Clinical-Genomics/housekeeper issues and pull requests

#203 - feat(poetry) Use

Pull Request - State: open - Opened by henrikstranneheim 25 days ago - 1 comment

#202 - feat(update): Linters

Pull Request - State: closed - Opened by henrikstranneheim about 2 months ago - 2 comments
Labels: Enhancement

#201 - Use poetry

Issue - State: open - Opened by seallard 3 months ago

#200 - Add cryptography to dependencies

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

#199 - feat(CLI get) Improve get bundle command

Pull Request - State: closed - Opened by Vince-janv 5 months ago - 3 comments

#198 - Update QA test deployment instructions

Pull Request - State: closed - Opened by seallard 5 months ago - 2 comments

#197 - Improve housekeeper CLI visualisation

Issue - State: closed - Opened by Vince-janv 5 months ago - 1 comment

#196 - Separate remote and local files

Pull Request - State: closed - Opened by seallard 5 months ago - 2 comments

#195 - Visualise archived files in get bundle command

Issue - State: closed - Opened by Vince-janv 5 months ago - 1 comment

#193 - feat(sql): Rename filter attributes

Pull Request - State: closed - Opened by henrikstranneheim 7 months ago - 3 comments
Labels: Enhancement

#192 - Housekeeper bundle version naming

Issue - State: open - Opened by seallard 8 months ago - 4 comments
Labels: Bug, Needs Refinement

#191 - Refactor sql handlers

Pull Request - State: closed - Opened by henrikstranneheim 8 months ago - 3 comments
Labels: Enhancement

#190 - feat(update): Black

Pull Request - State: closed - Opened by henrikstranneheim 8 months ago - 2 comments
Labels: Enhancement

#189 - (Archiving) Filter on tags in get_retrieved_files

Pull Request - State: closed - Opened by islean 9 months ago - 3 comments

#188 - (Archiving) Add retrieved_at filter

Pull Request - State: closed - Opened by islean 9 months ago - 3 comments

#187 - (Archiving) Find retrieved files

Pull Request - State: closed - Opened by islean 10 months ago - 2 comments

#186 - (Archiving) Abort delete file command when file is archived

Pull Request - State: closed - Opened by islean 10 months ago - 3 comments

#185 - Raise error when deleting archived file

Issue - State: closed - Opened by islean 10 months ago - 1 comment

#184 - (Archiving) Add cascade property to Archive

Pull Request - State: closed - Opened by islean 10 months ago - 4 comments

#183 - feat(update): Ruff and Black

Pull Request - State: closed - Opened by henrikstranneheim 10 months ago - 2 comments

#182 - feat(refactor): List

Pull Request - State: closed - Opened by henrikstranneheim 10 months ago - 3 comments

#181 - (Archiving) Add support for limited fetching

Pull Request - State: closed - Opened by islean 10 months ago - 3 comments

#180 - Fetch non-archived files with limit

Pull Request - State: closed - Opened by islean 10 months ago - 2 comments

#179 - Refactor to pep 0604

Pull Request - State: closed - Opened by henrikstranneheim 10 months ago - 2 comments
Labels: Enhancement

#178 - Some fastq files have the wrong flow cell as tag or in their file path

Issue - State: closed - Opened by diitaz93 11 months ago - 9 comments

#177 - Add missing dependency

Pull Request - State: closed - Opened by seallard 11 months ago - 1 comment

#176 - Update templates

Pull Request - State: closed - Opened by seallard 11 months ago - 1 comment

#175 - Fix deprecation warnings in actions

Pull Request - State: closed - Opened by seallard 11 months ago - 1 comment

#174 - Fix docker credentials in workflow

Pull Request - State: closed - Opened by seallard 11 months ago - 1 comment

#173 - Add missing latest tag

Pull Request - State: closed - Opened by seallard 11 months ago - 1 comment

#172 - Fix action workflows

Pull Request - State: closed - Opened by seallard 11 months ago - 1 comment

#171 - Add poetry

Pull Request - State: closed - Opened by seallard 11 months ago - 3 comments

#170 - Containerize housekeeper CLI

Pull Request - State: closed - Opened by seallard 11 months ago - 1 comment

#169 - feat(sample sheet) Add delete sample sheet command

Pull Request - State: closed - Opened by Vince-janv 12 months ago - 2 comments

#168 - Upgrade SQLAlchemy to 2.0

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#167 - Set future flag on session

Pull Request - State: closed - Opened by seallard 12 months ago - 2 comments

#166 - Use future flag on engine

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#165 - Return full archive model

Pull Request - State: closed - Opened by islean 12 months ago - 3 comments

#164 - (Archive) Get archive entries by archival/retrieval id

Pull Request - State: closed - Opened by islean 12 months ago - 3 comments

#163 - feat(CLI command for delete tag)

Pull Request - State: closed - Opened by diitaz93 12 months ago - 4 comments

#162 - Update PULL_REQUEST_TEMPLATE

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 1 comment

#161 - Fix session merge warnings

Pull Request - State: open - Opened by seallard 12 months ago - 6 comments

#160 - Refactor to pep 0585

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 5 comments
Labels: Enhancement

#159 - Add Ruff to pyproject.toml

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 2 comments

#158 - feat(black): Action

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 2 comments

#157 - feat(black): Update

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 1 comment
Labels: Enhancement

#156 - Refactor to PEP 0585

Issue - State: closed - Opened by henrikstranneheim 12 months ago
Labels: Enhancement

