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v2.1.0: Clinical discovery and bugfixes #23

Merged
merged 56 commits into from
Mar 7, 2024
Merged

v2.1.0: Clinical discovery and bugfixes #23

merged 56 commits into from
Mar 7, 2024

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OrdiNeu
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@OrdiNeu OrdiNeu commented Mar 5, 2024 •
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v2.1.0: Description

  • Update versions of Alpine and Python and other dependencies
  • Several fixes to make it work with the new frontend, including genomic search fixes, etc.
  • Fix a miscount on donors contributing to age summary stats once per treatment
  • Tagged as a release in this repo
  • Passes integration tests on a development instance
  • Images pushed to Dockerhub

OrdiNeu and others added 30 commits December 7, 2023 13:53
@OrdiNeu
Fix an issue where an unknown date of birth or diagnosis would fail
17dbced
@OrdiNeu
Fix an issue where NoneType keys would crash Flask
25f5112
@OrdiNeu
Fix the page/size being strings instead of ints
4d4938c
@OrdiNeu
[wip]
a815e77
@OrdiNeu
Fixup completeness query to split out genomic/transcriptome
d816ffd
@OrdiNeu
Add fixes for things that changed with the Katsu UUID fix
49aa245
@OrdiNeu
Fix the usage of the candig user
6a77553
@daisieh
remove libressl-dev
5751be5
@daisieh
update uwsgi
35b54a9
@OrdiNeu
Merge pull request #6 from CanDIG/fnguyen/uuid-fix
5eeb286 
Add fixes for things that changed with the Katsu UUID fix
@OrdiNeu
Merge pull request #8 from CanDIG/daisieh/alpine-318
e874d7b 
DIG-1149: Update Alpine to 3.18
@OrdiNeu
Merge pull request #7 from CanDIG/fnguyen/candig-user
660e812 
DIG-1377: Be consistent in our use of candig user inside containers
@OrdiNeu
Add workflow file (copied from HTSGet)
6d5af3d
@daisieh
Merge pull request #9 from CanDIG/daisieh/python-312
b9fa433 
DIG-1144: update to python 3.12
@daisieh
add candigv2-authx
9d39313
@daisieh
gene search is one-by-one
56eea2f
@daisieh
it's possible to have no "chr" prefix
3426351
@daisieh
add X-Service-Token to headers
a2be027
@daisieh
UPDATE THIS: this is how you'd get info for discovery
85c8b15
@OrdiNeu
Fix for the search page on query
21f67fb
@OrdiNeu
Merge pull request #12 from CanDIG/fnguyen/uuid-fix-2
46777eb 
Fix for the search page on query
@daisieh
update authx to v2.1.0
26ff100
@daisieh
Merge pull request #11 from CanDIG/daisieh/query-token
ad51ae9 
DIG-1382, DIG-1384: query uses a service token with htsget
@mshadbolt
add libffi-dev dependency
9fb1fbf
@OrdiNeu
Fix the miscount on donors contributing to age summary stats once per…
29624fd 
… treatment
@OrdiNeu
Fix the HTSGet search
da9fe06
@OrdiNeu
Remove debugging code
ae1ef3c
@OrdiNeu
Merge pull request #13 from CanDIG/mshadbolt/fix-cffi-install-fail
7811729 
add libffi-dev dependency
@OrdiNeu
Merge pull request #14 from CanDIG/fnguyen/donor-doublecount-fix
7d89a4b 
Fix the miscount on donors contributing to age summary stats once per treatment
@OrdiNeu
Merge pull request #15 from CanDIG/fnguyen/htsget-fix
ba31023 
Genomic search fix
OrdiNeu and others added 26 commits February 7, 2024 10:54
@OrdiNeu
[wip] Add intervals support
c5158b7
@OrdiNeu
Merge pull request #10 from CanDIG/fnguyen/workflow
db6edcc 
Add workflow file (copied from HTSGet)
@SonQBChau
Update query_operations.py
a2e4ac4 
- get floor age
- replace donor_date_of_births by donors
@OrdiNeu
Remove debugging statement
8c42d40
@OrdiNeu @mshadbolt
[wip] Add intervals support
a483584
@SonQBChau @mshadbolt
Update query_operations.py
56cbfb5 
- get floor age
- replace donor_date_of_births by donors
@OrdiNeu @mshadbolt
Remove debugging statement
8856343
@mshadbolt
Merge branch 'fnguyen/intervals_support' of github.com:CanDIG/query i…
58fbcc0 
…nto fnguyen/intervals_support
@OrdiNeu
Reduce number of per-donor iterations
e4825f2
@OrdiNeu
Merge pull request #17 from CanDIG/fnguyen/intervals_support
742c259 
DIG-1416: Add intervals support
@OrdiNeu
Add discovery queries for clinical data
980de1f
@OrdiNeu
Missing cases_missing_data metadata
f6cbb50
@OrdiNeu
Update openapi schema
838dcfc
@mshadbolt
Update candig-dispatch.yml
1ed50ef
@OrdiNeu
Merge pull request #18 from CanDIG/fnguyen/clinical_discovery
fffbc96 
Add clinical discovery queries
@mshadbolt
Merge pull request #19 from CanDIG/mshadbolt/update-gh-action
6317082 
DIG-1376 :Update GH Action to improve PR title and description
@OrdiNeu
Fix NREs with missing required data
16303ff
@OrdiNeu
Use the Query token when talking to Katsu/HTSGet
78f56c2
@OrdiNeu
Merge pull request #20 from CanDIG/bugfix/genomic-completeness
eac49e5 
Bugfix: Missing data and completeness data
@OrdiNeu
Bump versions to fix Snyk vulnerabilities
378c9ca
@OrdiNeu
Also update authx?
a4e0a6f
@OrdiNeu
Prune the HTSGet responses by what donors were found in Katsu
19c8c6a
@OrdiNeu
Fixup: grab the proper ID and check against the real program/donor
8da1bd6
@OrdiNeu
Merge pull request #21 from CanDIG/bugfix/snyk-vulnerabilities-20240301
37d5a46 
Bump versions to fix Snyk vulnerabilities
@OrdiNeu
Merge pull request #22 from CanDIG/bugfix/htsget-pruning
cd22b9b 
Bugfix/htsget pruning
@OrdiNeu
Merge branch 'stable' into stable-candidate-v.2.1.0
4a3a779
@OrdiNeu OrdiNeu merged commit bc1c393 into stable Mar 7, 2024
@OrdiNeu OrdiNeu deleted the stable-candidate-v.2.1.0 branch March 7, 2024 15:25
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4 participants
@OrdiNeu @daisieh @mshadbolt @SonQBChau