DB?
Pandas-db is a read-only package that allows you to view, analyze and explore all the content in a given Database (supported file extensions: db, sql, and sqlite)
The advantage of using this over something like Pandas is that your not storing anything onto memory and therefore the db object is very light compared to a regular Pandas DataFrame
How does it work?
The instance only stores the names of the tables as attributes (which is great for auto-complete), the Table and Column objects as the attribute values, and of course a reference to the SQLite connection object.
So whenever you call a method to get some data, for ex: db.table.data(10) or db.column.describe();
the function runs a query that gets the data directly from the Database, so there is no need to store anything in memory.
You can think of it as a wrapper for SQL so there is no need to type SQL queries manually, but also has some of the most common methods and functions from Pandas so you also don't need to store the table data onto memory.
And to top it off, it makes it easy to import the tables from a database onto pandas for further analysis, for ex:
from pandasdb2 import Database
db = Database(db_path='data/parch-and-posey.sql')
db.tables
['web_events', 'sales_reps', 'region', 'orders', 'accounts']
df1 = db.orders.to_df()
df2 = db.accounts.to_df()
type(df1), type(df2)
(pandas.core.frame.DataFrame, pandas.core.frame.DataFrame)
Memory Usage
Now let's visualize this and see the amount of memory a Database object consumes compared to a Pandas DataFrame
Import the package:
from pandasdb2 import Database
Create a connection:
db = Database(db_path='.../yfin_data.db')
For example, this Database contains one table with more than 18 million rows:
db.tables, db.stock_data.shape
(['stock_data'], (18078890, 9))
db object size:
from pandasdb2.utils import get_gb_size
get_gb_size(db)
0.000005 GB
dataframe object size:
dataframe = db.stock_data.to_df()
get_gb_size(dataframe)
6.961891 GB
As you can see, while the Database object remains almost the same size the Dataframe increases exponentially.
Now let's dive onto the pandasdb package
Once you have the package installed, import the package:
from pandasdb2 import Database
To instantiate the Database class you need to pass the path to the Database file, which could be one of the following extensions: db, sql, or sqlite
db = Database(db_path='data/forestation.db')
Tables
Get a list of all the tables
db.tables
['forest_area', 'land_area', 'regions']
To get the table object we can either use square brackets or type the name as an attribute, just like in Pandas
db['forest_area']
country_code country_name year forest_area_sqkm
0 ABW Aruba 2016 4.20000
1 AFG Afghanistan 2016 13500.00000
2 AGO Angola 2016 577311.99220
3 ALB Albania 2016 7705.39978
4 AND Andorra 2016 160.00000
... ... ... ...
5881 XKX Kosovo 1990 NaN
5882 YEM Yemen, Rep. 1990 5490.00000
5883 ZAF South Africa 1990 92410.00000
5884 ZMB Zambia 1990 528000.00000
5885 ZWE Zimbabwe 1990 221640.00000
[5886 rows x 4 columns]
Or:
db.forest_area
country_code country_name year forest_area_sqkm
0 ABW Aruba 2016 4.20000
1 AFG Afghanistan 2016 13500.00000
2 AGO Angola 2016 577311.99220
3 ALB Albania 2016 7705.39978
4 AND Andorra 2016 160.00000
... ... ... ...
5881 XKX Kosovo 1990 NaN
5882 YEM Yemen, Rep. 1990 5490.00000
5883 ZAF South Africa 1990 92410.00000
5884 ZMB Zambia 1990 528000.00000
5885 ZWE Zimbabwe 1990 221640.00000
[5886 rows x 4 columns]
Get a list of the table columns
db.forest_area.columns
['country_code', 'country_name', 'year', 'forest_area_sqkm']
Get table shape:
db.forest_area.shape
(5886, 4)
Get the first 20 rows
db.forest_area.data(20)
[('ABW', 'Aruba', 2016, 4.199999869),
('AFG', 'Afghanistan', 2016, 13500.0),
('AGO', 'Angola', 2016, 577311.9922),
('ALB', 'Albania', 2016, 7705.39978),
('AND', 'Andorra', 2016, 160.0),
...
