Code

Devex: Resolve merge conflicts dev#143

Code

Merged

aclark02-arcus merged 88 commits intodevexopenpharma/clinsight:devexfrom jt-resolve_merge_conflicts_devopenpharma/clinsight:jt-resolve_merge_conflicts_devCopy head branch name to clipboardNov 20, 2024

+662-182

Commits

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 28, 2024

• Update db_save_review to update instead of append

  jthompson-arcus

  committed
  0b2eb31

• Repair tests from db_save_review() changes

  jthompson-arcus

  committed
  37a7c11

Commits on Oct 29, 2024

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

  jthompson-arcus

  committed
  91a8c49

• Only store old records in logging table

  jthompson-arcus

  committed
  f98f0d2

• 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 4, 2024

• Resolve merge conflicts with dev

  Show description for f299d4a
  jthompson-arcus

  committed
  f299d4a

Commits on Nov 5, 2024

• Resolve merge conflicts with dev

  Show description for 63dc37d
  jthompson-arcus

  committed
  63dc37d

• Update version number

  jthompson-arcus

  committed
  0e6b4af

• 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 15, 2024

• 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)

  Show description for dfdf945
  LDSamson

  committed
  dfdf945

• Update news and version

  Show description for dda0b05
  LDSamson

  committed
  dda0b05

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

  Show description for d56c4b1
  LDSamson

  committed
  d56c4b1

• Update test database so a form with different review status per item is also covered.

  LDSamson

  committed
  bab7a92

• Update mod_review_forms logic to ensure review was saved successfully

  LDSamson

  committed
  a37ff1d

• Update mod_review_forms tests

  LDSamson

  committed
  7ac3278

• Add all common vars to rows_update, so that review status is only updated if changed within a form

  LDSamson

  committed
  29eb7a0

• Update news and description

  LDSamson

  committed
  9940944

• Resolve R CMD documentation note

  LDSamson

  committed
  bafae70

• Mark functions as internal for package website

  LDSamson

  committed
  d21f519

• Increase wait time to pass tests within Alpine Docker

  LDSamson

  committed
  7efa574

• Update Alpine Docker test results

  LDSamson

  committed
  9d8555b

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

• Add pkgdown gha workflow

  Show description for 5d52f83
  

  aclark02-arcus

  authored and

  LDSamson

  committed
  5d52f83

• don't rely on renv.lock

  Show description for bbf2b53
  

  aclark02-arcus

  authored and

  LDSamson

  committed
  bbf2b53

• update news

  Show description for e9ed1a4
  

  aclark02-arcus

  authored and

  LDSamson

  committed
  e9ed1a4

• Update pkgdown workflow for use on dev and devex

  LDSamson

  committed
  734f9ca

• Small NEWS.md wording update

  jthompson-arcus

  authored
  92677b0

• Merge pull request #138 from openpharma/ls_create_v0.1.1

  Show description for 573c633
  jthompson-arcus

  authored
  573c633

• 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 conflicts with dev

  Show description for 993035f
  jthompson-arcus

  committed
  993035f