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Diff: dev vs main #140

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Diff: dev vs main #140

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Commits on Sep 30, 2024

  1. Increment version number to 0.1.0.9000

    @LDSamson
    LDSamson committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. Add pkgdown gha workflow

    @aclark02-arcus
    aclark02-arcus committed Oct 1, 2024
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  2. don't rely on renv.lock

    @aclark02-arcus
    aclark02-arcus committed Oct 1, 2024
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  3. update certain functions with '@Keywords internal' for pkddown

    @aclark02-arcus
    aclark02-arcus committed Oct 1, 2024
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  4. Increment version number to 0.1.0.9000

    @aclark02-arcus
    aclark02-arcus committed Oct 1, 2024
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  5. update news

    @aclark02-arcus
    aclark02-arcus committed Oct 1, 2024
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  6. Merge branch 'dev' into ac-95

    @aclark02-arcus
    aclark02-arcus authored Oct 1, 2024
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  7. Update golem config with new app version

    @aclark02-arcus
    aclark02-arcus committed Oct 1, 2024
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  8. Merge branch 'ac-95' of https://github.com/openpharma/clinsight into … 

    …ac-95
    @aclark02-arcus
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Commits on Oct 8, 2024

  1. Add callback to "go to form" on double click event

    @jthompson-arcus
    jthompson-arcus committed Oct 8, 2024
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Commits on Oct 9, 2024

  1. Pass additional modifying functions in arguments of `merge_meta_with_… 

    …data()`
    @jthompson-arcus
    jthompson-arcus committed Oct 9, 2024
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  2. Recode to use base R and character values

    @jthompson-arcus
    jthompson-arcus committed Oct 9, 2024
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  3. Move additional merging functions to metadata

    @jthompson-arcus
    jthompson-arcus committed Oct 9, 2024
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Commits on Oct 10, 2024

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

    @jthompson-arcus
    jthompson-arcus committed Oct 10, 2024
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  2. Specify add_fns as post_merge_fns

    @jthompson-arcus
    jthompson-arcus committed Oct 10, 2024
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  3. Add pre_merge_fns setting

    @jthompson-arcus
    jthompson-arcus committed Oct 10, 2024
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  4. Add inline function to check existence of an object for dplyr mutat… 

    …ions
    @jthompson-arcus
    jthompson-arcus committed Oct 10, 2024
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  5. Impute event_name from event instead of event_name

    @jthompson-arcus
    jthompson-arcus committed Oct 10, 2024
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  6. Fix broken tests

    @jthompson-arcus
    jthompson-arcus committed Oct 10, 2024
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  7. Further generalize add_timevars_to_data()

    @jthompson-arcus
    jthompson-arcus committed Oct 10, 2024
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  8. Initialize region field

    @jthompson-arcus
    jthompson-arcus committed Oct 10, 2024
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Commits on Oct 11, 2024

  1. Add mid-merging functions

    @jthompson-arcus
    jthompson-arcus committed Oct 11, 2024
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  2. Update version and NEWS

    @jthompson-arcus
    jthompson-arcus committed Oct 11, 2024
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  3. Move logic to dblclick_to_form() function

    @jthompson-arcus
    jthompson-arcus committed Oct 11, 2024
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Commits on Oct 14, 2024

  1. Remove duplicate type conversion

    @jthompson-arcus
    jthompson-arcus committed Oct 14, 2024
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  2. Create apply_custom_functions() to handle

    @jthompson-arcus
    jthompson-arcus committed Oct 14, 2024
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  3. Clean up metadata settings element generation

    @jthompson-arcus
    jthompson-arcus committed Oct 14, 2024
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  4. Remove extraneous pipe

    @jthompson-arcus
    jthompson-arcus committed Oct 14, 2024
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  5. Reset %||% to standard evaluation

    @jthompson-arcus
    jthompson-arcus committed Oct 14, 2024
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  6. Display message if using user supplied data.

