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Feature/sdev 3256 gene list updates pharma cancer predisp #72

Merged
merged 11 commits into from
Dec 8, 2022
Merged

Feature/sdev 3256 gene list updates pharma cancer predisp #72

merged 11 commits into from
Dec 8, 2022

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dustinbleile
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Migrate get_cancer_predisposition_info and get_pharmacogenomic_info from gsc_report added to genes.py

These functions use a preferred gene_name to replace transcripts, alternated representations. Added an equivalent function to genes.py, get_preferred_gene_name.

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codecov bot commented Oct 19, 2022 •
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Codecov Report

Base: 89.21% // Head: 89.50% // Increases project coverage by +0.28% 🎉

Coverage data is based on head (0512830) compared to base (13a8d9d).
Patch coverage: 84.67% of modified lines in pull request are covered.

Additional details and impacted files 
@@             Coverage Diff             @@
##           develop      #72      +/-   ##
===========================================
+ Coverage    89.21%   89.50%   +0.28%     
===========================================
  Files            8        7       -1     
  Lines          473      581     +108     
===========================================
+ Hits           422      520      +98     
- Misses          51       61      +10
Flag Coverage Δ
unittests 89.50% <84.67%> (+0.28%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
graphkb/util.py 81.69% <77.77%> (-8.31%) ⬇️
graphkb/genes.py 90.07% <89.21%> (-4.21%) ⬇️
graphkb/constants.py 92.30% <91.17%> (-7.70%) ⬇️
graphkb/match.py 91.66% <100.00%> (-0.70%) ⬇️
graphkb/vocab.py 93.47% <100.00%> (+2.36%) ⬆️

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dustinbleile
dustinbleile commented Oct 21, 2022
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Updated

@dustinbleile
Release v1.8.0
ba11684 
New Features:
 - new list in genes.py - get_therapeutic_associated_genes
 - constants.py - expanded with commonly used GKB return properties.
 - GraphKBConnection login on init if given username and password.
 - typing_extensions>=3.7.4.2,<4.4
Improvements:
 - new test - match TERT:c.-124C>T
 - skipped test GERO-299 - test_missense_is_not_nonsense - not yet fixed.  (Intercepted by pori_ipr_python).
 - Refactor - simplify __init__.py - move GraphKBConnection to util.py
 - Refactor - simplify - remove custom VERBOSE logging level.
 - update tests - fix test_known_fusion_single_gene_no_match
@dustinbleile dustinbleile self-assigned this Nov 2, 2022
dustinbleile and others added 2 commits November 2, 2022 13:26
@dustinbleile
Merge pull request #73 from bcgsc/release/v1.8.0_constants_usablity
101b616 
Release/v1.8.0 constants usablity
@dustinbleile
Merge branch 'master' of https://github.com/bcgsc/pori_graphkb_python …
dd165f5 
…into feature/SDEV-3256_gene_list_updates_pharma_cancer_predisp
mattdoug604
mattdoug604 reviewed Nov 15, 2022
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@dustinbleile
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Hi @mattdoug604, @creisle,
Can we try to add Caleb and David as reviewers for this project?
I can't seem to figure out how. Maybe I do not have those permissions?

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creisle commented Nov 17, 2022

Hi @mattdoug604, @creisle, Can we try to add Caleb and David as reviewers for this project? I can't seem to figure out how. Maybe I do not have those permissions?

I'm making an sdev team and I will add them to the repo permissions that way all at once. What is david's github handle? and who else should be on sdev

https://github.com/orgs/bcgsc/teams/sdev/members

@dustinbleile
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Ping - new reviewers

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Hi @calchoo & @darenillas

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Hi @darenillas, @calchoo, @mattdoug604

pinging for some review

@dustinbleile dustinbleile merged commit 2ed3616 into develop Dec 8, 2022
@dustinbleile dustinbleile deleted the feature/SDEV-3256_gene_list_updates_pharma_cancer_predisp branch March 29, 2023 22:15
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@mattdoug604 mattdoug604 mattdoug604 left review comments

@calchoo calchoo calchoo approved these changes

@mathieulemieux mathieulemieux Awaiting requested review from mathieulemieux

@creisle creisle Awaiting requested review from creisle

@elewis2 elewis2 Awaiting requested review from elewis2

@kttkjl kttkjl Awaiting requested review from kttkjl

@Nithriel Nithriel Awaiting requested review from Nithriel

@darenillas darenillas Awaiting requested review from darenillas

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@dustinbleile @creisle @mattdoug604 @calchoo