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Need to remember not to use the 'current' url when adding a new reference.
This is still a work in progress. Need to clean up a buch of stuff. Thinking about revisiting the sample handler to add necessary functionality to make this easier.
| md = markdown.Markdown(output_format='html5') | ||
| tp = ENV.get_template('base.html') | ||
| return tp.render(content=md.convert(dedent(string).format(**kwargs))) | ||
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Still trying to decide how to build table and figure html representations. Right now I am doing it with a rule and saving the HTML chunk. Then importing the report rule. If we think this is best then probably should add a file importing here instead of assuming **kwargs is a string ready for injection.
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Just a note that de-indention is huge, because if tabs are not removed then Markdown.convert thinks you are trying to do a code block. I think this should take care of it, but something to look for as we write real reports.
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Just to clarify: in this system, each logical chunk of a report will have its own rule to create some HTML. The snakemake infrastructure will identify which rules will need to run and will thereforel be used to determine whether a chunk needs to be built. The final report rule in turn will essentially stitch together the various chunks into one final HTML report. Is that right?
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Yes, I think the cleanest/easiest way is to just have a rule for each HTML blob and then use the report rule to write the text and insert the blobs in the correct order.
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This is just a dummy pull request for discussion.
I have added a working example to the mapping workflow. Did a quick and dirty for the count generation, a little hackish but it works.
I am not happy with the interface tool. I think I need to re-vist it now. It needs simplified and I can see some more functionality to add.
I have attached the report (note had to rename to a .txt for upload to github)
report.txt
I will go through on the PR and make some comments line by line.