Or you can use the iloc property to get a slice:
db.regions.iloc[5:10]
[('Angola', 'AGO', 'Sub-Saharan Africa', 'Lower middle income'),
('Antigua and Barbuda', 'ATG', 'Latin America & Caribbean', 'High income'),
('Argentina', 'ARG', 'Latin America & Caribbean', 'High income'),
('Armenia', 'ARM', 'Europe & Central Asia', 'Upper middle income'),
('Aruba', 'ABW', 'Latin America & Caribbean', 'High income')]
Columns:
db.regions.region
Out[18]:
0 South Asia
1 Europe & Central Asia
2 Middle East & North Africa
3 East Asia & Pacific
4 Europe & Central Asia
...
214 Middle East & North Africa
215 Middle East & North Africa
216 Sub-Saharan Africa
217 Sub-Saharan Africa
218 World
Name: region, Length: 219, dtype: object
Get the Python and SQL data type of the column:
db.regions.region.type, db.regions.region.sql_type
(str, 'TEXT')
Describe the column:
db.forest_area.country_name.describe()
{'len': 5886,
'count': 5886,
'min': 'Afghanistan',
'max': 'Zimbabwe',
'unique': 218}
Note that the len returns the number of rows/ items in the column, while count excludes None values
Describe a numeric column:
db.forest_area.forest_area_sqkm.describe()
{'len': 5886,
'count': 5570,
'min': 0.799999982,
'max': 41282694.9,
'sum': 2178158753.6738772,
'avg': 391051.84087502287,
'median': 20513.00049}
Get a dictionary with each distinct value and its count:
db.regions.region.value_counts()
{'Europe & Central Asia': 58,
'Sub-Saharan Africa': 48,
'Latin America & Caribbean': 42,
'East Asia & Pacific': 38,
'Middle East & North Africa': 21,
'South Asia': 8,
'North America': 3,
Get the most common value:
db.regions.income_group.mode()
{'High income': 81}
Get all unique/ distinct values in a column:
db.forest_area.country_name.unique()
['Aruba',
'Afghanistan',
'Angola',
...
'Zambia',
'Zimbabwe']
When you're done you should always call the exit() method to close the SQL connection safely
db.exit()
Now let's use another Database
db = Database(db_path='data/parch-and-posey.sql')
for table in db.tables:
print(table, db.get_columns(table_name=table))
web_events ['id', 'account_id', 'occurred_at', 'channel']
sales_reps ['id', 'name', 'region_id']
region ['id', 'name']
orders ['id', 'account_id', 'occurred_at', 'standard_qty', 'gloss_qty', 'poster_qty', 'total', 'standard_amt_usd', 'gloss_amt_usd', 'poster_amt_usd', 'total_amt_usd']
accounts ['id', 'name', 'website', 'lat', 'long', 'primary_poc', 'sales_rep_id']
You can apply a function to the whole column like so:
column = db.accounts.primary_poc.apply(lambda x: x.split(' ')[-1])
for last_name in column:
print(last_name)
Tuma
Shields
Lupo
Banda
Crusoe
...
Similarly, the Table object has an applymap method, which maps/ applies the function on each cell in the table
First, let's have a look at the table:
db.sales_reps
id name region_id
0 321500 Samuel Racine 1
1 321510 Eugena Esser 1
2 321520 Michel Averette 1
3 321530 Renetta Carew 1
4 321540 Cara Clarke 1
.. ... ... ...
45 321950 Elwood Shutt 4
46 321960 Maryanna Fiorentino 4
47 321970 Georgianna Chisholm 4
48 321980 Micha Woodford 4
49 321990 Dawna Agnew 4
[50 rows x 3 columns]
And now we're going to pass a lambda function that will take the cell value and return the number of characters by converting it to a string:
table = db.sales_reps.applymap(lambda x: len(str(x)))
for row in table:
print(row)
(6, 13, 1)
(6, 12, 1)
(6, 15, 1)
(6, 13, 1)
(6, 11, 1)
...
You can also iterate directly on the table/ column object:
for row in db.sales_reps:
print(row)
(321500, 'Samuel Racine', 1)
(321510, 'Eugena Esser', 1)
(321520, 'Michel Averette', 1)
(321530, 'Renetta Carew', 1)
(321540, 'Cara Clarke', 1)
...
