031-data-wrangling-with-mongodb
April 23, 2022
3.1. Wrangling Data with MongoDB ��
[2]: from pprint import PrettyPrinter
import pandas as pd
from IPython.display import VimeoVideo
from pymongo import MongoClient
[3]: VimeoVideo("665412094", h="8334dfab2e", width=600)
[3]: <IPython.lib.display.VimeoVideo at 0x7fb54447b460>
[4]: VimeoVideo("665412135", h="dcff7ab83a", width=600)
[4]: <IPython.lib.display.VimeoVideo at 0x7fb54447b1c0>
Task 3.1.1: Instantiate a PrettyPrinter, and assign it to the variable pp.
• Construct a PrettyPrinter instance in pprint.
[5]: pp = PrettyPrinter(indent = 2)
1 Prepare Data
1.1 Connect
[6]: VimeoVideo("665412155", h="1ca0dd03d0", width=600)
[6]: <IPython.lib.display.VimeoVideo at 0x7fb54447ba30>
Task 3.1.2: Create a client that connects to the database running at localhost on port 27017.
• What’s a database client?
• What’s a database server?
• Create a client object for a MongoDB instance.
[7]: client = MongoClient(host="localhost", port=27017)
1
1.2 Explore
[8]: VimeoVideo("665412176", h="6fea7c6346", width=600)
[8]: <IPython.lib.display.VimeoVideo at 0x7fb54437fd60>
[9]: from sys import getsizeof
my_list = [0,1,2,3,4,5] #list/ array
my_range = range(0,8_000_000) #iterator
# for i in my_list:
# print(i)
# for i in my_range:
# print(i)
print(getsizeof(my_list))
print(getsizeof(my_range))
152
48
Task 3.1.3: Print a list of the databases available on client.
• What’s an iterator?
• List the databases of a server using PyMongo.
• Print output using pprint.
[10]: db_list = list(client.list_databases())
#print(getsizeof(db_list))
pp.pprint(db_list)
[ {'empty': False, 'name': 'admin', 'sizeOnDisk': 40960},
{'empty': False, 'name': 'air-quality', 'sizeOnDisk': 6987776},
{'empty': False, 'name': 'config', 'sizeOnDisk': 12288},
{'empty': False, 'name': 'local', 'sizeOnDisk': 73728}]
[11]: VimeoVideo("665412216", h="7d4027dc33", width=600)
[11]: <IPython.lib.display.VimeoVideo at 0x7fb542b112b0>
Task 3.1.4: Assign the "air-quality" database to the variable db.
• What’s a MongoDB database?
• Access a database using PyMongo.
[12]: db = client["air-quality"]
[13]: VimeoVideo("665412231", h="89c546b00f", width=600)
2
[13]: <IPython.lib.display.VimeoVideo at 0x7fb542b118b0>
Task 3.1.5: Use the list_collections method to print a list of the collections available in db.
• What’s a MongoDB collection?
• List the collections in a database using PyMongo.
[14]: #list(db.list_collections())[0]
for c in db.list_collections():
print(c["name"])
lagos
system.buckets.lagos
nairobi
system.buckets.nairobi
system.views
dar-es-salaam
system.buckets.dar-es-salaam
[15]: VimeoVideo("665412252", h="bff2abbdc0", width=600)
[15]: <IPython.lib.display.VimeoVideo at 0x7fb542b11a30>
Task 3.1.6: Assign the "nairobi" collection in db to the variable name nairobi.
• Access a collection in a database using PyMongo.
[16]: nairobi = db["nairobi"]
[17]: VimeoVideo("665412270", h="e4a5f5c84b", width=600)
[17]: <IPython.lib.display.VimeoVideo at 0x7fb542b32370>
Task 3.1.7: Use the count_documents method to see how many documents are in the nairobi
collection.
• What’s a MongoDB document?
• Count the documents in a collection using PyMongo.
