Notebooks2

[vkt1414]

This PR address #5

• Described what each notebook does and tried to improve the readability of the notebooks.
• Provided a sample papermill command wherever applicable

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[fedorov]

@vkt1414 is it necessary to keep the output cells in the notebooks?

[vkt1414]

@vkt1414 is it necessary to keep the output cells in the notebooks?

Not necessary..would you like me to clear the output for all notebooks?

[fedorov]

Here are suggested updates:

• remove output (to make it easier to open the notebook in GitHub)
• do not use aws_url in any intermediate queries to reduce complexity and cost
• start using CONCAT(aws_bucket,'/',crdc_series_uuid) for forming the series folder path
• instead of pasting the binary of the images, let's keep all images in a dedicated folder, and insert them by references (you can see an example in https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/getting_started/part1_prerequisites.ipynb - but don't use dropbox links like I did for that notebook - let's put the links into "images" folder, for example)

Once these are fixed, let's just merge this, and I will review by experimenting with the notebooks.

[vkt1414]

• remove output (to make it easier to open the notebook in GitHub)

Done

• do not use aws_url in any intermediate queries to reduce complexity and cost
• start using CONCAT(aws_bucket,'/',crdc_series_uuid) for forming the series folder path

Will be addressing these from sqlqueryfix branch

• instead of pasting the binary of the images, let's keep all images in a dedicated folder, and insert them by references (you can see an example in https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/getting_started/part1_prerequisites.ipynb - but don't use dropbox links like I did for that notebook - let's put the links into "images" folder, for example)

Done

Once these are fixed, let's just merge this, and I will review by experimenting with the notebooks.

Please go ahead