WIP: DB changes for EBI

[josenavas]

This PR modifies the DB to store all the information that EBI returns when we are doing a submission.
Storing all this information (in the correct place) will help us to do a better usage of the EBI structure (which actually fits pretty nicely with our structure) as well as being able to do EBI updates in the future.

Tests are currently failing, and I'm fixing them right now.

[antgonza]

What about transferring the error status from submitted_to_insdc_status? Currently, you are simply ignoring those.

[josenavas]

Is it useful? In the current deployed implementation it only reads failed. Do we want to keep track of those too, or just set them up as not submitted?

[antgonza]

Good point, we are not storing any useful information and the reason we need these changes ...

[antgonza]

One question. If all that block is tested 👍

[ElDeveloper]

under the given column -> in column

As it stands it isn't incorrect, but it reads kinda funny.

[josenavas]

Done

[ElDeveloper]

Ok, I think I'm done with my review, should be ready to go afterwards.

[ElDeveloper]

I just tested out a minimal example and this doesn't work , I think @antgonza once came up with a way to format data inside a docstring, can't remember where though.

(ipy)yoshikivazquezbaeza:qiita@db-changes-ebi$ python -c 'from py import fun; print help(fun)'
# should have displayed the help here, but it doesn't :( 
(ipy)yoshikivazquezbaeza:qiita@db-changes-ebi$ cat py.py
def fun(x):
    """Lolercoaster

    Has the following values {%s}
    """.format(['foo', 'bar', 'baz'])
    pass

[antgonza]

http://stackoverflow.com/questions/10307696/how-to-put-a-variable-into-python-docstring

[josenavas]

Thanks for the link @antgonza fixed.
I think at some point we did it as I had it, but then we find out that it doesn't work.

[ElDeveloper]

Great, thanks!

On (Oct-06-15|17:00), Jose Navas wrote:

•        return TRN.execute_fetchlast()
  
• @ebi_submission_status.setter
• def ebi_submission_status(self, value):

•    """Sets the study's EBI submission status
  

•    Parameters
  

---

•    value : str {%s}
  

•        The new EBI submission status
  

•    Raises
  

---

•    ValueError
  

•        If the status is not known
  

•    """.format(', '.join(self._valid_ebi_status))
  

Thanks for the link @antgonza fixed.
I think at some point we did it as I had it, but then we find out that it doesn't work.

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[josenavas]

@ElDeveloper Only the expected qiita-pet errors here. There was a flake8 error but I fixed in my last push, so I don't think that is worth waiting for that one to be done to merge this. Thanks!