Convert a table to a DataFrame:
df = db.orders.to_df()
type(df)
pandas.core.frame.DataFrame
Similarly, you can convert a column to a Pandas Series
ser = db.orders.occurred_at.to_series()
type(ser)
pandas.core.series.Series
Filtering
Just like Pandas you can filter a given table by passing a column object with an operator, eg: col >= 32
db = Database('data/parch-and-posey.sql')
db.tables
['web_events', 'sales_reps', 'region', 'orders', 'accounts']
Lets save the table that we'll be working with as df
df = db.orders
id account_id occurred_at standard_qty gloss_qty poster_qty total standard_amt_usd gloss_amt_usd poster_amt_usd total_amt_usd
0 1 1001 2015-10-06 17:31:14 123 22 24 169 613.77 164.78 194.88 973.43
1 2 1001 2015-11-05 03:34:33 190 41 57 288 948.10 307.09 462.84 1718.03
2 3 1001 2015-12-04 04:21:55 85 47 0 132 424.15 352.03 0.00 776.18
3 4 1001 2016-01-02 01:18:24 144 32 0 176 718.56 239.68 0.00 958.24
4 5 1001 2016-02-01 19:27:27 108 29 28 165 538.92 217.21 227.36 983.49
... ... ... ... ... ... ... ... ... ... ...
6907 6908 4501 2016-06-29 04:03:39 11 199 59 269 54.89 1490.51 479.08 2024.48
6908 6909 4501 2016-07-29 19:58:32 5 91 96 192 24.95 681.59 779.52 1486.06
6909 6910 4501 2016-08-27 00:58:11 16 94 82 192 79.84 704.06 665.84 1449.74
6910 6911 4501 2016-11-22 06:52:22 63 67 81 211 314.37 501.83 657.72 1473.92
6911 6912 4501 2016-12-21 13:30:42 61 150 52 263 304.39 1123.50 422.24 1850.13
[6912 rows x 11 columns]
Get all the orders where the account-id is equal to 4091
df[df.account_id == 4091]
id account_id occurred_at standard_qty gloss_qty poster_qty total standard_amt_usd gloss_amt_usd poster_amt_usd total_amt_usd
0 3775 4091 2016-11-22 07:33:05 325 36 46 407 1621.75 269.64 373.52 2264.91
1 3776 4091 2016-12-21 09:22:20 300 28 0 328 1497.00 209.72 0.00 1706.72
2 6573 4091 2016-11-22 07:57:27 45 482 305 832 224.55 3610.18 2476.60 6311.33
[3 rows x 11 columns]
Get all the orders where the total quantity is between 300 - 500
df[df.total.between(300, 500)]
id account_id occurred_at standard_qty gloss_qty poster_qty total standard_amt_usd gloss_amt_usd poster_amt_usd total_amt_usd
0 25 1041 2016-10-14 23:54:21 298 28 69 395 1487.02 209.72 560.28 2257.02
1 26 1041 2016-11-13 10:11:52 307 22 0 329 1531.93 164.78 0.00 1696.71
2 30 1051 2016-10-01 00:48:28 486 0 1 487 2425.14 0.00 8.12 2433.26
3 33 1051 2016-12-30 08:45:43 495 1 1 497 2470.05 7.49 8.12 2485.66
4 34 1061 2016-10-19 16:04:11 290 52 23 365 1447.10 389.48 186.76 2023.34
... ... ... ... ... ... ... ... ... ... ...
1693 6596 4121 2016-11-20 13:47:32 172 63 219 454 858.28 471.87 1778.28 3108.43
1694 6634 4161 2014-06-17 14:02:42 33 305 40 378 164.67 2284.45 324.80 2773.92
1695 6663 4181 2016-06-24 07:40:53 426 59 0 485 2125.74 441.91 0.00 2567.65
1696 6855 4451 2014-03-09 07:21:16 241 27 42 310 1202.59 202.23 341.04 1745.86
1697 6868 4461 2014-08-25 04:07:47 22 185 291 498 109.78 1385.65 2362.92 3858.35
[1698 rows x 11 columns]
Pass multiple conditions:
df[(df.total >= 500) & (df.total_amt_usd > 6700)]
id account_id occurred_at standard_qty gloss_qty poster_qty total standard_amt_usd gloss_amt_usd poster_amt_usd total_amt_usd
0 24 1031 2016-12-25 03:54:27 1148 0 215 1363 5728.52 0.00 1745.80 7474.32
1 129 1141 2016-12-21 15:52:58 143 1045 2157 3345 713.57 7827.05 17514.84 26055.46
2 176 1181 2016-04-24 16:47:51 2188 50 12 2250 10918.12 374.50 97.44 11390.06
3 214 1221 2016-02-04 20:17:54 485 1345 21 1851 2420.15 10074.05 170.52 12664.72
4 234 1231 2016-11-20 15:16:58 505 0 1355 1860 2519.95 0.00 11002.60 13522.55
.. ... ... ... ... ... ... ... ... ... ... ...
