feat(poetry) Use - Githubissues

henrikstranneheim commented 2 months ago

Description

Added

-

Changed

-

Fixed

-

Testing

How to prepare for test

[ ] ssh to Hasta
[ ] Test your branch with

housekeeper-test-deploy use-poetry
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 2 months 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 2 months ago

Image runs on Hasta, 👍


alias hk='singularity run --bind /home/proj/stage:/home/proj/stage docker://clinicalgenomics/housekeeper:use-poetry --config /home/proj/stage/servers/config/hasta.scilifelab.se/housekeeper-stage.yaml'
    /usr/bin/singularity
[henrik.stranneheim@hasta:~] [base] $ hk --version
housekeeper, version 4.13.2
[henrik.stranneheim@hasta:~] [base] $ hk --help
Usage: python -m 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.

k.stranneheim@hasta:~] [base] $ hk get bundle justhusky
2024-09-11 09:46:47 hasta.scilifelab.se housekeeper.cli.core[127814] 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 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md.cram.crai                                   │ earlycasualcaiman, cram, scout                      │
│ 6273865 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/hugelymodelbat_lanes_1_fastp_sorted_md.cram                                           │ hugelymodelbat, cram, scout                         │
│ 6273866 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/hugelymodelbat_lanes_1_fastp_sorted_md.cram.crai                                      │ hugelymodelbat, cram, scout                         │
│ 6273867 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/slowlycivilbuck_lanes_1_fastp_sorted_md.cram                                          │ slowlycivilbuck, cram, scout                        │
│ 6273868 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/slowlycivilbuck_lanes_1_fastp_sorted_md.cram.crai                                     │ slowlycivilbuck, cram, scout                        │
│ 6273869 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_sex.tsv                                     │ sex-check, earlycasualcaiman, chanjo, scout         │
│ 6273870 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/hugelymodelbat_lanes_1_fastp_sorted_md_sex.tsv                                        │ sex-check, hugelymodelbat, chanjo, scout            │
│ 6273871 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/slowlycivilbuck_lanes_1_fastp_sorted_md_sex.tsv                                       │ sex-check, slowlycivilbuck, chanjo, scout           │
│ 6273872 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_subsample_MT.bam                            │ bam-mt, earlycasualcaiman, scout                    │
│ 6273873 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_subsample_MT.bam.bai                        │ bam-mt, earlycasualcaiman, scout                    │
│ 6273874 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/hugelymodelbat_lanes_1_fastp_sorted_md_subsample_MT.bam                               │ bam-mt, hugelymodelbat, scout                       │
│ 6273875 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/hugelymodelbat_lanes_1_fastp_sorted_md_subsample_MT.bam.bai                           │ bam-mt, hugelymodelbat, scout                       │
│ 6273876 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/slowlycivilbuck_lanes_1_fastp_sorted_md_subsample_MT.bam                              │ bam-mt, slowlycivilbuck, scout                      │
│ 6273877 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/slowlycivilbuck_lanes_1_fastp_sorted_md_subsample_MT.bam.bai                          │ bam-mt, slowlycivilbuck, scout                      │
│ 6273878 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_tcov.bw                                     │ earlycasualcaiman, bigwig, tiddit-coverage, scout   │
│ 6273879 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/hugelymodelbat_lanes_1_fastp_sorted_md_tcov.bw                                        │ hugelymodelbat, bigwig, tiddit-coverage, scout      │
│ 6273880 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/slowlycivilbuck_lanes_1_fastp_sorted_md_tcov.bw                                       │ slowlycivilbuck, bigwig, tiddit-coverage, scout     │
│ 6273881 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_tcov_1.png                                  │ earlycasualcaiman, chromograph, tcov, scout         │
│ 6273882 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_tcov_2.png                                  │ earlycasualcaiman, chromograph, tcov, scout         │
│ 6273883 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_tcov_3.png                                  │ earlycasualcaiman, chromograph, tcov, scout         │
│ 6273884 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_tcov_4.png                                  │ earlycasualcaiman, chromograph, tcov, scout         │
│ 6273885 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_tcov_5.png                                  │ earlycasualcaiman, chromograph, tcov, scout         │
│ 6273886 │ /home/proj/stage/housekeeper-bundles/justhusky/2024-06-24/earlycasualcaiman_lanes_1_fastp_sorted_md_tcov_6.png                                  │ earlycasualcaiman, chromograph, tcov, scout         │

henrikstranneheim commented 2 months ago

Hasta via bashrc, 👍

enrik.stranneheim@hasta:~] [S_base] $ source /home/proj/stage/servers/config/hasta.scilifelab.se/bashrc
[henrik.stranneheim@hasta:~] [base] $ housekeeper-test-deploy use-poetry
Pulling image for feature branch: use-poetry...
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
Skipping fetch of repeat blob sha256:08f50f4aa3e31a96a57373f7ea3ddef9e7ef3a5f5b0a994d1eb79ff9eca9b54e
Skipping fetch of repeat blob sha256:002765cbf0130f5bdfda89ed8eac8db091f835d90e8510920556efd8ff6f97e1
Skipping fetch of repeat blob sha256:1b88a5c811e52abd109fb8e2f2a4ae8f7ecd300aabe760ba63b1c1cbf6b8a296
Skipping fetch of repeat blob sha256:456f848e2c2877ed34dbab37fd4a5381632f6d6ecbd517a355874e2f220ac181
Skipping fetch of repeat blob sha256:b96b6c0e36897de16a321301cf1e3cec823ac7e26ba2b9c138349652ee55ee18
Skipping fetch of repeat blob sha256:d5905a977cbc5deb8e63cd67d1344da50aa6b9f5efd327859655f2e35e4d7b46
Skipping fetch of repeat blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
Skipping fetch of repeat blob sha256:b7b091d8dcacc7ba29227ddeebf0f71ecef0b0d69f12d68e2a0eab3deb5787f8
Copying config sha256:25eda4fc4c4c0190a752e8753316e0726d3306b2435eb1592ae129a9b8bd390f
 8.09 KiB / 8.09 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/proj/stage/singularity_containers/housekeeper_use-poetry.sif
You can now run 'housekeeper-test --help' to test the feature branch: use-poetry.
[henrik.stranneheim@hasta:~] [base] $ housekeeper-test --help
Usage: python -m 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.

henrikstranneheim commented 2 months ago

Together with https://github.com/Clinical-Genomics/servers/pull/1451

henrikstranneheim commented 2 months ago

Deployed to prod, but the bump-version action needs a fix.

Clinical-Genomics / housekeeper

feat(poetry) Use #203

Description

Added

Changed

Fixed

Testing

How to prepare for test

How to test

Expected test outcome

Review

Quality Gate passed

Image runs on Hasta, 👍

Hasta via bashrc, 👍