Lund merge - Githubissues

Clinical-Genomics / gens

Mozilla Public License 2.0

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Lund merge #42

Closed raysloks closed 1 year ago

raysloks commented 1 year ago

This PR adds a functionality or fixes a bug. OR This PR marks a new Gens release. We apply semantic versioning. This is a major/minor/patch release for reasons.

How to test:

how to test it, possibly with real cases/data

Expected outcome: The functionality should be working Take a screenshot and attach or copy/paste the output.

Review:

[ ] code approved by

coveralls commented 1 year ago

Pull Request Test Coverage Report for Build 6893146065

2 of 7 (28.57%) changed or added relevant lines in 3 files are covered.
2 unchanged lines in 2 files lost coverage.
Overall coverage decreased (-0.08%) to 18.895%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
gens/app.py	1	2	50.0%
gens/api.py	0	4	0.0%
<!--	Total:	2	7	28.57%	-->

Files with Coverage Reduction	New Missed Lines	%
gens/api.py	1	0.0%
gens/app.py	1	45.83%
<!--	Total:	2		-->

Totals
Change from base Build 6889604914:	-0.08%
Covered Lines:	195
Relevant Lines:	1032

💛 - Coveralls

dnil commented 1 year ago

Ahem, woopsie! The npm 17 tests fail; some frozen package versions that need thawing perhaps?

dnil commented 11 months ago

Obtaining file:///home/daniel.nilsson/sandbox/gens
  Preparing metadata (setup.py) ... done
Requirement already satisfied: Click in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (8.1.3)
Requirement already satisfied: Flask in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (2.2.3)
Requirement already satisfied: flask-caching in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (2.0.2)
Requirement already satisfied: pymongo>=3.9.0 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (4.3.3)
Requirement already satisfied: gtfparse>=1.2.0 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (2.0.1)
Requirement already satisfied: pysam>=0.15.4 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (0.20.0)
Requirement already satisfied: pyyaml in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (6.0)
Requirement already satisfied: attrs in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (22.2.0)
Requirement already satisfied: cattrs in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (22.2.0)
Requirement already satisfied: connexion==2.14.2 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (2.14.2)
Requirement already satisfied: flask-compress in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (1.13)
Requirement already satisfied: tabulate in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gens==2.1.1) (0.9.0)
Requirement already satisfied: jsonschema<5,>=2.5.1 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from connexion==2.14.2->gens==2.1.1) (4.17.3)
Requirement already satisfied: inflection<0.6,>=0.3.1 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from connexion==2.14.2->gens==2.1.1) (0.5.1)
Requirement already satisfied: packaging>=20 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from connexion==2.14.2->gens==2.1.1) (23.0)
Requirement already satisfied: itsdangerous>=0.24 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from connexion==2.14.2->gens==2.1.1) (2.1.2)
Requirement already satisfied: werkzeug<2.3,>=1.0 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from connexion==2.14.2->gens==2.1.1) (2.2.3)
Requirement already satisfied: requests<3,>=2.9.1 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from connexion==2.14.2->gens==2.1.1) (2.28.2)
Requirement already satisfied: clickclick<21,>=1.2 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from connexion==2.14.2->gens==2.1.1) (20.10.2)
Requirement already satisfied: Jinja2>=3.0 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from Flask->gens==2.1.1) (3.1.2)
Requirement already satisfied: polars in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from gtfparse>=1.2.0->gens==2.1.1) (0.16.8)
Requirement already satisfied: dnspython<3.0.0,>=1.16.0 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from pymongo>=3.9.0->gens==2.1.1) (2.3.0)
Requirement already satisfied: exceptiongroup in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from cattrs->gens==2.1.1) (1.1.0)
Requirement already satisfied: cachelib<0.10.0,>=0.9.0 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from flask-caching->gens==2.1.1) (0.9.0)
Requirement already satisfied: brotli in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from flask-compress->gens==2.1.1) (1.0.9)
Requirement already satisfied: MarkupSafe>=2.0 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from Jinja2>=3.0->Flask->gens==2.1.1) (2.1.2)
Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from jsonschema<5,>=2.5.1->connexion==2.14.2->gens==2.1.1) (0.19.3)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from requests<3,>=2.9.1->connexion==2.14.2->gens==2.1.1) (3.0.1)
Requirement already satisfied: idna<4,>=2.5 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from requests<3,>=2.9.1->connexion==2.14.2->gens==2.1.1) (3.4)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from requests<3,>=2.9.1->connexion==2.14.2->gens==2.1.1) (1.26.14)
Requirement already satisfied: certifi>=2017.4.17 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from requests<3,>=2.9.1->connexion==2.14.2->gens==2.1.1) (2022.12.7)
Requirement already satisfied: typing_extensions>=4.0.1 in /home/proj/stage/bin/miniconda3/envs/S_gens/lib/python3.10/site-packages (from polars->gtfparse>=1.2.0->gens==2.1.1) (4.5.0)
Installing collected packages: gens
  Attempting uninstall: gens
    Found existing installation: gens 2.0.0
    Uninstalling gens-2.0.0:
      Successfully uninstalled gens-2.0.0
  Running setup.py develop for gens
Successfully installed gens-2.1.1

