Enabling Agile Data Analysis with AWS and Greenplum

Enabling Agile Data Analysis with AWS and Greenplum

Enabling Agile Data Analysis with AWS and Greenplum

Business Problem

At Pivotal we get to work with many customers who are looking to adopt an agile approach to how they develop and deploy applications.  For applications, this is done by utilizing continuous integration with products like Pivotal Cloud Foundry and methodologies of extreme programming and test-driven development.  A common request is how can we apply these types of methodologies for data when many of our customers are still struggling to just get access to data that they need to analyze?  The time it takes to get data loaded just to determine if there is any value in the data presents a problem towards a “fail fast” model of development (nothing useful in this data, let’s throw this dataset out and try a new one).  Our customers and their data scientists really need a way to get data into a database like Greenplum quickly so they can iterate on the data, perform the necessary analysis, and provide data “rules” for database designers and developers to incorporate this data into modeled data warehouses.

The solution presented in this post utilizes Greenplum on AWS along with several AWS components in order to automate a “no-IT touch” mechanism to upload data to AWS S3 and quickly be able to access this data using standard reporting and SQL-based tools from Greenplum.

Components highlighted in this post include:

  • AWS S3
  • AWS S3 Notifications and Lambda handler
  • AWS SES for email notifications
  • Greenplum on AWS
  • Greenplum S3 connector
  • Custom scripts

High level flow

Extended version of the AWS lamdba tutorial at: https://docs.aws.amazon.com/lambda/latest/dg/with-s3-example.html

  1. A user uploads an object to the source bucket in Amazon S3.
  2. Amazon S3 detects the object-created event.
  3. Amazon S3 publishes the s3:ObjectCreated:* event to AWS Lambda by invoking the Lambda function and passing event data as a function parameter.
  4. AWS Lambda executes under the role that you specified at the time you created the Lambda function.
  5. AWS Lambda executes the Lambda function.
  6. Lambda function ssh’s to EC2 Greenplum master instance and executes the script for generating the objects in Greenplum.  The function passes the S3 bucket, key, and optionally the table name to create (from S3 metadata)
  7. Script determines the external table headings by parsing the “header” row from the S3 key in the bucket (assumed to be the first row).  The Greenplum S3 connector is used in the creation of the external table.  Admin permissions are optionally granted to the generated external table to the specified admin_role from the scripts configuration file.
  8. Script generates a user view on the external table as a level of abstraction between the user and the underlying table.   Admin and Viewer permissions are optionally granted to the generated view to the specified admin_role and viewer_roles from the scripts configuration file.
  9. Lambda function receives response from the script, determines if response was successful or failed, and sends email to the configured email recipients.

At this point users can start querying the views from their tool of choice connected to Greenplum using the full supported ANSI SQL.

Implementation Steps

The name of the project is greenplumSailfish.  The name was chosen because the sailfish is the fastest fish in the sea and this project is enabling you to quickly “fish” for data.  Below are implementation steps to complete the project:

Greenplum

  1. Install Greenplum on AWS if it’s not already installed.  For this blog post I’ve used the Pivotal Greenplum marketplace offering from  https://aws.amazon.com/marketplace/pp/B06XKQ8Z3H?qid=1518113568120&sr=0-1&ref_=srh_res_product_title
  2. For ease of deployment for this blog post set an Inbound Rule on the AWS Greenplum marketplace security group to open up SSH fully.  This will allow the lambda function to invoke the code on the EC2 instance without the added complexity of custom AWS VPC’s, Subnets, etc:
  3. Note the greenplum master’s public IP address, you’ll use this later in the steps.  If you use the Greenplum marketplace and provided Cloudformation scripts, the master IP address can be found in the output of the Cloudformation (MasterHost line below):
  1. Git clone the greenplumSailfish repo onto the Greenplum master.  You can put the code under any directory owned by gpadmin.  If you can’t clone then you just need to copy greenplumSailfish.py, greenplumSailfish_cfg.py and argparse.py.  Note the full path to the scripts, you’ll use this later in the steps.  The code is available in a github repository for downloading onto your Greenplum master:
git clone https://github.com/lmugnano/greenplum-sailfish