774 6885 4461 2016-02-04 21:12:41 52 581 276 909 259.48 4351.69 2241.12 6852.29
775 6890 4461 2016-09-26 08:44:11 42 538 313 893 209.58 4029.62 2541.56 6780.76
776 6899 4491 2014-03-06 05:22:25 549 523 245 1317 2739.51 3917.27 1989.40 8646.18
777 6903 4491 2014-09-28 15:53:06 52 601 360 1013 259.48 4501.49 2923.20 7684.17
778 6906 4491 2015-01-24 07:15:47 54 621 282 957 269.46 4651.29 2289.84 7210.59
[779 rows x 11 columns]
Just like in Pandas you can also save the filtered dataframe/table to a variable and perform operations on it
filtered_df = df[(df.total >= 500) & (df.total_amt_usd > 4700)]
filtered_df.shape
(1491, 11)
filtered_df.account_id.value_counts()
{3411: 33,
2591: 30,
4211: 30,
1561: 29,
2181: 29,
4151: 29,
1401: 28,
...}
Sort a table:
filtered_df.sort_values('total_amt_usd', ascending=False)
id account_id occurred_at standard_qty gloss_qty poster_qty total standard_amt_usd gloss_amt_usd poster_amt_usd total_amt_usd
0 4016 4251 2016-12-26 08:53:24 521 16 28262 28799 2599.79 119.84 229487.44 232207.07
1 3892 4161 2016-06-24 13:32:55 22591 13 6 22610 112729.09 97.37 48.72 112875.18
2 3963 4211 2015-03-30 00:05:30 114 14281 0 14395 568.86 106964.69 0.00 107533.55
3 5791 2861 2014-10-24 12:06:22 0 10 11691 11701 0.00 74.90 94930.92 95005.82
4 3778 4101 2016-07-17 14:50:43 475 3 11226 11704 2370.25 22.47 91155.12 93547.84
... ... ... ... ... ... ... ... ... ... ...
1486 4721 1491 2015-06-13 21:50:46 46 426 160 632 229.54 3190.74 1299.20 4719.48
1487 6528 3991 2016-11-17 06:56:25 0 63 523 586 0.00 471.87 4246.76 4718.63
1488 4719 1491 2015-04-15 14:19:14 54 485 100 639 269.46 3632.65 812.00 4714.11
1489 5214 2081 2014-06-06 16:55:16 44 600 0 644 219.56 4494.00 0.00 4713.56
1490 4081 4291 2015-08-09 17:47:52 302 416 11 729 1506.98 3115.84 89.32 4712.14
[1491 rows x 11 columns]
You can also sort by multiple columns with either a list or dict'
filtered_df.sort_values({'account_id': 'asc', 'total_amt_usd': 'desc'})
id account_id occurred_at standard_qty gloss_qty poster_qty total standard_amt_usd gloss_amt_usd poster_amt_usd total_amt_usd
0 4308 1001 2015-12-04 04:01:09 526 597 287 1410 2624.74 4471.53 2330.44 9426.71
1 4309 1001 2016-01-02 00:59:09 566 645 194 1405 2824.34 4831.05 1575.28 9230.67
2 4316 1001 2016-08-28 06:50:58 557 572 255 1384 2779.43 4284.28 2070.60 9134.31
3 4317 1001 2016-09-26 23:22:47 507 614 226 1347 2529.93 4598.86 1835.12 8963.91
4 4314 1001 2016-05-31 21:09:48 531 603 209 1343 2649.69 4516.47 1697.08 8863.24
... ... ... ... ... ... ... ... ... ... ...
