initial database setup for travis

[squirrelo]

Fixes #50

[josenavas]

This PR is ready to review (yay!!)

The additions included in this PR are:

• The SQL layout have been modified to be able to successfully add a study to the database, including raw, preprocessed and processed data.
• A SQL file has been added that populates the database with some test data.
• A test has been added to check that the previous test data was able to be inserted in the database.
• Since it is quite easy to break a production database when running the test code, a safeguard mechanism has been introduced. This mechanism consists on 2 points:
  (1) A config file has been added, parsed with the python ConfigParser, which includes a TEST_ENVIRONMENT variable.
  (2) A new settings table has been added to the database, which holds if the database is a test database or a production one.
• This mechanism have been implemented through a decorator: qiita_test_checker. The decorator prevents the execution of the test if the database is a production db. Furthermore, this decorator (which should decorate the Test class) automatically decorates the setUp and tearDown functions to populate and clean up the test database, so each test is independent of each other and can assume the same exact data.
• click has been added to the dependencies. A new command qiita_db make_test_env has been added. This command creates the qiita_test database in the postgres server. This way, we have complete control over the test database, since we are creating it.

Although there are 27 files modifies, a lot of them are the sql files and the placeholder files for the test_data folder (probably will hold data in the future or we'll make Travis download it through wget).

[squirrelo]

No issue here, just want to say this is a bad ass way of setting this up.

[squirrelo]

Also, you can safely ignore checking the qiita-db.html and qiita-db.dbs files. They are auto-generated saves from DbSchema.

[squirrelo]

I'm assuming this file change-of-name is just git weirdness?

[josenavas]

Yup

[teravest]

YAY!

[wasade]

Cogent?
On May 22, 2014 8:16 AM, "teravest" notifications@github.com wrote:

In .travis.yml:

@@ -3,12 +3,9 @@ python:

• "2.7"
  install:
  • pip install numpy
    • • pip install cogent

YAY!

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/52/files#r12955383
.

[josenavas]

hahaha, yup, it was there... removing cogent speeded-up the travis runs 😄

[adamrp]

Thanks for adding all these checks -- I think this should be plenty enough to make sure people don't accidentally blow away their database! They'd really have to intentionally screw up three things simultaneously (I think)

[josenavas]

I think I've addressed all your comment. Let me know if I missed something!

[adamrp]

For these, it could be a nice use of functools.partial to do something like:

get_support_file = partial(join, join(dirname(abspath(__file__)), 'support_files'))

DFLT_BASE_DATA_FOLDER = get_support_file('test_data')
SETTINGS_FP = get_support_file('qiita-db-settings.sql')
LAYOUT_FP = get_support_file('qiita-db.sql')
INITIALIZE_FP = get_support_file('initialize.sql')
POPULATE_FP = get_support_file('populate_test_db.sql')

[adamrp]

👍

[josenavas]

Thank you all for the comments! and thanks @squirrelo for the help to get this done!