Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / clinical-genomics/chanjo2 issues and pull requests

#100 - Coverage for all samples of a case

Issue - State: closed - Opened by northwestwitch almost 2 years ago

#99 - Coverage and completeness over exons of a sample endpoint

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments

#98 - Transcripts completeness

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments
Labels: Enhancement

#97 - Gene coverage completeness over a list of thresholds alongside coverage stats

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments
Labels: Enhancement, Gain L

#96 - Sample mean transcript coverage over a list of genes

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 5 comments

#95 - Add instructions on how to use a dockerized chanjo2 on the fly to get coverage data from files

Issue - State: closed - Opened by northwestwitch almost 2 years ago - 1 comment
Labels: Documentation, Enhancement

#94 - Sample coverage over a gene list

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments

#92 - Increase size of the HGNC symbol field in genes table

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments

#91 - Infinite loop when loading genes in genome build 38

Issue - State: closed - Opened by northwestwitch almost 2 years ago - 1 comment
Labels: Bug

#90 - Remove transcripts and exons on gene update

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments

#89 - Updating genes can't be done unless transcripts are removed first

Issue - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments

#88 - Add completeness to the coverage metrics returned

Issue - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments

#87 - Endpoints: separate intervals from coverage

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments
Labels: Effort S, Refactor

#86 - Move coverage endpoints to a dedicated file

Issue - State: closed - Opened by northwestwitch almost 2 years ago
Labels: Enhancement

#85 - Filter exons by Ensmbl IDs, Ensembl gene IDs, HGNC IDs, HGNC symbols

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments

#84 - Simplified tests using demo instance of database that already contains data

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments
Labels: Enhancement, Refactor

#83 - Merge 2 Biomart download functions into 1

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments

#82 - Filter transcripts by Ensembl ID, Ensembl gene ID, HGNC gene ID, HGNC gene symbol

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 4 comments

#81 - Add demo intervals (genes, transcripts, exons) when launching the demo instance

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments

#80 - Filter genes by Ensembl ID, HGNC ID or HGNC symbol

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 4 comments

#79 - Fix Dockerfiles to run without problems on ARM arch

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments

#78 - Poor performance of Docker image on ARM architecture

Issue - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments
Labels: Enhancement

#77 - Load env vars from file

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 4 comments

#76 - Direct support for an env file when launching the app

Issue - State: closed - Opened by northwestwitch almost 2 years ago
Labels: Enhancement

#75 - Include in howto that Rust is a requirement for conda installation

Issue - State: closed - Opened by northwestwitch almost 2 years ago
Labels: Documentation

#74 - Fix saved build

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 4 comments

#73 - Wrong build value in genes, transcripts, exons

Issue - State: closed - Opened by northwestwitch almost 2 years ago - 1 comment
Labels: Bug

#72 - Add VARCHAR length to sample.coverage_file_path SQL field

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 5 comments
Labels: Effort S, Gain L

#71 - VARCHAR requires a length on dialect mysql

Issue - State: closed - Opened by northwestwitch almost 2 years ago
Labels: Bug

#69 - Update and fix deprecated GitHub actions

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 3 comments

#68 - Simplify reading of resource files and load intervals in batches

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 4 comments

#67 - Load exons endpoint

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 4 comments

#66 - Load transcripts endpoint

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 5 comments

#65 - Coverage not updated when merging PRs

Issue - State: closed - Opened by northwestwitch almost 2 years ago - 1 comment

#64 - Rename 2 intervals endpoints

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments

#63 - API endpoint to load genes

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 5 comments

#62 - Schug and chanjo2 libs are not compatible

Issue - State: closed - Opened by northwestwitch almost 2 years ago - 1 comment

#61 - Endpoint to load gene intervals

Issue - State: closed - Opened by northwestwitch almost 2 years ago

#60 - Add support for multitrack D4 files

Issue - State: open - Opened by northwestwitch almost 2 years ago

#59 - Multi-interval coverage endpoint

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments

#58 - Run multi-interval queries over .d4 files

Issue - State: closed - Opened by northwestwitch almost 2 years ago
Labels: Enhancement

#57 - Load a demo case when demo app is launched

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 2 comments

#56 - Fix missing dependency in Dockerfile

Pull Request - State: closed - Opened by northwestwitch almost 2 years ago - 1 comment
Labels: Effort S, Gain L

#55 - Some warnings from the docker-image-push GitHub action

Issue - State: closed - Opened by northwestwitch about 2 years ago

#54 - Quick D4 interval coverage endpoint

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 4 comments

#53 - Remote coverage files - once more because of a mistake, sorry!

