Added mapreduce with python using mrjob IPython Notebook.

This commit is contained in:
Donne Martin 2015-04-15 15:18:15 -04:00
parent 6109274ff0
commit 0890d2b2dc
3 changed files with 676 additions and 0 deletions

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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Hadoop MapReduce: Python Streaming with mrjob\n",
"\n",
"* Introduction\n",
"* Setup\n",
"* Processing S3 Logs\n",
"* Running Amazon Elastic MapReduce (EMR) Jobs\n",
"* Unit Testing S3 Logs\n",
"* Running S3 Logs Unit Test\n",
"* Sample .mrjob.conf"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Introduction\n",
"\n",
"[mrjob](https://pythonhosted.org/mrjob/) lets you write MapReduce jobs in Python 2.5+ and run them on several platforms. You can:\n",
"\n",
"* Write multi-step MapReduce jobs in pure Python\n",
"* Test on your local machine\n",
"* Run on a Hadoop cluster\n",
"* Run in the cloud using Amazon Elastic MapReduce (EMR)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Setup\n",
"\n",
"From PyPI:\n",
"\n",
"``pip install mrjob``\n",
"\n",
"From source:\n",
"\n",
"``python setup.py install``\n",
"\n",
"See \"Sample .mrjob.conf\" section for additional config details."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Processing S3 Logs\n",
"\n",
"Sample mrjob code that processes log files on Amazon S3 based on the [S3 logging format](http://docs.aws.amazon.com/AmazonS3/latest/dev/LogFormat.html):"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"%%file mr_s3_log_parser.py\n",
"\n",
"import time\n",
"from mrjob.job import MRJob\n",
"from mrjob.protocol import RawValueProtocol, ReprProtocol\n",
"import re\n",
"\n",
"\n",
"class MrS3LogParser(MRJob):\n",
" \"\"\"Parses the logs from S3 based on the S3 logging format:\n",
" http://docs.aws.amazon.com/AmazonS3/latest/dev/LogFormat.html\n",
" \n",
" Aggregates a user's daily requests by user agent and operation\n",
" \n",
" Outputs date_time, requester, user_agent, operation, count\n",
" \"\"\"\n",
"\n",
" LOGPATS = r'(\\S+) (\\S+) \\[(.*?)\\] (\\S+) (\\S+) ' \\\n",
" r'(\\S+) (\\S+) (\\S+) (\"([^\"]+)\"|-) ' \\\n",
" r'(\\S+) (\\S+) (\\S+) (\\S+) (\\S+) (\\S+) ' \\\n",
" r'(\"([^\"]+)\"|-) (\"([^\"]+)\"|-)'\n",
" NUM_ENTRIES_PER_LINE = 17\n",
" logpat = re.compile(LOGPATS)\n",
"\n",
" (S3_LOG_BUCKET_OWNER, \n",
" S3_LOG_BUCKET, \n",
" S3_LOG_DATE_TIME,\n",
" S3_LOG_IP, \n",
" S3_LOG_REQUESTER_ID, \n",
" S3_LOG_REQUEST_ID,\n",
" S3_LOG_OPERATION, \n",
" S3_LOG_KEY, \n",
" S3_LOG_HTTP_METHOD,\n",
" S3_LOG_HTTP_STATUS, \n",
" S3_LOG_S3_ERROR, \n",
" S3_LOG_BYTES_SENT,\n",
" S3_LOG_OBJECT_SIZE, \n",
" S3_LOG_TOTAL_TIME, \n",
" S3_LOG_TURN_AROUND_TIME,\n",
" S3_LOG_REFERER, \n",
" S3_LOG_USER_AGENT) = range(NUM_ENTRIES_PER_LINE)\n",
"\n",
" DELIMITER = '\\t'\n",
"\n",
" # We use RawValueProtocol for input to be format agnostic\n",
" # and avoid any type of parsing errors\n",
" INPUT_PROTOCOL = RawValueProtocol\n",
"\n",
" # We use RawValueProtocol for output so we can output raw lines\n",
" # instead of (k, v) pairs\n",
" OUTPUT_PROTOCOL = RawValueProtocol\n",
"\n",
" # Encode the intermediate records using repr() instead of JSON, so the\n",
" # record doesn't get Unicode-encoded\n",
" INTERNAL_PROTOCOL = ReprProtocol\n",
"\n",
" def clean_date_time_zone(self, raw_date_time_zone):\n",
" \"\"\"Converts entry 22/Jul/2013:21:04:17 +0000 to the format\n",
" 'YYYY-MM-DD HH:MM:SS' which is more suitable for loading into\n",
