Labman minimal changes

[antgonza]

This adds the minimal changes to join labman to qiita via an api. Note that this does not block being able to delete a sample but will be added in a follow up PR.

[ElDeveloper]

Just a couple of comments, would likely be useful to have someone else look over.

[ElDeveloper]

Perhaps I am missing a high-level design consideration but can you explain the motivation behind allowing consumers to query for a user's password?

[antgonza]

So labman/other-tool can authenticate. Things to consider, the communication is started via keys that only live in qiita/other-tool (like plugins); qiita only stores hashed passwords, so the retrieve should be "safe". In the other tool, we will have a user add their log/pass, the other tool will hash the pass and then compare to this info.

[ElDeveloper]

I believe you should be able to add an argument to this method call asjson=True so that the returned data in body is already parsed as a JSON object.

[ElDeveloper]

If this work, can you fix where appropriate in this PR?

[antgonza]

k

[antgonza]

tried, and didn't work, perhaps we are using an older version

[ElDeveloper]

Thanks for giving that a shot. I'm surprised that's the case, maybe there are slightly different test classes in Qiita.

[ElDeveloper]

I would probably change this to be 'id=%s: %s: % (sid, str(e)). So the message would be clear about what that number is, for example:

Error instantiating sample information id=11: Internal server error .....

If this makes sense, then it would be worth doing the same in the User's case.

[antgonza]

k

[ElDeveloper]

Looks like _get_user_info and _get_sample_info are essentially the same function except for the class instantiating it. I would probably try to facto these two things into a single function and then make _get_sample_info a shortcut for a call to this new function. Something like:

def _get_instance(object_id, klass, reason):
    """ """
    try:
        object = klass(object_id)
    except qdb.exceptions.QiitaDBUnknownIDError:
        raise HTTPError(404)
    except Exception as e:
        raise HTTPError(500, reason=reason + ' %s: %s' % (object_id, str(e)))


def _get_study_info(sid):
    return _get_instance(email, qdb.user.User, 'Error instantiating user')

def _get_study_info(sid):
    return _get_instance(int(sid), qdb.metadata_template.sample_template.SampleTemplate, 'Error instantiating sample information')

Should ultimately reduce needed code and tests 👍

[antgonza]

k

[codecov-io]

Codecov Report

Merging #2633 into dev will increase coverage by <.01%.
The diff coverage is 95.19%.

@@            Coverage Diff             @@
##              dev    #2633      +/-   ##
==========================================
+ Coverage   94.47%   94.47%   +<.01%     
==========================================
  Files         160      166       +6     
  Lines       19596    19698     +102     
==========================================
+ Hits        18513    18610      +97     
- Misses       1083     1088       +5

Impacted Files	Coverage Δ
qiita_db/test/test_user.py	99.65% <100%> (ø)	⬆️
qiita_db/handlers/sample_information.py	100% <100%> (ø)
qiita_db/user.py	94.92% <100%> (+0.09%)	⬆️
qiita_db/handlers/user.py	100% <100%> (ø)
qiita_pet/webserver.py	100% <100%> (ø)	⬆️
qiita_db/handlers/util.py	80% <80%> (ø)
qiita_db/handlers/tests/test_user.py	95% <95%> (ø)
qiita_db/handlers/tests/test_util.py	95.23% <95.23%> (ø)
qiita_db/handlers/tests/test_sample_information.py	95.65% <95.65%> (ø)
... and 5 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update cd3061e...4a36750. Read the comment docs.