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Scottx611x/td api #1646

Merged
merged 269 commits into from
Mar 28, 2017
Merged

Scottx611x/td api #1646

merged 269 commits into from
Mar 28, 2017
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Oct 21, 2016

  1. Cleanup some more tests

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    scottx611x committed Oct 21, 2016
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  2. Add id to aid testing

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    scottx611x committed Oct 21, 2016
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  3. Add id to aid testing

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    scottx611x committed Oct 21, 2016
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  4. Cleanup login method

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    scottx611x committed Oct 21, 2016
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  5. Abstract out reused login moethod

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    scottx611x committed Oct 21, 2016
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  6. Utilize relative import

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    scottx611x committed Oct 21, 2016
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  7. Merge branch 'develop' of https://github.com/parklab/refinery-platform … 

    …into scottx611x/acceptance_testing
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    scottx611x committed Oct 21, 2016
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Commits on Oct 22, 2016

  1. PEP8

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    scottx611x committed Oct 22, 2016
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Commits on Nov 1, 2016

  1. only run acceptance tests if we detect a build for a PR

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    scottx611x committed Nov 1, 2016
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Commits on Nov 2, 2016

  1. Always run our acceptance tests

    @scottx611x
    scottx611x committed Nov 2, 2016
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  2. Add acceptance tests for user registration and login

    @scottx611x
    scottx611x committed Nov 2, 2016
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  3. Don't use separate shell script (for now)

    @scottx611x
    scottx611x committed Nov 2, 2016
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Commits on Nov 3, 2016

  1. Remove cd comands

    @scottx611x
    scottx611x committed Nov 3, 2016
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  2. Refactor selenium utility functions

    @scottx611x
    scottx611x committed Nov 3, 2016
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Commits on Nov 16, 2016

  1. Add script to run acceptance tests on vagrant or travis

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    scottx611x committed Nov 16, 2016
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  2. Lower DEFAULT_WAIT Now that we aren't relying on SauceLabs VMs

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    scottx611x committed Nov 16, 2016
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  3. Cleanup setting of breakpoints, and refactor cleanup_on_error decor… 

    …ator
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    scottx611x committed Nov 16, 2016
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  4. Remove unnecessary env var, and re-add global as to ensure a single… 

    … build
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    scottx611x committed Nov 16, 2016
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  5. Sauce_connect isn't needed

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    scottx611x committed Nov 16, 2016
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  6. pip caching seems stable

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    scottx611x committed Nov 16, 2016
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  7. PEP8

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  8. Fail shell script if any step doesn't work properly

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    scottx611x committed Nov 16, 2016
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  9. GeckoDriver expects a more recent version of Firefox

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    scottx611x committed Nov 16, 2016
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Commits on Nov 17, 2016

  1. Remove Comments

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    scottx611x committed Nov 17, 2016
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  2. Update Default wait time

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    scottx611x committed Nov 17, 2016
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  3. Bump pytest-selenium version

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    scottx611x committed Nov 17, 2016
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  4. Update Comment

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    scottx611x committed Nov 17, 2016
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  5. Utilize wait_until_id_clickable

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    scottx611x committed Nov 17, 2016
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  6. Add tests for global analysis popover

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    scottx611x committed Nov 17, 2016
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  7. Add tests for Datasets panel

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    scottx611x committed Nov 17, 2016
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  8. Update comment

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    scottx611x committed Nov 17, 2016
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  9. Add a status to all generated Analyses

    @scottx611x
    scottx611x committed Nov 17, 2016
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  10. Update stats test to check for actual object counts

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    scottx611x committed Nov 17, 2016
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Commits on Dec 7, 2016

  1. Merge remote-tracking branch 'origin/develop' into scottx611x/accepta… 

    …nce_testing
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    scottx611x committed Dec 7, 2016
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Commits on Dec 14, 2016