    @jthompson-arcus
    jthompson-arcus committed Oct 14, 2024
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  7. Remove event_name from required columns

    @jthompson-arcus
    jthompson-arcus committed Oct 14, 2024
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  8. Resolve test errors

    @jthompson-arcus
    jthompson-arcus committed Oct 14, 2024
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Commits on Oct 15, 2024

  1. Specify the parent.frame() as the environment to check existence wi… 

    …thin
    @jthompson-arcus
    jthompson-arcus committed Oct 15, 2024
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  2. Add tests for %|_|%

    @jthompson-arcus
    jthompson-arcus committed Oct 15, 2024
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  3. Change warning() to cat()

    @jthompson-arcus
    jthompson-arcus committed Oct 15, 2024
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  4. Merge pull request #104 from openpharma/jt-generalize_meta_merging 

    Generalize metadata merging with data
    @LDSamson
    LDSamson authored Oct 15, 2024
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Commits on Oct 16, 2024

  1. Add primary key field to tables

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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  2. Temporary fix to preserve current functionality

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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  3. Re-create review_testdb.sqlite

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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  4. Repair mod_review_form tests

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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  5. Repair fct_SQLite tests

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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  6. Rebuild testdb.sqlite

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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  7. Temporary fix for adding queries to work as expected

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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  8. Add preliminary logging table

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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  9. Add "all_review_data_log" to list of expected tables

    @jthompson-arcus
    jthompson-arcus committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. Merge branch 'dev' into jt-dblclick_overview_tbl

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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  2. Add dblclick callback to other appropriate tables

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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  3. Remove unnecessary session$

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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  4. Repair mod_navigate_review tests

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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  5. Repair app feature 3 tests

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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  6. Repair app feature 2 tests

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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  7. Repair app feature 1 tests

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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  8. Add help files

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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  9. Make sure expression is appropriately defined for %|_|% in `add_tim… 

    …evars_to_data()`
    @jthompson-arcus
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  10. Update version

    @jthompson-arcus
    jthompson-arcus committed Oct 17, 2024
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Commits on Oct 18, 2024

  1. Further generalization

    @jthompson-arcus
    jthompson-arcus committed Oct 18, 2024
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  2. Repair fct_appdata tests

    @jthompson-arcus
    jthompson-arcus committed Oct 18, 2024
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  3. Repair custom metadata test

    @jthompson-arcus
    jthompson-arcus committed Oct 18, 2024
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  4. Update documentation

    @jthompson-arcus
    jthompson-arcus committed Oct 18, 2024
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  5. Update global variables

    @jthompson-arcus
    jthompson-arcus committed Oct 18, 2024
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Commits on Oct 22, 2024

  1. Resolve issue with unit derivation

    @jthompson-arcus
    jthompson-arcus committed Oct 22, 2024
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Commits on Oct 23, 2024

  1. Add form_type class to app data

    @jthompson-arcus
    jthompson-arcus committed Oct 23, 2024
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  2. Minimal solution

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    jthompson-arcus committed Oct 23, 2024
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Commits on Oct 24, 2024

  1. Revert to old code for units

    @jthompson-arcus
    jthompson-arcus committed Oct 24, 2024
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  2. Merge pull request #116 from openpharma/jt-gmm_follow_up 

    Follow up to generalizing metadata merge
    @LDSamson
    LDSamson authored Oct 24, 2024
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  3. Merge branch 'dev' into jt-107-extend_create_table

    @jthompson-arcus
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  4. Merge branch 'dev' into jt-dblclick_overview_tbl

    @jthompson-arcus
    jthompson-arcus committed Oct 24, 2024
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  5. Incorporate "dblclick" to app feature 1 test

    @jthompson-arcus
    jthompson-arcus committed Oct 24, 2024
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  6. Update version and NEWS

    @jthompson-arcus
    jthompson-arcus committed Oct 24, 2024
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Commits on Oct 25, 2024

  1. Update feature 01 test description, add back test of navigating by cl… 

    …icking on the header widget.
    @LDSamson
    LDSamson committed Oct 25, 2024
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Commits on Oct 28, 2024

