Code

Diff: dev vs main#140

Code

Draft

jthompson-arcus wants to merge 228 commits intomainopenpharma/clinsight:mainfrom devopenpharma/clinsight:devCopy head branch name to clipboard

+10,611-536

Commits

Commits on Sep 30, 2024

• Increment version number to 0.1.0.9000

  LDSamson

  committed
  92d4659

Commits on Oct 1, 2024

• Add pkgdown gha workflow

  aclark02-arcus

  committed
  d62de80

• don't rely on renv.lock

  aclark02-arcus

  committed
  3381f26

• update certain functions with '@Keywords internal' for pkddown

  aclark02-arcus

  committed
  78e9927

• Increment version number to 0.1.0.9000

  aclark02-arcus

  committed
  19b8f83

• update news

  aclark02-arcus

  committed
  279bc5c

• Merge branch 'dev' into ac-95

  aclark02-arcus

  authored
  9c03622

• Update golem config with new app version

  aclark02-arcus

  committed
  0aff3a9

• Merge branch 'ac-95' of https://github.com/openpharma/clinsight into ac-95

  aclark02-arcus

  committed
  0f08edf

Commits on Oct 8, 2024

• Add callback to "go to form" on double click event

  jthompson-arcus

  committed
  f927749

Commits on Oct 9, 2024

• Pass additional modifying functions in arguments of merge_meta_with_data()

  jthompson-arcus

  committed
  a7b8eaa

• Recode to use base R and character values

  jthompson-arcus

  committed
  f091000

• Move additional merging functions to metadata

  jthompson-arcus

  committed
  1ff5c2d

Commits on Oct 10, 2024

• Adjust %||% to check for empty values, not just NULL

  jthompson-arcus

  committed
  5d4a444

• Specify add_fns as post_merge_fns

  jthompson-arcus

  committed
  6451405

• Add pre_merge_fns setting

  jthompson-arcus

  committed
  2270fdc

• Add inline function to check existence of an object for dplyr mutations

  jthompson-arcus

  committed
  7cf9ee4

• Impute event_name from event instead of event_name

  jthompson-arcus

  committed
  ba6c086

• Fix broken tests

  jthompson-arcus

  committed
  8dc00e0

• Further generalize add_timevars_to_data()

  jthompson-arcus

  committed
  8154349

• Initialize region field

  jthompson-arcus

  committed
  325c27d

Commits on Oct 11, 2024

• Add mid-merging functions

  jthompson-arcus

  committed
  2506500

• Update version and NEWS

  jthompson-arcus

  committed
  c9755b7

• Move logic to dblclick_to_form() function

  jthompson-arcus

  committed
  ed64d65

Commits on Oct 14, 2024

• Remove duplicate type conversion

  jthompson-arcus

  committed
  f48ebac

• Create apply_custom_functions() to handle

  jthompson-arcus

  committed
  6087b0e

• Clean up metadata settings element generation

  jthompson-arcus

  committed
  a980920

• Remove extraneous pipe

  jthompson-arcus

  committed
  c90e778

• Reset %||% to standard evaluation

  jthompson-arcus

  committed
  4d7fd45

• Display message if using user supplied data.

  jthompson-arcus

  committed
  6adecea

• Remove event_name from required columns

  jthompson-arcus

  committed
  b001c9b

• Resolve test errors

  jthompson-arcus

  committed
  568a05f

Commits on Oct 15, 2024

• Specify the parent.frame() as the environment to check existence within

  jthompson-arcus

  committed
  12b28f1

• Add tests for %|_|%

  jthompson-arcus

  committed
  ea4714a

• Change warning() to cat()