Pull Request - State: closed - Opened by northwestwitch about 2 years ago

#52 - Provide coverage files hosted on a remote HTTP(s) server

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 3 comments

#50 - Dockerfile should contain Rust and d4tools

Issue - State: closed - Opened by northwestwitch about 2 years ago - 3 comments
Labels: Bug

#49 - Prepare for SQLAlchemy 2.0

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 2 comments
Labels: Effort S, Enhancement, Gain L

#48 - Deprecated code in dbutil.py

Issue - State: closed - Opened by northwestwitch about 2 years ago - 1 comment

#47 - Samples and cases endpoints - move DB connection code to CRUD utils file

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 4 comments

#46 - Use uvicorn's log system and avoid printing double logs

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 1 comment

#45 - Move code running the queries to a separate API

Issue - State: closed - Opened by northwestwitch about 2 years ago - 1 comment
Labels: Enhancement, Refactor

#44 - Adds badges on README page

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 1 comment
Labels: Effort S

#43 - Created docs via mkdocs or some other package

Issue - State: closed - Opened by northwestwitch about 2 years ago

#42 - Logs printed twice

Issue - State: closed - Opened by northwestwitch about 2 years ago - 2 comments
Labels: Bug

#41 - Launch demo via uvicorn command

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 2 comments
Labels: Effort S

#40 - Demo app is launched twice because of gunicorn settings

Issue - State: closed - Opened by northwestwitch about 2 years ago

#39 - Added colored logs

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 2 comments
Labels: Effort S

#38 - Add logging system to the app

Issue - State: closed - Opened by northwestwitch about 2 years ago

#37 - Fixed SQL models and added a test

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 3 comments
Labels: Refactor

#36 - Use a temporary file when running the demo app

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 2 comments

#35 - Removed broken bumpversion action and added vulture

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 3 comments

#33 - SQLite as demo database and simpler docker-compose setup

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 2 comments

#32 - Demo data in docker-compose

Issue - State: closed - Opened by northwestwitch about 2 years ago - 1 comment

#31 - Change this repo from private to public

Issue - State: closed - Opened by northwestwitch about 2 years ago - 4 comments

#30 - Add Codecov steps to Tests GitHub action

Pull Request - State: closed - Opened by northwestwitch about 2 years ago

#29 - Do not crash on SQLAlchemy connection error

Issue - State: open - Opened by northwestwitch about 2 years ago

#28 - Use SQLAlchemy 2.0

Issue - State: closed - Opened by northwestwitch about 2 years ago - 2 comments
Labels: Enhancement, Refactor

#27 - Track code coverage using codecov

Issue - State: closed - Opened by northwestwitch about 2 years ago
Labels: Enhancement

#26 - Test root endpoint with mocked DB and automated tests workflow

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 2 comments

#24 - Docker demo howto

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 1 comment

#23 - Minimize the size of the docker image

Issue - State: closed - Opened by ramprasadn about 2 years ago - 3 comments

#22 - Bumpversion workflow is broken

Issue - State: closed - Opened by northwestwitch about 2 years ago
Labels: Bug

#21 - Fix gunicorn launch and add conda install howto

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 1 comment

#20 - Can't launch the app via docker-compose or direct gunicorn command

Issue - State: closed - Opened by northwestwitch about 2 years ago - 2 comments

#19 - Add option to display only MANE transcripts in coverage module

Issue - State: open - Opened by ehre over 2 years ago - 1 comment

#18 - Add demo

Pull Request - State: closed - Opened by ramprasadn almost 3 years ago

#17 - Add push to PyPI on release

Pull Request - State: closed - Opened by Vince-janv almost 3 years ago - 2 comments

#16 - add bumpversion

Pull Request - State: closed - Opened by ramprasadn almost 3 years ago

#15 - build docker on push

Pull Request - State: closed - Opened by ramprasadn almost 3 years ago

#14 - add docker build on release

Pull Request - State: closed - Opened by ramprasadn almost 3 years ago

#13 - add black

Pull Request - State: closed - Opened by ramprasadn almost 3 years ago

#12 - Feat/add workflows reqs

Pull Request - State: closed - Opened by ramprasadn almost 3 years ago

#11 - add/dockerfile, fixes imports, and endpoint parameter

Pull Request - State: closed - Opened by Vince-janv about 3 years ago - 1 comment

#10 - Restructure endpoints and models

Pull Request - State: closed - Opened by Vince-janv about 3 years ago

#9 - Enable d4 on hasta

Issue - State: open - Opened by Mropat about 3 years ago

#8 - Establish MVP for chanjo-report

Issue - State: closed - Opened by Mropat about 3 years ago - 1 comment

#7 - Create a dockerfile

Issue - State: closed - Opened by Mropat about 3 years ago - 2 comments

#6 - Create endpoint for fetching coverage statistics from a bed file

Issue - State: closed - Opened by Mropat about 3 years ago - 2 comments

#5 - Create endpoint for fetching coverage data from a genomic range

Issue - State: closed - Opened by Mropat about 3 years ago - 2 comments

#4 - Create database models

Issue - State: closed - Opened by Mropat about 3 years ago

#3 - Generate d4 test data

Issue - State: open - Opened by Mropat about 3 years ago

#2 - Create a skeleton

Issue - State: closed - Opened by moonso over 3 years ago

#1 - Validate region files on post

Issue - State: open - Opened by moonso over 3 years ago