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patch - Concatenate Microbial fastq files #3958

Merged

diitaz93 merged 13 commits into master from concatenate-w-pseudo-workflow

Nov 25, 2024

Merged

patch - Concatenate Microbial fastq files #3958

diitaz93 merged 13 commits into master from concatenate-w-pseudo-workflow

Nov 25, 2024

Conversation 29 Commits 13 Checks 8 Files changed

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diitaz93 commented Nov 20, 2024 •

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Description

Addresses https://github.com/Clinical-Genomics/bug-reports/issues/17
The Microbial fastq orders currently behave in the backend as a normal fastq order, while in reality, they should have a hybrid functionality between Microsalt and fastq. This is, the raw data fastq files should be concatenated for a sample (the replicates in multiple lanes) as it is done in Microsalt, but no analysis should start, as in fastq orders.

This PR overwrites the Workflow of Microbial-fastq cases from Workflow.RAW_DATA to Workflow.MICROSALT just for the delivery service.

Added

Static method _convert_workflow in DeliveryServiceFactory that patches the workflow of microbial fastq cases as Microsalt
Unit test for new function

Changed

The parameters of the public function build_delivery_service from DeliveryServiceFactory to receive case and delivery_type instead of Workflow and delivery_type

Fixed

All calls to build_delivery_service with the new parameters
Tests for build_delivery_service

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 concatenate-w-pseudo-workflow -a

How to test

Copy housekeeper bundle fastq files from prod to stage
Do cg -l DEBUG deliver ticket -t 1001074 --dry-run

Expected test outcome

Check that a folder with the ticket id was created in home/proj/stage/customers/cust121
Check that the folder has concatenated fastq files

Review

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

This version is a

PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

Deployed to stage:

Deployed to production:

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          add pseudo workflow to delivery

7d34554

ChrOertlin reviewed

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cg/constants/constants.py Outdated Show resolved Hide resolved

cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py Outdated Show resolved Hide resolved

cg/cli/deliver/base.py Outdated Show resolved Hide resolved

cg/cli/deliver/utils.py Outdated Show resolved Hide resolved

diitaz93 added 6 commits

November 21, 2024 10:06


          refactor service factory to receive case


          remove pseudo-workflow function

1b9521c


          implemented suggestion by CO

5665cae


          fix tests

c0dcbb6


          Merge branch 'master' into concatenate-w-pseudo-workflow

903cc6a


          fix type hint

a9ad9ed

diitaz93 commented

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cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py Outdated Show resolved Hide resolved

diitaz93 commented

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tests/services/file_delivery/delivery_file_service/test_service_builder.py Outdated Show resolved Hide resolved

diitaz93 commented

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cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py Outdated Show resolved Hide resolved


          remove unused store

fb3a93c

diitaz93 changed the title ~~add pseudo workflow to delivery~~ patch - Concatenate Microbial fastq files

diitaz93 marked this pull request as ready for review

November 21, 2024 10:59

diitaz93 requested a review from a team as a code owner

November 21, 2024 10:59

ChrOertlin approved these changes

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Looks good.

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          remove unused import

diitaz93 mentioned this pull request

fix(samplefileformatter apptag base) #3930

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15 tasks

islean reviewed

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          implement comments

fc0b4df

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Added some comments! I think it makes sense to check apptags in statusdb since then we do not need to apply changes to the code when entries are changed. I also think we can clarify the intent of a method by changing its return type to bool

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diitaz93 added 3 commits

November 22, 2024 10:38


          change constants for fetching app tags from statusdb

af476ca


          delete constant

f0d7eda


          reorder functions

5c8e60d

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sonarcloud bot commented Nov 22, 2024

Quality Gate passed

Issues
2 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 SonarQube Cloud

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diitaz93 commented Nov 22, 2024

Tests on stage

Command finished without errors
Concatenated files are shown in customer folder in hasta

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diitaz93 merged commit db9214d into master

9 checks passed

diitaz93 deleted the concatenate-w-pseudo-workflow branch

November 25, 2024 06:36

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ChrOertlin ChrOertlin approved these changes

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