Issues

• Various issues identified during tabular-to-stf skill writing in dataset-curator

  bug
  VEuPathDB/study-wrangler#94 · Filter by author bobular opened on Oct 24, 2026
  5

• entity_from_file should handle completely empty lines in the input file

  bug
  VEuPathDB/study-wrangler#88 · Filter by author bobular opened on Jul 15, 2026

• Add EDA validation to forbid integer categorical variables

  VEuPathDB/study-wrangler#82 · Filter by author bobular opened on Jun 17, 2026

• Check binWidth calculations on single-value columns and fix if needed

  bug
  VEuPathDB/study-wrangler#76 · Filter by author bobular opened on Apr 28, 2026

• Possibly add semicolon-delimited support to entity_from_file? (already supports CSV and TSV)

  VEuPathDB/study-wrangler#66 · Filter by author bobular opened on Mar 9, 2026

• inspect(entity) is unusably slow with large data, e.g. RNA-Seq assays

  bug
  VEuPathDB/study-wrangler#41 · Filter by author bobular opened on Jun 23, 2025

• Confirm collections display_range behaviour

  VEuPathDB/study-wrangler#40 · Filter by author bobular opened on Jun 4, 2025
  1

• Convenience functions maybe needed

  enhancement
  VEuPathDB/study-wrangler#39 · Filter by author bobular opened on May 23, 2025

• Write documentation for all entity and variable metadata fields

  documentation
  VEuPathDB/study-wrangler#32 · Filter by author bobular opened on Mar 17, 2025

• Have entity_from_file work from CSV too

  enhancement
  VEuPathDB/study-wrangler#30 · Filter by author bobular opened on Mar 11, 2025

• Data dictionary wrangling

  enhancement
  VEuPathDB/study-wrangler#29 · Filter by author bobular opened on Feb 5, 2025

• Consider harmonising terminology with ClinEpi documentation

  enhancement
  VEuPathDB/study-wrangler#28 · Filter by author bobular opened on Feb 5, 2025

• Categories in STF YAML shouldn't require has_values: no

  enhancement
  VEuPathDB/study-wrangler#27 · Filter by author bobular opened on Feb 5, 2025

• Figure out (at least a tutorial) how to deal with single merged file (multi-entity)

  enhancement
  VEuPathDB/study-wrangler#26 · Filter by author bobular opened on Feb 5, 2025

• Don't forget these clinepi-related variable annotations

  enhancement
  VEuPathDB/study-wrangler#25 · Filter by author bobular opened on Feb 5, 2025

• Warn/flag about PII

  enhancement
  VEuPathDB/study-wrangler#24 · Filter by author bobular opened on Feb 5, 2025

• STF tsv files contain NA and should probably just have empty cells.

  bug
  VEuPathDB/study-wrangler#23 · Filter by author bobular opened on Feb 5, 2025
  1

• inspect(entity, category_name) lists many fields that are irrelevant to category 'variables'

  bug
  VEuPathDB/study-wrangler#22 · Filter by author bobular opened on Feb 5, 2025

• Check that hidden variable annotation is output to VDI properly

  VEuPathDB/study-wrangler#20 · Filter by author bobular opened on Jan 29, 2025

• Set is_temporal on date variables automatically

  Feature

  VEuPathDB/study-wrangler#18 · Filter by author bobular opened on Jan 28, 2025

• Validation should detect problems with very small numbers not working in EDA Number vars

  enhancement
  VEuPathDB/study-wrangler#13 · Filter by author bobular opened on Jan 22, 2025
  1

• Take care of entitygraph attributes has_attribute_collections and is_many_to_one_with_parent

  VEuPathDB/study-wrangler#11 · Filter by author bobular opened on Jan 17, 2025
  1

• Provide no-ID column guidance in inspect(entity)

  enhancement
  VEuPathDB/study-wrangler#10 · Filter by author bobular opened on Jan 17, 2025

• Perform metadata<->data synchronisation checks in modify_data(entity) before returning result

  enhancement
  VEuPathDB/study-wrangler#9 · Filter by author bobular opened on Jan 17, 2025
  1

• Add caching to get_hydrated_variable_metadata()

  enhancement
  VEuPathDB/study-wrangler#8 · Filter by author bobular opened on Jan 17, 2025