monarch-initiative koza issues

monarch-initiative / koza

Data transformation framework for LinkML data models

https://koza.monarchinitiative.org/

BSD 3-Clause "New" or "Revised" License

48 stars 4 forks source link

issues

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Handling of archives (tar, zip) not well defined

#160 ptgolden opened 2 weeks ago
1
Lint/Format fixes

#159 amc-corey-cox closed 2 weeks ago
0
If skip_blank_lines is False in CSVReader, garbage data is read out in all cases

#158 ptgolden opened 3 weeks ago
2
What is the purpose of "is not None" in the the transform.py idiom?

#157 ptgolden opened 3 weeks ago
0
`split_file` references output format that doesn't exist

#156 ptgolden opened 3 weeks ago
2
KozaApp.schema is never initialized

#155 ptgolden opened 4 weeks ago
0
Throw an error in writer if property isn't defined

#154 amc-corey-cox opened 4 weeks ago
6
Move to development on 3.9, 3.10, and 3.11

#153 amc-corey-cox opened 4 weeks ago
1
Add some sort of progress bar to Koza.

#152 amc-corey-cox opened 1 month ago
1
Add in_exact to filtercode enum

#151 kevinschaper closed 1 month ago
0
Remove filer values print statement

#150 kevinschaper closed 1 month ago
0
Make koza able to handle yamls with multiple Source configurations

#149 DnlRKorn opened 1 month ago
0
Add LinkML based writer support, with explicit definitions of multiple writers

#148 kevinschaper opened 1 month ago
0
Fix bug in row filter parser causing GOA parsing error

#147 DnlRKorn opened 3 months ago
0
Added changes to make row_filter 'inlist' function give better results on common use cases.

#146 DnlRKorn closed 3 months ago
0
Potentially undesired behavior with "in" filter in row_filter.py

#145 DnlRKorn closed 3 months ago
2
Koza doesn't play nicely with generators

#144 DnlRKorn opened 3 months ago
2
First row drops when ingesting with Koza (at least in some cases)

#143 DnlRKorn closed 3 months ago
1
Update source.py _get_row to help with readability.

#142 DnlRKorn closed 3 months ago
0
Fixed truthiness error that made the tsv writer ignore zero values

#141 kevinschaper closed 3 months ago
0
Add support for multiple writers

#140 kevinschaper opened 4 months ago
10
Add koza split cli command to split up a kgx file based on field values

#139 kevinschaper closed 1 month ago
3
Add in flags which enable creation of nodes grouped by source

#138 DnlRKorn opened 4 months ago
3
Allow external setter alternatives to `transform.yaml`

#137 hrshdhgd opened 4 months ago
2
Update docs to reflect name change for import

#136 caufieldjh opened 6 months ago
0
Consider adding ability to generate node/edge count reports

#135 glass-ships opened 6 months ago
0
Add dynamic versioning via releases

#134 glass-ships closed 6 months ago
0
Update docs, other changes for cookiecutter usage

#133 glass-ships closed 6 months ago
0
Make necessary changes for modular ingests

#132 glass-ships closed 6 months ago
0
Source Config: Metadata - Revisit `DatasetDescription` fields

#131 glass-ships opened 7 months ago
1
Source: log filtered rows during _get_row()

#130 glass-ships opened 7 months ago
0
Curie Cleaner: Mappings should be in a yaml somewhere?

#129 glass-ships opened 7 months ago
2
New command: Create a koza project?

#128 glass-ships opened 7 months ago
2
Source Config: Better exception message during field map creation

#127 glass-ships opened 7 months ago
0
Source Config: Try type-coercing if filter code

#126 glass-ships opened 7 months ago
0
Source Config: Exception check when attempting to load metadata file

#125 glass-ships opened 7 months ago
0
Source Config: Concatenate files and file_archive?

#124 glass-ships opened 7 months ago
0
Source Config: Constrain id to be a curie?

#123 glass-ships opened 7 months ago
0
CSV Reader: Handle varying line lengths

#122 glass-ships opened 7 months ago
2
CSV Reader: Handle delimiter being more than 1 character

#121 glass-ships opened 7 months ago
0
Implement XML Reader

#120 glass-ships opened 7 months ago
0
Update deprecated import for pydantic.Validation

#119 glass-ships closed 7 months ago
0
Current `sssom` pin does not install versions compatible with recent oaklib

#118 caufieldjh closed 11 months ago
3
add header prefix config field

#117 glass-ships closed 12 months ago
0
Implement Zip decompression

#116 glass-ships closed 1 year ago
0
Update validation

#115 glass-ships closed 1 year ago
0
Expand SSSOM Config to include narrow and broad matches

#114 glass-ships opened 1 year ago
0
Clarify examples

#113 glass-ships opened 1 year ago
0
Update to Pydantic v2

#112 glass-ships closed 1 year ago
1
Update to Pydantic v2

#111 glass-ships closed 1 year ago
1