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Release 1.5.0 #135

Merged
merged 37 commits into from
Nov 7, 2019
Merged

Release 1.5.0 #135

merged 37 commits into from
Nov 7, 2019

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@blankdots blankdots commented Nov 6, 2019 •
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Description

Implementing GA4GH passports, in order to adapt to ELIXIR JWT and userinfo endpoint.

Related issues

Releasing updated version.

Type of change

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)

Changes Made

  1. GA4GH Passports according to https://github.com/ga4gh/data-security/blob/master/AAI/AAIConnectProfile.md fixes Update GA4GH Permissions #130
  2. bumped unit tests to 96%
  3. Fix integer overflow in beacon_dataset_counts_table
  4. updated documentation
  5. Beacon erros are now derived from aiotthp HTTP Exceptions
  6. other fixes

Testing

  • Unit Tests
  • Integration Tests

Mentions

@teemukataja awesome work

teemukataja and others added 30 commits September 5, 2019 09:13
@teemukataja
update ga4gh service info endpoint, with tests and docs
c32f766
@blankdots
Merge pull request #129 from CSCfi/feature/ga4gh
2026232 
Update for GA4GH Service-info
@ooobik
Fix integer overflow in beacon_dataset_counts_table
51afbbd 
Simple fix in init.sql currently seems all that is needed. When updating callcounts and variantcounts variant count is likely to overflow on even medium-sized datasets.
@teemukataja
Merge pull request #132 from ooobik/patch-1
c70bd0a 
Fix integer overflow in beacon_dataset_counts_table
@blankdots
fix typose deploy docs
f3534f4
@blankdots
test exceptions db calls
2b3ae66
@blankdots
checking the request here is a bit redundant
a337e6a
@blankdots
fail coverage under 80%
0bc3883
@blankdots
verify aud claim in a function
ce54db1
@blankdots
test token scheme just to be sure
026a602
@blankdots
fix docs for validate
c9a64a3
@blankdots
exclude lines teste in integration tests
8224cad
@blankdots
fixes for db_load and its tests
3f42e2f
@blankdots
update jsonschema package
9b94677
@blankdots
outdated pipfile
c01be2e
@blankdots
bump db_load coverage
cff5bcb
@blankdots
updates to tox
b5aa2b2
@blankdots
no invalid request is ever going to reach this
90c8bc1
@blankdots
fix bug in handover
f1c538a
@blankdots
test actual db responses
dc614f1
@blankdots
do not test some lines as of problematic to unit test
0f281d6
@blankdots
test db load close db connection exception
9275ecb
@blankdots
test aud claim
1b4cf69
@teemukataja
Merge pull request #133 from CSCfi/bugfix/review-code
564aace 
Sanity check and review code for small improvements
@teemukataja @blankdots
first test at parsing new ga4gh passports #130
aab89ea
@teemukataja @blankdots
fix controlled datasets, move validation and decoding into function #130
ff4151b
@teemukataja @blankdots
check for scopes before parsing token
5e663b1
@blankdots
fix documentation link
a340551
@blankdots
update ga4gh with fixes
3245e6e
@blankdots
fix ga4gh unit tests
85e885f
@blankdots blankdots added performance For when we need to scale release For when we need to make it official testing For when one needs more QA ga4gh Global Alliance for Genomic and Health labels Nov 6, 2019
@blankdots blankdots added this to the Version 1.5rc0 milestone Nov 6, 2019
@teemukataja teemukataja merged commit 6dcf156 into master Nov 7, 2019
@teemukataja teemukataja mentioned this pull request Nov 12, 2019
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@teemukataja teemukataja teemukataja approved these changes

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ga4gh Global Alliance for Genomic and Health performance For when we need to scale release For when we need to make it official testing For when one needs more QA

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Version 1.5rc0

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Successfully merging this pull request may close these issues.

Update GA4GH Permissions

4 participants

@blankdots @teemukataja @ooobik