 

  1. Edit the greenplumSailfish_cfg.py script to set the static parameters for the script.  Below is sample settings:
import sys

sys.dont_write_bytecode = True

# Operation

action = ‘genS3externalTable’

”’ Valid values are

genS3externalTable

”’

# Connection Configuration

host = ‘localhost’

port = 6432

db = ‘gpadmin’

user = ‘gpadmin’

# Greenplum S3 Connector Configuration file

s3_config = ‘/home/gpadmin/s3/s3.conf’

# Naming convention for generated objects

ext_tbl_prefix = ‘ext_’

ext_tbl_suffix = ”

view_prefix = ‘vw_’

view_suffix = ”

# Permissions of generated objects

admin_role = ‘admin_role’

viewer_role = ‘ro_role’

Amazon Web Services (AWS)

  1. If you aren’t already using AWS SES, validate the email address you want to use for sending email from the lamdba function.  Please see the following AWS documentation on this step:

https://docs.aws.amazon.com/ses/latest/DeveloperGuide/send-using-sdk-python.html

  1. Create a new S3 bucket if you don’t already have one ( https://aws.amazon.com/documentation/s3/ ).  In your S3 bucket create a folder called sandbox.  This will be the folder that we’ll trigger off of later in the steps. No special properties or permissions are set on the example bucket used in this example.   As the owner of the bucket my AWS login has permissions to “list objects”, “write objects”, “read bucket permissions” and “write bucket permissions”.  The required permissions for the functionality in this post are just “list objects” and “write objects” for users who would be putting files into the bucket.  
  2. In your sandbox folder create a new folder called config.
  3. Put the following files into the sandbox/config folder on your S3 bucket:
    1. The pem file for connecting via ssh to your Greenplum master EC2 instance.  Name this file “PivotalGreenplum_master.pem”
    2. A file named sandbox_config.json.  Here is an example file that can be edited for your specific implementation:

 

{

“email_sender”:”<email address validated via SES>“,

“email_recipient”:”<email recipients for email notification>“,

“aws_region”:”us-east-1″,

“gpdb_master_host”:”<Greenplum master host IP>“,

“script”:”source .bashrc; cd <dir where you put python code on master>; python greenplumSailfish.py -cfg greenplumSailfish_cfg”

}

 

  1. Create a new role for the lambda function.  When creating the role choose lambda as a trusted resource

The following policies are required

 

AWSLambdaBasicExecution

AmazonS3ReadOnlyAccess

Required for lambda functions using S3
AmazonSESFullAccess This is specifically needed since our lambda function sends email using the SES service
AmazonVPCFullAccess Gives permissions for Lambda to access your EC2 instance

 

  1. Create a lambda function (I used python for language) and chose blueprint s3-get-object-python from: https://docs.aws.amazon.com/lambda/latest/dg/get-started-create-function.html
  1. Manually edit and package up the lambda function
    1. Building dependency package for Lambda function is in Appendix 1
    2. Lambda function itself is in Appendix 2
  2. Upload zip package to lambda function and save
  1. Copy a csv file into your S3 bucket under the sandbox directory, first line should be the header for the columns in the file (you can pick a file from the Greenplum sandbox tutorial faa dataset at https://github.com/greenplum-db/gpdb-sandbox-tutorials, the test in this post uses L_AIRPORTS.csv).  Configure test event (I named it s3notifytest).  If you copy the test from Appendix 3 in you just need to change the items in Bold to match the specifics of the test file you have under your s3 bucket.
  1. Run the test by choosing the s3notifytest test and pressing the “Test” button:
  1. Double check and then enable the S3 notification:
  1. Save the function
  2. Test by uploading a file to S3 bucket.  When a file is uploaded you should get an email with:

Email Subject example:

SUCCESS: Amazon S3 file upload on bucket cf-pde-lmugnano-us-east-1

 

Email Body example:

File sandbox/otp200912.gz was uploaded to S3 bucket cf-pde-lmugnano-us-east-1

Analytics auto enablement process returned with:

SUCCESS: File uploaded and is available for reporting with view s3_sandbox.vw_otp200912

 

  1. You can view logs for lambda functions from CloudWatch: https://console.aws.amazon.com/cloudwatch/home?region=us-east-1#logs:
  2. You can monitor invocations via CloudWatch: https://console.aws.amazon.com/lambda/home?region=us-east-1#/functions/s3_function?tab=monitoring

 

Additional Tasks / Future Considerations

  1. This post has intentionally left out topics around VPC and security groups since those would differ from customer to customer.  As part of the lambda function configuration you can specify that the lambda function run under your specific VPC and security groups.  See AWS documentation for details on this.
  2. The initial minimum custom code built for the greenplum portion of the implementation is being provided via a static public github at the time of this writing.  This code is a Minimum Viable Product for purposes of this post and the code will continue to add functionality as we work with our customers and iterate on the development.  Greenplum customers can gain access to the newest code by emailing the author and being added to the private Git repository.  To just get an idea of what the code generates, I included examples of log output from a sample run in Appendix 4.
  3. Accessing data from S3 directly via Greenplum enables quick data analysis and allows you to exploit the full capabilities of the database but for performance reasons it would often make sense to load the data directly into Greenplum internal tables.  This is left out of the blog post but one thought to enable this is to utilize user defined metadata on the S3 object where the user can decide to “cache” the data in Greenplum.  Based on that the greenplumSailfish.py script would generate a permanent table and load the data directly into Greenplum.  The main reason for the view abstraction is so that this decision can be made later simply by repointing the view to the internal table vs the external table without impacting the users accessing the data.
  4. With implementation of #3 a data lifecycle management policy also needs to be defined with the users so that space on the database can be managed properly (ie. At some point we’ll “flush the cache”)
  5. Heavy usage of a mechanism like this will bloat the catalog due to the creating and dropping of multiple objects throughout the process.  Catalog maintenance is critical for performance of any Greenplum database where users are allowed to directly create objects in the database.

 

Conclusion

This post includes the “long version” of the steps involved to set up an end to end solution like this.  Most of the steps can and will ultimately be scripted and Pivotal will look at how to simplify the configuration of a solution like this within our marketplace offerings.  Even with these simplifications we create it’s still beneficial to understand what’s “under the hood” which is what this post provides.   I want to thank my colleague Antonio Petrole for reviewing the doc and providing me with super valuable input.

Appendix 1 (lamdba function dependency .zip pkg)

Below are the steps I used to build the lambda_function.zip package for uploading to AWS Lamdba.  This package is needed because Lambda doesn’t include some of the python dependencies required by the script:

 

Note: The already built package (lambda_function.zip) is available for you on the greenplumSailfish Git repo if you don’t want to build it yourself.

 

  1. Spin up a AWS Redhat linux EC2 instance (t2micro is fine)
  2. Ssh to AWS instance
  3. Sudo to root: sudo su – root
  4. Install pip:
    1. curl “https://bootstrap.pypa.io/get-pip.py” -o “get-pip.py”
    2. python get-pip.py
    3. pip -V
  5. Install virtualenv: pip install virtualenv
  6. Install python in virtualenv: virtualenv -p /usr/bin/python2.7 /root/code
  7. Activate environment: source /root/code/bin/activate
  8. Install pycrypto: pip install pycrypto
  9. Install paramiko: pip install paramiko
  10. Install zip: yum install zip -y
  11. Install unzip: yum install unzip -y
  12. Add libraries to zip:
    1. cd path/to/my/helloworld-env/lib/python2.7/site-packages
    2. zip -r ~/lambda_function.zip .
    3. cd path/to/my/helloworld-env/lib64/python2.7/site-packages
    4. zip -r ~/lambda_function.zip .
  13. Download lambda_function.zip and add any handwritten python code to the zip file for deployment to AWS.  The custom lambda_function is in Appendix 2 below.

