rm get_reference_fp and ontology download deprecated functionality

[sjanssen2]

I think the local filenames of the GG 13.8 reference, used in the qp-target-sequencing plugin, is out of sync between qiita environment manager here:

qiita/qiita_db/environment_manager.py

Lines 100 to 108 in 57d1b14

	files = {'tree': (get_reference_fp('gg_13_8-97_otus.tree'),
	'ftp://ftp.microbio.me/greengenes_release/'
	'gg_13_8_otus/trees/97_otus.tree'),
	'taxonomy': (get_reference_fp('gg_13_8-97_otu_taxonomy.txt'),
	'ftp://ftp.microbio.me/greengenes_release/'
	'gg_13_8_otus/taxonomy/97_otu_taxonomy.txt'),
	'sequence': (get_reference_fp('gg_13_8-97_otus.fasta'),
	'ftp://ftp.microbio.me/greengenes_release/'
	'gg_13_8_otus/rep_set/97_otus.fasta')}

and in the plugin itself:

https://github.com/qiita-spots/qp-target-gene/blob/858436ee6d4a1fccd35faee0b156a12953b5774a/qp_target_gene/__init__.py#L148-L149

I figure the plugin is correct, see this screenshot from qiita.ucsd.edu

[sjanssen2]

hm, is there maybe even a way to overwrite these filepaths, provided by the plugin, when registering into qiita? Thus, the filepaths could point to those files that have actually downloaded through qiita-env make --download-references?!

[antgonza]

In the original (like 10 years ago) Qiita design, the idea was that everything was self contained; however, we then realized that using plugins was the way to go. The old download-references is really deprecated.

Maybe this is a good opportunity, if you have the chance, to remove those old functionalities and just rely on the newest code. BTW this issue reminded me of this other one: #3197.

[antgonza]

FWIW I think your effort might be better focus if we had a quick call to see what you are trying to achieve and maybe summarize all your open issues into one. Anyway, you have my email ...

[antgonza]

After #3403 was merged, we should be able to easily and (almost) cleanly remove the old and deprecated ontology and reference download and processing; thus, changing the name of this issue so it can be addressed.