  1. include gecko driver in our build process for ease of local selenium-… 

    …based testing
    @scottx611x
    scottx611x committed Dec 14, 2016
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  2. Refactor old acceptance test implementation in favor of simplicity an… 

    …d uniformness with our current Django unit tests
    @scottx611x
    scottx611x committed Dec 14, 2016
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Commits on Dec 16, 2016

  1. Make virtual display bigger

    @scottx611x
    scottx611x committed Dec 16, 2016
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  2. Update selenium testing utils

    @scottx611x
    scottx611x committed Dec 16, 2016
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  3. Update assert body text method

    @scottx611x
    scottx611x committed Dec 16, 2016
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  4. Update selenium tests

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    scottx611x committed Dec 16, 2016
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  5. Update wait_until_id_visible()

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    scottx611x committed Dec 16, 2016
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Commits on Dec 19, 2016

  1. bump Factory-Boy requirement

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    scottx611x committed Dec 19, 2016
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  2. Update travis as mentioned issue has been closed

    @scottx611x
    scottx611x committed Dec 19, 2016
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  3. Clean up gecko driver Puppet install

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    scottx611x committed Dec 19, 2016
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  4. Update docstrings

    @scottx611x
    scottx611x committed Dec 19, 2016
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  5. Remove unnecessary tests

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    scottx611x committed Dec 19, 2016
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  6. more geckodriver install cleanup

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    scottx611x committed Dec 19, 2016
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  7. Change Default wait

    @scottx611x
    scottx611x committed Dec 19, 2016
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  8. update wait_until_id_visible()

    @scottx611x
    scottx611x committed Dec 19, 2016
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  9. pull out duplicated code into ui-deletion helper method

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    scottx611x committed Dec 19, 2016
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  10. Update acceptance tests

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    scottx611x committed Dec 19, 2016
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  11. Minor changes due to abstraction of deletion code

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    scottx611x committed Dec 19, 2016
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  12. Fix typo

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    scottx611x committed Dec 19, 2016
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  13. Merge branch 'develop' into scottx611x/acceptance_testing

    @scottx611x
    scottx611x committed Dec 19, 2016
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  14. guest user creation isn't needed here anymore

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    scottx611x committed Dec 19, 2016
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  15. Merge branch 'scottx611x/acceptance_testing' of https://github.com/pa… 

    …rklab/refinery-platform into scottx611x/acceptance_testing
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    scottx611x committed Dec 19, 2016
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Commits on Dec 20, 2016

  1. Merge branch scottx611x/django_1.7_upgrade into scottx611x/acceptance… 

    …_testing
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    scottx611x committed Dec 20, 2016
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  2. Flip the order of some installed apps due to Django 1.7 ContentType l… 

    …oading
    @scottx611x
    scottx611x committed Dec 20, 2016
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  3. Decorate function as to not test 3rd party code's functionality

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    scottx611x committed Dec 20, 2016
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  4. Utilize StaticLiveServerTestCase

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    scottx611x committed Dec 20, 2016
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  5. Update delete_from_ui() helper

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    scottx611x committed Dec 20, 2016
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  6. Refactor decorator name to be more verbose

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    scottx611x committed Dec 20, 2016
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  7. Don't need to take a screenshot here

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Commits on Jan 5, 2017

  1. Merge branch 'develop' of https://github.com/parklab/refinery-platform … 

    …into scottx611x/acceptance_testing

# Conflicts:
#	.travis.yml
#	deployment/apache.conf.erb
#	deployment/manifests/default.pp
#	fabfile.py
#	refinery/config/settings/base.py
#	refinery/templates/base.html
#	refinery/templates/core/user.html
#	requirements.txt
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Commits on Jan 6, 2017

  1. Add xvfb and python3 to travis

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    scottx611x committed Jan 6, 2017
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  2. add pyvirtualdisplay req

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    scottx611x committed Jan 6, 2017
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  3. Rename geckodriver class to selenium

