VEuPathDB/study-wrangler

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Code to keep study data tidy

Stars: 0
Forks: 0
Open beginner issues: 0
Indexed issues: 25
Avg merge: 2d 1h
Merged PRs (30d): 1

Dominant language: R
License: Apache-2.0
Last GitHub push: Sep 6, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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25 open issues indexed

`entity_from_file` should handle completely empty lines in the input file Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 68/100

VEuPathDB/study-wrangler#88 · Opened Jul 15, 2026
Add EDA validation to forbid integer categorical variables Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/study-wrangler#82 · Opened Jun 17, 2026
Check binWidth calculations on single-value columns and fix if needed Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 52/100

VEuPathDB/study-wrangler#76 · Opened Apr 28, 2026
Possibly add semicolon-delimited support to `entity_from_file`? (already supports CSV and TSV) Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

VEuPathDB/study-wrangler#66 · Opened Mar 9, 2026
`inspect(entity)` is unusably slow with large data, e.g. RNA-Seq assays Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 20/100

VEuPathDB/study-wrangler#41 · Opened Jun 23, 2025
Confirm collections display_range behaviour Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

VEuPathDB/study-wrangler#40 · 1 comment · Opened Jun 4, 2025
Convenience functions maybe needed Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

VEuPathDB/study-wrangler#39 · Opened May 23, 2025
Write documentation for all entity and variable metadata fields Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/study-wrangler#32 · Opened Mar 17, 2025
Have `entity_from_file` work from CSV too Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 25/100

VEuPathDB/study-wrangler#30 · Opened Mar 11, 2025
Data dictionary wrangling Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

VEuPathDB/study-wrangler#29 · Opened Feb 5, 2025
Consider harmonising terminology with ClinEpi documentation Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

VEuPathDB/study-wrangler#28 · Opened Feb 5, 2025
Categories in STF YAML shouldn't require `has_values: no` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

VEuPathDB/study-wrangler#27 · Opened Feb 5, 2025
Figure out (at least a tutorial) how to deal with single merged file (multi-entity) Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

VEuPathDB/study-wrangler#26 · Opened Feb 5, 2025
Don't forget these clinepi-related variable annotations Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

VEuPathDB/study-wrangler#25 · Opened Feb 5, 2025
Warn/flag about PII Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

VEuPathDB/study-wrangler#24 · Opened Feb 5, 2025
STF tsv files contain `NA` and should probably just have empty cells. Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

VEuPathDB/study-wrangler#23 · 1 comment · Opened Feb 5, 2025
`inspect(entity, category_name)` lists many fields that are irrelevant to category 'variables' Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

VEuPathDB/study-wrangler#22 · Opened Feb 5, 2025
Check that `hidden` variable annotation is output to VDI properly Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

VEuPathDB/study-wrangler#20 · Opened Jan 29, 2025
Set `is_temporal` on date variables automatically Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

VEuPathDB/study-wrangler#18 · Opened Jan 28, 2025
Validation should detect problems with very small numbers not working in EDA Number vars Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/study-wrangler#13 · 1 comment · Opened Jan 22, 2025
Take care of entitygraph attributes `has_attribute_collections` and `is_many_to_one_with_parent` Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

VEuPathDB/study-wrangler#11 · 1 comment · Opened Jan 17, 2025
Provide no-ID column guidance in `inspect(entity)` Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

VEuPathDB/study-wrangler#10 · Opened Jan 17, 2025
Perform metadata<->data synchronisation checks in `modify_data(entity)` before returning result Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/study-wrangler#9 · 1 comment · Opened Jan 17, 2025
Add caching to `get_hydrated_variable_metadata()` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

VEuPathDB/study-wrangler#8 · Opened Jan 17, 2025
Capitalise entity display name defaults Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

VEuPathDB/study-wrangler#3 · Opened Jan 4, 2025

VEuPathDB/study-wrangler

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