Code

Early wrangling#1

Code

Draft

bobular wants to merge 70 commits intomainVEuPathDB/study-wrangler:mainfrom first-draftVEuPathDB/study-wrangler:first-draftCopy head branch name to clipboard

+2,769-22

Commits

Commits on Nov 27, 2024

• changes to improve dev workflow

  bobular

  committed
  71a078d

Commits on Dec 2, 2024

• first class, function and tests

  bobular

  committed
  89874e5

• Initial implementation of entity_from_file

  Show description for 72c3afd
  bobular

  committed
  72c3afd

• Implement data_type and data_shape detection in entity_from_file

  Show description for e0d8b6f
  bobular

  committed
  e0d8b6f

• oopsie with expected test outputs

  bobular

  committed
  c1c852f

• Add preprocess_fn to entity_from_file with warning embellishment and tests

  Show description for 70de463
  bobular

  committed
  70de463

• removed test.R boilerplate

  bobular

  committed
  bb951bb

Commits on Dec 3, 2024

• added roxygen2 docs for entity_from_file; updated README and dependencies

  bobular

  committed
  75762c1

• add skimr dependency

  bobular

  committed
  05fe81d

• Implement inspect() method for Entity objects

  Show description for c09dc99
  bobular

  committed
  c09dc99

• Add inspect_variable() method for Entity objects

  Show description for ff2c6a1
  bobular

  committed
  ff2c6a1

• treat categoricals as factors, fix skim behaviour with factors

  bobular

  committed
  f65a09d

Commits on Dec 5, 2024

• add test for inspect(entity) and long categorical values

  bobular

  committed
  7bb6dc8

• improve docs on inspect

  bobular

  committed
  b35cb4a

• add basic test for inspect_variable()

  bobular

  committed
  a05cb27

• made a start on validate(entity) - WIP

  bobular

  committed
  419b196

• added quiet option to validate()

  bobular

  committed
  0f430df

• added basic tests for validate()

  bobular

  committed
  24c519f

Commits on Dec 6, 2024

• tiny tweak to port number in examples

  bobular

  committed
  1c06e0a

• add setwd() advice in README

  bobular

  committed
  6f53f3c

• improve preprocess_fn documentation

  bobular

  committed
  cbedf09

• major refactor to separate concerns and add all metadata columns

  bobular

  committed
  e5b7f5a

• more of the refactor

  bobular

  committed
  ded4179

• tidied up handling of factors and vocabularies

  bobular

  committed
  382c52a

Commits on Dec 7, 2024

• improve inspect() output

  bobular

  committed
  a683b70

• tidy up entity metadata slots

  bobular

  committed
  8922aa9

• big rename of Entity metadata slot to 'variables'

  bobular

  committed
  730edc2

• document Entity class; add entity metadata handling in constructor

  bobular

  committed
  6c4fceb

• added set_entity_metadata and tests and fallbacks for display_name and display_name_plural

  bobular

  committed
  2a7955b

• refined set_entity_metadata and tests

  bobular

  committed
  a0424c1

• more tidying of inspect*() reports

  bobular

  committed
  0167192

Commits on Dec 8, 2024

• object arg renamed to entity

  bobular

  committed
  2d650db

• improve data-metadata validation messaging

  bobular

  committed
  27c9505

• added sync_variable_metadata and tests

  bobular

  committed
  d2c8593

• add set_entity_name and set_variable_metadata and tests for multiple ID columns

  bobular

  committed
  4cc3f59

• improve validation feedback

  bobular

  committed
  12ff5b4

• better entity_name validation and testing

  bobular

  committed
  ba11c3d

• use provider_label as default variable display_name

  bobular

  committed
  6b9cc96

• variable display_name stats, tests and convenience function with very long name

  bobular

  committed
  35bca81

Commits on Dec 9, 2024

• added missing tests for ID column checks

  bobular

  committed
  068429d

• tidy some base R

  bobular

  committed
  3fb6939

• categorical factor column validation and make data-variables mismatch errors fatal

  bobular

  committed
  19b3627

• remove as a variables metadata column

  bobular

  committed
  e9d0d54

• improve factor validation and testing

  bobular

  committed
  f9993ef

• add support for large vocabs/factors

  bobular

  committed
  17b9984

• added extensive variable metadata validation

  bobular

  committed
  f245db7

• added more fixtures - not checked yet

  bobular

  committed
  ad7ce09

Commits on Dec 10, 2024

• added convenience redirect from inspect() to inspect_variable()

  bobular

  committed
  bc56ef5

• add basic participants test

  bobular

  committed
  e3aa05a

• change guidance for inspecting variables

  bobular

  committed
  8b2e71d

• add set_parents() and tests and fct_mutate()

  bobular

  committed
  5b016ea

• started tests for fct_mutate()

  bobular

  committed
  3cc88cb

• added essential fct_mutate tests

  bobular

  committed
  78a2cdf

• fixed buggy fixture data and provided parsing error reporting

  bobular

  committed
  91499d8

Commits on Dec 11, 2024

• allow mutation to NA for factors

  bobular

  committed
  e8b4ceb

• big changes but mostly redo_type_detection_as_variables_only()

  bobular

  committed
  9b14e32

• tidy inspect() guidance

  bobular

  committed
  0845232

• better naming/tagging of built docker image

  bobular

  committed
  d5e31ec

• avoid error when there are no variables

  bobular

  committed
  b396239

• complete move of fixture data

  bobular

  committed
  086925f

• add basic vignette and figure out most of skim/kable issues

  bobular

  committed
  f6e51bc

• vignette/build-related tweaks

  bobular

  committed
  d6fd203

• improve comments

  bobular

  committed
  4dad26e

Commits on Dec 12, 2024

• inspect(entity) now produces consistent all-text report in console and notebook

  bobular

  committed
  1bdc73b

• inspect_variable() now console/notebook friendly, continue with vignette

  bobular

  committed
  98ca02a

• add get_variable_metadata and get_id_column_metadata helpers and use them in a few places - fix tests that were broken with using kable simple format

  bobular

  committed
  9c452c2

• added validation and test for no ID column

  bobular

  committed
  54cf647

• cleanup and vignette work

  bobular

  committed
  ac9a1e7

• add set_data() convenience and adapt tests and vignette, make vignette wider

  bobular

  committed
  39d79ec

• add tests for participants and observations loading

  bobular

  committed
  8768a3a