  jthompson-arcus

  committed
  3e9dc7b

• Merge pull request #104 from openpharma/jt-generalize_meta_merging

  Show description for a4d88ba
  LDSamson

  authored
  a4d88ba

Commits on Oct 16, 2024

• Add primary key field to tables

  jthompson-arcus

  committed
  e5e4da4

• Temporary fix to preserve current functionality

  jthompson-arcus

  committed
  1cffcdf

• Re-create review_testdb.sqlite

  jthompson-arcus

  committed
  ec0c753

• Repair mod_review_form tests

  jthompson-arcus

  committed
  193f05d

• Repair fct_SQLite tests

  jthompson-arcus

  committed
  58435dc

• Rebuild testdb.sqlite

  jthompson-arcus

  committed
  8f59b04

• Temporary fix for adding queries to work as expected

  jthompson-arcus

  committed
  ec868d8

• Add preliminary logging table

  jthompson-arcus

  committed
  804f7de

• Add "all_review_data_log" to list of expected tables

  jthompson-arcus

  committed
  48314ae

Commits on Oct 17, 2024

• Merge branch 'dev' into jt-dblclick_overview_tbl

  jthompson-arcus

  committed
  53bb43b

• Add dblclick callback to other appropriate tables

  jthompson-arcus

  committed
  4201ebe

• Remove unnecessary session$

  jthompson-arcus

  committed
  14a96fa

• Repair mod_navigate_review tests

  jthompson-arcus

  committed
  4f78d7b

• Repair app feature 3 tests

  jthompson-arcus

  committed
  0c5cbe0

• Repair app feature 2 tests

  jthompson-arcus

  committed
  d4d041d

• Repair app feature 1 tests

  jthompson-arcus

  committed
  85b492e

• Add help files

  jthompson-arcus

  committed
  9ce1c9b

• Make sure expression is appropriately defined for %|_|% in add_timevars_to_data()

  jthompson-arcus

  committed
  60b748a

• Update version

  jthompson-arcus

  committed
  f35e21d

Commits on Oct 18, 2024

• Further generalization

  jthompson-arcus

  committed
  5b4faed

• Repair fct_appdata tests

  jthompson-arcus

  committed
  d5d1d52

• Repair custom metadata test

  jthompson-arcus

  committed
  6aa89a3

• Update documentation

  jthompson-arcus

  committed
  abdcde2

• Update global variables

  jthompson-arcus

  committed
  9eb651a

Commits on Oct 22, 2024

• Resolve issue with unit derivation

  jthompson-arcus

  committed
  2cc5bcf

Commits on Oct 23, 2024

• Add form_type class to app data

  jthompson-arcus

  committed
  6461997

• Minimal solution

  jthompson-arcus

  committed
  05b869c

Commits on Oct 24, 2024

• Revert to old code for units

  jthompson-arcus

  committed
  33742e1

• Merge pull request #116 from openpharma/jt-gmm_follow_up

  Show description for 46b0489
  LDSamson

  authored
  46b0489

• Merge branch 'dev' into jt-107-extend_create_table

  jthompson-arcus

  committed
  655662b

• Merge branch 'dev' into jt-dblclick_overview_tbl

  jthompson-arcus

  committed
  9a616fb

• Incorporate "dblclick" to app feature 1 test

  jthompson-arcus

  committed
  a84a230

• Update version and NEWS

  jthompson-arcus

  committed
  b30627c

Commits on Oct 25, 2024

• Update feature 01 test description, add back test of navigating by clicking on the header widget.

