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v0.1.0 release #94

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merged 391 commits into from
Sep 30, 2024
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d58ce42
fix add_timevars_to_data within merge_meta_with_data
LDSamson Aug 1, 2024
7120125
Fix R CMD check error
LDSamson Aug 1, 2024
cdcaaa5
Also remove example from .Rd file
LDSamson Aug 1, 2024
8cdbdba
revert changes for #51
aclark02-arcus Aug 1, 2024
0ffa578
add column specs to internal data
LDSamson Aug 2, 2024
f67e271
Renaming the metadata tab `column_specs` to the more fitting name `co…
LDSamson Aug 2, 2024
8da18fe
Perform type conversion with the internally stored column types
LDSamson Aug 2, 2024
cc2ab12
use readr instead of vroom for reading csv files, since we are now us…
LDSamson Aug 2, 2024
6e2e6bd
Update renv lockfile, update appdata testthat snapshot
LDSamson Aug 2, 2024
a154359
update data_spec vignette
LDSamson Aug 2, 2024
66ab364
Remove line for creating day variable second time.
LDSamson Jul 12, 2024
3d368bf
add synch_time attribute to merged data
LDSamson Jul 12, 2024
23454f1
Remove rows with missing subject_id, if they exist.
LDSamson Jul 12, 2024
edc839c
update_review_data: make update_time available as function option, se…
LDSamson Jul 12, 2024
27366fe
Add synch time to merged data and database, part two
LDSamson Jul 12, 2024
ff791f7
Update tests
LDSamson Jul 12, 2024
356783f
Update snapshots and documentation
LDSamson Jul 12, 2024
0350241
Fix app feature 4
LDSamson Jul 19, 2024
2d71804
Update version and news, update test results
LDSamson Jul 23, 2024
a8b2fd6
Merge pull request #47 from openpharma/ls-045-restructure-data-import
jthompson-arcus Aug 6, 2024
8972a69
Merge branch 'dev' into ls-046-improve-synch-time-notification
LDSamson Aug 7, 2024
844e839
ensure sycnh_time attribute is created in merged data even if it is m…
LDSamson Aug 7, 2024
2a5cbdf
Add synch_time to raw data, and clearly describe the default.
LDSamson Aug 7, 2024
ea7c696
keep db_update time the same time as the synch_time in study_data, ev…
LDSamson Aug 7, 2024
58e1da4
Merge pull request #60 from openpharma/ls-046-improve-synch-time-noti…
jthompson-arcus Aug 16, 2024
2ad41dd
Add user roles to config in a more machine-readable format
LDSamson Aug 9, 2024
803426b
Ensure only the valid and available roles are passed onto the applica…
LDSamson Aug 9, 2024
9607772
review config: Implement that roles can be selected if multiple valid…
LDSamson Aug 9, 2024
63e10fd
review config: add separate helper function to set user role in mod_r…
LDSamson Aug 9, 2024
626a084
review_config: Add test for feature of changing user role in mod_revi…
LDSamson Aug 20, 2024
5edc33c
Update version
LDSamson Aug 20, 2024
a787d6e
Improve sanitizing role input. Rename app role helper functions (to a…
LDSamson Aug 21, 2024
500c9cb
Fix all_roles argument in get_valid_roles, for consistency within the…
LDSamson Aug 21, 2024
7ea477c
Allow list-type input format for user roles roles.
