added bulk load gff3

[nathandunn]

• [x] fix load_legacy_gff3
• [x] find why we get full CDS on creation by dragging, but not when making the API call (do a full CDS)
• [x] add timing code per https://github.com/nathandunn/apollo-performance/issues/13
• [x] make batch-size an option
• [x] update RST for actual usage
• [x] move "add_feature" to add_one_feature, and fix tests
• [x] add add_tarnscripts and moveadd_one_transcript` and fix tests
• [x] split into add_features and add_transcripts depending on type to add
• [x] from https://github.com/GMOD/Apollo/issues/2410 we want to be able to add:
  • [x] test
  • [x] disable_cds
  • [x] use_name
• [x] validate the GFF3 by adding more stuff here if necessary https://github.com/galaxy-genome-annotation/python-apollo/blob/master/apollo/util.py#L91
• [x] add source to feature as attribute (provided in legacy code)
• [x] fix empty lines

---

• [x] creates a new bulk load gff3 without specific entries
• [x] rename the old gff3 to legacy gff3 loader
• [x] add bulk gff3 load to load and submit in large chunks
• [x] remove bulk pieces script
• [ ] review
• [ ] merge
• [ ] deploy

[nathandunn]

Thanks. I'll see where I get by the end of the day . . .if @abretaud has a chance to review it great. Worst-case we could always re-patch it if needed.

[nathandunn]

@abretaud I am going to add some timing code and reduce the verbosity a little bit, but nothing more. At some point (lateR) this will get expanded, so the method pulling attributes off of the gff3 to put in JSON may get bigger.

[nathandunn]

But it is still ready for review.

[nathandunn]

Note @abretaud it still isn't loading the legacy_gff3 properly . . . I'll try to fix that prior to a merge.

[nathandunn]

@abretaud Okay, I fixed the legacy load stuff.

[nathandunn]

@abretaud if it looks good, I would say go ahead and merge it and publish it (not entirely sure how to publish it)

[abretaud]

@nathandunn I have a few comments pending + making some tests, still working on it ;)

[nathandunn]

@nathandunn I have a few comments pending + making some tests, still working on it ;)

Awesome thanks!

[nathandunn]

Just as an FYI @abretaud load_legacy_gff3 produces errors for me so I removed it form the bootstrap_apollo.sh script if that is okay.

[nathandunn]

I meant . . it produced errors for me in the upgraded server.

[hexylena]

amazing, super improvement :)