  LDSamson

  committed
  1d5bdd5

Commits on Oct 28, 2024

• Improve news description

  LDSamson

  committed
  278b99c

• Merge pull request #103 from openpharma/jt-dblclick_overview_tbl

  Show description for 24d8ea9
  LDSamson

  authored
  24d8ea9

• Fix warnings in apply_edc_specific_changes

  LDSamson

  committed
  492945b

• Update news and version

  LDSamson

  committed
  cafe81d

• Merge pull request #120 from openpharma/ls_119_fix_warnings

  Show description for 37d46c1
  jthompson-arcus

  authored
  37d46c1

• Update db_save_review to update instead of append

  jthompson-arcus

  committed
  0b2eb31

• Repair tests from db_save_review() changes

  jthompson-arcus

  committed
  37a7c11

• Merge branch 'dev' into ac-95

  aclark02-arcus

  authored
  07e67c3

• Merge branch 'dev' into jt-107-extend_create_table

  jthompson-arcus

  committed
  6a06ffc

• Simplify form_types creation

  jthompson-arcus

  committed
  3f38993

• Update version and NEWS

  jthompson-arcus

  committed
  802bc29

• Resolve merge conflicts with dev

  Show description for d220c70
  jthompson-arcus

  committed
  d220c70

Commits on Oct 29, 2024

• update news and golem-config veresion

  aclark02-arcus

  committed
  f3a5562

• merge conflic on golem_version (again)

  aclark02-arcus

  committed
  10f1c5f

• update a few functions with '@Keywords internal' for pkgdown build

  aclark02-arcus

  committed
  08a9aad

• Merge pull request #102 from openpharma/ac-95

  Show description for 151e465
  LDSamson

  authored
  151e465

• Merge branch 'dev' into jt-107-extend_create_table

  jthompson-arcus

  committed
  4f9ba5e

• Update version number

  jthompson-arcus

  committed
  f884d68

• Merge branch 'dev' into jt-113-logging_tables

  jthompson-arcus

  committed
  91a8c49

• Only store old records in logging table

  jthompson-arcus

  committed
  f98f0d2

• Add S3 generic to _pkgdown.yml

  jthompson-arcus

  committed
  056b99e

• Modify update process to only updated/append appropriate records

  jthompson-arcus

  committed
  9e55193

• Actually pull the newer record when updated

  jthompson-arcus

  committed
  f66f758

Commits on Oct 30, 2024

• Add db_version table to DB

  jthompson-arcus

  committed
  2ad8cc7

• Add edit_date_time to logging table

  jthompson-arcus

  committed
  75ad1d1

• Update all columns not considered in common

  jthompson-arcus

  committed
  4c8e2e5

• Correct error in creating primary key tables

  jthompson-arcus

  committed
  3f32584

• Update fct_SQLite.R tests to reflect changes

  jthompson-arcus

  committed
  b81500d

• Update test DB

  jthompson-arcus

  committed
  d268d14

• Incorporate review logging tests into test-fct_SQLite.R

  jthompson-arcus

  committed
  1cb9afa

• Add logging tests to test-mod_review_forms.R

  jthompson-arcus

  committed
  c6dace0

• Add index to all_review_data table

  jthompson-arcus

  committed
  7effc4c

Commits on Oct 31, 2024

• Utilize UPSERT for DB append/update procedure

  jthompson-arcus

  committed
  cd5d630

• Make UPSERT process more robust

  jthompson-arcus

  committed
  564d0f9

• Add function update_db_version() to migrate old DBs

  jthompson-arcus

  committed
  af8f76c

• Update version and NEWS

  jthompson-arcus

  committed
  f2ef3a6

• Fix warning message popping up in tests

  jthompson-arcus

  committed
  2c633d2

Commits on Nov 1, 2024

• Change create_table.common_events to create_table.common_forms

  jthompson-arcus

  committed
  746033a

• Add form_type to metadata$item_expanded

  jthompson-arcus

  committed
  5121075

• Repair fct_appdata.R tests

  jthompson-arcus

  committed
  cf53ca7

• Add create_table.common_forms() tests

  jthompson-arcus

  committed
  f159dd3

Commits on Nov 4, 2024

• Increment version number to 0.1.0.9005

  aclark02-arcus

  committed
  6779999

• Decode shinyproxy user name with base64 encoding, and return a warning if the result is not UTF8 (i.e. if the string was initially not encoded)