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    scottx611x committed Jan 6, 2017
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  4. Update order

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  5. Update order of INSTALLED_APPS for testing purposes

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  6. Update logging levels

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    scottx611x committed Jan 6, 2017
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  7. Update TEST_RUNNER per Django system-check suggestion

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Commits on Jan 9, 2017

  1. Update tests

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    scottx611x committed Jan 9, 2017
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  2. Fix get_or_create()

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    scottx611x committed Jan 9, 2017
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  3. Access actual object returned from get_or_create() tuple

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    scottx611x committed Jan 9, 2017
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  4. Update logger statement

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    scottx611x committed Jan 9, 2017
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  5. Do not need to specify live server here since it has a default value

    @scottx611x
    scottx611x committed Jan 9, 2017
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  6. Update string formatting to work properly

    @scottx611x
    scottx611x committed Jan 9, 2017
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  7. Update isa/pre-isa archive deletion to produce less unnecessary errors

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    scottx611x committed Jan 9, 2017
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  8. Update Tests

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  9. Manually save public group to sync db between threads (Specific to us… 

    …e of StaticLiveServerTestCase)
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  10. Update DEFAULT_WAIT

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  11. Share Datasets upon factory_boy creation

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    scottx611x committed Jan 9, 2017
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  12. Create public group for APIV2 test case

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  13. Added group creation to the wrong TestCase

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Commits on Jan 11, 2017

  1. Remove django-nose in favor of Django's new: DiscoverTestRunner

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  2. Merge remote-tracking branch 'origin/develop' into scottx611x/accepta… 

    …nce_testing
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  3. This file shouldn't exist anymore. Probably wasn't caught in the merg… 

    …e here: 0c727cc
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  4. Include ontology fixture content inside of a Data migration (#1581)

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    scottx611x committed Jan 11, 2017
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  5. Update puppet-archive version

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  6. Utilize puppet-archive and clean up neo4j.pp

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  7. Cleanup selenium manifest

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  8. Factor out solr class from init.pp

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  9. don't need to chmod here

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Commits on Jan 12, 2017

  1. Merge remote-tracking branch 'origin/scottx611x/puppet_refactoring' i… 

    …nto scottx611x/acceptance_testing
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  2. We are now using StaticLiveServerTestCase

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  3. "Users of the puppet-archivemodule are responsible for archive pack… 

    …age dependencies"
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  4. Remove unused var

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  5. Point to new archive download location

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    scottx611x committed Jan 12, 2017
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  6. Fix string formatting error

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  7. Add TEST_RUNNER setting to base.py so that someone testing on `prod… 

    …` locally could also benefeit
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  8. update order of INSTALLED_APPS addresses: #1353

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  9. Refactor all tests that interact with the ORM to inherit from `Transa… 

    …ctionTestCase` (removes need for crazy tearDown()'s)
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  10. DEFAULT_WAIT Shouldn't be that long

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  11. Manually save public group as to persist data between test and web … 

    …driver threads
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  12. Update comment

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  13. Don't need to optimize sole's index in tests

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  14. Inherit from TransactionTestCase here

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  15. 20 was actually a good fail-safe if things get slow for one reason … 

    …or another
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Commits on Jan 17, 2017

  1. Merge remote-tracking branch 'origin/develop' into scottx611x/accepta… 

    …nce_testing

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  2. switch order of INSTALLED APPS

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  3. Cleanup selenium test cases

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Commits on Jan 27, 2017

  1. Merge remote-tracking branch 'origin/develop' into scottx611x/accepta… 

    …nce_testing

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  2. Merge remote-tracking branch 'origin/develop' into scottx611x/accepta… 

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  3. Remove other unittest usages and unnecessary tests

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  4. Override setUp() in a cleaner manner

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Commits on Feb 13, 2017

  1. Add a travis fold

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  2. Merge remote-tracking branch 'origin/develop' into scottx611x/accepta… 

