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matthewhirschey / ddh.org

datadrivenhypothesis.org is a resource to query 100+ GB of raw biological science data to develop data-driven hypotheses
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simplify report generation #105

Closed johnbradley closed 4 years ago

johnbradley commented 4 years ago

Moves logic to create and run in a temp directory to one location. Removes duplicate Rmd filenames.

Adds a new report directory used for PDF generation. Inside this directory new temporary directories will be created when rendering reports.

Adds achilles to fix rendering report_dummy_app.Rmd (example gene WASH7P).

Updates OpenShift deployment template to create a temporary reports directory.

Fixes #104

matthewhirschey commented 4 years ago

Why is the default dir in your new fun() still code/?

To get the template?

I think it looks good. 👍

johnbradley commented 4 years ago

Why is the default dir in your new fun() still code/? To get the template?

I not sure I understand the question. I moved the changing directory logic to the end of the process. When we enter the new function render_rmarkdown_in_tempdir we are still in the /code directory. At the point we run file.copy we are inside the temp directory. The rmd_path variable needs to be an absolute path or the file.copy function will fail.