WIP: Artifact changes

[josenavas]

This is the PR from upstream artifact against upstream master, and this will be used to keep track of remaining changes. More details will be added as needed.

• Modify populate_test_db.sql to be adapted to the new schema (Artifact populate db changes #1524)
• Add software, command and parameters objects (Software, Command and Parameters objects #1525)
• Add artifact object (Artifact obj #1527)
• Remove qiita_db/data.py and qiita_db/test/test_data.py and fix all tests in qiita_db (@josenavas - I'm fixing all these at once)
• Put in place minimal plugin system
• Move current target gene pipeline to its own plugin (inside the repo)
• Put in place minimal execution system environment
• **kwargs -> dict in create new parameter
• Adopt GUI to use new system (I think we should include here the work that @antgonza is doing)
• submit_to_VAMPS function needs to check if the artifact is being submitted or not in order to raise if it has been already submitted
• Make sure that the new artifacts that represent preprocessed data have the same ids as this will allow us to have the same names for EBI submission. (Artifact retain ppd #1565)
• Add admin documentation in how the plugin launcher script should look like
• If you add a raw data from another study, you can see the preprocessed data from the other study (Fixing raw data sharing #1572)
• Then you can't delete the raw data cause it has children (Fixing raw data sharing #1572)
• If you change the processed data (artifact) visibility it doesn't propagate to other artifacts (this might be OK to leave until the new GUI is ready) Propagate artifact visibility #1578
• Add a minimal documentation about the new configuration requirements and how to restart jobs. Don't forget all the things that you helped me with to set up this in my laptop.
• There is no way to delete a raw data and return the files to the upload folder (Fixing raw data sharing #1572)
• Regenerate the new config file

[ElDeveloper]

There should be a special consideration for positional arguments, as briefly discussed in #1525.

We should also think about what kind of commands we want to run without arguments.

[antgonza]

Merging after discussion in Qiita meeting. We need all the help we can get, so:
in nomine Patris et Filii et Spiritus Sancti