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  3. Clean up FileStoreitem and InvestigationLink error handling

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  4. Clean up error handling for isa & pre-isa archives

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  5. Update comments

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  6. Cleanup factory_boy factories and utils

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  7. This is already a default value

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  8. DRY

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  9. Update existing DataMigrations to a more easily manageable format

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Commits on Feb 14, 2017

  1. More robust Data migrations

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  2. Remove pk

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  3. Merge remote-tracking branch 'origin/develop' into scottx611x/td_api

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Commits on Feb 16, 2017

  1. Bump DRF version to latest that supports Django 1.7

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  2. Add tools app

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  3. Add models

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  4. Configure admin ui for new models

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  5. Add migration

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  6. Add tools/definitions/ endpoint

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Commits on Feb 17, 2017

  1. Wrap deletion operations in transactions

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  2. Merge remote-tracking branch 'origin/scottx611x/safer_object_deletion… 

    …' into scottx611x/td_api
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  3. Merge remote-tracking branch 'origin/scottx611x/acceptance_testing' i… 

    …nto scottx611x/td_api

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  4. Add tools app

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  5. Add factories and utils method to create dummy ToolDefinitions for Te… 

    …sting
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  6. We don't need django.setup() here unless script is being run as a s… 

    …tandalone
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Commits on Feb 21, 2017

  1. RunPython is already encapsulated in a transaction

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  2. refactor get_isa_archive() & get_pre_isa_archive()

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  3. Analysis.status isn't necessary for testing

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  4. Add Error Handling to SeleniumTestBase.setUp()

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  5. Allow for proper rendering of self-referential Many-to-Many rels.

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  6. Update models & serializers

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  7. Add basic ToolDefinition API test case

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Commits on Feb 22, 2017

  1. Update Models and Migrations file

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  2. Add creation of LIST:LIST:PAIR ToolDef to utils script

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  3. Update Serializer for more easily readble API Responses

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  4. Update Tests

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Commits on Feb 23, 2017

  1. Add MGMT command to genereate Smaple ToolDefinitions

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  2. Demand users be authenticated to access DRF api endpoints

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  3. Add more tests for ToolDef API

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  4. Refactor DRF API related tests due to newly required Authentication

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  5. Remove unused nesting_type field

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  6. Add comment

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  7. Add AdminFieldPopulator class

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  8. Update MGMT command

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Commits on Feb 24, 2017

  1. Add TEST_NON_SERIALIZED_APPS setting due to pre Django 1.9 bug

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  2. Don't need to share datasets pubilcly in acceptance tests

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  3. Utilize serialized_rollback to ensure migration data persists in St… 

    …aticLiveServerTestCases
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  4. Merge branch 'develop' into scottx611x/acceptance_testing

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Commits on Feb 27, 2017

  1. Refactor isa/pre_isa archive fetching into one method

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  2. Merge branch 'scottx611x/acceptance_testing' of https://github.com/re… 

    …finery-platform/refinery-platform into scottx611x/acceptance_testing
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  3. Remove other unnecessary instances of tearDown()

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  4. Update method signature

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  5. Update comment

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  6. Fix Test

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  7. Revert "Fix Test" 

    This reverts commit 673827a.
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  8. Don't bundle (pre)isa_archive fetching functionality & Utilize existi… 

    …ng `get_investigation()`
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  9. Handle potential AttributeErrors that could occcur

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  10. Rename tools to tool_manager

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  11. Merge remote-tracking branch 'origin/scottx611x/acceptance_testing' i… 

    …nto scottx611x/td_api

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  12. Favor APITestCase to ensure initial DB state persists throughout tests

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  13. Provide request auth in test for newly secured endpoints

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Commits on Feb 28, 2017

  1. Remove transaction context manager

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  2. Refactor method name

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  3. Keeping Python 3 in mind

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  4. Rename field for clarity

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  5. Add comments

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  6. Fix serializer for newly added fieldname

