Denormalize a GCS file before uploading to BigQuery - google-bigquery

I have written a Cloud Run API in .Net Core that reads files from a GCS location and then is supposed to denormalize (i.e. add more information for each row to include textual descriptions) and then write that to a BigQuery table. I have two options:
My cloud run API could create denormalized CSV files and write them to another GCS location. Then another cloud run API could pick up those denormalized CSV files and write them straight to BigQuery.
My cloud run API could read the original CSV file, denormalize them in memory (filestream) and then somehow write from the in memory filestream straight to the BigQuery table.
What is the best way to write to BigQuery in this scenario if performance (speed) and cost (monetary) is my goal. These files are roughly 10KB each before denormalizing. Each row is roughly 1000 characters. After denormalizing it is about three times as much. I do not need to keep denormalized files after they are successfully loaded in BigQuery. I am concerned about performance, as well as any specific BigQuery daily quotas around inserts/writes. I don't think there are any unless you are doing DML statements but correct me if I'm wrong.

I would use Cloud Functions that are triggered when you upload a file to a bucket.
It is so common that Google has a repo a tutorial just for this for JSON files Streaming data from Cloud Storage into BigQuery using Cloud Functions.
Then, I would modify the example main.py file from:
def streaming(data, context):
'''This function is executed whenever a file is added to Cloud Storage'''
bucket_name = data['bucket']
file_name = data['name']
db_ref = DB.document(u'streaming_files/%s' % file_name)
if _was_already_ingested(db_ref):
_handle_duplication(db_ref)
else:
try:
_insert_into_bigquery(bucket_name, file_name)
_handle_success(db_ref)
except Exception:
_handle_error(db_ref)
To this that accepts CSV files:
import json
import csv
import logging
import os
import traceback
from datetime import datetime
from google.api_core import retry
from google.cloud import bigquery
from google.cloud import storage
import pytz
PROJECT_ID = os.getenv('GCP_PROJECT')
BQ_DATASET = 'fromCloudFunction'
BQ_TABLE = 'mytable'
CS = storage.Client()
BQ = bigquery.Client()
def streaming(data, context):
'''This function is executed whenever a file is added to Cloud Storage'''
bucket_name = data['bucket']
file_name = data['name']
newRows = postProcessing(bucket_name, file_name)
# It is recommended that you save
# what you process for debugging reasons.
destination_bucket = 'post-processed' # gs://post-processed/
destination_name = file_name
# saveRowsToBucket(newRows,destination_bucket,destination_name)
rowsInsertIntoBigquery(newRows)
class BigQueryError(Exception):
'''Exception raised whenever a BigQuery error happened'''
def __init__(self, errors):
super().__init__(self._format(errors))
self.errors = errors
def _format(self, errors):
err = []
for error in errors:
err.extend(error['errors'])
return json.dumps(err)
def postProcessing(bucket_name, file_name):
blob = CS.get_bucket(bucket_name).blob(file_name)
my_str = blob.download_as_string().decode('utf-8')
csv_reader = csv.DictReader(my_str.split('\n'))
newRows = []
for row in csv_reader:
modified_row = row # Add your logic
newRows.append(modified_row)
return newRows
def rowsInsertIntoBigquery(rows):
table = BQ.dataset(BQ_DATASET).table(BQ_TABLE)
errors = BQ.insert_rows_json(table,rows)
if errors != []:
raise BigQueryError(errors)
It would be still necesssary to define your map(row->newRow) and the function saveRowsToBucket if you needed it.

