Python Papermill - execute_notebook - Azure Python function

DataWrangler1980
April 22, 2024
134 views
1 vote
2 Answers

I can create an Azure Functions project (V2) – Python 3.11
After publishing all functions work – they all work on my local dev laptop – however there is one function that does not work when hosted as an Azure Function.

papermill ..

I have the python file downloaded, I can verify that it is in the tmp folder where the Azure Function downloads the file, as well as I have the metadata file there < – same as when debugging locally.

however, when i call execute_notebook function in papermill I get this error immediately?

Kernel died before replying to kernel_info

what does this mean? and how can I make this work when running on Azure Function hosted?

Answers

Chosen as BEST ANSWER

I managed to make Papermill work by installing the kernel each time the function starts up - since I want to keep on using Azure Serverless (consumption plan):

def RunJupyterNotebookPapermill(inputFile, outputFile): 
    inputFile = GetAbsoluteFilePath(inputFile)
    outputFile = GetAbsoluteFilePath(outputFile)

    pm.execute_notebook(
    inputFile,
    outputFile,
    kernel_name="python3"
    )    
    pass

Here is a more detailed flow, of some of the key elements, which allow me to download notebooks from kaggle, run them in azure serverless function and then push them back to Kaggle, tested it and it is working ;-)

remember to configure KAGGLE_USERNAME and KAGGLE_KEY with your API in local.settings.json - and ALSO in your Azure Functions Project Config in the Portal - or your functions won't show up online until you add those two configuration keys and values.

import logging 
import azure.functions as func 
import os

from kaggle.api.kaggle_api_extended import KaggleApi

import tempfile

import papermill as pm
import subprocess 
import json 



BlueprintJupyter = func.Blueprint() 

@BlueprintJupyter.route(route="KaggleRefresh", methods=['POST'])
def KaggleRefresh(req: func.HttpRequest) -> func.HttpResponse: 

    try:
        #no longer required
        #req_body = json.loads(req.get_body().decode())
        #papermill = req_body.get('Papermill')
       
        # install jupyter kernel 
        InstallJupyterKernel()

        # prepare files 
        tempPath = GetTempPath()
        inputFile = GetFilePath(tempPath, "schedule-run-test.ipynb")
        outputFile =  GetFilePath(tempPath, "schedule-run-test-output.ipynb")

        # pull
        KagglePull(tempPath) 

        files = "" + ListFiles(tempPath)
        files = files + "n" 

        files = files + "n" + "Absolute Paths:"
        files = files + "n" + GetAbsoluteFilePath(inputFile)
        files = files + "n" + GetAbsoluteFilePath(outputFile)

        # execute
        RunJupyterNotebookPapermill(inputFile, outputFile)

        # push 
        KagglePush(tempPath) 

        return func.HttpResponse( 
            f"Hello, This HTTP-triggered function " 
            f"executed successfully."
            f"Files: {files}")         
    except Exception as ex: 
        return func.HttpResponse( 
            f"This HTTP-triggered function failed." 
            f"{str(ex)}" 
            f"Files: {files}",
            status_code=200 
        )    
    
def KagglePull(tempPath): 
    api = KaggleApi()
    api.authenticate()    

    api.kernels_pull('myusername/schedule-run-test', path=tempPath, metadata=True)

    pass 

def KagglePush(tempPath):  
    api = KaggleApi()
    api.authenticate()

    #api.kernels_push(tempPath)
    api.kernels_push_cli(tempPath)
    pass

def RunJupyterNotebookPapermill(inputFile, outputFile): 
    inputFile = GetAbsoluteFilePath(inputFile)
    outputFile = GetAbsoluteFilePath(outputFile)

    pm.execute_notebook(
    inputFile,
    outputFile,
    kernel_name="python3"
    )    
    pass 

def GetTempPath(): 
    temp_dir = tempfile.gettempdir()
    subfolder_name = "tmpnotebook"
    full_path = os.path.join(temp_dir, subfolder_name)
    return full_path 

def GetFilePath(tempPath, fileName): 
    return os.path.join(tempPath, fileName)

def GetAbsoluteFilePath(fileName): 
    return os.path.abspath(fileName)

def ListFiles(tempPath):
    files = ""
    fileList = [] 
    
    for x in os.listdir(tempPath): 
        y = os.path.join(tempPath, x)
        if (os.path.isfile(y)): 
            fileList.append(y)

    files = '' + 'n' + '; n'.join(fileList)

    return files

def InstallJupyterKernel():
    os.system('pip install ipykernel')
    os.system('python -m ipykernel install --user --name python3')
    pass

(Edit)

You need to install the kernel by visiting Advance tool kudu and SSH'ing into Azure Function app. Make sure you have created your Azure Function app in Premium or Dedicated app service plan for the ssh to work:-

My function app kudu ssh commands to install kernel:-

pip install ipykernel
python -m ipykernel install --user --name jupytersiddhesh

Azure function app > Development Tools > Advanced Tools > Go:-

My Function app code:-

import azure.functions as func
import logging
import papermill as pm
import tempfile
import os
app = func.FunctionApp(http_auth_level=func.AuthLevel.ANONYMOUS)

@app.route(route="http_trigger")
def http_trigger(req: func.HttpRequest) -> func.HttpResponse:
    logging.info('Python HTTP trigger function processed a request.')

    name = req.params.get('name')
    if not name:
        try:
            req_body = req.get_json()
            name = req_body.get('name')
        except ValueError:
            pass

    if name:
        temp_dir = tempfile.mkdtemp()
        input_notebook = os.path.join(temp_dir, "input_notebook.ipynb")
        output_notebook = os.path.join(os.getenv('HOME', 'D:\home\data\temp'), "output_notebook.ipynb")

        with open(input_notebook, 'w') as file:
            file.write("""
            # Sample Notebook
            print(f'Hello, {name}. This is a sample notebook execution.')
            """)

        pm.execute_notebook(
            input_path=input_notebook,
            output_path=output_notebook,
            parameters=dict(name=name),
            kernel_name='jupytersiddhesh'
        )

        with open(output_notebook, 'r') as file:
            output_content = file.read()
            
        return func.HttpResponse(output_content, status_code=200)
    else:
        return func.HttpResponse(
            "Please provide 'name' parameter.",
            status_code=400
        )

Refer my SO answer for the same error.

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Python Papermill – execute_notebook – Azure Python function

Answers