Merge pull request #94 from openpharma/ls_v0.1.0_release

v0.1.0 release

.Rbuildignore

@@ -14,3 +14,9 @@ _\.new\.png$
 ^docs$
 ^dev$
 ^Meta$
+^pkgdown$
+^test_data$
+^app\.R$
+^rsconnect$
+^manifest.json$
+^\.rscignore$

.github/workflows/R-CMD-check.yaml

@@ -12,7 +12,7 @@ jobs:
   R-CMD-check:
     runs-on: ubuntu-latest
     env:
-      RENV_PROFILE: "dev"
+      RENV_PROFILE: "full"
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
@@ -22,7 +22,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: '4.3.1'
+          r-version: '4.4.1'
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-tinytex@v2
@@ -35,5 +35,5 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          upload-snapshots: true
+          upload-snapshots: false
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -13,7 +13,7 @@ jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
-      RENV_PROFILE: "dev"
+      RENV_PROFILE: "full"
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       RENV_CONFIG_SANDBOX_ENABLED: false
@@ -26,11 +26,15 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          r-version: '4.3.1'
+          r-version: '4.4.1'
 
       - uses: r-lib/actions/setup-tinytex@v2
       - run: tlmgr --version    
 
+      - name: add libcurl Linux dependency
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y libcurl4-openssl-dev
+
       - uses: r-lib/actions/setup-renv@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2

.gitignore

@@ -11,4 +11,7 @@ docs/*
 inst/doc
 /doc/
 /Meta/
-*.sqlite
+*.sqlite
+/pkgdown/
+/test_data/
+*.rds

.rscignore

@@ -0,0 +1,7 @@
+dev
+vignettes
+tests
+man
+.Rprofile
+data-raw
+.github

DESCRIPTION

@@ -1,8 +1,13 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.0.0.9000
+Version: 0.1.0
 Authors@R: c(
-    person("Leonard Daniël", "Samson", , "[email protected]", role = c("cre", "aut")),
+    person("Leonard Daniël", "Samson", , "[email protected]", role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0002-6252-7639")),
+    person("Aaron", "Clark", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-0123-0970")),
+    person("Jeff", "Thompson", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0009-0007-3640-1075")),
     person("GCP-Service International Ltd.& Co. KG", role = "fnd")
   )
 Description: Interactive application to monitor patient safety during
@@ -11,12 +16,12 @@ Description: Interactive application to monitor patient safety during
     assessments of the patients' safety. Secondary goal is to improve data
     quality by identifying suspicious outliers.
 License: Apache License (>= 2) | file LICENSE
-URL: https://github.com/LDSamson/clinsight
-BugReports: https://github.com/LDSamson/clinsight/issues
+URL: https://github.com/openpharma/clinsight
+BugReports: https://github.com/openpharma/clinsight/issues
 Depends: 
     R (>= 4.1)
 Imports: 
-    bslib,
+    bslib (>= 0.6.2),
     config,
     DBI,
     dbplyr (>= 2.4.0),
@@ -26,34 +31,35 @@ Imports:
     golem,
     htmltools,
     plotly,
+    readr,
     readxl,
     rlang,
     rmarkdown,
     RSQLite,
     shiny,
     shinycssloaders,
     shinyjs,
-    shinymanager,
     shinyWidgets,
     stats,
     tidyr,
     timevis,
     tools,
-    vroom,
     withr
 Suggests: 
     kableExtra,
     knitr,
+    pkgload,
     purrr,
+    shinymanager,
     shinytest2,
     stringr,
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
-Config/renv/profiles/dev/dependencies: pkgdown, stringr, kableExtra,
-    usethis, cowplot
+Config/renv/profiles/full/dependencies: pkgdown, stringr, kableExtra,
+    usethis, cowplot, covr, devtools, shinymanager
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

NAMESPACE

@@ -13,7 +13,6 @@ export(adjust_colnames)
 export(app_ui)
 export(bind_rows_custom)
 export(check_appdata)
-export(check_available_data)
 export(clean_dates)
 export(collapse_column_vals)
 export(collapse_fct_levels)
@@ -26,8 +25,8 @@ export(custom_plot_theme)
 export(datatable_custom)
 export(date_cols_to_char)
 export(db_create)
-export(db_get_latest_query)
-export(db_get_latest_review)
+export(db_get_query)
+export(db_get_review)
 export(db_save)
 export(db_save_review)
 export(db_slice_rows)
@@ -38,7 +37,6 @@ export(fig_barplot)
 export(fig_boxplots)
 export(fig_timeline)
 export(fig_timeseries)
-export(filter_data)
 export(fix_multiple_choice_vars)
 export(get_appdata)
 export(get_available_data)
@@ -47,7 +45,8 @@ export(get_db_connection)
 export(get_ggplot_layer_names)
 export(get_max_time)
 export(get_meta_vars)
-export(get_raw_data)
+export(get_metadata)
+export(get_raw_csv_data)
 export(get_review_data)
 export(get_static_overview_data)
 export(get_test_results)
@@ -81,3 +80,4 @@ importFrom(shiny,shinyApp)
 importFrom(shiny,tagList)
 importFrom(stats,na.omit)
 importFrom(stats,setNames)
+importFrom(utils,modifyList)

NEWS.md

@@ -1,17 +1,35 @@
-# clinsight 0.0.9000 (development version)
+# clinsight 0.1.0
 
 ## Changed
 
+- Improved metadata so that external file can be used. 
+- Improved data loading by using a config file.
 - Created two renv profiles, one for development and one for production. Goal is 
 to minimize the package dependencies of the production version.
 - Removed development package dependencies (for example devtools) that were not needed to run the application.  
-- Improved data anonimization 
+- Improved data anonymization.
 - Changed license.
-
 - Updated Description file.
 - Improved reading of data files within clinsight::run_app()
 - Improved creating test result report.
+- Added data specification to `run_app()` documentation
+- Improved function `get_test_results()`.
+- Merged data now has an attribute 'synch_time' which will be used to update the synchronization information in the side bar.
+- user roles as defined in the config.yml will now be shown at several places in the application and will be documented alongside the user name if needed. 
+- Provided scaffolding for developers who plan to deploy on Posit Connect
+- Improved dataTable outputs
+- Move `shinymanager` to suggests since it is optional to use it.
+- Add functionality to mark which forms are required to review and which are not.
+- Improved required column verification of metadata columns when reading metadata using `get_metadata()`.
+- Improved visibility of queries, especially with longer query text and with smaller screen resolutions. Adds option to view query details in full screen.
 
 ## Bug fixes
 
 - Fixed error of creating adverse events table with empty data frame input. 
+- Properly handled zero regions selected in review configuration and provided user feedback.
+- Fixed issue with the timeline figure when a subject had no completed events.
+- Fixed pre-processing bug where `get_metadata()` would error when a metadata.xlsx tab exist, but were empty
+- Fixed error when running `golem::run_dev()` when `clinsight` was not installed.
+- Fixed error that the app did not recognize the user roles when using `shinymanager`. 
+- Fixed issue that item names and query types were not showing up in queries in PDF report.
+- Fixed an issue in the query system that duplicate item names in the same person and same form could not be distinguished from each other. 

R/_disable_autoload.R

@@ -0,0 +1,3 @@
+# Disabling shiny autoload
+
+# See ?shiny::loadSupport for more information