Feat/55 link to data source

.gitignore

@@ -2,4 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
+.Renviron
 docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DataTools
 Type: Package
 Title: Data Tools for Shiny Apps
-Version: 24.01.0
+Version: 24.03.0
 Authors@R: c(
             person("Antonia", "Runge", email = "antonia.runge@inwt-statistics.de", role = c("cre", "aut"))
             )
@@ -17,6 +17,7 @@ Imports:
   htmltools,
   httr,
   futile.logger,
+  jsonlite,
   magrittr,
   openxlsx,
   readxl,
@@ -37,5 +38,5 @@ Suggests:
   devtools,
   lintr (>= 1.0.2),
   testthat (>= 2.0.0)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://pandora-isomemo.github.io/data-tools/

NAMESPACE

@@ -23,6 +23,7 @@ export(startApplication)
 export(tryCatchWithWarningsAndErrors)
 export(updateListNamesIfDuplicate)
 export(updateNameEntryIfDuplicate)
+export(updateUserInputs)
 export(uploadModelServer)
 export(uploadModelUI)
 import(shiny, except = c(renderDataTable, dataTableOutput))
@@ -40,6 +41,7 @@ importFrom(RSQLite,SQLite)
 importFrom(RSQLite,dbConnect)
 importFrom(RSQLite,dbGetQuery)
 importFrom(RSQLite,dbListTables)
+importFrom(RSQLite,dbRemoveTable)
 importFrom(RSQLite,dbWriteTable)
 importFrom(dplyr,full_join)
 importFrom(dplyr,inner_join)
@@ -49,6 +51,8 @@ importFrom(htmltools,save_html)
 importFrom(httr,GET)
 importFrom(httr,content)
 importFrom(httr,timeout)
+importFrom(jsonlite,read_json)
+importFrom(jsonlite,write_json)
 importFrom(magrittr,"%>%")
 importFrom(openxlsx,loadWorkbook)
 importFrom(readxl,excel_sheets)

NEWS.md

@@ -1,5 +1,12 @@
 # DataTools
 
+## Version 24.03.0
+
+- option to download 'import links' to the imported data if data loading was successful in advance (#55)
+  - stores only user inputs to file imports, not the data itself
+  - all links to data that were 'submitted for data preparation' are stored also
+- option to upload 'import links' containing user inputs for data imports from a local .json file (#55)
+
 ## Version 24.01.0
 
 Integration of rgpt3 functions into data tools package

R/00-NAMESPACE.R

@@ -3,11 +3,12 @@
 #' @importFrom DT datatable renderDataTable dataTableOutput
 #' @importFrom htmltools save_html
 #' @importFrom httr GET content timeout
+#' @importFrom jsonlite read_json write_json
 #' @importFrom openxlsx loadWorkbook
 #' @importFrom Pandora callAPI getFileTypes getNetworks getRepositories getResources loadData
 #'  formatRepositoryList
 #' @importFrom readxl excel_sheets
-#' @importFrom RSQLite dbConnect dbGetQuery dbListTables dbWriteTable SQLite
+#' @importFrom RSQLite dbConnect dbGetQuery dbListTables dbWriteTable dbRemoveTable SQLite
 #' @importFrom shinyAce aceEditor updateAceEditor
 #' @importFrom shinyalert shinyalert
 #' @importFrom shinyjs alert disable disabled enable hide hidden info reset runjs show useShinyjs

R/01-toolsPanel.R

@@ -10,7 +10,7 @@ toolsImportUI <- function(id) {
     sidebarPanel(
       width = 2,
       style = "position:fixed; width:15%; max-width:350px; overflow-y:auto; height:88%",
-      importDataUI(ns("localData"), "Import Data"),
+      importDataUI(ns("localData"), "Import Data (local)"),
       tags$br(),
       tags$br(),
       importDataUI(ns("ckanData"), "Import CKAN Data"),
@@ -51,7 +51,8 @@ toolsImportServer <- function(id) {
                    customErrorChecks = list(reactive(checkErrorNoNumericColumns)),
                    ckanFileTypes = config()[["ckanFileTypes"]],
                    ignoreWarnings = TRUE,
-                   defaultSource = "ckan"
+                   defaultSource = "ckan",
+                   rPackageName = config()[["rPackageName"]]
                  )
 
                  importedBatchData <- importDataServer(
@@ -62,7 +63,8 @@ toolsImportServer <- function(id) {
                    ignoreWarnings = TRUE,
                    defaultSource = config()[["defaultSource"]],
                    batch = TRUE,
-                   outputAsMatrix = TRUE
+                   outputAsMatrix = TRUE,
+                   rPackageName = config()[["rPackageName"]]
                  )
 
                  importedModel <- importDataServer(
@@ -73,7 +75,6 @@ toolsImportServer <- function(id) {
                    ignoreWarnings = TRUE,
                    defaultSource = config()[["defaultSource"]],
                    importType = "model",
-                   mainFolder = config()[["mainFolder"]],
                    fileExtension = config()[["fileExtension"]],
                    rPackageName = config()[["rPackageName"]]
                  )

R/02-downAndUpload.R

@@ -19,9 +19,8 @@ downUploadButtonUI <-
 #' downUploadButton module server
 #'
 #' @param id module id
-#' @param rPackageName (character) name of the package (as in the description file) in which this
-#'  module is applied, e.g. "mpiBpred"
 #' @param title title used inside the modal
+#' @inheritParams importOptions
 #' @inheritParams downloadModelServer
 #' @inheritParams uploadModelUI
 #' @inheritParams uploadModelServer
@@ -147,8 +146,6 @@ downloadModelUI <- function(id, title = NULL, label = "Download", width = NULL)
 #' @param dat (reactive) user data
 #' @param inputs (reactiveValues) reactiveValues list of user inputs, in most cases just the "inputs" list
 #' @param model (reactive) model output object
-#' @param rPackageName (character) name of the package (as in the description file) in which this
-#'  module is applied, e.g. "mpiBpred"
 #' @param subFolder (character) (optional) subfolder containing loadable .zip files
 #' @param fileExtension (character) (optional) app specific file extension, e.g. "resources",
 #'  "bpred", "bmsc"
@@ -162,6 +159,7 @@ downloadModelUI <- function(id, title = NULL, label = "Download", width = NULL)
 #'  file is a connection.
 #' @param compressionLevel A number between 1 and 9. 9 compresses best, but it also takes the
 #'  longest.
+#' @inheritParams importOptions
 #'
 #' @export
 downloadModelServer <-
@@ -334,8 +332,7 @@ uploadModelUI <- function(id,
 #' @param mainFolder (character) folder containing all loadable .zip files. For most apps this
 #' is folder "predefinedModels". In most apps it can be found under "inst/app/".
 #' @param subFolder (character) (optional) subfolder containing loadable .zip files
-#' @param rPackageName (character) If not NULL, than the uploaded file must come from this R
-#'  package
+#' @inheritParams importOptions
 #' @inheritParams remoteModelsServer
 #'
 #' @export
@@ -422,6 +419,19 @@ getPathToLocal <- function(mainFolder, subFolder, rPackageName = NULL) {
   }
 }
 
+getSpecsForRemotes <- function(importType) {
+  if (importType != "data") {
+    folder <- "predefinedModels"
+    extension <- "zip"
+  } else {
+    folder <- "dataLinks"
+    extension <- "json"
+  }
+
+  list(folder = folder,
+       extension = extension)
+}
+
 dataLoadedAlert <-
   function(warnings,
            uploadedVersion,