From 1856552f4bed33a521e63b0d0117ca0c108fee05 Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Tue, 30 Sep 2025 14:53:20 +0200 Subject: [PATCH 1/9] import for module DT import for missing module DT --- app.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app.R b/app.R index 65fd238..338bed4 100644 --- a/app.R +++ b/app.R @@ -33,7 +33,7 @@ library(magrittr) library(rjson) # write JSON files library(jsonlite) # read JSON files - +library(DT) # interactive Tables in shiny library(igraph) From b46d2ae0dc107c20bc43669e9d5c48c121c2e4b3 Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Tue, 30 Sep 2025 15:32:15 +0200 Subject: [PATCH 2/9] bugfix: correct zip download in preprocessing zip download of preprocessed data was faulty; fixed by using zipr instead of zip function. Additionally small cosmetics to the code. --- app.R | 30 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 16 deletions(-) diff --git a/app.R b/app.R index 338bed4..285a754 100644 --- a/app.R +++ b/app.R @@ -736,7 +736,7 @@ fluidPage(clusteringCAMs_overallLevelUI("clusteringCAMs_overallLevel")) ) } - if ("approximateMatching" %in% globals$condition || + if ("approximateMatching" %in% globals$condition || "searchTerms" %in% globals$condition || "findSynonyms" %in% globals$condition || "word2vec" %in% globals$condition) { @@ -810,7 +810,7 @@ fluidPage(clusteringCAMs_overallLevelUI("clusteringCAMs_overallLevel")) ) } - if ("networkIndicators" %in% globals$condition) { + if ("networkIndicators" %in% globals$condition) { write( "\nnetworkIndicators: .txt file of all computed network indicators", path, @@ -836,7 +836,7 @@ fluidPage(clusteringCAMs_overallLevelUI("clusteringCAMs_overallLevel")) ) } - if ("networkNeighborhoodIndicators" %in% globals$condition) { + if ("networkNeighborhoodIndicators" %in% globals$condition) { write( "\nnetworkNeighborhoodIndicators: .txt file of all computed neighborhood indicators", path, @@ -861,31 +861,31 @@ fluidPage(clusteringCAMs_overallLevelUI("clusteringCAMs_overallLevel")) path, append = TRUE ) - } + } - if ("wordlistOverallCreated" %in% globals$condition) { - write( + if ("wordlistOverallCreated" %in% globals$condition) { + write( "\nwordlistOverall: .txt file of overall wordlist", path, append = TRUE ) - write( + write( "wordlistOverall: .xlsx (Excel) file of overall wordlist", path, append = TRUE ) } - if ("singleConceptsTable" %in% globals$condition) { - write( + if ("singleConceptsTable" %in% globals$condition) { + write( "\nsingleConceptsTable: .txt file of all drawn single concepts seperated by CAMs", path, append = TRUE ) - write( + write( "singleConceptsTable: .xlsx (Excel) file of all drawn single concepts seperated by CAMs", path, append = TRUE @@ -893,14 +893,14 @@ fluidPage(clusteringCAMs_overallLevelUI("clusteringCAMs_overallLevel")) } - if ("CAMsSlicedCreated" %in% globals$condition) { - write( + if ("CAMsSlicedCreated" %in% globals$condition) { + write( paste0("\nCAMs sliced datasets: .txt files (nodes, connectors, merged) created for central concept: ", globals$namingSlicedCAMs[1]), path, append = TRUE ) - write( + write( paste0("CAMs sliced datasets: .txt files (nodes, connectors, merged) created for central concept: ", globals$namingSlicedCAMs[2]), path, append = TRUE @@ -925,9 +925,7 @@ fluidPage(clusteringCAMs_overallLevelUI("clusteringCAMs_overallLevel")) # write(rjson::toJSON(globals$protocol), path) #jsonlite::write_json(x = globals$protocol, path = path) - - - zip(zipfile = fname, files = fs) + zip::zipr(zipfile = fname, files = fs) }, contentType = "application/zip" ) From 08f72becfcc226a8897e23c9833d286f6191373f Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Tue, 30 Sep 2025 16:03:41 +0200 Subject: [PATCH 3/9] bugfix: upload of protocol on local machine Now reads the text only once in correct encoding. --- www/modules/uploadServer.R | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/www/modules/uploadServer.R b/www/modules/uploadServer.R index 844427c..c00b5d4 100644 --- a/www/modules/uploadServer.R +++ b/www/modules/uploadServer.R @@ -292,16 +292,17 @@ uploadServer <- function(id, parent, globals) { ### upload protocol dataset protocol <- reactive({ ## to test validity of JSON file - text <- readLines(input$uploadProtocol$datapath, warn = FALSE) - text <- readLines(textConnection(text, encoding="UTF-8"), encoding="UTF-8") - if (testIfJson(file = text)) { + protocol <- reactive({ + req(input$uploadProtocol) + if (testIfJson(file = readLines(input$uploadProtocol$datapath, warn = FALSE, encoding="UTF-8"))) { protocol <- rjson::fromJSON(file = input$uploadProtocol$datapath) - return(protocol) - } else{ + } else { print("Invalid protocol uploaded") return(NULL) } + }) + # ## alternative From 69dfa13204dda2f81d278bbf13b7f35ee35c8f48 Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Tue, 30 Sep 2025 16:20:24 +0200 Subject: [PATCH 4/9] TEMP bugfix: accessing analysis part on local machine Was prohibited because of closure-error. Has to be fixed correctly by not using a list for "cleanValence" in the protocoll. --- www/modules/uploadServer.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/www/modules/uploadServer.R b/www/modules/uploadServer.R index c00b5d4..58e8e53 100644 --- a/www/modules/uploadServer.R +++ b/www/modules/uploadServer.R @@ -1079,7 +1079,7 @@ uploadServer <- function(id, parent, globals) { verbose = FALSE) ## set protocol to true - globals$protocol$cleanValence <- TRUE + globals$protocol()$cleanValence <- TRUE v$dfClean <- clean_ValenceData v$df <- clean_ValenceData From cf1d94515401a02c7b7a3ef9877f214b723e4a54 Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Tue, 30 Sep 2025 16:48:52 +0200 Subject: [PATCH 5/9] Revert "TEMP bugfix: accessing analysis part on local machine" This reverts commit 69dfa13204dda2f81d278bbf13b7f35ee35c8f48. --- www/modules/uploadServer.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/www/modules/uploadServer.R b/www/modules/uploadServer.R index 58e8e53..c00b5d4 100644 --- a/www/modules/uploadServer.R +++ b/www/modules/uploadServer.R @@ -1079,7 +1079,7 @@ uploadServer <- function(id, parent, globals) { verbose = FALSE) ## set protocol to true - globals$protocol()$cleanValence <- TRUE + globals$protocol$cleanValence <- TRUE v$dfClean <- clean_ValenceData v$df <- clean_ValenceData From e1c1d5333c0853348728e1e042e40ed1c7250be0 Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Tue, 30 Sep 2025 20:42:35 +0200 Subject: [PATCH 6/9] import for module stringdist --- app.R | 1 + 1 file changed, 1 insertion(+) diff --git a/app.R b/app.R index 285a754..d3417de 100644 --- a/app.R +++ b/app.R @@ -38,6 +38,7 @@ library(DT) # interactive Tables in shiny library(igraph) library(sortable) +library(stringdist) library(vroom) library(xlsx) From c9ef3b148879bdc89c39c29860c32d5c9ea05cbf Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Tue, 30 Sep 2025 20:48:10 +0200 Subject: [PATCH 7/9] bugfix and code-cleaning Fixed my own bug (had protocol <- reactive nested