Add raredisease panel cmd #2718

henrikstranneheim · 2023-11-29T16:13:37Z

Description

Added

Panel CLI
Test and fixtures

Changed

Refactored panel functions and gene panel constants

How to prepare for test

Ssh to relevant server (depending on type of change)
Use stage: us
Paxa the environment: paxa

Install on stage (example for Hasta):

bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b add-raredisease-panel-cmd -a

How to test

Do ...

Expected test outcome

Check that ...
Take a screenshot and attach or copy/paste the output.

Review

Tests executed by
"Merge and deploy" approved by
Thanks for filling in who performed the code review and the test!

This version is a

MAJOR - when you make incompatible API changes
MINOR - when you add functionality in a backwards compatible manner
PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

Document in ...
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# Conflicts: # cg/constants/__init__.py # cg/constants/gene_panel.py # cg/meta/workflow/analysis.py # cg/store/api/status.py

henrikstranneheim · 2023-12-05T11:50:52Z

@rannick @peterpru @jemten Ready for review!

jemten

Looks good to me! Although, you should probably get someone more cg savvy then me to review it :)

henrikstranneheim · 2023-12-06T07:46:02Z

https://github.com/Clinical-Genomics/servers/pull/1208

henrikstranneheim · 2023-12-06T08:22:46Z

cg workflow mip-dna panel justhusky ✅

[henrik.stranneheim@hasta:~] [S_base] 48s $ cg workflow mip-dna panel justhusky
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Case justhusky exists in Status DB
Running command /home/proj/stage/bin/miniconda3/envs/S_scout/bin/scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml export panel --bed BRAIN Cardiology CILM CH CTD DIAB ENDO EP HEARING HYDRO IBMFS IEM IF mcarta MHT MIT MOVE mtDNA NBS-M NEURODEG NMD OMIM-AUTO PANELAPP-GREEN PEDHEP PID PIDCAD RETINA SKD SOVM STROKE AID --build 37
θ60° [henrik.stranneheim@hasta:~] [S_base] 51s $ head /home/proj/stage/rare-disease/cases/justhusky/gene_panels.bed
##genome_build=37
##gene_panel=BRAIN,version=1.0,updated_at=2020-02-14,display_name=BRAIN
##gene_panel=Cardiology,version=1.0,updated_at=2020-01-21,display_name=Cardiology
##gene_panel=CILM,version=59.0,updated_at=2018-03-22,display_name=Ciliopathy
##gene_panel=CTD,version=55.0,updated_at=2021-12-13,display_name=Connective Tissue Diseases
##gene_panel=DIAB,version=17.0,updated_at=2023-03-20,display_name=DIAB
##gene_panel=ENDO,version=12.0,updated_at=2018-02-05,display_name=Endocrinology
##gene_panel=EP,version=15.0,updated_at=2021-12-10,display_name=Epilepsy
##gene_panel=HYDRO,version=4.0,updated_at=2018-01-19,display_name=Hydropspanel
##gene_panel=IBMFS,version=13.0,updated_at=2018-01-31,display_name=Inherited Bone Marrow Failure Syndromes

henrikstranneheim · 2023-12-06T08:27:21Z

No raredisease case in statusDB to test with but we have no live functionality yet and raredisease uses identical functions as mip-dna so this is good enough I think.

ChrOertlin

👍 Looks good!

cg/constants/constants.py

cg/meta/workflow/mip_dna.py

cg/meta/workflow/mip_rna.py

cg/meta/workflow/raredisease.py

tests/cli/workflow/mip/test_cli_mip_dna_panel.py

tests/cli/workflow/raredisease/test_cli_raredisease_compound_commands.py

diitaz93

Looks good! Made some suggestions about the code duplication

cg/meta/workflow/analysis.py

cg/meta/workflow/mip_dna.py

cg/meta/workflow/raredisease.py

tests/conftest.py

tests/io/test_io_controller.py

tests/io/test_io_txt.py

tests/mocks/mip_analysis_mock.py

cg/constants/gene_panel.py

…add-raredisease-panel-cmd

Co-authored-by: Sebastian Diaz <[email protected]>

cg/constants/gene_panel.py

# Conflicts: # cg/constants/constants.py # cg/meta/workflow/mip.py

…add-raredisease-panel-cmd

henrikstranneheim · 2023-12-07T07:52:14Z

cg workflow mip-dna panel justhusky ✅

[henrik.stranneheim@hasta:~] [S_base] 13s $ cg workflow mip-dna panel justhusky
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Case justhusky exists in Status DB
Running command /home/proj/stage/bin/miniconda3/envs/S_scout/bin/scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml export panel --bed BRAIN Cardiology CILM CH CTD DIAB ENDO EP HEARING HYDRO IBMFS IEM IF mcarta MHT MIT MOVE mtDNA NBS-M NEURODEG NMD OMIM-AUTO PANELAPP-GREEN PEDHEP PID PIDCAD RETINA SKD SOVM STROKE AID --build 37

henrikstranneheim · 2023-12-07T08:10:35Z

cg, version 53.5.4
[henrik.stranneheim@hasta:~] [S_base] 2m59s $ cg workflow raredisease --help
Usage: cg workflow raredisease [OPTIONS] COMMAND [ARGS]...

