feat(python): Update - Githubissues

henrikstranneheim commented 1 month ago

Description

Added

-

Changed

-

Fixed

-

Testing

How to prepare for test

[ ] ssh to Hasta
[ ] Test your branch with

housekeeper-test-deploy update-python
housekeeper-test --help

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

How to test

[ ] login to ...
[ ] do ...

Expected test outcome

[ ] check that ...
[ ] 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
[ ] MINOR - when you add functionality in a backwards compatible manner
[x] PATCH - when you make backwards compatible bug fixes or documentation/instructions

sonarcloud[bot] commented 1 month ago

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

henrikstranneheim commented 1 month ago

CLI, 👍


henrik.stranneheim@hasta:~] [S_base] $ housekeeper-test-deploy update-python
Pulling image for feature branch: update-python...
WARNING: Authentication token file not found : Only pulls of public images will succeed
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:6533c3eba3f3cd4c840877f9245b26929fc8c22a39f42c872aa314c32c6d654b
Copying blob sha256:6671afbf80d520b90e6bc20b00bf42d8c8b9b03f37e60a0bdb47ee01564df8b7
 1.03 MiB / 1.03 MiB [======================================================] 0s
Copying blob sha256:035d07709dfb5588e1576091d0f994ee2c7ec39e89150803ff8ef975a9034596
 12.04 MiB / 12.04 MiB [====================================================] 0s
Copying blob sha256:102a6e7f7a21934a56851632b76315e0c2067b22256a4543c859a1c561bd957b
 251 B / 251 B [============================================================] 0s
Copying blob sha256:8ad6980d5df958828580d8ce6e8fd6af57c10b73686b68ed3ccafbd6100c3cb4
 93 B / 93 B [==============================================================] 0s
Copying blob sha256:bf8dede5700d875623223e81eca7fcf67ee5cd18511a008fc5a574a88b715eb4
 454.95 KiB / 454.95 KiB [==================================================] 0s
Copying blob sha256:c8744c00155339fc743b20210547e0c655c0832418e55b57dd5fe4d8b8812471
 64.06 MiB / 64.06 MiB [====================================================] 1s
Copying config sha256:814efa25ef4ff28bffaee12cade1cd22aa85bc5b5128ebfe0d1a0f3fa05c587b
 5.85 KiB / 5.85 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/proj/stage/singularity_containers/housekeeper_update-python.sif
You can now run 'housekeeper-test --help' to test the feature branch: update-python.
[henrik.stranneheim@hasta:~] [base] $ housekeeper-test --help
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:6533c3eba3f3cd4c840877f9245b26929fc8c22a39f42c872aa314c32c6d654b
Skipping fetch of repeat blob sha256:6671afbf80d520b90e6bc20b00bf42d8c8b9b03f37e60a0bdb47ee01564df8b7
Skipping fetch of repeat blob sha256:035d07709dfb5588e1576091d0f994ee2c7ec39e89150803ff8ef975a9034596
Skipping fetch of repeat blob sha256:102a6e7f7a21934a56851632b76315e0c2067b22256a4543c859a1c561bd957b
Skipping fetch of repeat blob sha256:8ad6980d5df958828580d8ce6e8fd6af57c10b73686b68ed3ccafbd6100c3cb4
Skipping fetch of repeat blob sha256:bf8dede5700d875623223e81eca7fcf67ee5cd18511a008fc5a574a88b715eb4
Skipping fetch of repeat blob sha256:c8744c00155339fc743b20210547e0c655c0832418e55b57dd5fe4d8b8812471
Copying config sha256:814efa25ef4ff28bffaee12cade1cd22aa85bc5b5128ebfe0d1a0f3fa05c587b
 5.85 KiB / 5.85 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/henrik.stranneheim/.singularity/cache/oci-tmp/d8b5b6aceea8a58b738f23f70686e5514861385cdd9c9e88d35ad1806314af6b/housekeeper_update-python.sif
INFO:    Image cached as SIF at /home/henrik.stranneheim/.singularity/cache/oci-tmp/d8b5b6aceea8a58b738f23f70686e5514861385cdd9c9e88d35ad1806314af6b/housekeeper_update-python.sif
/app/housekeeper/services/file_report_service/utils.py:111: SyntaxWarning: invalid escape sequence '\d'
  parsed = re.split("(\d+)\.(\w{2,3}$)", filename)
Usage: housekeeper [OPTIONS] COMMAND [ARGS]...

  Housekeeper - Access your files!

Options:
  -c, --config FILENAME
  -d, --database TEXT    path/URI of the SQL database
  -r, --root PATH        Housekeeper root dir
  -l, --log-level TEXT
  --version              Show the version and exit.
  --help                 Show this message and exit.

Commands:
  add      Add things to the store.
  delete   Delete things in the database.
  get      Get info from database
  include  Include a bundle of files into the internal space.
  init     Setup the database.

[henrik.stranneheim@hasta:~] [base] $ housekeeper-test get bundle justhusky
/app/housekeeper/services/file_report_service/utils.py:111: SyntaxWarning: invalid escape sequence '\d'
  parsed = re.split("(\d+)\.(\w{2,3}$)", filename)
2024-09-24 11:19:07 hasta.scilifelab.se housekeeper.cli.core[168690] INFO Use root path /home/proj/stage/housekeeper-bundles
                                              📦 Bundle table 📦
┏━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓
┃ ID   ┃ Bundle name ┃ Version IDs                                                               ┃ Created    ┃
┡━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
│ 8925 │ justhusky   │ 191243, 178836, 167748, 140963, 136933, 120104, 51171, 42582, 16939, 9523 │ 2019-06-11 │
└──────┴─────────────┴───────────────────────────────────────────────────────────────────────────┴────────────┘
                               📕 Version table 📕
┏━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━┓
┃ ID     ┃ Bundle name ┃ Nr files ┃ Included   ┃ Archived ┃ Created    ┃ Expires ┃
┡━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━┩
│ 191243 │ justhusky   │ 356      │ 2024-06-25 │          │ 2024-06-24 │         │
└────────┴─────────────┴──────────┴────────────┴──────────┴────────────┴─────────┘
                                                                                                 📜 Local files 📜
┏━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ID      ┃ File name                                                                                                                                       ┃ Tags                                                ┃
┡━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ 6273863 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md.cram                                        │ earlycasualcaiman, cram, scout                      │
│ 6273864 │

henrikstranneheim commented 1 month ago

Deployed in prod

Clinical-Genomics / housekeeper

feat(python): Update #208

Description

Added

Changed

Fixed

Testing

How to prepare for test

How to test

Expected test outcome

Review

Quality Gate passed

CLI, 👍