Merge pull request #141 from RE-QDA/dev

Thuringothyris

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

@@ -54,7 +54,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 1
+          cache-version: 2
           extra-packages: any::rcmdcheck
           needs: check
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: requal
 Title: Shiny Application for Computer-Assisted Qualitative Data Analysis
-Version: 1.1.1.9006
+Version: 1.1.2
 Authors@R:
     c(
      person(given = "Radim",

NEWS.md

@@ -1,3 +1,18 @@
+# requal 1.1.2 Thuringothyris
+
+__Release notes:__  
+
+- Export functions
+  - Export enabled for memos and codebooks. Segments export now includes character positions.
+- Citation information
+  - Updated citation information for proper referencing.
+- User Interface
+  - Minor UI updates plus a new logo.
+- Improved testing
+  - Certain behaviors are now formally tested with the integration of `shinytest2`.
+- Permission controls in server mode
+  - Project owners will no longer be able to inadvertently revoke their own permission privileges.
+
 # requal 1.1.1
 
 - export memos

R/app_ui.R

@@ -12,14 +12,14 @@ app_ui <- function(request, mode = NULL, access = NULL) {
     golem_add_external_resources(),
     # Your application UI logic
     dashboardPage(
-      title = "reQual",
+      title = "requal",
       options = list(sidebarExpandOnHover = FALSE),
       header = dashboardHeader(
         title = tags$span(
           tags$img(
             src = "www/requal_logo.png",
             height = "70%", style = "margin-right: 20px"
-          ), "reQual"
+          ), "requal"
         ),
         controlbarIcon = icon("ellipsis-v", id = "launchpad_icon"),
         dropdownBlock2(
@@ -62,7 +62,7 @@ golem_add_external_resources <- function() {
     favicon(),
     bundle_resources(
       path = app_sys("app/www"),
-      app_title = "reQual"
+      app_title = "requal"
     ),
     # Add here other external resources
     # for example, you can add shinyalert::useShinyalert()

R/db_startup.R

@@ -392,7 +392,7 @@ update_db_schema <- function(pool) {
 
       purrr::walk(to_create_tables$sql, ~ DBI::dbExecute(pool, .x))
     }
-    message("Updated reQual schema.")
+    message("Updated requal schema.")
   } else {
     NULL
   }
@@ -423,7 +423,7 @@ update_db_schema <- function(pool) {
 
       purrr::walk(to_create_tables$sql, ~ DBI::dbExecute(pool, .x))
     }
-    message("Updated reQual schema.")
+    message("Updated requal schema.")
   } else {
     NULL
   }

R/mod_about.R

@@ -10,7 +10,7 @@
 mod_about_ui <- function(id) {
   ns <- NS(id)
   # Citation info ----
-  rql_citation <- citation("requal")
+  rql_citation <- utils::citation("requal")
   # Extract authors
   authors <- sapply(as.character(rql_citation$author), function(x) strsplit(x, " ")) # Split the author names into first and last names
   # Format the authors as "Last name, Initial."
@@ -30,14 +30,14 @@ mod_about_ui <- function(id) {
         href = "https://requal.fsv.cuni.cz/",
         tags$img(src = "www/requal_logo.png", width = "5%"), target = "_blank"
       ),
-      "reQual CAQDAS"
+      "requal CAQDAS"
     ),
     textOutput(ns("version_project")),
     textOutput(ns("version_package")),
     p(),
     p(
       "For help, consult ",
-      a("reQual Wiki", href = "https://github.com/RE-QDA/requal/wiki", target = "_blank"),
+      a("requal Wiki", href = "https://github.com/RE-QDA/requal/wiki", target = "_blank"),
       ".",
       br(),
       "Leave feedback on our ",
@@ -68,7 +68,7 @@ mod_about_ui <- function(id) {
     p("To cite package", tags$code("requal"), "in publications use:"),
     HTML(apa_citation), p(),
     p("A BibTeX entry for LaTeX users:"),
-    tags$pre(paste(toBibtex(citation("requal")), collapse = "\n"))
+    tags$pre(paste(utils::toBibtex(utils::citation("requal")), collapse = "\n"))
   )
 }
 

R/mod_codebook.R

@@ -198,11 +198,11 @@ mod_codebook_server <- function(id, glob) {
 
    output$export_codebook <- downloadHandler(
      filename = function() {
-       "requal_codebook_export.csv"
+       "requal_codebook.csv"
      },
      content = function(file) {
        codebook <- get_codebook_export_table(glob)
-       write.csv(codebook, file)
+       utils::write.csv(codebook, file)
      }
    )
 