" a database such as Redshift or RDS\n",
"\n",
" Note: requires the chars \"[ ]\" to be stripped prior to input\n",
" Returns the converted datetime annd timezone\n",
" or None for both values if failed\n",
"\n",
" TODO: Needs to combine timezone with date as one field\n",
" \"\"\"\n",
" date_time = None\n",
" time_zone_parsed = None\n",
"\n",
" # TODO: Probably cleaner to parse this with a regex\n",
" date_parsed = raw_date_time_zone[:raw_date_time_zone.find(\":\")]\n",
" time_parsed = raw_date_time_zone[raw_date_time_zone.find(\":\") + 1:\n",
" raw_date_time_zone.find(\"+\") - 1]\n",
" time_zone_parsed = raw_date_time_zone[raw_date_time_zone.find(\"+\"):]\n",
"\n",
" try:\n",
" date_struct = time.strptime(date_parsed, \"%d/%b/%Y\")\n",
" converted_date = time.strftime(\"%Y-%m-%d\", date_struct)\n",
" date_time = converted_date + \" \" + time_parsed\n",
"\n",
" # Throws a ValueError exception if the operation fails that is\n",
" # caught by the calling function and is handled appropriately\n",
" except ValueError as error:\n",
" raise ValueError(error)\n",
" else:\n",
" return converted_date, date_time, time_zone_parsed\n",
"\n",
" def mapper(self, _, line):\n",
" line = line.strip()\n",
" match = self.logpat.search(line)\n",
"\n",
" date_time = None\n",
" requester = None\n",
" user_agent = None\n",
" operation = None\n",
"\n",
" try:\n",
" for n in range(self.NUM_ENTRIES_PER_LINE):\n",
" group = match.group(1 + n)\n",
"\n",
" if n == self.S3_LOG_DATE_TIME:\n",
" date, date_time, time_zone_parsed = \\\n",
" self.clean_date_time_zone(group)\n",
" # Leave the following line of code if \n",
" # you want to aggregate by date\n",
" date_time = date + \" 00:00:00\"\n",
" elif n == self.S3_LOG_REQUESTER_ID:\n",
" requester = group\n",
" elif n == self.S3_LOG_USER_AGENT:\n",
" user_agent = group\n",
" elif n == self.S3_LOG_OPERATION:\n",
" operation = group\n",
" else:\n",
" pass\n",
"\n",
" except Exception:\n",
" yield ((\"Error while parsing line: %s\", line), 1)\n",
" else:\n",
" yield ((date_time, requester, user_agent, operation), 1)\n",
"\n",
" def reducer(self, key, values):\n",
" output = list(key)\n",
" output = self.DELIMITER.join(output) + \\\n",
" self.DELIMITER + \\\n",
" str(sum(values))\n",
"\n",
" yield None, output\n",
"\n",
" def steps(self):\n",
" return [\n",
" self.mr(mapper=self.mapper,\n",
" reducer=self.reducer)\n",
" ]\n",
"\n",
"\n",
"if __name__ == '__main__':\n",
" MrS3LogParser.run()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Running Amazon Elastic MapReduce (EMR) Jobs"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Run an Amazon EMR job on the given input (must be a flat file hierarchy), placing the results in the output (output directory must not exist):"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"!python mr-mr_s3_log_parser.py -r emr s3://bucket-source/ --output-dir=s3://bucket-dest/"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Run a MapReduce job locally on the specified input file, sending the results to the specified output file:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"!python mr_s3_log_parser.py input_data.txt > output_data.txt"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Unit Testing S3 Logs"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Accompanying unit test:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"%%file test_mr_s3_log_parser.py\n",
"\n",
"from StringIO import StringIO\n",
"import unittest2 as unittest\n",
