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https://github.com/codait/covid-notebooks

Jupyter notebooks that analyze COVID-19 time series data
https://github.com/codait/covid-notebooks

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Jupyter notebooks that analyze COVID-19 time series data

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# Analyzing COVID-19 time series data



This repository provides a set of [Jupyter Notebooks](https://jupyter.org) that augment and 

analyze COVID-19 time series data.



While working on this scenario, we identified that building a pipeline would help organize the

notebooks and simplify running the full workflow to process and analyze new data. For this, we leveraged

[Elyra's](https://github.com/elyra-ai/elyra) ability to build 

[notebook pipelines](https://elyra.readthedocs.io/en/latest/getting_started/overview.html#notebook-pipelines-visual-editor)

to orchestrate the running of the full scenario on a [Kubeflow Pipeline](https://www.kubeflow.org/docs/pipelines/overview/pipelines-overview/)

runtime.



![COVID-19 Analytics Pipeline](docs/source/images/covid-19-pipeline.png)



### Configuring the local development environment



**WARNING: Do not run these notebooks from your system Python environment.**



Use the following steps to create a consistent Python environment for running the

notebooks in this repository:



1. Install [Anaconda](https://docs.anaconda.com/anaconda/install/)

   or [Miniconda](https://docs.conda.io/en/latest/miniconda.html)

1. Navigate to your local copy of this repository.

1. Run the script `env.sh` to create an Anaconda environment in the directory `./env`:

   ```console

   $ bash env.sh

   ```

   Note: This script takes a while to run.

1. Activate the new environment and start JupyterLab:

   ```console

   $ conda activate ./env

   $ jupyter lab --debug

   ```



#### Configuring a local Kubeflow Pipeline runtime



[Elyra's Notebook pipeline visual editor](https://elyra.readthedocs.io/en/latest/getting_started/overview.html#notebook-pipelines-visual-editor)

currently supports running these pipelines in a Kubeflow Pipeline runtime.  If required, these are

[the steps to install a local deployment of KFP](https://elyra.readthedocs.io/en/latest/recipes/deploying-kubeflow-locally-for-dev.html).



After installing your Kubeflow Pipeline runtime, use the command below (with proper updates) to configure the new

KFP runtime with Elyra.



```bash

elyra-metadata install runtimes --replace=true \

       --schema_name=kfp \

       --name=kfp-local \

       --display_name="Kubeflow Pipeline (local)" \

       --api_endpoint=http://[host]:[api port]/pipeline \

       --cos_endpoint=http://[host]:[cos port] \

       --cos_username=[cos username] \

       --cos_password=[cos password] \

       --cos_bucket=covid

``` 



**Note:** The cloud object storage above is a local minio object storage but other cloud-based object storage 

services could be configured and used in this scenario.



## Elyra Notebook pipelines



Elyra provides a visual editor for building Notebook-based AI pipelines, simplifying the conversion of 

multiple notebooks into batch jobs or workflows. By leveraging cloud-based resources to run their 

experiments faster, the data scientists, machine learning engineers, and AI developers are then more productive,

allowing them to spend their time using their technical skills.



![Notebook pipeline](https://raw.githubusercontent.com/elyra-ai/community/master/resources/blog-announcement/elyra-pipelines.gif)



### Running the Elyra pipeline



The Elyra pipeline `us_data.pipeline`, which is located in the `pipeline` directory, can be run by clicking

on the `play` button as seen on the image above. The `submit` dialog will request two inputs from the user: a name 

for the pipeline and a runtime to use while executing the pipeline. The list of available runtimes comes from

the registered Kubeflow Pipelines runtimes documented above. After submission, Elyra will show a dialog with a direct

link to where the experiment is being executed on Kubeflow Piplines. 



The user can access the pipelines, and respective experiment runs, via the `api_endpoint` of the Kubeflow Pipelines

runtime (e.g. `http://[host]:[port]/pipeline`)



![Pipeline experiment run](docs/source/images/kfp-experiment.png)



The output from the executed experiments are then available in the associated `object storage`

and the executed notebooks are available as native ipynb notebooks and also in html format

to facilitate the visualization and sharing of the results.



![Pipeline experiment results in object storage](docs/source/images/object-storage-results.png)



### References



Find more project details on [Elyra's GitHub](https://github.com/elyra-ai/elyra) or watching the

[Elyra's demo](https://www.youtube.com/watch?v=Nj0yga6T4U8).