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add(delivery file formatter) #3626

Merged
merged 30 commits into from
Aug 29, 2024
Merged

add(delivery file formatter) #3626

merged 30 commits into from
Aug 29, 2024

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ChrOertlin
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Description

delivery file formatter

Added

Changed

Fixed

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 [THIS-BRANCH-NAME] -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 ...
  • Deploy this branch on ...
  • Inform to ...

@ChrOertlin ChrOertlin requested a review from a team as a code owner August 22, 2024 12:42
@ChrOertlin ChrOertlin marked this pull request as draft August 22, 2024 12:42
@ChrOertlin ChrOertlin marked this pull request as ready for review August 27, 2024 09:33
henrikstranneheim
henrikstranneheim reviewed Aug 27, 2024
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@henrikstranneheim henrikstranneheim left a comment

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Nice work! Leaving some comments and questions.

...rvices/file_delivery/file_formatter_service/concatenation_delivery_file_formatter_service.py Outdated Show resolved Hide resolved
...rvices/file_delivery/file_formatter_service/concatenation_delivery_file_formatter_service.py Outdated Show resolved Hide resolved
...rvices/file_delivery/file_formatter_service/concatenation_delivery_file_formatter_service.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/generic_delivery_file_formatter_service.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/generic_delivery_file_formatter_service.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_concatenation_formatter.py Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_concatenation_formatter.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_concatenation_formatter.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_concatenation_formatter.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_concatenation_formatter.py Outdated Show resolved Hide resolved
Vince-janv
Vince-janv reviewed Aug 28, 2024
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@Vince-janv Vince-janv left a comment

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Nice! I especially like the classes for passing the data around, it makes the implementation so much cleaner!

cg/services/file_delivery/file_formatter_service/utils/case_file_formatter.py Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/case_file_formatter.py Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/delivery_file_formatter.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/delivery_file_formatter.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_concatenation_formatter.py Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_concatenation_formatter.py Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_formatter.py Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_formatter.py Show resolved Hide resolved
cg/services/fastq_concatenation_service/utils.py Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/utils.py Outdated Show resolved Hide resolved
islean
islean approved these changes Aug 28, 2024
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@islean islean left a comment

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Looks super nice!

cg/services/file_delivery/file_formatter_service/delivery_file_formatter.py Outdated Show resolved Hide resolved
cg/services/file_delivery/file_formatter_service/utils/sample_file_concatenation_formatter.py Show resolved Hide resolved
tests/fixture_plugins/delivery_fixtures/delivery_formatted_files_fixtures.py Show resolved Hide resolved
tests/services/file_delivery/format_deliver_files_service/test_format_delivery_files_service.py Show resolved Hide resolved
tests/services/file_delivery/format_deliver_files_service/utils/test_formatter_utils.py Show resolved Hide resolved
@sonarqubecloud SonarQubeCloud
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Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

@ChrOertlin ChrOertlin merged commit 79d5ca3 into dev-new-delivery-service Aug 29, 2024
7 checks passed
@ChrOertlin ChrOertlin deleted the add-file-reformatters branch August 29, 2024 06:36
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@Vince-janv Vince-janv Vince-janv left review comments

@henrikstranneheim henrikstranneheim henrikstranneheim left review comments

@islean islean islean approved these changes

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4 participants
@ChrOertlin @henrikstranneheim @islean @Vince-janv