Integrating Pipestat Summarize with PEPHub

[donaldcampbelljr]

Idea: Could pephub actually generate the summarized html page automatically?

Originally posted by @donaldcampbelljr in #191 (comment)

Notes from discussion:

We could allow Pipestat to push items to s3. We currently do this in bbclient:
https://github.com/databio/geniml_dev/blob/4657e53d8de0720c7041aff5f6143a4694b19f40/geniml/bbclient/bbclient.py#L193-L205

• Would need to allow s3 database configuration.

• Leave the output schema as is, but have the user configuration editable to flag which results would get pushed to s3 vs local.

• For example: the output schema can define the option with s3 potential. but in the pipestat config file, maybe the config options in pipestat have includes, excludes, provide list of values.

• • • We probably don't want to push ALL files. For example, some outputs are large and not helpful for results summary. Therefore the user define which results are to be pushed to s3

• In the future have the output schema simply live remotely on the repository, so the end user doesn't need to change it.

• Add a "Generate Report" button to generate a results report. pephub#314

[donaldcampbelljr]

• Per discussion we would like to have the ability to do both a local html report AND the PEPhub generate report button when using the Pephub backend

[nsheff]

What's the status of this? I see v0.12 is released.

[donaldcampbelljr]

These items have not been started. I forgot to take it off the 0.12 milestone.