 

Appendix 2 (Lambda function)

Create a file called lambda_function.py and put the following code into the file.  Include this file into the lambda_function.zip package you created in Appendix 1.

 

Note: The already built package (lambda_function.zip) is available for you on the greenplumSailfish Git repo if you don’t want to build it yourself.  This code is included into the lambda_function.zip package.

 

from __future__ import print_function

import json

from pprint import pprint

import urllib

import boto3

from botocore.exceptions import ClientError

import paramiko

print(‘Loading function’)

# —————————————————————————

# Global Variables

# —————————————————————————

s3 = boto3.client(‘s3’)

gpdb_host = ”

email_sender = ”

email_recipient = ”

aws_region = ”

config_dir = ‘sandbox/config/’

script = ”

# —————————————————————————

# Init

# —————————————————————————

def initialize(bucket):

   global gpdb_host

   global email_sender

   global email_recipient

   global aws_region

   global script

   

   try:

       data = s3.get_object(Bucket=bucket, Key=config_dir + “sandbox_config.json”)

       json_config = json.loads(data[‘Body’].read())

       pprint(json_config)

       gpdb_host = json_config[“gpdb_master_host”]

       email_sender = json_config[“email_sender”]

       email_recipient = json_config[“email_recipient”]

       aws_region = json_config[“aws_region”]

       script = json_config[“script”]

   except Exception as e:

       print(e)

       print(‘Error getting sandbox_config object from bucket {}. Make sure it exists and your bucket is in the same region as this function.’.format(bucket))

       raise e

# —————————————————————————

# Function to send mail

#

# How to send email is from:

# https://docs.aws.amazon.com/ses/latest/DeveloperGuide/send-using-sdk-python.html

# Had to add AmazonSESFullAccess to the role and had to verify email address from SES

# —————————————————————————

def send_mail(bucket, key, rc, response):

   

   SENDER = email_sender

   RECIPIENT = email_recipient

   AWS_REGION = aws_region

   # The subject line for the email.

   if rc==0:

       SUBJECT = “SUCCESS: “

   else:

       SUBJECT = “FAILED: “

   SUBJECT += “Amazon S3 file upload on bucket ” + bucket

   # The email body for recipients with non-HTML email clients.

   BODY_TEXT = (“File ” + key + ” was uploaded to S3 bucket ” + bucket + “\r\n\r\n”

                “Analytics auto enablement process returned with:\r\n” +

                response)

   # The character encoding for the email.

   CHARSET = “UTF-8”

   # Create a new SES resource and specify a region.

   client = boto3.client(‘ses’,region_name=AWS_REGION)

   # Try to send the email.

   try:

       #Provide the contents of the email.

       mail_response = client.send_email (

           Destination={

               ‘ToAddresses’: [

                   RECIPIENT,

               ],

           },

           Message={

               ‘Body’: {

                   ‘Text’: {

                       ‘Charset’: CHARSET,

                       ‘Data’: BODY_TEXT,

                   },

               },

               ‘Subject’: {

                   ‘Charset’: CHARSET,

                   ‘Data’: SUBJECT,

               },

           },

           Source=SENDER,

       )        

   # Display an error if something goes wrong.

   except ClientError as e:

       print(e.mail_response[‘Error’][‘Message’])

       return -1

   else:

       print(“Email sent! Message ID:”),

       print(mail_response[‘ResponseMetadata’][‘RequestId’])

       return 0

       