  1. Improve news description

    @LDSamson
    LDSamson committed Oct 28, 2024
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  2. Merge pull request #103 from openpharma/jt-dblclick_overview_tbl 

    Add callback to "go to form" on double click event
    @LDSamson
    LDSamson authored Oct 28, 2024
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  3. Fix warnings in apply_edc_specific_changes

    @LDSamson
    LDSamson committed Oct 28, 2024
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  4. Update news and version

    @LDSamson
    LDSamson committed Oct 28, 2024
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  5. Merge pull request #120 from openpharma/ls_119_fix_warnings 

    Fix warnings in `apply_edc_specific_changes`
    @jthompson-arcus
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  6. Update db_save_review to update instead of append

    @jthompson-arcus
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  7. Repair tests from db_save_review() changes

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  8. Merge branch 'dev' into ac-95

    @aclark02-arcus
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  9. Merge branch 'dev' into jt-107-extend_create_table

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  10. Simplify form_types creation

    @jthompson-arcus
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  11. Update version and NEWS

    @jthompson-arcus
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  12. Resolve merge conflicts with dev 

    Merge branch 'dev' into jt-107-extend_create_table

# Conflicts:
#	NEWS.md
    @jthompson-arcus
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Commits on Oct 29, 2024

  1. update news and golem-config veresion

    @aclark02-arcus
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  2. merge conflic on golem_version (again)

    @aclark02-arcus
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  3. update a few functions with '@Keywords internal' for pkgdown build

    @aclark02-arcus
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  4. Merge pull request #102 from openpharma/ac-95 

    Add `pkgdown` gha workflow
    @LDSamson
    LDSamson authored Oct 29, 2024
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  5. Merge branch 'dev' into jt-107-extend_create_table

    @jthompson-arcus
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  6. Update version number

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  7. Merge branch 'dev' into jt-113-logging_tables

    @jthompson-arcus
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  8. Only store old records in logging table

    @jthompson-arcus
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  9. Add S3 generic to _pkgdown.yml

    @jthompson-arcus
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  10. Modify update process to only updated/append appropriate records

    @jthompson-arcus
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  11. Actually pull the newer record when updated

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Commits on Oct 30, 2024

  1. Add db_version table to DB

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  2. Add edit_date_time to logging table

    @jthompson-arcus
    jthompson-arcus committed Oct 30, 2024
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  3. Update all columns not considered in common

    @jthompson-arcus
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  4. Correct error in creating primary key tables

    @jthompson-arcus
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  5. Update fct_SQLite.R tests to reflect changes

    @jthompson-arcus
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  6. Update test DB

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  7. Incorporate review logging tests into test-fct_SQLite.R

    @jthompson-arcus
    jthompson-arcus committed Oct 30, 2024
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  8. Add logging tests to test-mod_review_forms.R

    @jthompson-arcus
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  9. Add index to all_review_data table

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Commits on Oct 31, 2024

  1. Utilize UPSERT for DB append/update procedure

    @jthompson-arcus
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  2. Make UPSERT process more robust

    @jthompson-arcus
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  3. Add function update_db_version() to migrate old DBs

    @jthompson-arcus
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  4. Update version and NEWS

    @jthompson-arcus
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  5. Fix warning message popping up in tests

    @jthompson-arcus
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Commits on Nov 1, 2024

  1. Change create_table.common_events to create_table.common_forms

    @jthompson-arcus
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  2. Add form_type to metadata$item_expanded

    @jthompson-arcus
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  3. Repair fct_appdata.R tests

    @jthompson-arcus
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  4. Add create_table.common_forms() tests

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Commits on Nov 4, 2024

  1. Increment version number to 0.1.0.9005

    @aclark02-arcus
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  2. Decode shinyproxy user name with base64 encoding, and return a warnin… 

    …g if the result is not UTF8 (i.e. if the string was initially not encoded)
    @LDSamson
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  3. Update news and version

