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save a zip file downloaded in AWS EC2 to a gzip file in S3, using python boto3 in memory

I appreciate this question is quite specific, but I believe it should be a common problem. I've solved parts of it but not the entire chain.
Input:
in AWS EC2 instance, I download a zip-compressed file from the internet
Output:
I save the gzip-compressed file to an S3 bucket
I see 2 ways of doing this:
saving temporary files in EC2, and then copying them to S3
converting the data in memory in EC2, and saving directly to S3
I know how to do the first option, but because of resource constraints, and because I need to download a lot of files, I would like to try the second option. This is what I have so far:
import requests, boto3, gzip
zip_data = requests.get(url).content
#I can save a temp zip file in EC2 like this, but I would like to avoid it
with open(zip_temp, 'wb') as w:
w.write(zip_data)
#missing line that decompresses the zipped file in memory and returns a byte-object, I think?
#like: data = SOMETHING (zip_data)
gz_data = gzip.compress(data)
client = boto3.client('s3')
output = client.put_object(
Bucket = 'my-bucket',
Body = gz_data,
Key = filename)
Besides, are there any general considerations I should think about when deciding which option to go for?

turns out it was quite simple:
import requests, boto3, gzip
from zipfile import ZipFile
from io import BytesIO
zip_data = requests.get(url).content
with ZipFile(BytesIO(zip_data)) as myzip:
with myzip.open('zip_file_inside.csv') as mycsv:
gz_data = gzip.compress(mycsv.read())
client = boto3.client('s3')
output = client.put_object(
Bucket = 'my-bucket',
Body = gz_data,
Key = filename)

writing a simple text file with no key value pair to cloud storage storage

My requirement is to export the data from BQ to GCS in a particular sorted order which I am not able to get using automatic export and hence trying to write a manual export for this.
File format is like below:
HDR001||5378473972abc||20101|182082||
DTL001||436282798101|
DTL002||QS
DTL005||3733|8
DTL002||QA
DTL005||3733|8
DTL002||QP
DTL005||3733|8
DTL001||436282798111|
DTL002||QS
DTL005||3133|2
DTL002||QA
DTL005||3133|8
DTL002||QP
DTL005||3133|0
I am very new to this and am able to write the file in local disk but I am not sure how I can write this to file to GCS. I tried to use the write_to_file but I seem to be missing something.
import pandas as pd
import pickle as pkl
import tempfile
from google.colab import auth
from google.cloud import bigquery, storage
#import cloudstorage as gcs
auth.authenticate_user()
df = pd.DataFrame(data=job)
sc = storage.Client(project='temp-project')
with tempfile.NamedTemporaryFile(mode='w+b', buffering=- 1,prefix='test',suffix='temp') as fh:
with open(fh.name,'w+',newline='') as f:
dfAsString = df.to_string(header=" ", index=False)
fh.name = fh.write(dfAsString)
fh.close()
bucket = sc.get_bucket('my-bucket')
target_fn = 'test.csv'
source_fn = fh.name
destination_blob_name = bucket.blob('test.csv')
bucket.blob(destination_blob_name).upload_from_file(source_fn)
Can someone please help?
Thank You.

I would suggest to upload an object through a Cloud Storage bucket. Instead of upload_from_file, you need to use upload_from_filename. Your code should look like this:
bucket.blob(destination_blob_name).upload_from_filename(source_fn)
Here are links for the documentation on how to upload an object to Cloud Storage bucket and Client library docs.
EDIT:
The reason why you're getting that is because somewhere in your code, you're passing a Blob object, rather than a String. Currently your destination variable is a Blob Object, change it to String instead:
destination_blob_name = bucket.blob('test.csv')
to
destination_blob_name = 'test.csv'