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  7. django.setup() not necessary (unless running as a standalone script)

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  8. Change nested_elements -> file_relationship per Model field rename

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  9. Reflect lack of POSTing in comment

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  10. Fix import ordering

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  11. Merge remote-tracking branch 'origin/develop' into scottx611x/td_api

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  12. Merge branch 'develop' into scottx611x/td_api

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  13. Remove MGMT command since its only needed for a short period of time

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  14. Migrations due to GalaxyParameter child class

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  15. Add useful comment

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  16. Remove already default values

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  17. Revert from usage of Generic DRF api perm classes

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  18. Change sample data generation to reflect new schema

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  19. Ensure that Users accessing ToolDefinitions are authenticated

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  20. Rename GalaxyToolParameter to GalaxyParameter

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  21. Squash migrations

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  22. Old isa_archive deletion tests were of better form

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  23. Quoted references only necessary for manual avoidance of circ. imports

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  24. We could have a tool without any Parameters

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  25. Cleanup imports

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  26. Remove unutilized APIClient

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  27. Fix ordering of imports

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  28. Fix migration

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  29. Remove unnesscessary user creation

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Commits on Mar 1, 2017

  1. Remove TearDown

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Commits on Mar 2, 2017

  1. Remove constraint on ToolDefinition description & rename is_editable … 

    …field
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  2. Add galaxy_workflow_step field and squash migrations

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Commits on Mar 3, 2017

  1. Scottx611x/td api url routing (#1622) 

    * Add RouterCombiner class to allow for url definitions to be app specific

* Don't really need `import as`

* Relative import

* Fix import ordering

* Place hard-coded DRF api urls into their own apps

* Fix Import ordering
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Commits on Mar 16, 2017

  1. Merge remote-tracking branch 'origin/develop' into scottx611x/td_api

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Commits on Mar 20, 2017

  1. Add the ability to generate basic ToolDefinitons from properly annota… ( 

    #1624)

* Add the ability to generate basic ToolDefinitons from properly annotated Galaxy WFs

* Add `galaxy_workflow_step` field

* Validate incoming workflow annotation data

* Add Factory for GalaxyParameter creation

* Add tests to ensure proper creation of ToolDefinitions from Galaxy workflow annotations

* Handle ConnectionError if we can't reach Galaxy

* Rename `create_nesting()`

* Add custom Exception

* Refactor `validate_workflow_annotation()`

* Refactor ToolDefinition generation MGMT command

* Update tests

* Simplfy validation logic in mgmt command

* Utilize jsonschema to validate incoming ToolDefinitions

* Update mgmt command

* Update tests and test data

* Add `jsonschema` requirement

* Rename some things for clarity

* Add & Rename test data

* Properly handle invalid FileTypes in workflow annotations

* Fix Typo

* Add helpful comment

* jsonschema.validate is None upon successful validation, otherwise a ValidaationError is raised

* Cleanup generate_tool_definitions mgmt command

* Remove old clunky method to create ToolDefs in favor of new one

* Fix tests

* Clean up utils.py

* Update docstring

* Changes suggested from CR

* Directly access key rather that iterating through

* Split large ToolDefinition schema into individual files

* We don't need to use `hyper-schema`

* Let an empty object denote that we're at the bottom-most FileRelationship

* Travis didn't seem to like `os.path.abspath` so lets try `TRAVIS_BUILD_DIR` env var

* Try to fix Travis

* Trying out paths again

* Git doesn't automatically recognize case-sensitive only filename changes

* Remove blank lines and "..."