    @LDSamson
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  4. Update workflows

    @jthompson-arcus
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  5. Only update website on pushes to main

    @jthompson-arcus
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  6. Add workflow_dispatch to R CMD check

    @jthompson-arcus
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  7. Merge pull request #127 from openpharma/jt-update_devex_workflows 

    Update workflows
    @LDSamson
    LDSamson authored Nov 4, 2024
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  8. update 'default_opts' instead and update function documentation

    @aclark02-arcus
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  9. Add a check if the package base64enc is installed within the `decode_… 

    …base64` function
    @LDSamson
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  10. Merge pull request #123 from openpharma/ls_use_base64_encoded_usernames 

    Use base64 encoding for usernames in http headers (shinyproxy specific)
    @jthompson-arcus
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  11. Simplify form string

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  12. Update version

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  13. Resolve merge conflicts with dev 

    Merge branch 'dev' into jt-107-extend_create_table

# Conflicts:
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#	inst/golem-config.yml
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  14. Resolve merge conflicts with dev 

    Merge branch 'dev' into jt-113-logging_tables

# Conflicts:
#	DESCRIPTION
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  15. Merge branch 'dev' into ac-colorder

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Commits on Nov 5, 2024

  1. update test snapshots with colReorder extension

    @aclark02-arcus
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  2. Merge branch 'ac-colorder' of https://github.com/openpharma/clinsight … 

    …into ac-colorder
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  3. add snap from feature 02

    @aclark02-arcus
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  4. update snaps for feature 03

    @aclark02-arcus
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  5. update the rest of the snaps

    @aclark02-arcus
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  6. Merge pull request #124 from openpharma/ac-colorder 

    Give users ability to re-order columns
    @aclark02-arcus
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  7. Resolve merge conflicts with dev 

    Merge branch 'dev' into jt-107-extend_create_table

# Conflicts:
#	NEWS.md
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  8. Update version number

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  9. Resolve merge conflicts with dev 

    Merge branch 'dev' into jt-113-logging_tables

# Conflicts:
#	NEWS.md
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  10. Update version number

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

    Extend `create_table()`
    @LDSamson
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  12. Resolve merge conflicts with dev 

    Merge branch 'dev' into jt-113-logging_tables

# Conflicts:
#	NEWS.md
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Commits on Nov 7, 2024

  1. Revert changes to mod_review_data_fct_helpers.R

    @jthompson-arcus
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  2. Update internal documentation

    @jthompson-arcus
    jthompson-arcus committed Nov 7, 2024
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  3. Add index columns and db version to internal data

    @jthompson-arcus
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  4. Create helper function to add new tables

    @jthompson-arcus
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  5. Oopsies

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    jthompson-arcus committed Nov 7, 2024
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  6. Update UPSERT documentation

    @jthompson-arcus
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Commits on Nov 8, 2024

  1. Ignore .Renviron on git

    @jthompson-arcus
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  2. Initialize db_get_table()

    @jthompson-arcus
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  3. Use db_get_table() instead of db_slice_rows() to retrieve review … 

    …rows
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  4. Use db_get_table() instead of db_slice_rows() in tests

    @jthompson-arcus
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  5. Remove unneeded slicing and filtering

    @jthompson-arcus
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  6. Capture second snapshot

    @jthompson-arcus
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Commits on Nov 11, 2024

  1. Add comment for idx_cols

    @jthompson-arcus
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  2. Use unique names in function arguments from internal package objects

    @jthompson-arcus
    jthompson-arcus committed Nov 11, 2024
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  3. Merge pull request #115 from openpharma/jt-113-logging_tables 

    Add logging tables
    @LDSamson
    LDSamson authored Nov 11, 2024
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  4. Merge branch 'dev' into jt-113-simplify_review_process

    @jthompson-arcus
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  5. Add trigger for update on id

    @jthompson-arcus
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  6. Check DB version at run time

    @jthompson-arcus
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  7. Update NEWS and version