LDSamson Aug 21, 2024
a9d9f82
merge conflict resolution, bumping dev version
aclark02-arcus Aug 21, 2024
2633316
Add purrr to suggests
aclark02-arcus Aug 21, 2024
00420f0
remove duplicate na.omit() calls and make it safer
aclark02-arcus Aug 21, 2024
fdd2ad6
Check for empty `completed_events` in `fig_timeline()`
jthompson-arcus Aug 21, 2024
f7996f6
Update version and NEWS
jthompson-arcus Aug 21, 2024
a5a986c
Correct version number
jthompson-arcus Aug 21, 2024
9f96c2a
Merge pull request #66 from openpharma/jt-fix_fig_timeline_bug
LDSamson Aug 22, 2024
ec33daf
Merge branch 'dev' into ls-061-make_roles_available
LDSamson Aug 22, 2024
70d4bee
Remove reactive() in reactiveValues() complexity. Fix tests
LDSamson Aug 22, 2024
980a7d5
Increment version number
jthompson-arcus Aug 22, 2024
0c918e0
Merge pull request #63 from openpharma/ls-061-make_roles_available
jthompson-arcus Aug 22, 2024
1f10fa4
query_add: Add user role when adding new query; remove redundant quer…
LDSamson Aug 9, 2024
f5ed728
update metdata.rda
aclark02-arcus Aug 22, 2024
a1b3e3a
update dev version
aclark02-arcus Aug 22, 2024
7761131
query_add: ensure that user without role cannot add a query. Add test…
LDSamson Aug 22, 2024
c0befec
query_follow_up: implement reviewer role in mod_query_follow_up
LDSamson Aug 9, 2024
03af5d5
query_follow_up: ensure a follow-up query can only be written if ther…
LDSamson Aug 22, 2024
9d4d2f7
Update internal datasets
LDSamson Aug 20, 2024
f8859d3
Update .png snapshots with correct fixed synch date in feature 1 test
LDSamson Aug 19, 2024
4ad386d
Fix some small minor errors (docs update, snapshot update)
LDSamson Aug 19, 2024
b621e3d
Update version and news
LDSamson Aug 20, 2024
f2253f2
update news
aclark02-arcus Aug 22, 2024
0eec2fd
Merge pull request #57 from openpharma/ac-50-51
LDSamson Aug 22, 2024
ffda246
Merge branch 'dev' into ls-061-add-roles-to-queries
LDSamson Aug 22, 2024
8058621
Increment version
LDSamson Aug 22, 2024
a2b09b0
Add roles to mod_report
LDSamson Aug 20, 2024
ba3f850
Add roles to review_forms
LDSamson Aug 22, 2024
f428123
Restrict roles allowed to review to the ones mentioned in the config …
LDSamson Aug 22, 2024
5c00d20
Update version and news
LDSamson Aug 20, 2024
5783594
Merge pull request #64 from openpharma/ls-061-add-roles-to-queries
jthompson-arcus Aug 27, 2024
4cd6562
Add more explicit warning if no user role or user name is available
LDSamson Aug 28, 2024
db0260a
make logical test slightly safer
LDSamson Aug 28, 2024
e552fac
Ensure app can handle an empty roles variable
LDSamson Aug 28, 2024
0efb311
Fix pkgdown yml file
LDSamson Aug 23, 2024
2e0e30e
Fix unintended randomness in test outcome
LDSamson Aug 28, 2024
42a328a
Merge branch 'dev' into ls-061-add-roles-to-form-review-and-report
LDSamson Aug 28, 2024
39ebcb7
Revert "Fix pkgdown yml file"
LDSamson Aug 29, 2024
26cfa5e
Merge branch 'dev' into ac-58
aclark02-arcus Aug 30, 2024
a138800
move pkgload to 'Suggests' and then revert changes to production/renv…
aclark02-arcus Aug 30, 2024
224ec6b
change renv profile back to dev
aclark02-arcus Aug 30, 2024
9d2b7ee
Add code that helps users update the manifest file for deployment to …
aclark02-arcus Aug 30, 2024
690744d
Add manifest.json file to .Rbuildignore
aclark02-arcus Aug 30, 2024
138c419
Add small description/purpose of the app.R file