# —————————————————————————

# Function to invoke remote script

#

# Code primarily from:

# https://aws.amazon.com/blogs/compute/scheduling-ssh-jobs-using-aws-lambda/

# —————————————————————————

def invoke_script(bucket, key, timeout=30, bg_run=False):

   

   s3.download_file(bucket, config_dir + ‘PivotalGreenplum_master.pem’, ‘/tmp/keyname.pem’)

   head = s3.head_object(Bucket=bucket, Key=key)

   if ‘dbtable’ in head[‘Metadata’]:

       dbtable = head[‘Metadata’][‘dbtable’]

   else:

       dbtable = ”

       

   host=gpdb_host

   user=’gpadmin’

   

   k = paramiko.RSAKey.from_private_key_file(“/tmp/keyname.pem”)

   c = paramiko.SSHClient()

   c.set_missing_host_key_policy(paramiko.AutoAddPolicy())

   #host=event[‘IP’]

   print (“Connecting to ” + host)

   c.connect( hostname = host, username = “ec2-user”, pkey = k, timeout = 10 )

   print (“Connected to ” + host)

   commands = [

       “sudo su – gpadmin ” + script

       ]

   for command in commands:

       print (“Executing {}”.format(command))

       stdin , stdout, stderr = c.exec_command(command + ‘ %s %s %s’ % (bucket, key, dbtable))

       rc = stdout.channel.recv_exit_status()

       stderr = stderr.readline()

       if rc != 0:

           return rc, “FAILED: File upload failed with error:\r\n    ” + stderr

   return rc, “SUCCESS: File uploaded and is available for reporting”

   

# —————————————————————————

# Event Handler for S3 notification

# —————————————————————————

def lambda_handler(event, context):

   #print(“Received event: ” + json.dumps(event, indent=2))

   # Get the object from the event

   bucket = event[‘Records’][0][‘s3’][‘bucket’][‘name’]

   key = urllib.unquote_plus(event[‘Records’][0][‘s3’][‘object’][‘key’].encode(‘utf8’))

   

   # Exit if file is part of config

   if key.startswith(config_dir):

       return ”

   

   try:

       response = s3.get_object(Bucket=bucket, Key=key)

   except Exception as e:

       print(e)

       print(‘Error getting object {} from bucket {}. Make sure they exist and your bucket is in the same region as this function.’.format(key, bucket))

       raise e   

   

   initialize(bucket)

   rc, script_response = invoke_script(bucket,key)

   send_mail(bucket,key,rc,script_response)

   

   # Return response

   return response[‘ContentType’]

Appendix 3 (Test)

{

 “Records”: [

   {

     “eventVersion”: “2.0”,

     “eventTime”: “1970-01-01T00:00:00.000Z”,

     “requestParameters”: {

       “sourceIPAddress”: “127.0.0.1”

     },

     “s3”: {

       “configurationId”: “testConfigRule”,

       “object”: {

         “eTag”: “3b0c8da017cfdb9e7e2f3da5b0f32b5a”,

         “sequencer”: “0A1B2C3D4E5F678901”,

         “key”: “sandbox/L_AIRPORTS.csv”,

         “size”: 200796

       },

       “bucket”: {

         “arn”: “arn:aws:s3:::cf-pde-lmugnano-us-east-1“,

         “name”: “cf-pde-lmugnano-us-east-1“,

         “ownerIdentity”: {

           “principalId”: “EXAMPLE”

         }

       },

       “s3SchemaVersion”: “1.0”

     },

     “responseElements”: {

       “x-amz-id-2”: “EXAMPLE123/5678abcdefghijklambdaisawesome/mnopqrstuvwxyzABCDEFGH”,

       “x-amz-request-id”: “EXAMPLE123456789”

     },

     “awsRegion”: “us-east-1”,

     “eventName”: “ObjectCreated:Put”,

     “userIdentity”: {

       “principalId”: “EXAMPLE”

     },

     “eventSource”: “aws:s3”

   }

 ]