    @jthompson-arcus
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Commits on Nov 13, 2024

  1. Migrate to review_records from review_row

    @jthompson-arcus
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  2. Update test-fct_SQLite.R

    @jthompson-arcus
    jthompson-arcus committed Nov 13, 2024
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  3. Update test-mod_review_forms.R

    @jthompson-arcus
    jthompson-arcus committed Nov 13, 2024
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  4. Update test-mod_main_sidebar.R

    @jthompson-arcus
    jthompson-arcus committed Nov 13, 2024
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  5. Fix R CMD checks

    @jthompson-arcus
    jthompson-arcus committed Nov 13, 2024
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  6. Fix db_get_review() example

    @jthompson-arcus
    jthompson-arcus committed Nov 13, 2024
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  7. Helps if you update documentation

    @jthompson-arcus
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Commits on Nov 14, 2024

  1. Only UPDATE reviews when review status is changed

    @jthompson-arcus
    jthompson-arcus committed Nov 14, 2024
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Commits on Nov 18, 2024

  1. Use DBI directly instead of tbl() and collect()

    @jthompson-arcus
    jthompson-arcus committed Nov 18, 2024
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  2. Fix typo in user_db version check

    @jthompson-arcus
    jthompson-arcus committed Nov 18, 2024
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  3. Only update records with new status.

    @jthompson-arcus
    jthompson-arcus committed Nov 18, 2024
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  4. Remove argument no longer used

    @jthompson-arcus
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  5. Remove common_vars from tests

    @jthompson-arcus
    jthompson-arcus committed Nov 18, 2024
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  6. Repair tests with db_get_table() returning data.frame not tibble

    @jthompson-arcus
    jthompson-arcus committed Nov 18, 2024
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  7. Update review_testdb.sqlite

    @jthompson-arcus
    jthompson-arcus committed Nov 18, 2024
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  8. Update mod_review_forms test with new testing DB

    @jthompson-arcus
    jthompson-arcus committed Nov 18, 2024
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  9. Update all_review_data_id_update_trigger to include idx_cols

    @jthompson-arcus
    jthompson-arcus committed Nov 18, 2024
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  10. Add keys argument to db_add_log()

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    jthompson-arcus committed Nov 18, 2024
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  11. Resolve some R CMD check issues

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    jthompson-arcus committed Nov 18, 2024
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Commits on Nov 19, 2024

  1. Resolve merge conflicts with jt-113-simplify_review_process 

    Merge branch 'jt-113-simplify_review_process' into jt-99-review_by_row

# Conflicts:
#	R/fct_SQLite.R
#	man/db_save_review.Rd
#	tests/testthat/test-fct_SQLite.R
#	tests/testthat/test-mod_review_forms.R
    @jthompson-arcus
    jthompson-arcus committed Nov 19, 2024
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  2. Keep current structure for enabling reviews

    @jthompson-arcus
    jthompson-arcus committed Nov 19, 2024
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  3. Resolve merge conflicts with main 

    Merge branch 'main' into jt-resolve_merge_conflicts_main

# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/fct_utils.R
#	inst/golem-config.yml
#	tests/testthat/_snaps/mod_review_forms.md
#	tests/testthat/fixtures/review_testdb.sqlite
#	tests/testthat/test-mod_review_forms.R
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Commits on Nov 20, 2024

  1. small alignment fix

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  2. Merge pull request #142 from openpharma/jt-resolve_merge_conflicts_main 

    Resolve merge conflicts `main`
    @LDSamson
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  3. Merge branch 'dev' into jt-113-simplify_review_process

    @LDSamson
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  4. Improve alignment according to https://style.tidyverse.org/syntax.htm… 

    …l#long-function-calls, improve db_add_log docs, add function argument check to db_add_log
    @LDSamson
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  5. Merge pull request #135 from openpharma/jt-113-simplify_review_process 

    Simplify review process
    @LDSamson
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  6. Resolve merge conflict with dev 

