monarch-initiative/koza issues and pull requests

#162 - (By May 2024) Preliminary work for KozaGX R03 - Build KG under various configurations with timing documented

Issue - State: open - Opened by DnlRKorn about 1 month ago
Labels: enhancement, good first issue

#161 - Filters (may) only work with CSV sources that have defined columns

Issue - State: open - Opened by ptgolden about 2 months ago - 1 comment

#160 - Handling of archives (tar, zip) not well defined

Issue - State: open - Opened by ptgolden 2 months ago - 2 comments

#159 - Lint/Format fixes

Pull Request - State: closed - Opened by amc-corey-cox 2 months ago

#158 - If skip_blank_lines is False in CSVReader, garbage data is read out in all cases

Issue - State: open - Opened by ptgolden 3 months ago - 3 comments

#157 - What is the purpose of "is not None" in the the transform.py idiom?

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

#156 - `split_file` references output format that doesn't exist

Issue - State: open - Opened by ptgolden 3 months ago - 2 comments

#155 - KozaApp.schema is never initialized

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

#154 - Throw an error in writer if property isn't defined

Pull Request - State: open - Opened by amc-corey-cox 3 months ago - 6 comments

#153 - Move to development on 3.9, 3.10, and 3.11

Issue - State: open - Opened by amc-corey-cox 3 months ago - 2 comments

#152 - Add some sort of progress bar to Koza.

Issue - State: open - Opened by amc-corey-cox 3 months ago - 1 comment

#151 - Add in_exact to filtercode enum

Pull Request - State: closed - Opened by kevinschaper 4 months ago

#150 - Remove filer values print statement

Pull Request - State: closed - Opened by kevinschaper 4 months ago

#149 - Make koza able to handle yamls with multiple Source configurations

Issue - State: open - Opened by DnlRKorn 4 months ago
Labels: enhancement

#148 - Add LinkML based writer support, with explicit definitions of multiple writers

Pull Request - State: open - Opened by kevinschaper 4 months ago

#147 - Fix bug in row filter parser causing GOA parsing error

Issue - State: open - Opened by DnlRKorn 5 months ago

#146 - Added changes to make row_filter 'inlist' function give better results on common use cases.

Pull Request - State: closed - Opened by DnlRKorn 5 months ago

#145 - Potentially undesired behavior with "in" filter in row_filter.py

Issue - State: closed - Opened by DnlRKorn 5 months ago - 2 comments

#144 - Koza doesn't play nicely with generators

Issue - State: open - Opened by DnlRKorn 5 months ago - 2 comments

#143 - First row drops when ingesting with Koza (at least in some cases)

Issue - State: closed - Opened by DnlRKorn 5 months ago - 1 comment
Labels: bug

#142 - Update source.py _get_row to help with readability.

Pull Request - State: closed - Opened by DnlRKorn 5 months ago

#141 - Fixed truthiness error that made the tsv writer ignore zero values

Pull Request - State: closed - Opened by kevinschaper 6 months ago

#140 - Add support for multiple writers

Pull Request - State: open - Opened by kevinschaper 6 months ago - 10 comments

#139 - Add koza split cli command to split up a kgx file based on field values

Pull Request - State: closed - Opened by kevinschaper 6 months ago - 3 comments

#138 - Add in flags which enable creation of nodes grouped by source

Issue - State: open - Opened by DnlRKorn 7 months ago - 3 comments

#137 - Allow external setter alternatives to `transform.yaml`

Issue - State: open - Opened by hrshdhgd 7 months ago - 2 comments

#136 - Update docs to reflect name change for import

Issue - State: open - Opened by caufieldjh 8 months ago

#135 - Consider adding ability to generate node/edge count reports

Issue - State: open - Opened by glass-ships 9 months ago

#134 - Add dynamic versioning via releases

Issue - State: closed - Opened by glass-ships 9 months ago

#133 - Update docs, other changes for cookiecutter usage

Pull Request - State: closed - Opened by glass-ships 9 months ago

#132 - Make necessary changes for modular ingests

Issue - State: closed - Opened by glass-ships 9 months ago

#131 - Source Config: Metadata - Revisit `DatasetDescription` fields

Issue - State: open - Opened by glass-ships 10 months ago - 1 comment
Labels: documentation, help wanted, question

#130 - Source: log filtered rows during _get_row()

Issue - State: open - Opened by glass-ships 10 months ago
Labels: enhancement, good first issue

#129 - Curie Cleaner: Mappings should be in a yaml somewhere?

Issue - State: open - Opened by glass-ships 10 months ago - 2 comments
Labels: question

#128 - New command: Create a koza project?

Issue - State: open - Opened by glass-ships 10 months ago - 2 comments

#127 - Source Config: Better exception message during field map creation

Issue - State: open - Opened by glass-ships 10 months ago
Labels: enhancement

#126 - Source Config: Try type-coercing if filter code

Issue - State: open - Opened by glass-ships 10 months ago
Labels: enhancement, good first issue

#125 - Source Config: Exception check when attempting to load metadata file

Issue - State: open - Opened by glass-ships 10 months ago
Labels: enhancement, good first issue

#124 - Source Config: Concatenate files and file_archive?