"from mr_s3_log_parser import MrS3LogParser\n",
"\n",
"\n",
"class MrTestsUtil:\n",
"\n",
" def run_mr_sandbox(self, mr_job, stdin):\n",
" # inline runs the job in the same process so small jobs tend to\n",
" # run faster and stack traces are simpler\n",
" # --no-conf prevents options from local mrjob.conf from polluting\n",
" # the testing environment\n",
" # \"-\" reads from standard in\n",
" mr_job.sandbox(stdin=stdin)\n",
"\n",
" # make_runner ensures job cleanup is performed regardless of\n",
" # success or failure\n",
" with mr_job.make_runner() as runner:\n",
" runner.run()\n",
" for line in runner.stream_output():\n",
" key, value = mr_job.parse_output_line(line)\n",
" yield value\n",
"\n",
" \n",
"class TestMrS3LogParser(unittest.TestCase):\n",
"\n",
" mr_job = None\n",
" mr_tests_util = None\n",
"\n",
" RAW_LOG_LINE_INVALID = \\\n",
" '00000fe9688b6e57f75bd2b7f7c1610689e8f01000000' \\\n",
" '00000388225bcc00000 ' \\\n",
" 's3-storage [22/Jul/2013:21:03:27 +0000] ' \\\n",
" '00.111.222.33 ' \\\n",
"\n",
" RAW_LOG_LINE_VALID = \\\n",
" '00000fe9688b6e57f75bd2b7f7c1610689e8f01000000' \\\n",
" '00000388225bcc00000 ' \\\n",
" 's3-storage [22/Jul/2013:21:03:27 +0000] ' \\\n",
" '00.111.222.33 ' \\\n",
" 'arn:aws:sts::000005646931:federated-user/user 00000AB825500000 ' \\\n",
" 'REST.HEAD.OBJECT user/file.pdf ' \\\n",
" '\"HEAD /user/file.pdf?versionId=00000XMHZJp6DjM9x500000' \\\n",
" '00000SDZk ' \\\n",
" 'HTTP/1.1\" 200 - - 4000272 18 - \"-\" ' \\\n",
" '\"Boto/2.5.1 (darwin) USER-AGENT/1.0.14.0\" ' \\\n",
" '00000XMHZJp6DjM9x5JVEAMo8MG00000'\n",
"\n",
" DATE_TIME_ZONE_INVALID = \"AB/Jul/2013:21:04:17 +0000\"\n",
" DATE_TIME_ZONE_VALID = \"22/Jul/2013:21:04:17 +0000\"\n",
" DATE_VALID = \"2013-07-22\"\n",
" DATE_TIME_VALID = \"2013-07-22 21:04:17\"\n",
" TIME_ZONE_VALID = \"+0000\"\n",
"\n",
" def __init__(self, *args, **kwargs):\n",
" super(TestMrS3LogParser, self).__init__(*args, **kwargs)\n",
" self.mr_job = MrS3LogParser(['-r', 'inline', '--no-conf', '-'])\n",
" self.mr_tests_util = MrTestsUtil()\n",
"\n",
" def test_invalid_log_lines(self):\n",
" stdin = StringIO(self.RAW_LOG_LINE_INVALID)\n",
"\n",
" for result in self.mr_tests_util.run_mr_sandbox(self.mr_job, stdin):\n",
" self.assertEqual(result.find(\"Error\"), 0)\n",
"\n",
" def test_valid_log_lines(self):\n",
" stdin = StringIO(self.RAW_LOG_LINE_VALID)\n",
"\n",
" for result in self.mr_tests_util.run_mr_sandbox(self.mr_job, stdin):\n",
" self.assertEqual(result.find(\"Error\"), -1)\n",
"\n",
" def test_clean_date_time_zone(self):\n",
" date, date_time, time_zone_parsed = \\\n",
" self.mr_job.clean_date_time_zone(self.DATE_TIME_ZONE_VALID)\n",
" self.assertEqual(date, self.DATE_VALID)\n",
" self.assertEqual(date_time, self.DATE_TIME_VALID)\n",
" self.assertEqual(time_zone_parsed, self.TIME_ZONE_VALID)\n",
"\n",
" # Use a lambda to delay the calling of clean_date_time_zone so that\n",
" # assertRaises has enough time to handle it properly\n",
" self.assertRaises(ValueError,\n",
" lambda: self.mr_job.clean_date_time_zone(\n",
" self.DATE_TIME_ZONE_INVALID))\n",
"\n",
"if __name__ == '__main__':\n",
" unittest.main()\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Running S3 Logs Unit Test"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Run the mrjob test:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"!python test_mr_s3_log_parser.py -v"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Sample .mrjob.conf"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"runners:\n",