  NF-core/raredisease analysis workflow.

Options:
  --help  Show this message and exit.

Commands:
  panel  Write aggregated gene panel file exported from Scout.
[henrik.stranneheim@hasta:~] [S_base] 23s $ cg workflow raredisease panel --help
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Usage: cg workflow raredisease panel [OPTIONS] CASE_ID

  Write aggregated gene panel file exported from Scout.

Options:
  -d, --dry-run  Simulate process without executing
  --help         Show this message and exit.

sonarqubecloud · 2023-12-07T10:41:43Z

SonarCloud Quality Gate failed.

0 Bugs
0 Vulnerabilities
0 Security Hotspots
1 Code Smell

No Coverage information
9.2% Duplication

Catch issues before they fail your Quality Gate with our IDE extension SonarLint

henrikstranneheim · 2023-12-07T10:58:19Z

Deployed to production:

Log deploy... done.
cg, version 53.6.0

henrikstranneheim added 3 commits November 29, 2023 16:10

feat(WIP)

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feat(WIP)

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feat(WIP)

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henrikstranneheim self-assigned this Nov 29, 2023

henrikstranneheim added 11 commits November 30, 2023 13:35

feat(constant): CustomerId

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feat(refactor):

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feat(WIP):

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feat(TXT): Add IO write

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feat(TXT): Use IO write

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WIP

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feat(test): Add

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Merge branch 'master' into add-raredisease-panel-cmd

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# Conflicts: # cg/constants/__init__.py # cg/constants/gene_panel.py # cg/meta/workflow/analysis.py # cg/store/api/status.py

feat(refactor)

49ecaf2

henrikstranneheim marked this pull request as ready for review December 5, 2023 09:17

henrikstranneheim requested a review from a team as a code owner December 5, 2023 09:17

henrikstranneheim added the Project Task Part of a quarterly project label Dec 5, 2023

jemten reviewed Dec 5, 2023

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Merge branch 'master' into add-raredisease-panel-cmd

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ChrOertlin approved these changes Dec 6, 2023

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diitaz93 approved these changes Dec 6, 2023

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beatrizsavinhas reviewed Dec 6, 2023

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henrikstranneheim added 3 commits December 6, 2023 13:26

Merge branch 'master' into add-raredisease-panel-cmd

db00e6b

fix(review)

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fix(review)

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henrikstranneheim and others added 3 commits December 6, 2023 14:07

fix(review)

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Merge remote-tracking branch 'origin/add-raredisease-panel-cmd' into …

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…add-raredisease-panel-cmd

Apply suggestions from code review

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Co-authored-by: Sebastian Diaz <[email protected]>

beatrizsavinhas reviewed Dec 6, 2023

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henrikstranneheim added 4 commits December 7, 2023 08:13

Merge branch 'master' into add-raredisease-panel-cmd

97d84a7

# Conflicts: # cg/constants/constants.py # cg/meta/workflow/mip.py

feat(refactor)

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Merge remote-tracking branch 'origin/add-raredisease-panel-cmd' into …

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…add-raredisease-panel-cmd

feat(refactor)

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feat(clo)

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fix(binary_path)

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henrikstranneheim merged commit c33d482 into master Dec 7, 2023
8 of 9 checks passed

henrikstranneheim deleted the add-raredisease-panel-cmd branch December 7, 2023 10:50

jemten added the raredisease Issues related to nextflow raredisease pipeline label Dec 11, 2023

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Add raredisease panel cmd #2718

Add raredisease panel cmd #2718

henrikstranneheim commented Nov 29, 2023 •

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henrikstranneheim commented Dec 7, 2023

Add raredisease panel cmd #2718

Add raredisease panel cmd #2718

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henrikstranneheim commented Nov 29, 2023 • edited Loading

Description

Added

Changed

How to prepare for test

How to test

Expected test outcome

Review

This version is a

Implementation Plan

henrikstranneheim commented Dec 5, 2023

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henrikstranneheim commented Dec 6, 2023

henrikstranneheim commented Dec 6, 2023

cg workflow mip-dna panel justhusky ✅

henrikstranneheim commented Dec 6, 2023

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henrikstranneheim commented Dec 7, 2023

cg workflow mip-dna panel justhusky ✅

henrikstranneheim commented Dec 7, 2023

sonarqubecloud bot commented Dec 7, 2023

henrikstranneheim commented Dec 7, 2023

henrikstranneheim commented Nov 29, 2023 •

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