  LDSamson

  committed
  a22a5b5

• Update news and version

  LDSamson

  committed
  1e72f44

• Update workflows

  jthompson-arcus

  committed
  80534e1

• Only update website on pushes to main

  jthompson-arcus

  committed
  3970db9

• Add workflow_dispatch to R CMD check

  jthompson-arcus

  committed
  a76fb98

• Merge pull request #127 from openpharma/jt-update_devex_workflows

  Show description for af8da6a
  LDSamson

  authored
  af8da6a

• update 'default_opts' instead and update function documentation

  aclark02-arcus

  committed
  3b46c22

• Add a check if the package base64enc is installed within the decode_base64 function

  LDSamson

  committed
  3f377a9

• Merge pull request #123 from openpharma/ls_use_base64_encoded_usernames

  Show description for 3290897
  jthompson-arcus

  authored
  3290897

• Simplify form string

  jthompson-arcus

  committed
  147c521

• Update version

  jthompson-arcus

  committed
  d3cf1b0

• Resolve merge conflicts with dev

  Show description for 3315a24
  jthompson-arcus

  committed
  3315a24

• Resolve merge conflicts with dev

  Show description for f299d4a
  jthompson-arcus

  committed
  f299d4a

• Merge branch 'dev' into ac-colorder

  aclark02-arcus

  authored
  35f49e7

Commits on Nov 5, 2024

• update test snapshots with colReorder extension

  aclark02-arcus

  committed
  0f03ad3

• Merge branch 'ac-colorder' of https://github.com/openpharma/clinsight into ac-colorder

  aclark02-arcus

  committed
  2c53b86

• add snap from feature 02

  aclark02-arcus

  committed
  a6b7659

• update snaps for feature 03

  aclark02-arcus

  committed
  4ff0813

• update the rest of the snaps

  aclark02-arcus

  committed
  6ce0001

• Merge pull request #124 from openpharma/ac-colorder

  Show description for 858bc30
  aclark02-arcus

  authored
  858bc30

• Resolve merge conflicts with dev

  Show description for 4b73522
  jthompson-arcus

  committed
  4b73522

• Update version number

  jthompson-arcus

  committed
  ce8bb74

• Resolve merge conflicts with dev

  Show description for 63dc37d
  jthompson-arcus

  committed
  63dc37d

• Update version number

  jthompson-arcus

  committed
  0e6b4af

• Merge pull request #118 from openpharma/jt-107-extend_create_table

  Show description for 02359d4
  LDSamson

  authored
  02359d4

• Resolve merge conflicts with dev

  Show description for c9b8cf8
  jthompson-arcus

  committed
  c9b8cf8

Commits on Nov 7, 2024

• Revert changes to mod_review_data_fct_helpers.R

  jthompson-arcus

  committed
  abe5703

• Update internal documentation

  jthompson-arcus

  committed
  9c4dc72

• Add index columns and db version to internal data

  jthompson-arcus

  committed
  62aa39d

• Create helper function to add new tables

  jthompson-arcus

  committed
  8e7f752

• Oopsies

  jthompson-arcus

  committed
  7b7114d

• Update UPSERT documentation

  jthompson-arcus

  committed
  6e65f04

Commits on Nov 8, 2024

• Ignore .Renviron on git

  jthompson-arcus

  committed
  4af9905

• Initialize db_get_table()