LDSamson Sep 2, 2024
9e809f7
Changing renv profile names to 'full' and 'minimal'
LDSamson Sep 2, 2024
2b0109e
Increment package version
LDSamson Sep 2, 2024
bcd7831
Merge pull request #59 from openpharma/ac-58
LDSamson Sep 2, 2024
5161fb1
Merge branch 'dev' into ls-061-add-roles-to-form-review-and-report
LDSamson Sep 2, 2024
12f82bc
Increment version
LDSamson Sep 2, 2024
5734e0b
Fix bug in output of get_valid_roles in case no valid role is available
LDSamson Sep 3, 2024
c5aaa44
ignore .rds files so that they are not accidentily shared in remote repo
aclark02-arcus Sep 3, 2024
5fca650
add .rscignore for posit connect deployers
aclark02-arcus Sep 3, 2024
80582f0
Increment version number to 0.0.0.9015
aclark02-arcus Sep 3, 2024
f3bfa6f
update news and version num
aclark02-arcus Sep 3, 2024
be68388
Merge pull request #65 from openpharma/ls-061-add-roles-to-form-revie…
jthompson-arcus Sep 3, 2024
4e97fdd
Merge branch 'dev' into ac-tiny
LDSamson Sep 4, 2024
b073e42
add .rscignore to .Rbuildignore
LDSamson Sep 4, 2024
4a50593
Increment version
LDSamson Sep 4, 2024
47e993a
Merge pull request #68 from openpharma/ac-tiny
LDSamson Sep 4, 2024
f98dd0b
Remove calls to the clinsight package to prevent an error when using …
LDSamson Sep 4, 2024
c7658f4
Update news
LDSamson Sep 4, 2024
0b6acb4
Increment version
LDSamson Sep 4, 2024
25012e5
Revert "Remove calls to the clinsight package to prevent an error whe…
LDSamson Sep 5, 2024
2999bfe
Fix bug by using the golem::pkg_path instead of the yaml for retrievi…
LDSamson Sep 5, 2024
88faf5b
Remove rogue comma
aclark02-arcus Sep 4, 2024
2345b75
Merge pull request #70 from openpharma/ls-69-bug-fix-run_dev
jthompson-arcus Sep 5, 2024
5d061e3
Add form-level default values and required metadata columns to intern…
LDSamson Sep 6, 2024
b0e1efc
Add get_form_level_data() to clean form-level data, including several…
LDSamson Sep 6, 2024
0e3777d
Update get_metadata() function to use get_form_level_data(), add some…
LDSamson Sep 6, 2024
48558c5
Update metadata.xlsx, renaming the groups tab to form_level_data, add…
LDSamson Sep 6, 2024
a63f0e3
Add form_level data in app_vars by adding it to get_meta_vars
LDSamson Sep 6, 2024
7956bd4
Ensure mod_study_forms uses the new location of form_level_data. Rest…
LDSamson Sep 6, 2024
ef6a2d8
Disable review options if review is not required
LDSamson Sep 6, 2024
78eadaf
Remove forms of which review is not required from the summary data se…
LDSamson Sep 6, 2024
2e4c6c7
Increment version
LDSamson Sep 6, 2024
b062b69
Update news
LDSamson Sep 6, 2024
67a1840
Fix metadata documentation
LDSamson Sep 6, 2024
d3c898e
Adjust `datatable_custom()` to include "Scroller" extension and "scro…
jthompson-arcus Sep 6, 2024
dd64ab9
Move caption/title to table wrapper
jthompson-arcus Sep 9, 2024
73cc3e7
Update snaps for 'app-feature-1'
jthompson-arcus Sep 9, 2024
b30e9c1
Update snaps for 'app-feature-2'
jthompson-arcus Sep 9, 2024
ac06e0a
Update snaps for 'app-feature-3'
jthompson-arcus Sep 9, 2024
b2f0079
Update snaps for 'mod_navigate_review'
jthompson-arcus Sep 9, 2024
9aa427e
Update snaps for 'mod_study_forms'
jthompson-arcus Sep 9, 2024
7e98d8d
Update `datatable_custom()` test
jthompson-arcus Sep 9, 2024
3773026
Update version and NEWS
jthompson-arcus Sep 9, 2024
d3baeba