Amazon Sagemaker open json from S3 bucket

I created a S3 bucket and placed both a data.csv and a data.json file inside it. I then created a Sagemaker notebook and specified this S3 bucket in the IAM role.
This now works from inside the notebook:
import pandas as pd
from sagemaker import get_execution_role
bucket='my-sagemaker-bucket'
data_key = 'data.csv'
data_location = 's3://{}/{}'.format(bucket, data_key)
data = pd.read_csv(data_location)
But this errors saying file doesn't exist:
import json
from sagemaker import get_execution_role
bucket='my-sagemaker-bucket'
data_key = 'data.json'
data_location = 's3://{}/{}'.format(bucket, data_key)
data = json.load(open(data_location))
Anyone know why I can read the csv but not the json? I also can't shutil.copy the csv to the notebook's current working directory (also says file doesn't exist). I'm not very well versed with S3 buckets or Sagemaker, so not sure if this is a permissions/policy issue or something else.

your SageMaker-ExecutionRole might have insufficient rights to access your S3-bucket. The default IAM-SageMaker Execution role has the permission: "AmazonSageMakerFullAccess" which uses the S3 RequestCondition "s3:ExistingObjectTag/SageMaker = true".
So maybe you could try to simply tag your S3 bucket (Tag: SageMaker:true). Control your IAM settings.
import pandas as pd
bucket='my-sagemaker-bucket'
data_key = 'data.json'
data_location = 's3://{}/{}'.format(bucket, data_key)
pd.read_json(data_location) # , orient='columns', typ='series'

Pandas can handle S3 URL using your AWS credentials. So you could use pd.read_csv or pd.read_json instead of json.load. The suggestion from #Michael_S should work.

How to load a model saved in joblib file from Google Cloud Storage bucket

I want to load a model which is saved as a joblib file from Google Cloud Storage bucket. When it is in local path, we can load it as follows (considering model_file is the full path in system):
loaded_model = joblib.load(model_file)
How can we do the same task with Google Cloud Storage?

For anyone googling around for an answer to this.
Here are two more options besides the obvious, to use Google AI platform for model hosting (and online predictions).
Option 1 is to use TemporaryFile like this:
from google.cloud import storage
from sklearn.externals import joblib
from tempfile import TemporaryFile
storage_client = storage.Client()
bucket_name=<bucket name>
model_bucket='model.joblib'
bucket = storage_client.get_bucket(bucket_name)
#select bucket file
blob = bucket.blob(model_bucket)
with TemporaryFile() as temp_file:
#download blob into temp file
blob.download_to_file(temp_file)
temp_file.seek(0)
#load into joblib
model=joblib.load(temp_file)
#use the model
model.predict(...)
Option 2 is to use BytesIO like this:
from google.cloud import storage
from sklearn.externals import joblib
from io import BytesIO
storage_client = storage.Client()
bucket_name=<bucket name>
model_bucket='model.joblib'
bucket = storage_client.get_bucket(bucket_name)
#select bucket file
blob = bucket.blob(model_bucket)
#download blob into an in-memory file object
model_file = BytesIO()
blob.download_to_file(model_file)
#load into joblib
model=joblib.load(model_local)

Alternate answer as of 2020 using tf2, you can do this:
import joblib
import tensorflow as tf
gcs_path = 'gs://yourpathtofile'
loaded_model = joblib.load(tf.io.gfile.GFile(gcs_path, 'rb'))

I found using gcsfs to be the fastest (and most compact) method to use:
def load_joblib(bucket_name, file_name):
fs = gcsfs.GCSFileSystem()
with fs.open(f'{bucket_name}/{file_name}') as f:
return joblib.load(f)

I don't think that's possible, at least in a direct way. I though about a workaround, but the might not be as efficient as you want.
By using the Google Cloud Storage client libraries [1] you can download the model file first, load it, and when your program ends, delete it. Of course, this means that you need to download the file every time you run the code. Here is a snippet:
from google.cloud import storage
from sklearn.externals import joblib
storage_client = storage.Client()
bucket_name=<bucket name>
model_bucket='model.joblib'
model_local='local.joblib'
bucket = storage_client.get_bucket(bucket_name)
#select bucket file
blob = bucket.blob(model_bucket)
#download that file and name it 'local.joblib'
blob.download_to_filename(model_local)
#load that file from local file
job=joblib.load(model_local)