Related

How to convert S3 bucket content(.csv format) into a dataframe in AWS Lambda

I am trying to ingest S3 data(csv file) to RDS(MSSQL) through lambda. Sample code:
s3 = boto3.client('s3')
if event:
file_obj = event["Records"][0]
bucketname = str(file_obj["s3"]["bucket"]["name"])
csv_filename = unquote_plus(str(file_obj["s3"]["object"]["key"]))
print("Filename: ", csv_filename)
csv_fileObj = s3.get_object(Bucket=bucketname, Key=csv_filename)
file_content = csv_fileObj["Body"].read().decode("utf-8").split()
I have tried put my csv contents into a list but didnt work.
results = []
for row in csv.DictReader(file_content):
results.append(row.values())
print(results)
print(file_content)
return {
'statusCode': 200,
'body': json.dumps('S3 file processed')
}
Is there anyway I could convert "file_content" into a dataframe in Lambda? I have multiple columns to load.
Later I would follow this approach to load the data into RDS
import pyodbc
import pandas as pd
# insert data from csv file into dataframe(df).
server = 'yourservername'
database = 'AdventureWorks'
username = 'username'
password = 'yourpassword'
cnxn = pyodbc.connect('DRIVER={SQL Server};SERVER='+server+';DATABASE='+database+';UID='+username+';PWD='+ password)
cursor = cnxn.cursor()
# Insert Dataframe into SQL Server:
for index, row in df.iterrows():
cursor.execute("INSERT INTO HumanResources.DepartmentTest (DepartmentID,Name,GroupName) values(?,?,?)", row.DepartmentID, row.Name, row.GroupName)
cnxn.commit()
cursor.close()
Can anyone suggest how to go about it?
You can use io.BytesIO to get the bytes data into memory and after that use pandasread_csv to transform it into a dataframe. Note that there is some strange SSL download limit for dataframes that will lead to issue when downloading data > 2GB. That is why I have used this chunking in the code below.
import io
obj = s3.get_object(Bucket=bucketname, Key=csv_filename)
# This should prevent the 2GB download limit from a python ssl internal
chunks = (chunk for chunk in obj["Body"].iter_chunks(chunk_size=1024**3))
data = io.BytesIO(b"".join(chunks)) # This keeps everything fully in memory
df = pd.read_csv(data) # here you can provide also some necessary args and kwargs
It appears that your goal is to load the contents of a CSV file from Amazon S3 into SQL Server.
You could do this without using Dataframes:
Loop through the Event Records (multiple can be passed-in)
For each object:
Download the object to /tmp/
Use the Python CSVReader to loop through the contents of the file
Generate INSERT statements to insert the data into the SQL Server table
You might also consider using aws-data-wrangler: Pandas on AWS, which is available as a Lambda Layer.

Exporting query results to an output file in cloud storage using Google bigquery

I'm working on a project involved with querying a bigquery server.
Until recently, the size of output was enough to fit in memeory as a pandas dataframe:
from google.cloud import bigquery
client = bigquery.Client(...)
query = client.query("SELECT * FROM my_table")
results = query.to_dataframe()
Now I got to a point where the result may be too large to fit in memory.
Ideally, I'd tel bigquery to export the results of a query as csv/parquet file into cloud storage.
Problem is, I'm not sure how can I do that using the python client library.
Is the mentioned above possible?
Many Thanks :)
Check out this official documentation
# from google.cloud import bigquery
# client = bigquery.Client()
# bucket_name = 'my-bucket'
project = "bigquery-public-data"
dataset_id = "samples"
table_id = "shakespeare"
destination_uri = "gs://{}/{}".format(bucket_name, "shakespeare.csv")
dataset_ref = bigquery.DatasetReference(project, dataset_id)
table_ref = dataset_ref.table(table_id)
extract_job = client.extract_table(
table_ref,
destination_uri,
# Location must match that of the source table.
location="US",
) # API request
extract_job.result() # Waits for job to complete.
print(
"Exported {}:{}.{} to {}".format(project, dataset_id, table_id, destination_uri)
)
Ideally, I'd tel bigquery to export the results of a query as csv/parquet file into cloud storage.
You can use below BigQuery statement
EXPORT DATA OPTIONS(
uri='gs://bucket/folder/*.csv',
format='CSV',
overwrite=true,
header=true,
field_delimiter=';') AS
SELECT * FROM my_table
Read more about EXPORT DATA statement

Google Cloud Storage Joining multiple csv files

I exported a dataset from Google BigQuery to Google Cloud Storage, given the size of the file BigQuery exported the file as 99 csv files.
However now I want to connect to my GCP Bucket and perform some analysis with Spark, yet I need to join all 99 files into a single large csv file to run my analysis.
How can this be achieved?
BigQuery splits the data exported into several files if it is larger than 1GB. But you can merge these files with the gsutil tool, check this official documentation to know how to perform object composition with gsutil.
As BigQuery export the files with the same prefix, you can use a wildcard * to merge them into one composite object:
gsutil compose gs://example-bucket/component-obj-* gs://example-bucket/composite-object
Note that there is a limit (currently 32) to the number of components that can be composed in a single operation.
The downside of this option is that the header row of each .csv file will be added in the composite object. But you can avoid this by modifiyng the jobConfig to set the print_header parameter to False.
Here is a Python sample code, but you can use any other BigQuery Client library:
from google.cloud import bigquery
client = bigquery.Client()
bucket_name = 'yourBucket'
project = 'bigquery-public-data'
dataset_id = 'libraries_io'
table_id = 'dependencies'
destination_uri = 'gs://{}/{}'.format(bucket_name, 'file-*.csv')
dataset_ref = client.dataset(dataset_id, project=project)
table_ref = dataset_ref.table(table_id)
job_config = bigquery.job.ExtractJobConfig(print_header=False)
extract_job = client.extract_table(
table_ref,
destination_uri,
# Location must match that of the source table.
location='US',
job_config=job_config) # API request
extract_job.result() # Waits for job to complete.
print('Exported {}:{}.{} to {}'.format(
project, dataset_id, table_id, destination_uri))
Finally, remember to compose an empty .csv with just the headers row.
I got tired kind tired of doing multiple recursive compose operations, stripping headers, etc... Especially when dealing with 3500 split gzipped csv files.
Therefore wrote a CSV Merge (Sorry windows only though) to solve exactly this problem.
https://github.com/tcwicks/DataUtilities
Download latest release, unzip and use.
Also wrote an article with a use case and usage example for it:
https://medium.com/#TCWicks/merge-multiple-csv-flat-files-exported-from-bigquery-redshift-etc-d10aa0a36826
Hope it is of use to someone.
p.s. Recommend tab delimited over CSV as it tends to have less data issues.