dnil commented 11 months ago

 [daniel.nilsson@hasta:~/sandbox/gens]└2 [P_gens] master 13s ± pip install .
Processing /home/daniel.nilsson/sandbox/gens
  Preparing metadata (setup.py) ... done
Requirement already satisfied: Click in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (8.1.3)
Requirement already satisfied: Flask in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (2.2.3)
Requirement already satisfied: flask-caching in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (2.0.2)
Requirement already satisfied: pymongo>=3.9.0 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (4.3.3)
Requirement already satisfied: gtfparse>=1.2.0 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (2.0.1)
Requirement already satisfied: pysam>=0.15.4 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (0.20.0)
Requirement already satisfied: pyyaml in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (6.0)
Requirement already satisfied: attrs in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (22.2.0)
Requirement already satisfied: cattrs in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (22.2.0)
Requirement already satisfied: connexion==2.14.2 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (2.14.2)
Requirement already satisfied: flask-compress in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (1.13)
Requirement already satisfied: tabulate in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gens==2.1.1) (0.9.0)
Requirement already satisfied: clickclick<21,>=1.2 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from connexion==2.14.2->gens==2.1.1) (20.10.2)
Requirement already satisfied: jsonschema<5,>=2.5.1 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from connexion==2.14.2->gens==2.1.1) (4.17.3)
Requirement already satisfied: requests<3,>=2.9.1 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from connexion==2.14.2->gens==2.1.1) (2.28.2)
Requirement already satisfied: inflection<0.6,>=0.3.1 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from connexion==2.14.2->gens==2.1.1) (0.5.1)
Requirement already satisfied: werkzeug<2.3,>=1.0 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from connexion==2.14.2->gens==2.1.1) (2.2.3)
Requirement already satisfied: packaging>=20 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from connexion==2.14.2->gens==2.1.1) (23.0)
Requirement already satisfied: itsdangerous>=0.24 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from connexion==2.14.2->gens==2.1.1) (2.1.2)
Requirement already satisfied: Jinja2>=3.0 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from Flask->gens==2.1.1) (3.1.2)
Requirement already satisfied: polars in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from gtfparse>=1.2.0->gens==2.1.1) (0.16.8)
Requirement already satisfied: dnspython<3.0.0,>=1.16.0 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from pymongo>=3.9.0->gens==2.1.1) (2.3.0)
Requirement already satisfied: cachelib<0.10.0,>=0.9.0 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from flask-caching->gens==2.1.1) (0.9.0)
Requirement already satisfied: brotli in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from flask-compress->gens==2.1.1) (1.0.9)
Requirement already satisfied: MarkupSafe>=2.0 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from Jinja2>=3.0->Flask->gens==2.1.1) (2.1.2)
Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from jsonschema<5,>=2.5.1->connexion==2.14.2->gens==2.1.1) (0.19.3)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from requests<3,>=2.9.1->connexion==2.14.2->gens==2.1.1) (3.0.1)
Requirement already satisfied: idna<4,>=2.5 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from requests<3,>=2.9.1->connexion==2.14.2->gens==2.1.1) (3.4)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from requests<3,>=2.9.1->connexion==2.14.2->gens==2.1.1) (1.26.14)
Requirement already satisfied: certifi>=2017.4.17 in /home/proj/production/bin/miniconda3/envs/P_gens/lib/python3.11/site-packages (from requests<3,>=2.9.1->connexion==2.14.2->gens==2.1.1) (2022.12.7)
Building wheels for collected packages: gens
  Building wheel for gens (setup.py) ... done
  Created wheel for gens: filename=gens-2.1.1-py3-none-any.whl size=67473 sha256=a839d90a18ef8d9b5a8359344bca77a0c68214127aa68d60766e4ce15cf66f5d
  Stored in directory: /home/daniel.nilsson/tmp/pip-ephem-wheel-cache-5blqgest/wheels/8d/0a/48/34a7045811ab0aacda8906950b96c9dc2edd14ba85d46c8a08
Successfully built gens
Installing collected packages: gens
  Attempting uninstall: gens
    Found existing installation: gens 2.0.0
    Uninstalling gens-2.0.0:
      Successfully uninstalled gens-2.0.0
Successfully installed gens-2.1.1

dnil commented 11 months ago

Deployed to cg-prod-services: Screenshot 2023-12-20 at 16 03 18

dnil commented 11 months ago

And annotations are loading:

θ65° [daniel.nilsson@hasta:~/sandbox/gens]└2 [P_gens] master 31s ± gens load annotations -b 37 -f /home/proj/production/rare-disease/gens-tracks
[2023-12-20 16:03:00,471] INFO in app: Using default Gens configuration
[2023-12-20 16:03:00,472] INFO in db: Initialize db connection
[2023-12-20 16:03:00,630] INFO in load: Processing files
[2023-12-20 16:03:00,631] INFO in load: Processing /home/proj/production/rare-disease/gens-tracks/Final_common_CNV_clusters_0.bed
[2023-12-20 16:03:00,659] INFO in load: Remove old entry in the database
[2023-12-20 16:03:00,777] INFO in load: Load annoatations in the database
[2023-12-20 16:03:00,860] INFO in load: Update height order
[2023-12-20 16:03:04,297] INFO in load: Processing /home/proj/production/rare-disease/gens-tracks/DGV_UCSC_2023-03-09.bed
[2023-12-20 16:03:08,621] INFO in load: Remove old entry in the database
[2023-12-20 16:03:39,035] INFO in load: Load annoatations in the database
[2023-12-20 16:04:05,417] INFO in load: Update height order

dnil commented 11 months ago

And done! ![Uploading Screenshot 2023-12-20 at 16.32.02.png…]()