* Styling fixes
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Commits on Mar 21, 2017

  1. Merge remote-tracking branch 'origin/develop' into scottx611x/td_api

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  2. Update Galaxy Parameter Model to include a single field

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    scottx611x committed Mar 21, 2017
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  3. Update ToolDefinition schema

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    scottx611x committed Mar 21, 2017
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  4. Separate Parameter and GalaxyParameter schemas

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    scottx611x committed Mar 21, 2017
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  5. Add new sample data utilizing Parameters

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    scottx611x committed Mar 21, 2017
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  6. Add tests to check for good and bad parameters in Annotation data

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    scottx611x committed Mar 21, 2017
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Commits on Mar 22, 2017

  1. Avoid code reuse by extending from other schema

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  2. Update test-data and tests to utilize Parameters

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    scottx611x committed Mar 22, 2017
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  3. Add proper deletion of a ToolDefinitions related objects + tests

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    scottx611x committed Mar 22, 2017
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Commits on Mar 23, 2017

  1. Update Parameter schema

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    scottx611x committed Mar 23, 2017
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  2. Update GalaxyParameter schema

    @scottx611x
    scottx611x committed Mar 23, 2017
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  3. Add schema to aid in validating Workflows individual step's annotations

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    scottx611x committed Mar 23, 2017
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  4. Add test-data and tests to validate Workflows step's annotations

    @scottx611x
    scottx611x committed Mar 23, 2017
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  5. Rename validate_workflow_annotation to validate_tool_annotation

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    scottx611x committed Mar 23, 2017
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  6. clear() is redundant if we are also performing delete() here

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    scottx611x committed Mar 23, 2017
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  7. Include parameter and output_file parsing from step annotations in MG… 

    …MT command
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  8. Update ParameterSerializer to include/disclude galaxy_workflow_step… 

    … based on its existance
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    scottx611x committed Mar 23, 2017
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  9. Add sample data and tests for a basic Visualization-based ToolDefinition

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    scottx611x committed Mar 23, 2017
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  10. Fix typo and update comment

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    scottx611x committed Mar 23, 2017
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  11. Update comments

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    scottx611x committed Mar 23, 2017
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  12. Remove extra space

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    scottx611x committed Mar 23, 2017
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  13. RuntimeError is actually being raised here

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    scottx611x committed Mar 23, 2017
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  14. Rename method to create_tool_definition

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    scottx611x committed Mar 23, 2017
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  15. Add API test to check for different Parameter Types

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    scottx611x committed Mar 23, 2017
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  16. Merge remote-tracking branch 'origin/develop' into scottx611x/td_api

    @scottx611x
    scottx611x committed Mar 23, 2017
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  17. Merge remote-tracking branch 'origin/develop' into scottx611x/td_api

    @scottx611x
    scottx611x committed Mar 23, 2017
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  18. Styling fixes

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    scottx611x committed Mar 23, 2017
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  19. Fix comment

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    scottx611x committed Mar 23, 2017
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Commits on Mar 27, 2017

  1. Rename pre/post delete handlers

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    scottx611x committed Mar 27, 2017
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  2. Fix styling

    @scottx611x
    scottx611x committed Mar 27, 2017
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  3. Fix more styling

    @scottx611x
    scottx611x committed Mar 27, 2017
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  4. Remove newline characters

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    scottx611x committed Mar 27, 2017
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  5. Factor out workflow fetching, and cleanup indentation.

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    scottx611x committed Mar 27, 2017
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  6. Add a sample galaxy get_workflows() response for testing purposes

    @scottx611x
    scottx611x committed Mar 27, 2017
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  7. Test management command functionality with proper mock usage

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    scottx611x committed Mar 27, 2017
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  8. Remove comment explaining "what"

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    scottx611x committed Mar 27, 2017
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  9. Revert "Remove comment explaining "what"" 

    This reverts commit 69d5c65.
    @scottx611x
    scottx611x committed Mar 27, 2017
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  10. Rename test-data to test_data

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    scottx611x committed Mar 27, 2017
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  11. Utilize logger statements since not in a MGMT command anymore

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    scottx611x committed Mar 27, 2017
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  12. Handle RuntimeError

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    scottx611x committed Mar 27, 2017
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