google-api-python-client is in maintenance only mode

[pumpikano]

The old Google client libraries (google-api-python-client) are now in maintenance only mode. They are superseded by google-cloud-python.

Most of the notebooks need to be updated to be kept up-to-date.

[smrgit]

thanks @pumpikano we'll add this to our to-do-list

[pumpikano]

I just went through and updated notebooks/Creating TCGA cohorts -- part 1.ipynb myself and can share some pointers that might be helpful to you. Unfortunately, it was not as straightforward as I had hoped.

My updated version of that notebook is here and includes all 3 types of changes described below.

There are basically 3 things that need to be updated:

1. As mentioned, the new client libraries are under the umbrella of google-cloud-python and versions past v0.28 differ in a variety of ways from their forebears. The latest release notes for google-cloud-bigquery v0.30 indicate that it is a v1.0 release candidate, so I suspect it is reasonable to develop against the API in v0.30, though waiting for v1.0 is also a reasonable thing to do. In any case, there is a good client migration guide that summarizes the changes.
2. There is a new version of the Datalab utilities package which provide the %sql and %bigquery magic commands. Those commands are now deprecated and superseded by the %bq magic command. There is a migration guide for this as well, and I found the new documentation to be a helpful reference.
3. Additionally, the notebooks currently use a legacy SQL dialect. Newer BigQuery clients now default to a new dialect called "Standard SQL" (though you can still override this and use legacy SQL). There is also a migration guide for Standard SQL, though I suspect Legacy SQL will be supported for some time if you chose to keep it.

Happy to answer specific questions about the updated notebook as well (esp. since notebooks are hard to diff).

[smrgit]

thank you @pumpikano! after a long delay we are finally getting back to using Datalab and will be updating our notebooks over the next couple of weeks