clinical-genomics/schug issues and pull requests

#91 - Swagger docs presents many endpoints that don't work

Issue - State: open - Opened by northwestwitch 15 days ago

#90 - Added retry logic to stream_resource to handle failed chunk downloads

Pull Request - State: open - Opened by northwestwitch 15 days ago - 1 comment

#89 - Error while downloading exons in build 37

Issue - State: open - Opened by northwestwitch 15 days ago - 2 comments
Labels: Bug

#88 - Minor release 1.8

Pull Request - State: closed - Opened by northwestwitch 22 days ago - 2 comments

#87 - Remove old code and apply fix also to transcripts and exons downloads

Pull Request - State: closed - Opened by northwestwitch 22 days ago - 1 comment

#86 - Add custom issue and PR templates

Pull Request - State: closed - Opened by northwestwitch 22 days ago - 1 comment

#85 - Remove old code initially used for downloading data from Ensembl

Issue - State: closed - Opened by northwestwitch 22 days ago - 1 comment

#84 - Do not include [success] lines in the streamed outfiles

Pull Request - State: closed - Opened by northwestwitch 22 days ago - 2 comments

#83 - Modify issue template

Issue - State: open - Opened by northwestwitch 22 days ago
Labels: Enhancement

#82 - Error parsing build 37 transcripts

Issue - State: closed - Opened by northwestwitch 23 days ago - 2 comments

#81 - Minor release 1.7

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

#80 - Deprecate Python 3.8 in Dockerfile and toml

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

#79 - Workaround to download all exons from the latest Ensembl BioMart

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 8 comments

#78 - Deprecate Python 3.8 all over the repo

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

#77 - Ensembl BioMart errors downloading genes and transcripts (Ensembl v.112)

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

#77 - Ensembl BioMart errors downloading genes and transcripts (Ensembl v.112)

Issue - State: open - Opened by northwestwitch about 2 months ago - 3 comments
Labels: Bug

#77 - Ensembl BioMart errors downloading genes and transcripts (Ensembl v.112)

Issue - State: open - Opened by northwestwitch about 2 months ago - 3 comments
Labels: Bug

#76 - Patch release 1.6.2

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

#76 - Patch release 1.6.2

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

#76 - Patch release 1.6.2

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

#75 - Use Ensembl v112 to temporarily address the missing exons issue

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

#75 - Use Ensembl v112 to temporarily address the missing exons issue

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

#74 - Exons not showing on gene report

Issue - State: closed - Opened by Jakob37 2 months ago - 23 comments
Labels: Bug

#73 - New minor release 1.6.1

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 1 comment

#72 - Address 3 security issues

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

#72 - Address 3 security issues

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

#72 - Address 3 security issues

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

#71 - Update starlette to address security issue

Issue - State: closed - Opened by northwestwitch 4 months ago

#71 - Update starlette to address security issue

Issue - State: closed - Opened by northwestwitch 4 months ago

#71 - Update starlette to address security issue

Issue - State: closed - Opened by northwestwitch 4 months ago

#70 - Minor release 1.6

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 1 comment

#70 - Minor release 1.6

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 1 comment

#70 - Minor release 1.6

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 1 comment

#69 - Update libraries

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 2 comments

#69 - Update libraries

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 2 comments

#68 - Fix URL to GRCh37 Biomart

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 5 comments

#68 - Fix URL to GRCh37 Biomart

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 5 comments

#67 - GRCh37 Resources are not downloaded from Ensembl

Issue - State: closed - Opened by northwestwitch 11 months ago - 6 comments
Labels: Bug

#66 - Patch release 1.5.1

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 2 comments

#65 - Revert to python 3.8 in Dockerfile

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 2 comments
Labels: Effort S, Gain L, Urgency L

#65 - Revert to python 3.8 in Dockerfile

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 2 comments
Labels: Effort S, Gain L, Urgency L

#64 - RuntimeError: can't start new thread

Issue - State: closed - Opened by northwestwitch about 1 year ago - 1 comment
Labels: Bug

#63 - Remove database-related functions from schug

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

#62 - Release version 1.5

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

#62 - Release version 1.5

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

#61 - Convert validators and Config to Pydantic 2

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 2 comments

#61 - Convert validators and Config to Pydantic 2

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 2 comments

#60 - Pydantic validators warnings

Issue - State: closed - Opened by northwestwitch about 1 year ago

#60 - Pydantic validators warnings

Issue - State: closed - Opened by northwestwitch about 1 year ago

#59 - Upgrade python version in tests action and remove pytest dependency

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

#59 - Upgrade python version in tests action and remove pytest dependency

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

#58 - Error using python=3.11 in tests GitHub action

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

#58 - Error using python=3.11 in tests GitHub action

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

#57 - Fix security issue in tj-actions/branch-names action and update version of other external images used in GitHub actions

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

#57 - Fix security issue in tj-actions/branch-names action and update version of other external images used in GitHub actions

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

#56 - Pydantic 2, Python>=3.8 & other updates

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

#56 - Pydantic 2, Python>=3.8 & other updates

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

#55 - Refactor to PEP 0585

Issue - State: open - Opened by henrikstranneheim over 1 year ago

#55 - Refactor to PEP 0585

Issue - State: open - Opened by henrikstranneheim over 1 year ago

#54 - Upgrade pydantic to v2

Issue - State: closed - Opened by northwestwitch over 1 year ago
Labels: Enhancement