export big query table locally

I have a big query table that I would like to run on using pandas DataFrame. The table is big and using the: pd.read_gpq() function gets stuck and does not manage to retrieve the data.
I implemented a chunk mechanism using pandas that works, but it takes a long time to fetch (an hour for 9M rows). So im looking into a new sulotion.
I would like to download the table to as a csv file and then read it. I saw this code in the google cloud docs:
# from google.cloud import bigquery
# client = bigquery.Client()
# bucket_name = 'my-bucket'
project = 'bigquery-public-data'
dataset_id = 'samples'
table_id = 'shakespeare'
destination_uri = 'gs://{}/{}'.format(bucket_name, 'shakespeare.csv')
dataset_ref = client.dataset(dataset_id, project=project)
table_ref = dataset_ref.table(table_id)
extract_job = client.extract_table(
table_ref,
destination_uri,
# Location must match that of the source table.
location='US') # API request
extract_job.result() # Waits for job to complete.
print('Exported {}:{}.{} to {}'.format(
project, dataset_id, table_id, destination_uri))
but all the URIs shown in the examples are google cloud buckets URIs and not local, and I didn't manage to download it (tried to put a local URI which gave me an error).
Is there a way to download the table's data as csv file without using a bucket?
As mentioned here
The limitation with bigquery export is - You cannot export data to a local file or to Google Drive, but you can save query results to a local file. The only supported export location is Cloud Storage.
Is there a way to download the table's data as csv file without using a bucket?
So now as we know that we can store query result to local file so you can use something like this :
from google.cloud import bigquery
client = bigquery.Client()
# Perform a query.
QUERY = (
'SELECT * FROM `project_name.dataset_name.table_name`')
query_job = client.query(QUERY) # API request
rows = query_job.result() # Waits for query to finish
for row in rows:
print(row.name)
this rows variable will have all the table rows and you can either directly use it or can write it to a local file.

How to list all databases and tables in AWS Glue Catalog?

I created a Development Endpoint in the AWS Glue console and now I have access to SparkContext and SQLContext in gluepyspark console.
How can I access the catalog and list all databases and tables? The usual sqlContext.sql("show tables").show() does not work.
What might help is the CatalogConnection Class but I have no idea in which package it is. I tried importing from awsglue.context and no success.
I spend several hours trying to find some info about CatalogConnection class but haven't found anything. (Even in the aws-glue-lib repository https://github.com/awslabs/aws-glue-libs)
In my case I needed table names in Glue Job Script console
Finally I used boto library and retrieved database and table names with Glue client:
import boto3
client = boto3.client('glue',region_name='us-east-1')
responseGetDatabases = client.get_databases()
databaseList = responseGetDatabases['DatabaseList']
for databaseDict in databaseList:
databaseName = databaseDict['Name']
print '\ndatabaseName: ' + databaseName
responseGetTables = client.get_tables( DatabaseName = databaseName )
tableList = responseGetTables['TableList']
for tableDict in tableList:
tableName = tableDict['Name']
print '\n-- tableName: '+tableName
Important thing is to setup the region properly
Reference:
get_databases - http://boto3.readthedocs.io/en/latest/reference/services/glue.html#Glue.Client.get_databases
get_tables - http://boto3.readthedocs.io/en/latest/reference/services/glue.html#Glue.Client.get_tables
Glue returns back one page per response. If you have more than 100 tables, make sure you use NextToken to retrieve all tables.
def get_glue_tables(database=None):
next_token = ""
while True:
response = glue_client.get_tables(
DatabaseName=database,
NextToken=next_token
)
for table in response.get('TableList'):
print(table.get('Name'))
next_token = response.get('NextToken')
if next_token is None:
break
The boto3 api also supports pagination, so you could use the following instead:
import boto3
glue = boto3.client('glue')
paginator = glue.get_paginator('get_tables')
page_iterator = paginator.paginate(
DatabaseName='database_name'
)
for page in page_iterator:
print(page['TableList'])
That way you don't have to mess with while loops or the next token.