Oops
jthompson-arcus Sep 9, 2024
c7d55c0
Fix roles are not read correctly when using shinymanager
LDSamson Sep 10, 2024
05eb57f
Fix error if an input is unavailable when using shinymanager
LDSamson Sep 10, 2024
507bb75
Test that no user name or user role error occurs with shinymanager
LDSamson Sep 10, 2024
3eacd33
Update news
LDSamson Sep 10, 2024
0b98c19
Update version
LDSamson Sep 10, 2024
2fa6356
Handle cases where code is inserted in table title
jthompson-arcus Sep 10, 2024
f4b88dd
Update R version and packages
LDSamson Sep 9, 2024
338f6d9
Fix golem_config
LDSamson Sep 9, 2024
42d3d05
disable 'compact' view for bslib::value_box() (see https://github.com…
LDSamson Sep 9, 2024
f987497
set bslib requirement to 0.6.2 to ensure we can set bslib-value-box-h…
LDSamson Sep 9, 2024
f82d891
tweak header widgets appearance a bit
LDSamson Sep 9, 2024
18a64b1
Use theme instead of deprecated argument theme_color
LDSamson Sep 9, 2024
87d3acd
Update app feature 1 test
LDSamson Sep 9, 2024
3a094b6
Update app feature 2 test
LDSamson Sep 9, 2024
4d187e7
Update app feature 3 test
LDSamson Sep 9, 2024
9a8c310
Update app feature 4 snapshots
LDSamson Sep 9, 2024
73457e3
Update mod_navigate_participants test snapshots
LDSamson Sep 9, 2024
59311e3
Update mod_study_forms, mod_nav_review, and mod_main_sidebar tests
LDSamson Sep 10, 2024
aba878a
Update authentication test snapshots
LDSamson Sep 10, 2024
ee65d55
Update R version in GHA yaml
LDSamson Sep 10, 2024
3d125dd
add libcurl system package manually to GHA
LDSamson Sep 10, 2024
3bba8fc
Prevent new ggplot2 warning by using geom_annotate in compact timeline
LDSamson Sep 11, 2024
3336342
Move shinymanager to suggest
LDSamson Sep 11, 2024
7ddb2c0
Ensure it is installed in the 'full' but not in the 'minimal' profile
LDSamson Sep 11, 2024
2acd34c
Create helpful prompts to install shinymanager if needed
LDSamson Sep 11, 2024
de0d78f
Skip shinymanager-related tests if shinymanager is not installed
LDSamson Sep 11, 2024
fd712a7
Update test descriptions of shinymanager function tests
LDSamson Sep 11, 2024
a69626a
Update news
LDSamson Sep 11, 2024
36d16d1
Increment version
LDSamson Sep 11, 2024
3c46cfb
Respect function arg `selection`
jthompson-arcus Sep 11, 2024
b5ab475
Merge pull request #78 from openpharma/ls_77_bug_fix_shinymanager
jthompson-arcus Sep 11, 2024
684af10
Merge branch 'dev' into ls-81-move-shinymanager-to-suggests
LDSamson Sep 11, 2024
bab150c
Merge branch 'dev' into jt-74-improve_datatables
jthompson-arcus Sep 11, 2024
9f7aaf0
Restructure `datatable_custom()`
jthompson-arcus Sep 11, 2024
771b6d9
Update documentation
jthompson-arcus Sep 11, 2024
14e9b67
Import `modifyList()`
jthompson-arcus Sep 11, 2024
b26335b
Update selected query dataTable
jthompson-arcus Sep 11, 2024
e515381
Update snaps
jthompson-arcus Sep 11, 2024
0eb51f8
Small documentation update
jthompson-arcus Sep 11, 2024
63e1d02
Tweak css for header widgets a bit more
LDSamson Sep 12, 2024
0b14be3
Update to snapshot of 12 September 2024
LDSamson Sep 12, 2024
0eac1f2
Reflow code for readability
jthompson-arcus Sep 13, 2024
c78fdb1
Fix issue when title is `NULL`
jthompson-arcus Sep 13, 2024
12697d6
Update snaps
jthompson-arcus Sep 13, 2024
af1dec5
Update version number
jthompson-arcus Sep 13, 2024
1a3c060
Update version number in config...