    Merge branch 'dev' into jt-99-review_by_row

# Conflicts:
#	R/mod_review_forms.R
#	tests/testthat/test-mod_review_forms.R
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  7. Generalize db_get_review()

    @jthompson-arcus
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  8. Update version and NEWS

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Commits on Nov 21, 2024

  1. Update scenario description for two rows

    @jthompson-arcus
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  2. Update language from row to records

    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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  3. Grab un-duplicated rv_records

    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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  4. Remove unnecessary dplyr::select()

    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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  5. Remove unneeded dplyr::distinct()

    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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  6. Return db_get_review() when ... is empty

    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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  7. Update to latest test-coverage. Remove package installation since it … 

    …is redundant
    @LDSamson
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  8. Fix codecov arguments for codecov-actvion V5 https://github.com/marke… 

    …tplace/actions/codecov#v5-release
    @LDSamson
    LDSamson committed Nov 21, 2024
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  9. Print codecov results again

    @LDSamson
    LDSamson committed Nov 21, 2024
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  10. Update test-mod_review_forms.R

    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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  11. Update version and news

    @LDSamson
    LDSamson committed Nov 21, 2024
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  12. Update only one table in db_save_review()

    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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  13. Fix oopsies

    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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  14. Merge pull request #139 from openpharma/ls_update_codecov 

    Fix codecov uploads
    @jthompson-arcus
    jthompson-arcus authored Nov 21, 2024
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  15. Fix merge conflict with dev 

    Merge branch 'dev' into jt-99-review_by_row

# Conflicts:
#	DESCRIPTION
#	inst/golem-config.yml
    @jthompson-arcus
    jthompson-arcus committed Nov 21, 2024
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Commits on Nov 22, 2024

  1. Add test for db_get_review() when no filters are specified

    @jthompson-arcus
    jthompson-arcus committed Nov 22, 2024
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  2. Fix updated_items_memory

    @jthompson-arcus
    jthompson-arcus committed Nov 22, 2024
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Commits on Nov 28, 2024

  1. Don't export db_get_review anymore

    @LDSamson
    LDSamson committed Nov 28, 2024
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  2. Update documentation

    @LDSamson
    LDSamson committed Nov 28, 2024
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  3. Ensure db_get_review errors before sending a db query if ... cannot… 

    … be coerced to a data frame
    @LDSamson
    LDSamson committed Nov 28, 2024
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  4. Add additional tests

    @LDSamson
    LDSamson committed Nov 28, 2024
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  5. Use more consistent naming in the save review process

    @LDSamson
    LDSamson committed Nov 28, 2024
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  6. Change a dplyr::filter call to base R filter for performance reasons

    @LDSamson
    LDSamson committed Nov 28, 2024
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  7. Ensure that updated_records_memory has the same columns as in the db

    @LDSamson
    LDSamson committed Nov 28, 2024
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  8. Ensure tests will fail if there is a review discrepancy

    @LDSamson
    LDSamson committed Nov 28, 2024
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  9. Export review_save_error to ensure errors are captured when saving re… 

    …view in in a shinytest2 test
    @LDSamson
    LDSamson committed Nov 28, 2024
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  10. Update snaps

    @LDSamson
    LDSamson committed Nov 28, 2024
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  11. Also update mod_main_sidebar snaps

    @LDSamson
    LDSamson committed Nov 28, 2024
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Commits on Dec 2, 2024

  1. Change to base R filter

    @LDSamson
    LDSamson committed Dec 2, 2024
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  2. Fix review saving by selecting correct rows to update within the appl… 

    …ication
    @LDSamson
    LDSamson committed Dec 2, 2024
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  3. Remove the (now) redundant filtering by timestamp for updated_records… 

    …_memory
    @LDSamson
    LDSamson committed Dec 2, 2024
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  4. Merge pull request #137 from openpharma/jt-99-review_by_row 

    Review by records instead of `subject_id` & `form_id` "rv_row"
    @LDSamson
    LDSamson authored Dec 2, 2024
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