[18]: nairobi.count_documents({})
[18]: 202212
[19]: VimeoVideo("665412279", h="c2315f3be1", width=600)
[19]: <IPython.lib.display.VimeoVideo at 0x7fb542b326d0>
Task 3.1.8: Use the find_one method to retrieve one document from the nairobi collection, and
assign it to the variable name result.
• What’s metadata?
3
• What’s semi-structured data?
• Retrieve a document from a collection using PyMongo.
[20]: result = nairobi.find_one({})
pp.pprint(result)
{ 'P1': 39.67,
'_id': ObjectId('6261a046e76424a61615daaf'),
'metadata': { 'lat': -1.3,
'lon': 36.785,
'measurement': 'P1',
'sensor_id': 57,
'sensor_type': 'SDS011',
'site': 29},
'timestamp': datetime.datetime(2018, 9, 1, 0, 0, 2, 472000)}
[21]: VimeoVideo("665412306", h="e1e913dfd1", width=600)
[21]: <IPython.lib.display.VimeoVideo at 0x7fb542b320a0>
Task 3.1.9: Use the distinct method to determine how many sensor sites are included in the
nairobi collection.
• Get a list of distinct values for a key among all documents using PyMongo.
[22]: nairobi.distinct("metadata.site")
[22]: [29, 6]
[23]: VimeoVideo("665412322", h="4776c6d548", width=600)
[23]: <IPython.lib.display.VimeoVideo at 0x7fb542b32eb0>
Task 3.1.10: Use the count_documents method to determine how many readings there are for
each site in the nairobi collection.
• Count the documents in a collection using PyMongo.
[24]: print("Documents from site 6:", nairobi.count_documents({"metadata.site":6}))
print("Documents from site 29:", nairobi.count_documents({"metadata.site":29}))
Documents from site 6: 70360
Documents from site 29: 131852
[25]: VimeoVideo("665412344", h="d2354584cd", width=600)
[25]: <IPython.lib.display.VimeoVideo at 0x7fb542b3d6d0>
Task 3.1.11: Use the aggregate method to determine how many readings there are for each site
in the nairobi collection.
4
• Perform aggregation calculations on documents using PyMongo.
[26]: result = nairobi.aggregate(
[
{"$group":{"_id":"$metadata.site","count":{"$count": {}}}}
]
)
pp.pprint(list(result))
[{'_id': 29, 'count': 131852}, {'_id': 6, 'count': 70360}]
[27]: VimeoVideo("665412372", h="565122c9cc", width=600)
[27]: <IPython.lib.display.VimeoVideo at 0x7fb542b3d7c0>
Task 3.1.12: Use the distinct method to determine how many types of measurements have been
taken in the nairobi collection.
• Get a list of distinct values for a key among all documents using PyMongo.
[28]: nairobi.distinct("metadata.measurement")
[28]: ['P2', 'humidity', 'temperature', 'P1']
[29]: VimeoVideo("665412380", h="f7f7a39bb3", width=600)
[29]: <IPython.lib.display.VimeoVideo at 0x7fb542b3d610>
Task 3.1.13: Use the find method to retrieve the PM 2.5 readings from all sites. Be sure to limit
your results to 3 records only.
• Query a collection using PyMongo.
