Release candidate (#2298)

[josenavas]

• replace printable for try/except utf-8

• add sleeps for tests

• moving wait_for_prep_information_job

• just leaving the changes on this pr

• Fixing tests

• Reverting changes

• dist: precise

• addressing @josenavas comments

• fix-2212

• Adding branch description to Contributing (Adding branch description to Contributing #2256)

• Adding branch description

• Adding spaces

• Adding timeline

• upgrading software

• mv r_client to qiita

• from redis import Redis

• rm moi and ipython

• Move qiita_db/private.py -> qiita_ware/private_plugin.py

• _system_call as system_call

• flake8

• rm create_raw_data

• Transferring VAMPS submission to internal job

• rm other unnecessary files

• addressing @josenavas comment

• Fixing merge conflicts

• Adding tests to private plugin

• rm wrapper.py

• Removing import

• Fixing import

• Modifying GUI to use the plugin

• moving qiita pet in .travis.yml

• Transfer submit to vamps (Transfer submit to vamps #2265)

• Move qiita_db/private.py -> qiita_ware/private_plugin.py

• Transferring VAMPS submission to internal job

• Fixing import

• some other .travis.yml fixes

• addressing @josenavas comment

• Adding success test

• adding some methods

• flake8

• Transfer copy raw data (Transfer copy raw data #2267)

• Move qiita_db/private.py -> qiita_ware/private_plugin.py

• Transferring VAMPS submission to internal job

• Fixing merge conflicts

• Adding tests to private plugin

• Removing import

• Fixing import

• Modifying GUI to use the plugin

• Adding success test

• change imports

• adding delete_artifact and create_sample_template

• fixing errors and gui

• fix delete error

• ENH: Make jobs list modal

With some recent changes to the position of the navigation bar, the
header of the jobs list is cut from screen. With this patch in place,
the jobs list will be shown as a modal window, so that won't be a
problem anymore.

• Transfer update delete templates (Transfer update delete templates #2274)

• Moving update_sample_template

• Transfer update_sample_template

• Porting update prep template

• Moving delete sample or column

• Removing tests

• Removing dispatchable and its tests

• Updating interface to use the new functionality'

• Adapting the prep template GUI

• Submitting jobs

• Fixing tests

• Removing qiita_ware/context.py

• flake8ing

• Fixing _system_call

• Safeguarding the call to rollback

• Unmasking more errors

• Forcing different connections on different processes

• Moving job completion to internal plugin structure

• Removing unused code

• Forcing the creation of a new transaction on the jobs

• Fixing tests

• forcing the commit

• Fixing all tests

• Addressing @antgonza's comments

• Addressing @antgonza's comment

• Addressing @ElDeveloper's comments

• BUG: Fix job updates

• Fixing the redis DB (Fixing the redis DB #2277)

• Fixing the redis DB

• Addressing @antgonza's comments

• redbiom install

• redbiom to install_requires

• mv moi-ws to qiita_websocket

• init commit

• addressing @wasade comment

• rm webdis.log

• cleaning code for initial review

• install latest redbiom

• fix test

• ENH: Change phrasing of upload text (ENH: Change phrasing of upload text #2281)

• ENH: Change phrasing of upload text

As per a user's request.

• Fix typo in docs

Fixes #2259

• addressing @wasade comments and adding other tests

• flake8

• addressing @josenavas comments

• fix admins don't have access to analysis #2258

• fix admins don't have access to analysis #2258

• fix Single study analysis shortcut #858 (fix #858 #2286)

• addressing @ElDeveloper and @josenavas comments

• @ElDeveloper :|

• redbiom now adds per sample studies to analysis

• jobs-list-as-modal

• addresssing @josenavas comments

• rm () from update_processing_job_data

• add prints to review errors

• rm prints

• Fix 2190 (Fix 2190 #2292)

• Adding patch to add the 'name' parameter to all validate commands

• Adding the parameter 'name' automatically and adding a test for it

• Removing extra blank line

• Adding dflt value to artifact name

• Edited the wrong file

• Adding user defined name at creation time

• Fixing test

• add is_from_analysis to artifact_handlers (add is_from_analysis to artifact_handlers #2293)

• add is_from_analysis to artifact_handlers

• fix test_post_metadata

• fix error

• WIP: rm sudo from travis

• adding sed for config file

• fix sed

• rm &

• cat redis.conf

• using local redis.conf

• protected-mode yes

• supervised no

• redis-server --port 7777 &

• Fix 1293 (Fix 1293 #2291)

• fix bulk delete #1293

• flake8

• fix errors

• addressing @ElDeveloper comments

• rm redis.conf

• fix awaiting_approval list bug

• Fix Trying to download a 'html summary dir' filepath type will fail #2276 (Fix #2276 #2294)

• Fix Trying to download a 'html summary dir' filepath type will fail #2276

• Factoring out generate nginx directory file list

• Factoring out the nginx file list writing

• Factoring out generating the file list of an artifact

• Factoring out the header setting

• Addressing @antgonza's comment

• Addressing @wasade's comments

[codecov-io]

Codecov Report

Merging #2299 into master will increase coverage by 0.98%.
The diff coverage is 90.68%.

@@            Coverage Diff            @@
##           master   #2299      +/-   ##
=========================================
+ Coverage   92.81%   93.8%   +0.98%     
=========================================
  Files         171     163       -8     
  Lines       18925   18581     -344     
=========================================
- Hits        17566   17430     -136     
+ Misses       1359    1151     -208

Impacted Files	Coverage Δ
qiita_db/commands.py	96.55% <ø> (-0.48%)	⬇️
qiita_db/metadata_template/constants.py	100% <ø> (ø)	⬆️
...ita_pet/handlers/study_handlers/tests/test_base.py	98.14% <ø> (-0.22%)	⬇️
qiita_pet/test/test_prep_template.py	97.87% <ø> (ø)	⬆️
qiita_db/test/test_commands.py	99.6% <ø> (+0.28%)	⬆️
qiita_db/test/test_artifact.py	99.84% <ø> (ø)	⬆️
qiita_db/__init__.py	100% <ø> (ø)	⬆️
qiita_db/software.py	97.9% <100%> (+0.76%)	⬆️
qiita_db/search.py	92.56% <100%> (+0.05%)	⬆️
...pet/handlers/analysis_handlers/sharing_handlers.py	100% <100%> (ø)	⬆️
... and 58 more

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[ElDeveloper]

🎉 😄 🚀