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[Master] Deploy #1367

Merged
merged 67 commits into from
Jul 3, 2019
Merged

[Master] Deploy #1367

merged 67 commits into from
Jul 3, 2019

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arielsvn
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@arielsvn arielsvn commented Jul 3, 2019

Api docs and other improvements

@arielsvn
update requirements for elastic search
91c1618
@arielsvn
add drf_yasg
e0994b7
@arielsvn
add redoc routes
0c04632
@arielsvn
Remove django documentation and make redoc api root
e178c4e
@arielsvn
Modify experiment api endpoints
f4a6d5d
@arielsvn
sample detail endpoint
5e93f16
@arielsvn
Refactor sample list endpoint and add docs
1eb8f6d
@arielsvn
use ListAPIView more
77a779c
@arielsvn
remove es router
4282106
@arielsvn
Add docs for search endpoint
15175bc
@arielsvn
docs for search parameters
9fa3821
@arielsvn
Add djangoFilterBackend to experiment endpoint
9bf0831
@arielsvn
Use method decorator for samples endpoint
33589bd
@arielsvn
update tests to only allow sample/experiment details with accession_code
ff1b470
@arielsvn
fix tests for experiments with no processed samples
072d2d4
@arielsvn
update /es/ endpoint in tests
a345b88
@arielsvn
experiment/sample detail lookup by accession
5373f6e
@arielsvn
Refactor ResultsList and add docs
377adde
@arielsvn
Add docs for dataset endpoint
5bb5d00
@arielsvn
hide dataset stats
9f2e434
@arielsvn
Remove dataset stats
c45d681
@arielsvn
Add docs about details parameter in dataset details
1171714
@arielsvn
remove old search tests. We have some tests for the ES search
64b383c
@arielsvn
remove dataset stats tests
4358e2d
@arielsvn
token view documentation
20eed2e
@arielsvn
Add compendia capabilities to the computed_files endpoint
e89fe62
@arielsvn
token and compendia tests
ddc9572
@arielsvn
remove compendia views
75498ff
@arielsvn
Revert "remove compendia views"
e20cb74 
This reverts commit 75498ff.
@arielsvn
add docs for computed files
1fffabf
arielsvn and others added 24 commits July 1, 2019 11:56
@arielsvn
Merge branch 'master' of github.com:AlexsLemonade/refinebio into arie…
a0df2dd 
…lsvn/687-api-docs
@arielsvn
Don't send download_url when token isn't present
928ad8e
@arielsvn
remove /docs url
885726e
@arielsvn
update migrations
b4dea33
@wvauclain
Made management command work on all source databases
a65df24
@wvauclain
Added filters for specific usernames in engagement-bot
e703ff9
@kurtwheeler
Uses a transcriptome index build using salmon v13 for salmon tests an…
db6baa3 
…d reenables them.
@kurtwheeler
Add 1 git-crypt collaborator
53b05d5 
New collaborators:

	B1A70025 Will Vauclain <will.vauclain@gmail.com>
@wvauclain
Merge branch 'dev' of github.com:AlexsLemonade/refinebio into dev
b80c76d
@wvauclain
Merge pull request #1363 from AlexsLemonade/kurtwheeler/readd-will-to…
a60071d 
…-git-crypt

Add 1 git-crypt collaborator
@wvauclain
Merge branch 'dev' of github.com:AlexsLemonade/refinebio into wvaucla…
7fb79d9 
…in/engagement-bot
@wvauclain
Added check for production in engagement-bot code
cb72ff5
@wvauclain
Get ENVIRONMENT gracefully
041489b
@arielsvn
Merge pull request #1330 from AlexsLemonade/arielsvn/687-api-docs
2f6a117 
Api Docs
@kurtwheeler
Fix salmon test data which involves updating the salmon test data in S3.
1c81ea5
@kurtwheeler
Make txindex errors from salmon an exception and fix a wget command t…
3c1304d 
…o download salmon test data correctly.
@wvauclain
Added 'age (yrs)' to harmonizer
f6aa928
@kurtwheeler
Move data for salmon tests that is in git repo out of salmon_tests so…
250e299 
… that can just be for data from S3.
@kurtwheeler
Fix s3 data cleanup for salmon tests.
6041acf
@wvauclain
Merge pull request #1365 from AlexsLemonade/wvauclain/1332
e24794f 
Added 'age (yrs)' to harmonizer
@wvauclain
Merge pull request #1355 from AlexsLemonade/wvauclain/SRA-metadata-ma…
7551a1d 
…nagement-command

Created a management command to refresh SRA metadata
@wvauclain
Merge pull request #1364 from AlexsLemonade/wvauclain/engagement-bot
da9300e 
Remove Us From Engagement Bot Messages
@kurtwheeler
Fix salmon tests to use simplified test data paths.
e6a5849
@wvauclain
Merge pull request #1366 from AlexsLemonade/kurtwheeler/reenable-salm…
b88e486 
…on-tests

Reenable salmon tests
@arielsvn arielsvn requested a review from kurtwheeler July 3, 2019 15:55
kurtwheeler
kurtwheeler approved these changes Jul 3, 2019
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Let's do it!

@arielsvn arielsvn merged commit bb9f5fb into master Jul 3, 2019
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@kurtwheeler kurtwheeler kurtwheeler approved these changes

@jaclyn-taroni jaclyn-taroni jaclyn-taroni approved these changes

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4 participants
@arielsvn @kurtwheeler @jaclyn-taroni @wvauclain