For folks who are Googling around with this problem - here's another option. The open source modelstore library is a wrapper that deals with the process of saving, uploading, and downloading models from Google Cloud Storage.
Under the hood, it saves scikit-learn models using joblib, creates a tar archive with the files, and up/downloads them from a Google Cloud Storage bucket using blob.upload_from_file() and blob.download_to_filename().
In practice it looks a bit like this (a full example is here):
# Create modelstore instance
from modelstore import ModelStore
ModelStore.from_gcloud(
os.environ["GCP_PROJECT_ID"], # Your GCP project ID
os.environ["GCP_BUCKET_NAME"], # Your Cloud Storage bucket name
)
# Train and upload a model (this currently works with 9 different ML frameworks)
model = train() # Replace with your code to train a model
meta_data = modelstore.sklearn.upload("my-model-domain", model=model)
# ... and later when you want to download it
model_path = modelstore.download(
local_path="/path/to/a/directory",
domain="my-model-domain",
model_id=meta_data["model"]["model_id"],
)
The full documentation is here.

This is the shortest way I found so far:
from google.cloud import storage
client = storage.Client()
bucket = client.get_bucket("my-gcs-bucket")
blob = bucket.blob("model.joblib")
with blob.open(mode="rb") as file:
model = joblib.load(file)

AWS uploading file into wrong bucket

I am using AWS Sagemaker and trying to upload a data folder into S3 from Sagemaker. I am trying to do is to upload my data into the s3_train_data directory (the directory exists in S3). However, it wouldn't upload it in that bucket, but in a default Bucket that has been created, and in turn creates a new folder directory with the S3_train_data variables.
code to input in directory
import os
import sagemaker
from sagemaker import get_execution_role
sagemaker_session = sagemaker.Session()
role = get_execution_role()
bucket = <bucket name>
prefix = <folders1/folders2>
key = <input>
s3_train_data = 's3://{}/{}/{}/'.format(bucket, prefix, key)
#path 'data' is the folder in the Jupyter Instance, contains all the training data
inputs = sagemaker_session.upload_data(path= 'data', key_prefix= s3_train_data)
Is the problem in the code or more in how I created the notebook?

You could look at the Sample notebooks, how to upload the data S3 bucket
There have many ways. I am just giving you hints to answer.
And you forgot create a boto3 session to access the S3 bucket
It is one of the ways to do it.
import os
import urllib.request
import boto3
def download(url):
filename = url.split("/")[-1]
if not os.path.exists(filename):
urllib.request.urlretrieve(url, filename)
def upload_to_s3(channel, file):
s3 = boto3.resource('s3')
data = open(file, "rb")
key = channel + '/' + file
s3.Bucket(bucket).put_object(Key=key, Body=data)
# caltech-256
download('http://data.mxnet.io/data/caltech-256/caltech-256-60-train.rec')
upload_to_s3('train', 'caltech-256-60-train.rec')
download('http://data.mxnet.io/data/caltech-256/caltech-256-60-val.rec')
upload_to_s3('validation', 'caltech-256-60-val.rec')
link : https://buildcustom.notebook.us-east-2.sagemaker.aws/notebooks/sample-notebooks/introduction_to_amazon_algorithms/imageclassification_caltech/Image-classification-fulltraining.ipynb
Another way to do it.
bucket = '<your_s3_bucket_name_here>'# enter your s3 bucket where you will copy data and model artifacts
prefix = 'sagemaker/breast_cancer_prediction' # place to upload training files within the bucket
# do some processing then prepare to push the data.
f = io.BytesIO()
smac.write_numpy_to_dense_tensor(f, train_X.astype('float32'), train_y.astype('float32'))
f.seek(0)
boto3.Session().resource('s3').Bucket(bucket).Object(os.path.join(prefix, 'train', train_file)).upload_fileobj(f)
Link : https://buildcustom.notebook.us-east-2.sagemaker.aws/notebooks/sample-notebooks/introduction_to_applying_machine_learning/breast_cancer_prediction/Breast%20Cancer%20Prediction.ipynb
Youtube link : https://www.youtube.com/watch?v=-YiHPIGyFGo - how to pull the data in S3 bucket.