jthompson-arcus Sep 13, 2024
26aed39
Merge pull request #75 from openpharma/jt-74-improve_datatables
LDSamson Sep 13, 2024
0eeb341
Merge branch 'dev' into ls-81-move-shinymanager-to-suggests
LDSamson Sep 13, 2024
a96a257
Generalize shinymanager login screen; use a non-existent mail address…
LDSamson Sep 13, 2024
89dd054
Increment version
LDSamson Sep 13, 2024
88e0301
Merge pull request #82 from openpharma/ls-81-move-shinymanager-to-sug…
jthompson-arcus Sep 13, 2024
8968b50
Merge branch 'dev' into ls-043-add-review-required-settings
LDSamson Sep 16, 2024
a0db067
Merge branch 'dev' into ls-29-update-R-and-packages
LDSamson Sep 16, 2024
c8a4cf9
Update snaps
LDSamson Sep 16, 2024
42ad0ec
Increment version
LDSamson Sep 16, 2024
488192f
Update contributing authors
jthompson-arcus Sep 16, 2024
7d85a69
Increment version number
jthompson-arcus Sep 16, 2024
ef5da53
add aaron's orcid to `DESCRIPTION`
aclark02-arcus Sep 16, 2024
5a649de
Update documentation
jthompson-arcus Sep 16, 2024
ea84049
Add ORCID from Leon
LDSamson Sep 17, 2024
6a9704e
Merge pull request #85 from openpharma/jt-update_contributors
LDSamson Sep 17, 2024
9aff424
Merge branch 'dev' into ls-29-update-R-and-packages
LDSamson Sep 17, 2024
e8fd4e6
Increment version
LDSamson Sep 17, 2024
02b41fe
Merge branch 'dev' into ls-043-add-review-required-settings
LDSamson Sep 17, 2024
9b6d166
Increment version
LDSamson Sep 17, 2024
63e22fe
Merge pull request #73 from openpharma/ls-043-add-review-required-set…
LDSamson Sep 18, 2024
563a5ad
Merge branch 'dev' into ls-29-update-R-and-packages
LDSamson Sep 18, 2024
35ae4c5
Increment version
LDSamson Sep 18, 2024
c4bb835
Use latest snapshot
LDSamson Sep 17, 2024
5478e67
Merge pull request #79 from openpharma/ls-29-update-R-and-packages
LDSamson Sep 18, 2024
50769c7
Improve mod_study_form ui layout
LDSamson Sep 12, 2024
f8f0efd
Use sidebar layout for mod_study_forms
LDSamson Sep 12, 2024
b78dfb4
Use sidebar layout for mod_common_forms
LDSamson Sep 12, 2024
8a33692
Improve figure legend - larger, and hidden with popover
LDSamson Sep 17, 2024
f3944a8
Align info text
LDSamson Sep 17, 2024
a38185a
remove css overflow.x=scroll for basic timeline (not needed with late…
LDSamson Sep 17, 2024
471e742
CSS: use minimum text size in app value boxes
LDSamson Sep 17, 2024
7939947
Slightly bigger figs if only one or two are shown
LDSamson Sep 17, 2024
7ec879e
Update snaps
LDSamson Sep 17, 2024
1d43648
link to homepage in logo
LDSamson Sep 18, 2024
5184bf8
Increment version
LDSamson Sep 18, 2024
d24fa2a
Merge pull request #87 from openpharma/ls-improve-UI
LDSamson Sep 19, 2024
854564b
Add form_repeat to common_forms table
LDSamson Sep 19, 2024
5ab8ee0
Change metadata table_names: form_repeat will now show as 'N' in a cu…
LDSamson Sep 19, 2024
7b4d166
Remove rownames from common_forms, since it is a bit redundant now we…
LDSamson Sep 19, 2024
26db26a
Add form_repeat number to the selected query item name, but only if t…
LDSamson Sep 19, 2024
1accb96
Improve visibility in tables with long query texts
LDSamson Sep 19, 2024
449b8d4
Update snaps
LDSamson Sep 19, 2024
a250a9c
Ensure query type shows up in query details
LDSamson Sep 19, 2024
8716a00
Add additional integration tests for viewing queries, responding to q…
LDSamson Sep 19, 2024
7c0a80b
Update news
LDSamson Sep 19, 2024
9d5080d
Increment version
LDSamson Sep 19, 2024
01063ce
Fix some issues with mod_report
LDSamson Sep 19, 2024
e133ad8
Ensure query type shows up in reports
LDSamson Sep 19, 2024
052bff0
Adjust test for mod_report
LDSamson Sep 19, 2024
1ac7f3f
Update news
LDSamson Sep 19, 2024
0e8cb22
Increment version
LDSamson Sep 19, 2024
6b5afe6
Remove flaky input values from new integration test
LDSamson Sep 19, 2024
1e58c61
of course that change also needs new snapshot files..