Issue - State: open - Opened by glass-ships 10 months ago - 1 comment
Labels: enhancement

#123 - Source Config: Constrain id to be a curie?

Issue - State: open - Opened by glass-ships 10 months ago
Labels: enhancement

#122 - CSV Reader: Handle varying line lengths

Issue - State: open - Opened by glass-ships 10 months ago - 2 comments
Labels: enhancement

#121 - CSV Reader: Handle delimiter being more than 1 character

Issue - State: open - Opened by glass-ships 10 months ago - 1 comment
Labels: enhancement

#120 - Implement XML Reader

Issue - State: open - Opened by glass-ships 10 months ago
Labels: enhancement

#119 - Update deprecated import for pydantic.Validation

Pull Request - State: closed - Opened by glass-ships 10 months ago

#118 - Current `sssom` pin does not install versions compatible with recent oaklib

Issue - State: closed - Opened by caufieldjh about 1 year ago - 3 comments

#117 - add header prefix config field

Pull Request - State: closed - Opened by glass-ships about 1 year ago

#116 - Implement Zip decompression

Pull Request - State: closed - Opened by glass-ships about 1 year ago

#115 - Update validation

Pull Request - State: closed - Opened by glass-ships about 1 year ago

#114 - Expand SSSOM Config to include narrow and broad matches

Issue - State: open - Opened by glass-ships about 1 year ago

#113 - Clarify examples

Issue - State: open - Opened by glass-ships about 1 year ago

#112 - Update to Pydantic v2

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

#111 - Update to Pydantic v2

Pull Request - State: closed - Opened by glass-ships over 1 year ago - 1 comment
Labels: blocked

#110 - Produce friendlier error from csv_reader on missing column

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

#109 - adding sssom support

Pull Request - State: closed - Opened by glass-ships over 1 year ago - 6 comments

#108 - Add SSSOM sssupport

Issue - State: closed - Opened by kevinschaper over 1 year ago - 7 comments

#107 - Relax dependencies to get along with the latest kgx release

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

#106 - Logging

Pull Request - State: closed - Opened by glass-ships almost 2 years ago - 1 comment

#105 - QoL updates

Pull Request - State: closed - Opened by glass-ships almost 2 years ago

#104 - Metadata.yaml opened as TextIOWrapper rather than a str

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

#103 - `**yaml.safe_load(`string-path`)` will not load the YAML file.

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

#102 - Generate new ingests from templates

Issue - State: open - Opened by kevinschaper about 2 years ago - 1 comment

#101 - Add cli & docstrings documentation

Issue - State: closed - Opened by kevinschaper about 2 years ago - 2 comments
Labels: documentation

#100 - Upgrade typer to 0.7, no longer needs to be locked lower

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

#99 - update linkml-validator, bug has been fixed

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

#98 - Further QoL updates to io modules

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

#97 - General QoL updates (WIP)

Pull Request - State: closed - Opened by glass-ships about 2 years ago - 1 comment
Labels: enhancement

#96 - Bump pyyaml to 6.0

Pull Request - State: closed - Opened by caufieldjh over 2 years ago - 1 comment

#95 - Remove beta disclaimer

Pull Request - State: closed - Opened by kevinschaper over 2 years ago

#94 - Add license to repo

Issue - State: closed - Opened by matentzn over 2 years ago - 1 comment

#93 - Add support for BaseModel entities

Pull Request - State: closed - Opened by kevinschaper over 2 years ago

#92 - Create CITATION.cff

Pull Request - State: closed - Opened by nlharris over 2 years ago - 2 comments

#91 - Refactoring Koza / KozaApp

Pull Request - State: closed - Opened by glass-ships over 2 years ago

#90 - Nested props

Pull Request - State: closed - Opened by glass-ships over 2 years ago

#89 - Logfile requires path structure

Pull Request - State: closed - Opened by sierra-moxon over 2 years ago

#88 - Update build.yml to test against Py 3.10

Pull Request - State: closed - Opened by glass-ships over 2 years ago

#87 - Raise an error if an entity property isn't defined in node/edge properties

Issue - State: open - Opened by kevinschaper over 2 years ago - 3 comments

#86 - Add support for nested classes to KGXConverter

Issue - State: closed - Opened by kevinschaper over 2 years ago - 1 comment

#85 - List only the columns that are needed for ingest in yaml config

Issue - State: closed - Opened by putmantime almost 3 years ago - 1 comment
Labels: enhancement

#84 - Koza --log flag (WIP)

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

#83 - Add support in the Koza singleton for multiple ingests running at once

Issue - State: closed - Opened by kevinschaper almost 3 years ago - 1 comment

#82 - Logging updates: quiet mode and option to write log files

Issue - State: closed - Opened by kevinschaper almost 3 years ago - 3 comments

#81 - Add "file_archive" attribute for SourceConfig

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

#80 - required_properties for nested JSON files tags

Issue - State: closed - Opened by RichardBruskiewich almost 3 years ago - 3 comments