R/mod_doc_manager.R

@@ -1,6 +1,6 @@
 #' doc_manager UI Function
 #'
-#' @description This module accept document inputs and writes them to ReQual database.
+#' @description This module accept document inputs and writes them to Requal database.
 #'
 #' @param id,input,output,session Internal parameters for {shiny}.
 #'

R/mod_download_html.R

@@ -43,7 +43,7 @@ mod_download_html_server <- function(id, glob){
                                         winslash = "/", mustWork = FALSE)
             fileConn<-file(tempReport)
             writeLines(c("---",
-                         "title: 'reQual report'",
+                         "title: 'requal report'",
                          "output: html_document",
                          "---",
                          "```{r, echo=FALSE}",

R/mod_memo.R

@@ -185,7 +185,7 @@ mod_memo_server <- function(id, glob) {
         },
         content = function(file) {
             memos <- export_memos(glob$pool, glob$active_project)
-            write.csv(memos, file)
+            utils::write.csv(memos, file)
         }
     )
 

R/mod_memo_utils_memo.R

@@ -1,3 +1,5 @@
+utils::globalVariables(c("memo_title"))
+
 # list existing memos ------
 list_memo_records <- function(pool, project) {
     dplyr::tbl(pool, "memos") %>%

R/mod_project.R

@@ -1,3 +1,5 @@
+utils::globalVariables(c("project_description"))
+
 #' project UI Function
 #'
 #' @description A shiny Module.

R/mod_user_manager.R

@@ -97,10 +97,10 @@ mod_user_manager_server <- function(id, glob) {
 
       modified_permissions_df <- loc$users_permissions_df %>%
       dplyr::filter(user_id %in% input$members_permissions) %>%
-      dplyr::mutate(across(matches("modify|view"), .fns = function(x) {
+      dplyr::mutate(dplyr::across(dplyr::matches("modify|view"), .fns = function(x) {
         x  <- 0 # reset permissions
       })) %>%
-      dplyr::mutate(across(all_of(input$permissions_list), .fns = function(x) {
+      dplyr::mutate(dplyr::across(dplyr::all_of(input$permissions_list), .fns = function(x) {
         x  <- 1 # apply new permissions
       }))
 

R/mod_user_manager_utils_user_manager.R

@@ -1,4 +1,4 @@
-utils::globalVariables(c("user", "user_mail", "value_old"))
+utils::globalVariables(c("user", "user_mail", "value_old", "user_login"))
 
 # disabled_checkbox <- function(inputId, label, value = FALSE, width = NULL){
 #   value <- shiny::restoreInput(id = inputId, default = value)

R/mod_user_utils_user.R

@@ -128,7 +128,7 @@ permission_button <- function(class, color, title) {
 
 transform_user_table <- function(user_table) {
   user_table %>%
-    dplyr::mutate(across(-c(user_id, created_at, user_mail, user_name, user_login),
+    dplyr::mutate(dplyr::across(-c(user_id, created_at, user_mail, user_name, user_login),
       .fn = function(x) {
         dplyr::case_when(
           x == 1 & stringr::str_detect(dplyr::cur_column(), "other_modify") ~ permission_button("fas fa-users", "black", "Can modify others"),

README.Rmd

@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# reQual
+# requal
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
@@ -70,7 +70,7 @@ On the first launch of the app, use the "Create" menu to set up a new project by
 
 `requal` is designed with reproducibility, openness, and transparency in mind, and these values are most evident when it's used collaboratively. You can achieve this by self-hosting `requal` on your own server. A server instance of `requal` can support multiple users and offers fine-grained permission settings, making it easier to form diverse teams and collaborate in real time. With `requal`, you can discuss codes, evaluate agreement on codes, and estimate the sensitivity of coding to the attributes of your team members. 
 
-However, setting up a server instance is not a simple task. It requires a basic level of system administration experience. If you need assistance, the IT department at your institution should be able to help set up an `requal` server instance by following these [instructions](https://github.com/RE-QDA/requal/wiki/Server-setup). To get a sense of how `requal` operates in server mode, take a look at the public demo available on the [reQual project website](https://requal.fsv.cuni.cz/).
+However, setting up a server instance is not a simple task. It requires a basic level of system administration experience. If you need assistance, the IT department at your institution should be able to help set up an `requal` server instance by following these [instructions](https://github.com/RE-QDA/requal/wiki/Server-setup). To get a sense of how `requal` operates in server mode, take a look at the public demo available on the [requal project website](https://requal.fsv.cuni.cz/).
 
