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Clinical-Genomics / housekeeper

File data orchestrator
MIT License
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feat(refactor): List #182

Closed henrikstranneheim closed 11 months ago

henrikstranneheim commented 11 months ago

Description

Refactor to pep 0604

Changed

Testing

How to prepare for test

housekeeper-test-deploy refactorto-PEP-0604_2
housekeeper-test get bundle -v justhusky

Any migrations need to be applied manually with alembic against the stage database.

How to test

Expected test outcome

Review

This version is a:

sonarcloud[bot] commented 11 months ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

henrikstranneheim commented 11 months ago

HK executes ✅

henrik.stranneheim@hasta:~] [base] $ housekeeper-test get bundle -v justhusky
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:b7f91549542cca4b35a34cdee5364339f17468971ea730bb072864d3e78c8b94
Skipping fetch of repeat blob sha256:4bb0f1d192947f14a4b39d3c834d07ba99bdd44fd87c51df64e0c443a9e2471c
Skipping fetch of repeat blob sha256:b95fe821a42071bc164d30f997ab2e9918018145f8d303ac5af44193429d0d30
Skipping fetch of repeat blob sha256:9342c96c14b444acc0906bd883c07423b8f4d31b7ad5a955a42a886e582b26f5
Skipping fetch of repeat blob sha256:ce51f6afce88199c94daac12dfbcc2cf14832feed0a86988709475364a7c276a
Skipping fetch of repeat blob sha256:849aa61d149c0ad8a117523410215fe479127a0b45934259364ff468fbbb9240
Skipping fetch of repeat blob sha256:c2d29d40aaa1b3aed76b644b56d34568bd6cbb99b73ccaa4fdb7432ead4bc8ed
Skipping fetch of repeat blob sha256:c0d14e80c4192cbfd7d411c0a3a6e3b209656bfd312697fda293822e1ee2e5b6
Skipping fetch of repeat blob sha256:af2d98d145bc2b277b63704b2ca6c812b18bbcd8ffc91fa3bb31d0c89a2a0095
Copying config sha256:680e8f786767a80e7ca2427ea1730a090fd0a4592b2e76c134ff05c5dfc2e59e
 7.75 KiB / 7.75 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/henrik.stranneheim/.singularity/cache/oci-tmp/c0b91c52493ca584fdeda5bdb6df0b4038a61a5942ed3f12210248ce50c5bdc9/housekeeper_refactorto-PEP-0604_2.sif
INFO:    Image cached as SIF at /home/henrik.stranneheim/.singularity/cache/oci-tmp/c0b91c52493ca584fdeda5bdb6df0b4038a61a5942ed3f12210248ce50c5bdc9/housekeeper_refactorto-PEP-0604_2.sif
2023-12-04 16:07:48 hasta.scilifelab.se housekeeper.cli.core[46811] INFO Use root path /home/proj/stage/housekeeper-bundles
                                  📦 Bundle table 📦
┏━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓
┃ ID   ┃ Bundle name ┃ Version IDs                                       ┃ Created    ┃
┡━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
│ 8925 │ justhusky   │ 140963, 136933, 120104, 51171, 42582, 16939, 9523 │ 2019-06-11 │
└──────┴─────────────┴───────────────────────────────────────────────────┴────────────┘
                               📕 Version table 📕
┏━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━┓
┃ ID     ┃ Bundle name ┃ Nr files ┃ Included   ┃ Archived ┃ Created    ┃ Expires ┃
┡━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━┩
│ 140963 │ justhusky   │ 355      │ 2023-05-05 │          │ 2023-05-04 │         │
└────────┴─────────────┴──────────┴────────────┴──────────┴────────────┴─────────┘
                                                                                  📜 Files table 📜
┏━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ID      ┃ File name                                                                                                          ┃ Tags                                                ┃
┡━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ 3985485 │ /home/proj/stage/housekeeper-bundles/justhusky/2023-05-04/earlycasualcaiman_lanes_1_sorted_md.cram                 │ earlycasualcaiman, cram, scout                      │
│ 3985486 │ /home/proj/stage/housekeeper-bundles/justhusky/2023-05-04/earlycasualcaiman_lanes_1_sorted_md.cram.crai            │ earlycasualcaiman, cram, scout                      │
│ 3985487 │ /home/proj/stage/housekeeper-bundles/justhusky/2023-05-04/hugelymodelbat_lanes_1_sorted_md.cram                    │ hugelymodelbat, cram, scout
henrikstranneheim commented 11 months ago

Deployed to production