}

Appendix 4 (greenplumSailfish.py sample log output)

The following shows sample log output of an execution of the greenplumSailfish.py script.  This shows the Greenplum SQL generated to build the objects in the database when the script is invoked by the S3 notification lamdba handler:

 

Invocation of script:

python ./greenplumSailfish.py -cfg greenplumSailfish_cfg -s3_bucket=’cf-pde-lmugnano-us-east-1′ -s3_key=’sandbox/otp200912.gz’

 

————-  CONNECTION CONFIGURATION  —————–

Host: localhost

Port: 6432

Database: gpadmin

———————————————————-

Generate External table for S3 Object

determine_headings-1:

   drop external table if exists s3_sandbox.ext_otp200912_head

determine_headings-2:

   create external table s3_sandbox.ext_otp200912_head ( header text ) location (‘s3://s3.amazonaws.com/cf-pde-lmugnano-us-east-1/sandbox/otp200912.gz config=/home/gpadmin/s3/s3.conf’) format ‘text’

determine_headings-3:

   select replace(unnest(header),'”‘,”) from (select string_to_array(header,’,’) as header from s3_sandbox.ext_otp200912_head limit 1) a

determine_headings-4:

   drop external table if exists s3_sandbox.ext_otp200912_head

create_ext_table-1:

   drop external table if exists s3_sandbox.ext_otp200912 cascade

create_ext_table-2:

   create external table s3_sandbox.ext_otp200912 ( year text, quarter text, month text, dayofmonth text, dayofweek text, flightdate text, uniquecarrier text, airlineid text, carrier text, tailnum text, flightnum text, origin text, origincityname text, originstate text, originstatefips text, originstatename text, originwac text, dest text, destcityname text, deststate text, deststatefips text, deststatename text, destwac text, crsdeptime text, deptime text, depdelay text, depdelayminutes text, depdel15 text, departuredelaygroups text, deptimeblk text, taxiout text, wheelsoff text, wheelson text, taxiin text, crsarrtime text, arrtime text, arrdelay text, arrdelayminutes text, arrdel15 text, arrivaldelaygroups text, arrtimeblk text, cancelled text, cancellationcode text, diverted text, crselapsedtime text, actualelapsedtime text, airtime text, flights text, distance text, distancegroup text, carrierdelay text, weatherdelay text, nasdelay text, securitydelay text, lateaircraftdelay text, firstdeptime text, totaladdgtime text, longestaddgtime text, divairportlandings text, divreacheddest text, divactualelapsedtime text, divarrdelay text, divdistance text, div1airport text, div1wheelson text, div1totalgtime text, div1longestgtime text, div1wheelsoff text, div1tailnum text, div2airport text, div2wheelson text, div2totalgtime text, div2longestgtime text, div2wheelsoff text, div2tailnum text, div3airport text, div3wheelson text, div3totalgtime text, div3longestgtime text, div3wheelsoff text, div3tailnum text, div4airport text, div4wheelson text, div4totalgtime text, div4longestgtime text, div4wheelsoff text, div4tailnum text, div5airport text, div5wheelson text, div5totalgtime text, div5longestgtime text, div5wheelsoff text, div5tailnum text, dummy_1 text ) location (‘s3://s3.amazonaws.com/cf-pde-lmugnano-us-east-1/sandbox/otp200912.gz config=/home/gpadmin/s3/s3.conf’) format ‘csv’ (header)

grant_to_role:

   grant ALL on s3_sandbox.ext_otp200912 to admin_role

create_user_view-1:

   drop view if exists s3_sandbox.vw_otp200912

create_user_view-2:

   create view s3_sandbox.vw_otp200912 as select * from s3_sandbox.ext_otp200912

grant_to_role:

   grant ALL on s3_sandbox.vw_otp200912 to admin_role

grant_to_role:

   grant SELECT on s3_sandbox.vw_otp200912 to ro_role

 

 

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