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feat(new delivery flow) #3598

Merged
merged 85 commits into from
Sep 10, 2024
Merged

feat(new delivery flow) #3598

merged 85 commits into from
Sep 10, 2024

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ChrOertlin
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@ChrOertlin ChrOertlin commented Aug 19, 2024 •
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Description

There have been multiple attempts to refactor the file delivery for workflows.

Here is an attempt to re write the logic from scratch instead.

REQUIRES: https://github.com/Clinical-Genomics/servers/pull/1447

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 dev-new-delivery-service -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 19, 2024 13:04
@ChrOertlin ChrOertlin marked this pull request as draft August 19, 2024 13:04
ChrOertlin and others added 18 commits August 21, 2024 11:59
@ChrOertlin
Merge branch 'master' into dev-new-delivery-service
f45df6e
@ChrOertlin
add(fetch delivery files service) (#3601)
5857eab 
# Description

adds tag and file fetchers for the delivery service
@ChrOertlin
fix imports
44bbe28
@ChrOertlin
initial commit
4dd94c8
@ChrOertlin
fixes
c09db2f
@ChrOertlin
fix
f449da4
@ChrOertlin
add test
33456ef
@ChrOertlin
fix test
f175540
@ChrOertlin
add exists assertion
511ed7f
@ChrOertlin
add func call
9063fc8
@ChrOertlin
initial commit
8a64d3b
@ChrOertlin @henrikstranneheim
Update tests/fixture_plugins/delivery_fixtures/delivery_files_models_…
83d6c9f 
…fixtures.py

Co-authored-by: Henrik Stranneheim <[email protected]>
@ChrOertlin @henrikstranneheim
Update tests/fixture_plugins/delivery_fixtures/delivery_files_models_…
bacaa11 
…fixtures.py

Co-authored-by: Henrik Stranneheim <[email protected]>
@ChrOertlin @henrikstranneheim
Apply suggestions from code review
0533071 
Co-authored-by: Henrik Stranneheim <[email protected]>
@ChrOertlin
review
3fbc9ef
@ChrOertlin
Merge branch 'add-file-mover' into add-file-reformatters
4eca28e
@ChrOertlin
feat(delivery file mover service) (#3622)
086c74d 
# Description 

move files service
@ChrOertlin
conflicsts
f83f694
@ChrOertlin ChrOertlin mentioned this pull request Aug 22, 2024
Closed
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delivero auto-raw-data

Runs through without failing on errors:
image

@ChrOertlin ChrOertlin marked this pull request as ready for review September 9, 2024 12:30
diitaz93
diitaz93 reviewed Sep 10, 2024
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@diitaz93 diitaz93 left a comment

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Will leave my first round, looks great until now ⭐

cg/meta/upload/error_handling.py Outdated Show resolved Hide resolved
cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py Show resolved Hide resolved
cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py Outdated Show resolved Hide resolved
cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py Outdated Show resolved Hide resolved
cg/services/deliver_files/delivery_file_formatter_service/utils/case_file_formatter.py Outdated Show resolved Hide resolved
...ices/deliver_files/delivery_file_fetcher_service/fastq_and_analysis_delivery_file_fetcher.py Outdated Show resolved Hide resolved
...ices/deliver_files/delivery_file_fetcher_service/fastq_and_analysis_delivery_file_fetcher.py Outdated Show resolved Hide resolved
cg/services/deliver_files/delivery_file_fetcher_service/fastq_delivery_file_fetcher.py Outdated Show resolved Hide resolved
cg/services/deliver_files/delivery_file_fetcher_service/analysis_delivery_file_fetcher.py Outdated Show resolved Hide resolved
cg/services/deliver_files/delivery_file_fetcher_service/analysis_delivery_file_fetcher.py Outdated Show resolved Hide resolved
diitaz93
diitaz93 approved these changes Sep 10, 2024
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Great work 💪

cg/services/deliver_files/deliver_files_service/deliver_files_service.py Outdated Show resolved Hide resolved
tests/services/file_delivery/rsync_service/conftest.py Outdated Show resolved Hide resolved
tests/services/file_delivery/rsync_service/conftest.py Outdated Show resolved Hide resolved
tests/services/file_delivery/rsync_service/conftest.py Outdated 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 6a221f1 into master Sep 10, 2024
9 checks passed
@ChrOertlin ChrOertlin deleted the dev-new-delivery-service branch September 10, 2024 13:18
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@diitaz93 diitaz93 diitaz93 approved these changes

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