1486 6900 4491 2014-05-05 00:03:19 33 508 283 824 164.67 3804.92 2297.96 6267.55
1487 6905 4491 2014-12-26 21:39:04 218 366 283 867 1087.82 2741.34 2297.96 6127.12
1488 6896 4491 2013-12-08 06:34:23 43 520 242 805 214.57 3894.80 1965.04 6074.41
1489 6901 4491 2014-07-31 05:05:06 12 509 262 783 59.88 3812.41 2127.44 5999.73
1490 6898 4491 2014-02-04 03:04:08 34 517 205 756 169.66 3872.33 1664.60 5706.59
[1491 rows x 11 columns]
sorted_df = filtered_df.sort_values({'account_id': 'asc', 'total_amt_usd': 'desc'})
for row in sorted_df:
print(row)
(4308, 1001, '2015-12-04 04:01:09', 526, 597, 287, 1410, 2624.74, 4471.53, 2330.44, 9426.71)
(4309, 1001, '2016-01-02 00:59:09', 566, 645, 194, 1405, 2824.34, 4831.05, 1575.28, 9230.67)
(4316, 1001, '2016-08-28 06:50:58', 557, 572, 255, 1384, 2779.43, 4284.28, 2070.6, 9134.31)
(4317, 1001, '2016-09-26 23:22:47', 507, 614, 226, 1347, 2529.93, 4598.86, 1835.12, 8963.91)
(4314, 1001, '2016-05-31 21:09:48', 531, 603, 209, 1343, 2649.69, 4516.47, 1697.08, 8863.24)
(4307, 1001, '2015-11-05 03:25:21', 506, 612, 203, 1321, 2524.94, 4583.88, 1648.36, 8757.18)
(4311, 1001, '2016-03-02 15:40:29', 498, 605, 204, 1307, 2485.02, 4531.45, 1656.48, 8672.95)
...
Cache
When initializing the Database() object there are a few parameters which will
determine how the output is cached (if it is at all).
cache(True/False, default True)
By default, all the SQL queries are cached,
so whenever you do db.table.col.median() it will calculate the median
and cache the result for next time, this is done for almost all Table and Column
properties (where the output is always the same or not very large).
populate_cache(True/False, default False)
If the parameter is set to True it will loop through all the tables and columns
in the database and populate the cache, so whenever you do table.shape or
col.avg() the result will already be there.
Note that populating the cache can take quite some time for larger databases.
max_item_size(int, default 2), andmax_dict_size(int, default 100)
The two parameters determine the maximum size in Megabytes for the element to be cached.
For example: if the output of col.value_counts() was 2.1MB and max_item_size is set to 2MB,
then the output would not be cached since it goes over the limit.
And if the output was 1.9MB and the current cache size was 99MB then it would not cache the output of the function because otherwise the whole cache-dict size would be above 100MB.
And finally, you can pass an SQL query to db.query() which will return a Pandas DataFrame with the results:
query = """
SELECT * FROM accounts
JOIN sales_reps
ON sales_reps.id = accounts.sales_rep_id
JOIN region
ON region.id = sales_reps.region_id
"""
db.query(query)
long ... id_2 name_2 region_id id_3 name_3
0 -75.103297 ... 321500 Samuel Racine 1 1 Northeast
1 -73.849374 ... 321510 Eugena Esser 1 1 Northeast
2 -76.084009 ... 321520 Michel Averette 1 1 Northeast
3 -75.763898 ... 321530 Renetta Carew 1 1 Northeast
4 -75.284998 ... 321540 Cara Clarke 1 1 Northeast
.. ... ... ... ... ... ... ...
346 -122.655247 ... 321970 Georgianna Chisholm 4 4 West
347 -122.681500 ... 321960 Maryanna Fiorentino 4 4 West
348 -122.669460 ... 321970 Georgianna Chisholm 4 4 West
349 -122.671880 ... 321960 Maryanna Fiorentino 4 4 West
350 -122.657145 ... 321970 Georgianna Chisholm 4 4 West
[351 rows x 12 columns]
Close the connection
db.exit()
TODO:
- Move Table and Column objects to a dictionary
- Support mathematical operations between Column objects (db.table.col1 * db.table.col2)
- Replace
to_string()in__repr__()with a custom one - Add filter function
- Add cache system for most common properties
- Add Group-By method
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