  jthompson-arcus

  committed
  7af507c

• Use db_get_table() instead of db_slice_rows() to retrieve review rows

  jthompson-arcus

  committed
  2191a04

• Use db_get_table() instead of db_slice_rows() in tests

  jthompson-arcus

  committed
  0582b3b

• Remove unneeded slicing and filtering

  jthompson-arcus

  committed
  b370ff5

• Capture second snapshot

  jthompson-arcus

  committed
  f0837f2

Commits on Nov 11, 2024

• Add comment for idx_cols

  jthompson-arcus

  committed
  27c9220

• Use unique names in function arguments from internal package objects

  jthompson-arcus

  committed
  d1c81ea

• Merge pull request #115 from openpharma/jt-113-logging_tables

  Show description for f271502
  LDSamson

  authored
  f271502

• Merge branch 'dev' into jt-113-simplify_review_process

  jthompson-arcus

  committed
  cea4d43

• Add trigger for update on id

  jthompson-arcus

  committed
  3e1a650

• Check DB version at run time

  jthompson-arcus

  committed
  851a5ba

• Update NEWS and version

  jthompson-arcus

  committed
  485f464

Commits on Nov 13, 2024

• Migrate to review_records from review_row

  jthompson-arcus

  committed
  7c58504

• Update test-fct_SQLite.R

  jthompson-arcus

  committed
  b271add

• Update test-mod_review_forms.R

  jthompson-arcus

  committed
  39d8da1

• Update test-mod_main_sidebar.R

  jthompson-arcus

  committed
  43931ed

• Fix R CMD checks

  jthompson-arcus

  committed
  d311ab1

• Fix db_get_review() example

  jthompson-arcus

  committed
  ccd9bb1

• Helps if you update documentation

  jthompson-arcus

  committed
  0743880

Commits on Nov 14, 2024

• Only UPDATE reviews when review status is changed

  jthompson-arcus

  committed
  e5e8acb

Commits on Nov 18, 2024

• Use DBI directly instead of tbl() and collect()

  jthompson-arcus

  committed
  0e266d7

• Fix typo in user_db version check

  jthompson-arcus

  committed
  1405702

• Only update records with new status.

  jthompson-arcus

  committed
  240c4e8

• Remove argument no longer used

  jthompson-arcus

  committed
  8085287

• Remove common_vars from tests

  jthompson-arcus

  committed
  a797883

• Repair tests with db_get_table() returning data.frame not tibble

  jthompson-arcus

  committed
  20f9528

• Update review_testdb.sqlite

  jthompson-arcus

  committed
  6fb21a6

• Update mod_review_forms test with new testing DB

  jthompson-arcus

  committed
  2a7b9e9

• Update all_review_data_id_update_trigger to include idx_cols

  jthompson-arcus

  committed
  c6ef19c

• Add keys argument to db_add_log()

  jthompson-arcus

  committed
  1a85f40

• Resolve some R CMD check issues

  jthompson-arcus

  committed
  c427f2d

Commits on Nov 19, 2024

• Resolve merge conflicts with jt-113-simplify_review_process

  Show description for 2551970
  jthompson-arcus

  committed
  2551970

• Keep current structure for enabling reviews

  jthompson-arcus

  committed
  d863300

• Resolve merge conflicts with main

  Show description for 0e8b655
  jthompson-arcus

  committed
  0e8b655

Commits on Nov 20, 2024

• small alignment fix

  LDSamson

  committed
  a9488cc

• Merge pull request #142 from openpharma/jt-resolve_merge_conflicts_main

  Show description for 906daf8
  LDSamson

  authored
  906daf8

• Merge branch 'dev' into jt-113-simplify_review_process

  LDSamson

  committed
  b8e598e

• Improve alignment according to https://style.tidyverse.org/syntax.html#long-function-calls, improve db_add_log docs, add function argument check to db_add_log

  LDSamson

  committed
  f57b549

• Merge pull request #135 from openpharma/jt-113-simplify_review_process

  Show description for 740a10a
  LDSamson

  authored
  740a10a

• Resolve merge conflict with dev

  Show description for 6ad27a6
  jthompson-arcus

  committed
  6ad27a6

• Generalize db_get_review()

  jthompson-arcus

  committed
  a23b462

• Update version and NEWS

  jthompson-arcus

  committed
  6990cf1

Commits on Nov 21, 2024

• Update scenario description for two rows

  jthompson-arcus

  committed
  3db4274

• Update language from row to records

  jthompson-arcus

  committed
  1c675a9

• Grab un-duplicated rv_records

  jthompson-arcus

  committed
  c177a30

• Remove unnecessary dplyr::select()

  jthompson-arcus

  committed
  d2fa0d6

• Remove unneeded dplyr::distinct()

  jthompson-arcus

  committed
  de24777

• Return db_get_review() when ... is empty

  jthompson-arcus

  committed
  d372afa

• Update to latest test-coverage. Remove package installation since it is redundant