 >NOTE: It is crucial to prioritize __data security__ when hosting your `requal` instance publicly over the internet. At the very least, enabling the TLS protocol is a necessary precaution. However, be aware that this measure alone will not fully protect you from knowledgeable attackers. Consequently, it is important that you only analyze public, GDPR-compliant, and non-confidential data via `requal` in server mode. If you intend to use `requal` for collaborative work involving confidential or sensitive data, ensure this is done behind adequate firewalls or on internal networks established in secure locations. Always consult with your data stewards and/or research ethics committee to determine the appropriate level of security control for your dataset. In the future, we plan to provide support for data de-identification. This will allow you to perform de-identification locally and collaboratively analyze the de-identified dataset online.
 

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# reQual
+# requal
 
 <!-- badges: start -->
 
@@ -88,7 +88,7 @@ assistance, the IT department at your institution should be able to help
 set up an `requal` server instance by following these
 [instructions](https://github.com/RE-QDA/requal/wiki/Server-setup). To
 get a sense of how `requal` operates in server mode, take a look at the
-public demo available on the [reQual project
+public demo available on the [requal project
 website](https://requal.fsv.cuni.cz/).
 
 > NOTE: It is crucial to prioritize **data security** when hosting your
@@ -106,7 +106,7 @@ website](https://requal.fsv.cuni.cz/).
 > de-identification. This will allow you to perform de-identification
 > locally and collaboratively analyze the de-identified dataset online.
 
-## Acknowledgement
+## Acknowledgment
 
 The application development has been supported by The Technology Agency
 of the Czech Republic, project n. TL05000054, and CLS INFRA Fellowship

inst/WORDLIST

@@ -1,6 +1,26 @@
+Acknowledgement
+CLS
 CMD
+Coelostegus
 DESC
+DEV
+GDPR
 Lifecycle
-Reproducibility
+Programme
+RQDA
+TLS
+Thuringothyris
+UI
+caselinkage
+codebook
+codebooks
+codecat
+colours
+de
+freecode
 golem
+magrittr
+md
 reproducibility
+shinymanager
+shinytest

inst/test_app/tests/testthat/_snaps/app-create-codes.md

@@ -1,4 +1,4 @@
 # {shinytest2} testing create codebook
 
-    "requal_codebook_export.csv"
+    "requal_codebook.csv"
 

inst/test_app/tests/testthat/_snaps/app-create-codes/createcode-001.json

@@ -1,13 +1,13 @@
 {
   "output": {
     "codebook_ui_1-codes_ui": {
-      "html": "<div data-code_id=\"1\" class=\"code_item\" style=\"max-width: 500px\">\n  <div class=\"box box-solid collapsed-box bg-light-blue\" id=\"1\">\n    <div class=\"box-header with-border\">\n      <h3 class=\"box-title\">Code1<\/h3>\n      <div class=\"box-tools pull-right\">\n        <span class=\"label label-warning custom_label\" style=\"background-color:rgb(255, 255, 0) !important;\">code<\/span>\n        <button class=\"btn btn-box-tool btn-md\" type=\"button\" data-widget=\"collapse\">\n          <i class=\"fa fa-plus\" role=\"presentation\" aria-label=\"plus icon\"><\/i>\n        <\/button>\n      <\/div>\n    <\/div>\n    <div class=\"box-body\">\n      Code description\n      \n    <\/div>\n  <\/div>\n  <script type=\"application/json\" data-for=\"1\">{\"title\":\"Code1\",\"solidHeader\":true,\"background\":\"light-blue\",\"collapsible\":true,\"closable\":false,\"gradient\":false}<\/script>\n<\/div>",
+      "html": "<div data-code_id=\"1\" class=\"code_item\" style=\"max-width: 500px\">\n  <div class=\"box box-solid collapsed-box bg-light-blue\" id=\"1\">\n    <div class=\"box-header with-border\">\n      <h3 class=\"box-title\">Code1<\/h3>\n      <div class=\"box-tools pull-right\">\n        <span class=\"label label-warning custom_label\" style=\"background-color:rgb(255, 255, 0) !important;\">code<\/span>\n        <button class=\"btn btn-box-tool btn-md\" type=\"button\" data-widget=\"collapse\">\n          <i class=\"fas fa-plus\" role=\"presentation\" aria-label=\"plus icon\"><\/i>\n        <\/button>\n      <\/div>\n    <\/div>\n    <div class=\"box-body\">\n      Code description\n      \n    <\/div>\n  <\/div>\n  <script type=\"application/json\" data-for=\"1\">{\"title\":\"Code1\",\"solidHeader\":true,\"background\":\"light-blue\",\"collapsible\":true,\"closable\":false,\"gradient\":false}<\/script>\n<\/div>",
       "deps": [
         {
           "name": "font-awesome",
-          "version": "5.15.3",
+          "version": "6.4.2",
           "src": {
-            "href": "font-awesome-5.15.3"
+            "href": "font-awesome-6.4.2"
           },
           "meta": null,
           "script": null,