Include bundle by default

islean commented 1 year ago

Description

Addresses issue #136 and adds an exclude flag to the add command. If not used, the add bundle command will include the bundle.

Added

Flag to exclude bundle when running housekeeper add bundle.

Changed

By default housekeeper add bundle includes the bundle.

Testing

How to prepare for test

[x] ssh to hasta (depending on type of change)
[x] install on stage: bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_main -t housekeeper -b include-bundle-by-default

How to test

[x] Add a bundle
[x] Add a file to the bundle

Expected test outcome

[x] Check that the bundle was added and included.
[x] Check that adding the file works without running include bundle.
[x] Take a screenshot and attach or copy/paste the output.

Review

[ ] code approved by
[ ] 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
[x] MINOR - when you add functionality in a backwards compatible manner
[ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

islean commented 1 year ago

Tests went well:

And now add file runs without needing to include the bundle beforehand.

sonarcloud[bot] commented 1 year ago

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

islean commented 1 year ago

Tests still successful with comments addressed:

θ67° [isak.ohlsson@hasta:/home/proj/stage] [S_base] 56s $ housekeeper add bundle TestBundle
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.cli.core[259560] INFO Use root path /home/proj/stage/housekeeper-bundles
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.cli.add[259560] INFO Running add bundle
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.store.api.handlers.read[259560] INFO Fetching bundle with name: TestBundle
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.files[259560] INFO Validating bundle schema
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.files[259560] INFO Validate marshmallow schema
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.files[259560] INFO Input looks fine
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.date[259560] INFO Trying to parse date string 2023-09-11 13:26:59.775662
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.store.api.handlers.read[259560] INFO Fetching bundle with name: TestBundle
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.store.api.handlers.create[259560] INFO Created new bundle: TestBundle
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.store.api.handlers.create[259560] INFO Created new version
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.include[259560] INFO Use global root path /home/proj/stage/housekeeper-bundles
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.include[259560] INFO created new bundle version dir: /home/proj/stage/housekeeper-bundles/TestBundle/2023-09-11
2023-09-11 13:26:59 hasta.scilifelab.se housekeeper.cli.add[259560] INFO new bundle added: TestBundle (150251)
θ65° [isak.ohlsson@hasta:/home/proj/stage] [S_base] 2s $ housekeeper add file -b TestBundle test_file.txt 
2023-09-11 13:27:22 hasta.scilifelab.se housekeeper.cli.core[8077] INFO Use root path /home/proj/stage/housekeeper-bundles
2023-09-11 13:27:23 hasta.scilifelab.se housekeeper.cli.add[8077] INFO Running add file
2023-09-11 13:27:23 hasta.scilifelab.se housekeeper.store.api.handlers.read[8077] INFO Fetching bundle with name: TestBundle
2023-09-11 13:27:24 hasta.scilifelab.se housekeeper.include[8077] INFO linked file: test_file.txt -> /home/proj/stage/housekeeper-bundles/TestBundle/2023-09-11/test_file.txt
2023-09-11 13:27:24 hasta.scilifelab.se housekeeper.cli.add[8077] INFO new file added: TestBundle/2023-09-11/test_file.txt (4483606)

islean commented 1 year ago

Deployed to stage 2023-09-11 by IO:

θ64° [isak.ohlsson@hasta:/home/proj/stage/housekeeper-bundles] [S_base] $ bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_main -t housekeeper -b master

...

repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/proj/stage/housekeeper-bundles
done.
Log deploy... done.
housekeeper, version 4.8.0

islean commented 1 year ago

Deployed to production 2023-09-11 by IO:

θ61° [isak.ohlsson@hasta:/home/proj/stage/housekeeper-bundles] [P_base] 6s $ bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-prod.sh -e P_main -t housekeeper -b master

...

repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/proj/stage/housekeeper-bundles
done.
Log deploy... done.
housekeeper, version 4.8.0

Clinical-Genomics / housekeeper