" emr:\n",
" aws_access_key_id: __ACCESS_KEY__\n",
" aws_secret_access_key: __SECRET_ACCESS_KEY__\n",
" aws_region: us-east-1\n",
" ec2_key_pair: EMR\n",
" ec2_key_pair_file: ~/.ssh/EMR.pem\n",
" ssh_tunnel_to_job_tracker: true\n",
" ec2_master_instance_type: m3.xlarge\n",
" ec2_instance_type: m3.xlarge\n",
" num_ec2_instances: 5\n",
" s3_scratch_uri: s3://bucket/tmp/\n",
" s3_log_uri: s3://bucket/tmp/logs/\n",
" enable_emr_debugging: True\n",
" bootstrap:\n",
" - sudo apt-get install -y python-pip\n",
" - sudo pip install --upgrade simplejson"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.9"
}
},
"nbformat": 4,
"nbformat_minor": 0
}

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import time
from mrjob.job import MRJob
from mrjob.protocol import RawValueProtocol, ReprProtocol
import re
class MrS3LogParser(MRJob):
"""Parses the logs from S3 based on the S3 logging format:
http://docs.aws.amazon.com/AmazonS3/latest/dev/LogFormat.html
Aggregates a user's daily requests by user agent and operation
Outputs date_time, requester, user_agent, operation, count
"""
LOGPATS = r'(\S+) (\S+) \[(.*?)\] (\S+) (\S+) ' \
r'(\S+) (\S+) (\S+) ("([^"]+)"|-) ' \
r'(\S+) (\S+) (\S+) (\S+) (\S+) (\S+) ' \
r'("([^"]+)"|-) ("([^"]+)"|-)'
NUM_ENTRIES_PER_LINE = 17
logpat = re.compile(LOGPATS)
(S3_LOG_BUCKET_OWNER,
S3_LOG_BUCKET,
S3_LOG_DATE_TIME,
S3_LOG_IP,
S3_LOG_REQUESTER_ID,
S3_LOG_REQUEST_ID,
S3_LOG_OPERATION,
S3_LOG_KEY,
S3_LOG_HTTP_METHOD,
S3_LOG_HTTP_STATUS,
S3_LOG_S3_ERROR,
S3_LOG_BYTES_SENT,
S3_LOG_OBJECT_SIZE,
S3_LOG_TOTAL_TIME,
S3_LOG_TURN_AROUND_TIME,
S3_LOG_REFERER,
S3_LOG_USER_AGENT) = range(NUM_ENTRIES_PER_LINE)
DELIMITER = '\t'
# We use RawValueProtocol for input to be format agnostic
# and avoid any type of parsing errors
INPUT_PROTOCOL = RawValueProtocol
# We use RawValueProtocol for output so we can output raw lines
# instead of (k, v) pairs
OUTPUT_PROTOCOL = RawValueProtocol
# Encode the intermediate records using repr() instead of JSON, so the
# record doesn't get Unicode-encoded
INTERNAL_PROTOCOL = ReprProtocol
def clean_date_time_zone(self, raw_date_time_zone):
"""Converts entry 22/Jul/2013:21:04:17 +0000 to the format
'YYYY-MM-DD HH:MM:SS' which is more suitable for loading into
a database such as Redshift or RDS
Note: requires the chars "[ ]" to be stripped prior to input
Returns the converted datetime annd timezone
or None for both values if failed
TODO: Needs to combine timezone with date as one field
"""
date_time = None
time_zone_parsed = None
# TODO: Probably cleaner to parse this with a regex
date_parsed = raw_date_time_zone[:raw_date_time_zone.find(":")]
time_parsed = raw_date_time_zone[raw_date_time_zone.find(":") + 1:
raw_date_time_zone.find("+") - 1]
time_zone_parsed = raw_date_time_zone[raw_date_time_zone.find("+"):]
try:
date_struct = time.strptime(date_parsed, "%d/%b/%Y")
converted_date = time.strftime("%Y-%m-%d", date_struct)
date_time = converted_date + " " + time_parsed
# Throws a ValueError exception if the operation fails that is
# caught by the calling function and is handled appropriately
except ValueError as error:
raise ValueError(error)
else:
return converted_date, date_time, time_zone_parsed
def mapper(self, _, line):
line = line.strip()
match = self.logpat.search(line)
date_time = None
requester = None
user_agent = None
operation = None
try:
for n in range(self.NUM_ENTRIES_PER_LINE):
group = match.group(1 + n)
if n == self.S3_LOG_DATE_TIME:
