Adding qiime map file

[antgonza]

This adds the creation of the qiime mapping file (combination of prep/sample template) at the when the prep template is added. Note that the code is ready for review, it tests pass, but we should merge #677 first.

[coveralls]

Coverage decreased (-0.14%) when pulling c07967b on antgonza:adding-qiime-map-file into d29f2fe on biocore:master.

[coveralls]

Coverage decreased (-0.14%) when pulling 4dae65c on antgonza:adding-qiime-map-file into d29f2fe on biocore:master.

[antgonza]

This is ready for review.

[ElDeveloper]

Can you revise this sentence?

[ElDeveloper]

This PR reminded me that we have not created that micro-package to deal with QIIME mapping files. Once we have that, we should replace as needed. Not sure if it would be worth creating an issue about that or not.

This works great, I applied the patch, accessed a study got a QIIME mapping file and then was able to open it (with vim) and started playing around with it! I was even able to get validate_mapping_file.py to go through an example and the only oddity it found were "extraneous" characters i. e. (, but that is not really a problem.

[coveralls]

Coverage decreased (-0.06%) when pulling 010332b on antgonza:adding-qiime-map-file into b5d257d on biocore:master.

[josenavas]

study -> sample

[josenavas]

Few comments @antgonza
It is a bit weird that we are relying on the filepaths to create the qiime mapping file (so we can parse them into pandas). I remember correctly, there is a function that @ElDeveloper wrote to transform a MetadataTemplate into a pandas DataFrame. I think the way to go is to make a function on the MetadataTemplate object called to_dataframe that returns a DataFrame with the template information.

[antgonza]

The new commit should address @josenavas comments, note that I have created #680 so we can discuss the refactoring of create_qiime_mapping_file.

[coveralls]

Coverage increased (+0.09%) when pulling e2e0a05 on antgonza:adding-qiime-map-file into b5d257d on biocore:master.

[ElDeveloper]

👍