  LDSamson

  committed
  8261441

• Fix codecov arguments for codecov-actvion V5 https://github.com/marketplace/actions/codecov#v5-release

  LDSamson

  committed
  0f4a693

• Print codecov results again

  LDSamson

  committed
  c547862

• Update test-mod_review_forms.R

  jthompson-arcus

  committed
  f28f174

• Update version and news

  LDSamson

  committed
  047b459

• Update only one table in db_save_review()

  jthompson-arcus

  committed
  7e26f83

• Fix oopsies

  jthompson-arcus

  committed
  ad3f05e

• Merge pull request #139 from openpharma/ls_update_codecov

  Show description for b2bd9bb
  jthompson-arcus

  authored
  b2bd9bb

• Fix merge conflict with dev

  Show description for 939566f
  jthompson-arcus

  committed
  939566f

• Actually use renv for GHA

  jthompson-arcus

  committed
  0880603

• Quote profile name

  jthompson-arcus

  committed
  3d2fd2c

• Set working directory

  jthompson-arcus

  committed
  b626a3f

• Re-hardcode R version

  jthompson-arcus

  committed
  36ea9c1

Commits on Nov 22, 2024

• Add test for db_get_review() when no filters are specified

  jthompson-arcus

  committed
  439d14b

• Fix updated_items_memory

  jthompson-arcus

  committed
  0079348

Commits on Nov 28, 2024

• Don't export db_get_review anymore

  LDSamson

  committed
  ca83997

• Update documentation

  LDSamson

  committed
  0f680cd

• Ensure db_get_review errors before sending a db query if ... cannot be coerced to a data frame

  LDSamson

  committed
  a08c510

• Add additional tests

  LDSamson

  committed
  f7ba04a

• Use more consistent naming in the save review process

  LDSamson

  committed
  205896f

• Change a dplyr::filter call to base R filter for performance reasons

  LDSamson

  committed
  b8f3f52

• Ensure that updated_records_memory has the same columns as in the db

  LDSamson

  committed
  0154355

• Ensure tests will fail if there is a review discrepancy

  LDSamson

  committed
  f0144a2

• Export review_save_error to ensure errors are captured when saving review in in a shinytest2 test

  LDSamson

  committed
  5360760

• Update snaps

  LDSamson

  committed
  88f5b04

• Also update mod_main_sidebar snaps

  LDSamson

  committed
  23b6e91

Commits on Dec 2, 2024

• Change to base R filter

  LDSamson

  committed
  6ce5827

• Fix review saving by selecting correct rows to update within the application

  LDSamson

  committed
  0e8ecc7

• Remove the (now) redundant filtering by timestamp for updated_records_memory

  LDSamson

  committed
  d8e24d4

• Merge pull request #137 from openpharma/jt-99-review_by_row

  Show description for 5845568
  LDSamson

  authored
  5845568

Commits on Dec 13, 2024

• Set pageLength to all when Scroller disabled

  jthompson-arcus

  committed
  e9f451d

• Update NEWS and version

  jthompson-arcus

  committed
  06d8948

• Repair tests

  jthompson-arcus

  committed
  8ba71a2

Commits on Dec 17, 2024

• Merge pull request #145 from openpharma/jt-GHA_renv

  Show description for 78ad0cf
  LDSamson

  authored
  78ad0cf

• Merge pull request #150 from openpharma/jt-fix_pageLength_bug

  Show description for d5b80d2
  LDSamson

  authored
  d5b80d2