[30]: result = nairobi.find({"metadata.measurement":"P2"}).limit(4)
pp.pprint(list(result))
[ { 'P2': 34.43,
'_id': ObjectId('6261a046e76424a616165b3a'),
'metadata': { 'lat': -1.3,
'lon': 36.785,
'measurement': 'P2',
'sensor_id': 57,
'sensor_type': 'SDS011',
'site': 29},
'timestamp': datetime.datetime(2018, 9, 1, 0, 0, 2, 472000)},
{ 'P2': 30.53,
'_id': ObjectId('6261a046e76424a616165b3b'),
'metadata': { 'lat': -1.3,
'lon': 36.785,
'measurement': 'P2',
5
'sensor_id': 57,
'sensor_type': 'SDS011',
'site': 29},
'timestamp': datetime.datetime(2018, 9, 1, 0, 5, 3, 941000)},
{ 'P2': 22.8,
'_id': ObjectId('6261a046e76424a616165b3c'),
'metadata': { 'lat': -1.3,
'lon': 36.785,
'measurement': 'P2',
'sensor_id': 57,
'sensor_type': 'SDS011',
'site': 29},
'timestamp': datetime.datetime(2018, 9, 1, 0, 10, 4, 374000)},
{ 'P2': 13.3,
'_id': ObjectId('6261a046e76424a616165b3d'),
'metadata': { 'lat': -1.3,
'lon': 36.785,
'measurement': 'P2',
'sensor_id': 57,
'sensor_type': 'SDS011',
'site': 29},
'timestamp': datetime.datetime(2018, 9, 1, 0, 15, 4, 245000)}]
[31]: VimeoVideo("665412389", h="8976ea3090", width=600)
[31]: <IPython.lib.display.VimeoVideo at 0x7fb542b3d2b0>
Task 3.1.14: Use the aggregate method to calculate how many readings there are for each type
("humidity", "temperature", "P2", and "P1") in site 6.
• Perform aggregation calculations on documents using PyMongo.
[32]: result = nairobi.aggregate(
[
{"$match": {"metadata.site":6}},
{"$group":{"_id":"$metadata.measurement","count":{"$count": {}}}}
]
)
pp.pprint(list(result))
[ {'_id': 'P2', 'count': 18169},
{'_id': 'humidity', 'count': 17011},
{'_id': 'temperature', 'count': 17011},
{'_id': 'P1', 'count': 18169}]
[33]: VimeoVideo("665412418", h="0c4b125254", width=600)
[33]: <IPython.lib.display.VimeoVideo at 0x7fb542b2f820>
6
Task 3.1.15: Use the aggregate method to calculate how many readings there are for each type
("humidity", "temperature", "P2", and "P1") in site 29.
• Perform aggregation calculations on documents using PyMongo.
[34]: result = nairobi.aggregate(
[
{"$match": {"metadata.site":29}},
{"$group":{"_id":"$metadata.measurement","count":{"$count": {}}}}
]
)
pp.pprint(list(result))
[ {'_id': 'P2', 'count': 32907},
{'_id': 'humidity', 'count': 33019},
{'_id': 'temperature', 'count': 33019},
{'_id': 'P1', 'count': 32907}]
1.3 Import
[35]: VimeoVideo("665412437", h="7a436c7e7e", width=600)
[35]: <IPython.lib.display.VimeoVideo at 0x7fb54437f9a0>
Task 3.1.16: Use the find method to retrieve the PM 2.5 readings from site 29. Be sure to limit
your results to 3 records only. Since we won’t need the metadata for our model, use the projection
argument to limit the results to the "P2" and "timestamp" keys only.
• Query a collection using PyMongo.
[42]: result = nairobi.find(
{"metadata.site":29, "metadata.measurement":"P2"},
projection={"P2":1, "timestamp":1, "_id":0}
)
#pp.pprint(result.next())
[39]: VimeoVideo("665412442", h="494636d1ea", width=600)
[39]: <IPython.lib.display.VimeoVideo at 0x7fb542b3db80>
Task 3.1.17: Read records from your result into the DataFrame df. Be sure to set the index to
"timestamp".
• Create a DataFrame from a dictionary using pandas.
[43]: df = pd.DataFrame(result).set_index("timestamp")
df.head()
[43]: P2
timestamp
7
2018-09-01 00:00:02.472 34.43
2018-09-01 00:05:03.941 30.53
2018-09-01 00:10:04.374 22.80
2018-09-01 00:15:04.245 13.30
2018-09-01 00:20:04.869 16.57
[44]: # Check your work
assert df.shape[1] == 1, f"`df` should have only one column, not {df.shape[1]}."
assert df.columns == [
"P2"
], f"The single column in `df` should be `'P2'`, not {df.columns[0]}."
assert isinstance(df.index, pd.DatetimeIndex), "`df` should have a␣
,→`DatetimeIndex`."
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