LDSamson Sep 19, 2024
3c29424
add some additional waiting time in new test
LDSamson Sep 19, 2024
4802815
Ensure break will not occur at a whitespace
LDSamson Sep 20, 2024
9b86234
Remove some unneeded default settings overrides in query tables
LDSamson Sep 20, 2024
e93fe08
Improve query table in mod_navigate_review (now also show query type …
LDSamson Sep 20, 2024
701a752
Update snaps
LDSamson Sep 20, 2024
308f101
Update some older .png shinytest2 snapshot so that the latest UI is s…
LDSamson Sep 20, 2024
933a000
Ensure that form_repeat_name displayed in duplicate query names can b…
LDSamson Sep 20, 2024
857d864
Add global vars to resolve some R package notes
LDSamson Sep 20, 2024
61c30b8
Update docs (resolves R CMD warning)
LDSamson Sep 20, 2024
207db4c
Merge pull request #92 from openpharma/ls-fix-mod_query_issues
jthompson-arcus Sep 20, 2024
fe74719
Merge branch 'dev' into ls-fix-reports
LDSamson Sep 20, 2024
8b79c33
Increment version
LDSamson Sep 20, 2024
145f89c
Show user role in prepare report modal in mod_report
LDSamson Sep 23, 2024
b01b565
Add additional test for downloading PDF report
LDSamson Sep 23, 2024
29a2aa5
Ensure report type is included in test of mod_report, test for creati…
LDSamson Sep 23, 2024
9b6e76e
Merge pull request #93 from openpharma/ls-fix-reports
LDSamson Sep 23, 2024
f7b6360
Increment version number to 0.1.0
LDSamson Sep 25, 2024
bce6538
don't use full_width=T for PDF since it relies on a deprecated latex …
LDSamson Sep 26, 2024
88cffc0
Delete unused old file
LDSamson Sep 26, 2024
4bfe038
Update test descriptions
LDSamson Sep 26, 2024
528e51b
Sort start page based on review status
LDSamson Sep 26, 2024
d41a50d
Update Snapshot headers after updatinng test descriptions
LDSamson Sep 26, 2024
329daea
Do not upload snapshots automatically with GHA; GHA fails if we reach…
LDSamson Sep 26, 2024
76b0c77
Fix that selected regions were not preserved after changing them and …
LDSamson Sep 26, 2024
5697a60
Add short feature description to all feature tests
LDSamson Sep 28, 2024
12cf77b
Update snapshots
LDSamson Sep 28, 2024
3e37045
Ensure that creating PDF reports does not error with long folder name…
LDSamson Sep 28, 2024
e5dcc31
Give shinytest2 some more time to think
LDSamson Sep 28, 2024
60f9a2e
Improve traceability matrix in report
LDSamson Sep 29, 2024
274a233
trim down validation report to only test report with traceabilty matrix
LDSamson Sep 30, 2024
9428066
Update test results
LDSamson Sep 30, 2024
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2 changes: 1 addition & 1 deletion R/mod_report_fct_helpers.R
Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,7 @@ create_report <- function(
# Knit the document, passing in the `params` list, and eval it in a
# child of the global environment (this isolates the code in the document
# from the code in this app).
rmarkdown::render(tempReport, output_file = fileinput,
rmarkdown::render(tempReport, output_file = basename(fileinput),
params = params,
Comment on lines 115 to 118
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@jthompson-arcus I suspect that this change could solve your problem of not being able to render PDF reports under Windows, closely related to this bug I reported previously: rstudio/rmarkdown#2556

envir = new.env(parent = globalenv())
)
Expand Down