date, date_time, time_zone_parsed = \
self.clean_date_time_zone(group)
# Leave the following line of code if
# you want to aggregate by date
date_time = date + " 00:00:00"
elif n == self.S3_LOG_REQUESTER_ID:
requester = group
elif n == self.S3_LOG_USER_AGENT:
user_agent = group
elif n == self.S3_LOG_OPERATION:
operation = group
else:
pass
except Exception:
yield (("Error while parsing line: %s", line), 1)
else:
yield ((date_time, requester, user_agent, operation), 1)
def reducer(self, key, values):
output = list(key)
output = self.DELIMITER.join(output) + \
self.DELIMITER + \
str(sum(values))
yield None, output
def steps(self):
return [
self.mr(mapper=self.mapper,
reducer=self.reducer)
]
if __name__ == '__main__':
MrS3LogParser.run()

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from StringIO import StringIO
import unittest2 as unittest
from mr_s3_log_parser import MrS3LogParser
class MrTestsUtil:
def run_mr_sandbox(self, mr_job, stdin):
# inline runs the job in the same process so small jobs tend to
# run faster and stack traces are simpler
# --no-conf prevents options from local mrjob.conf from polluting
# the testing environment
# "-" reads from standard in
mr_job.sandbox(stdin=stdin)
# make_runner ensures job cleanup is performed regardless of
# success or failure
with mr_job.make_runner() as runner:
runner.run()
for line in runner.stream_output():
key, value = mr_job.parse_output_line(line)
yield value
class TestMrS3LogParser(unittest.TestCase):
mr_job = None
mr_tests_util = None
RAW_LOG_LINE_INVALID = \
'00000fe9688b6e57f75bd2b7f7c1610689e8f01000000' \
'00000388225bcc00000 ' \
's3-storage [22/Jul/2013:21:03:27 +0000] ' \
'00.111.222.33 ' \
RAW_LOG_LINE_VALID = \
'00000fe9688b6e57f75bd2b7f7c1610689e8f01000000' \
'00000388225bcc00000 ' \
's3-storage [22/Jul/2013:21:03:27 +0000] ' \
'00.111.222.33 ' \
'arn:aws:sts::000005646931:federated-user/user 00000AB825500000 ' \
'REST.HEAD.OBJECT user/file.pdf ' \
'"HEAD /user/file.pdf?versionId=00000XMHZJp6DjM9x500000' \
'00000SDZk ' \
'HTTP/1.1" 200 - - 4000272 18 - "-" ' \
'"Boto/2.5.1 (darwin) USER-AGENT/1.0.14.0" ' \
'00000XMHZJp6DjM9x5JVEAMo8MG00000'
DATE_TIME_ZONE_INVALID = "AB/Jul/2013:21:04:17 +0000"
DATE_TIME_ZONE_VALID = "22/Jul/2013:21:04:17 +0000"
DATE_VALID = "2013-07-22"
DATE_TIME_VALID = "2013-07-22 21:04:17"
TIME_ZONE_VALID = "+0000"
def __init__(self, *args, **kwargs):
super(TestMrS3LogParser, self).__init__(*args, **kwargs)
self.mr_job = MrS3LogParser(['-r', 'inline', '--no-conf', '-'])
self.mr_tests_util = MrTestsUtil()
def test_invalid_log_lines(self):
stdin = StringIO(self.RAW_LOG_LINE_INVALID)
for result in self.mr_tests_util.run_mr_sandbox(self.mr_job, stdin):
self.assertEqual(result.find("Error"), 0)
def test_valid_log_lines(self):
stdin = StringIO(self.RAW_LOG_LINE_VALID)
for result in self.mr_tests_util.run_mr_sandbox(self.mr_job, stdin):
self.assertEqual(result.find("Error"), -1)
def test_clean_date_time_zone(self):
date, date_time, time_zone_parsed = \
self.mr_job.clean_date_time_zone(self.DATE_TIME_ZONE_VALID)
self.assertEqual(date, self.DATE_VALID)
self.assertEqual(date_time, self.DATE_TIME_VALID)
self.assertEqual(time_zone_parsed, self.TIME_ZONE_VALID)
# Use a lambda to delay the calling of clean_date_time_zone so that
# assertRaises has enough time to handle it properly
self.assertRaises(ValueError,
lambda: self.mr_job.clean_date_time_zone(
self.DATE_TIME_ZONE_INVALID))
if __name__ == '__main__':
unittest.main()