#155 - Fix version file warnings

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#154 - Fix deprecated joins

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#153 - Do not add directories to housekeeper

Issue - State: open - Opened by ChrOertlin 12 months ago

#152 - Remove models as properties

Pull Request - State: closed - Opened by seallard 12 months ago - 2 comments

#151 - Extract database initialisation

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#150 - Replace deprecated import

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#149 - feat(ruff): Add

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 1 comment
Labels: Enhancement

#148 - Upgrade Python 3.11

Pull Request - State: closed - Opened by seallard 12 months ago - 2 comments

#147 - Upgrade to Python 3.10

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#146 - Upgrade to Python 3.9

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#145 - Update instructions

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#144 - Upgrade to Python 3.8

Pull Request - State: closed - Opened by seallard 12 months ago - 3 comments

#143 - Upgrade to click 8

Pull Request - State: closed - Opened by seallard 12 months ago - 4 comments

#142 - Allow for latest 1.4 version

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

#141 - refactor(moving log info to debug)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 3 comments

#140 - Upgrade sqlalchemy to 1.4

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

#139 - feat(isort): Add

Pull Request - State: closed - Opened by henrikstranneheim about 1 year ago - 2 comments
Labels: Enhancement

#138 - Include bundle by default

Pull Request - State: closed - Opened by islean about 1 year ago - 5 comments

#137 - Remove pytest fixture prefix snd name arg in decorator

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

#136 - Include bundle by default

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

#135 - Deprecate tag `archived_sample_sheet` and replace by `samplesheet`

Issue - State: closed - Opened by diitaz93 about 1 year ago - 16 comments

#134 - Update CODEOWNERS

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

#133 - Error when adding samples to bundle

Issue - State: closed - Opened by seallard about 1 year ago - 7 comments
Labels: Bug, Needs Refinement

#132 - Functionality for updating archiving/retrieval task ids

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

#131 - removing wrongly assigned fastq files to sample bundle

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

#130 - feat(archiving) Add function to fetch all unarchived files

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

#129 - Adding files to an included bundle that are already in the target.

Issue - State: open - Opened by karlnyr over 1 year ago - 6 comments
Labels: Enhancement, Effort S, Gain M, Urgency S, Needs Refinement, Good first issue

#128 - housekeeper does not list file present in bundle

Issue - State: closed - Opened by seallard over 1 year ago - 2 comments
Labels: Bug, Effort M, Gain S, Urgency S

#127 - Fix forgotten code smells from issue 115

Pull Request - State: closed - Opened by islean over 1 year ago - 2 comments

#126 - Fix forgotten code smells from issue 115

Issue - State: closed - Opened by islean over 1 year ago - 1 comment

#125 - 115 - include file in housekeeper-bundles by default

Pull Request - State: closed - Opened by islean over 1 year ago - 8 comments

#124 - feat(archiving) Adds functions for task interactions

Pull Request - State: closed - Opened by Vince-janv over 1 year ago - 2 comments

#123 - Remove log with database connection string

Pull Request - State: closed - Opened by seallard over 1 year ago - 2 comments

#122 - feat(Archiving) Adds functions interacting with the new Archive table

Pull Request - State: closed - Opened by Vince-janv over 1 year ago - 3 comments

#121 - Add missing module

Pull Request - State: closed - Opened by seallard over 1 year ago - 1 comment

#120 - feat(Archiving) Add new database table

Pull Request - State: closed - Opened by Vince-janv over 1 year ago - 2 comments

#119 - Fix(Tests) Restructured test folders

Pull Request - State: closed - Opened by Vince-janv over 1 year ago - 1 comment

#118 - Review how sessions are managed

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

#117 - Move and rename handler files

Pull Request - State: closed - Opened by seallard over 1 year ago - 1 comment

#116 - Add(Archive) Creates and archive table linked to files

Pull Request - State: closed - Opened by Vince-janv over 1 year ago - 2 comments

#115 - add CLI command to include file in bundle

Issue - State: closed - Opened by Vince-janv over 1 year ago
Labels: Good first issue

#114 - Remove models from base handler

Pull Request - State: closed - Opened by seallard over 1 year ago - 1 comment

#113 - Cleaner way of accessing methods from other handlers

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

#112 - Remove alchy

Pull Request - State: closed - Opened by seallard over 1 year ago - 2 comments

#111 - implement crud

Pull Request - State: closed - Opened by ChrOertlin over 1 year ago - 2 comments
Labels: Project Task

#110 - Avoid returning queries in the API-layer

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

#109 - Move get_query into base handler

Pull Request - State: closed - Opened by seallard over 1 year ago - 1 comment
Labels: Project Task

#108 - Refer to database id:s in a consistent manner throughout the codebase

Issue - State: open - Opened by seallard over 1 year ago
Labels: Refactoring

#107 - Split get_files_before into smaller functions

Issue - State: closed - Opened by seallard over 1 year ago

#106 - Split get_files into smaller functions

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

#105 - Refactor long methods and parameters

Issue - State: open - Opened by seallard over 1 year ago
Labels: Refactoring

#104 - (fix) Publish to pypi on release action

Pull Request - State: closed - Opened by diitaz93 over 1 year ago - 1 comment

#103 - Broken link in README.md

Issue - State: closed - Opened by diitaz93 over 1 year ago - 1 comment
Labels: Bug, Effort S, Gain S, Urgency S

GitHub / Clinical-Genomics/housekeeper issues and pull requests