in itself) and also cleaned up the code a bit. --- www/modules/uploadServer.R | 303 ++++++++++++++++++++----------------- 1 file changed, 162 insertions(+), 141 deletions(-) diff --git a/www/modules/uploadServer.R b/www/modules/uploadServer.R index c00b5d4..5581972 100644 --- a/www/modules/uploadServer.R +++ b/www/modules/uploadServer.R @@ -290,45 +290,26 @@ uploadServer <- function(id, parent, globals) { #> Server ### upload protocol dataset + + ## to test validity of JSON file protocol <- reactive({ - ## to test validity of JSON file - protocol <- reactive({ - req(input$uploadProtocol) - if (testIfJson(file = readLines(input$uploadProtocol$datapath, warn = FALSE, encoding="UTF-8"))) { - protocol <- rjson::fromJSON(file = input$uploadProtocol$datapath) - return(protocol) - } else { - print("Invalid protocol uploaded") - return(NULL) - } - }) - - - - # ## alternative - # text <- readLines(input$uploadProtocol$datapath) - # text <- readLines(textConnection(text, encoding="UTF-8"), encoding="UTF-8") - # if (testIfJson(file = text)) { - # protocol <- jsonlite::fromJSON(txt = text) - # # jsonlite::read_json(path = input$uploadProtocol$datapath) - # # rjson::fromJSON(file = input$uploadProtocol$datapath) - # return(protocol) - # } else{ - # print("ERROR") - # return(NULL) - # } - # - # ## right encoding - # for(i in 1:length(protocol$approximateMatching)){ - # Encoding(x = protocol$approximateMatching[[i]]$wordsFound) <- "latin1" - # Encoding(x = protocol$approximateMatching[[i]]$supordinateWord) <- "latin1" - # } + req(input$uploadProtocol) + if (testIfJson(file = readLines(input$uploadProtocol$datapath, warn = FALSE, encoding="UTF-8"))) { + protocol <- rjson::fromJSON(file = input$uploadProtocol$datapath) + return(protocol) + } else { + print("Invalid protocol uploaded") + return(NULL) + } }) + observeEvent(input$uploadProtocol, { + print("observer for uploadProtocol is triggered") if (!is.null(protocol())) { message("successfully uploaded protocol!") v$protocol = TRUE + print(v$protocol) } else{ v$protocol = FALSE showModal( @@ -366,9 +347,10 @@ uploadServer <- function(id, parent, globals) { ### create three data sets with nodes / connectors / merged - data <- reactive({ - # wait for upload + uploadedData <- reactive({ req(ext()) + print("uploadedData ist being read") + print(ext()) ## if CAMEL data (checked by .txt ending) if (all(stringr::str_detect(string = ext(), pattern = "txt"))) { @@ -397,6 +379,7 @@ uploadServer <- function(id, parent, globals) { ) ) v$dataUploaded <- "no" + print("Uploaded raw_CAM Datei doesn't seem to be a valid Data Collection Tool dataset..") return(NULL) } } @@ -417,6 +400,7 @@ uploadServer <- function(id, parent, globals) { ) ) v$dataUploaded <- "no" + print("CAMs are not valid Data Collection Tool datasets or a empty") return(NULL) } @@ -428,13 +412,24 @@ uploadServer <- function(id, parent, globals) { ## if JSON file } else if (all(stringr::str_detect(string = ext(), pattern = "json"))) { + print("Starting JSON-Branch") + print(input$upload$datapath) + print(ext()) + print("testIfJson:") + print(testIfJson(input$upload$datapath)) + if(testIfJson(input$upload$datapath)) { raw <- jsonlite::fromJSON(input$upload$datapath, simplifyVector = FALSE) - + + #print("raw nach fromJSON:") + #str(raw, max.level=2) + # Then apply fromJSON again per CAM - this allows proper simplification dat <- lapply(raw, function(cam) { jsonlite::fromJSON(jsonlite::toJSON(cam, auto_unbox = TRUE)) }) + #print("dat nach lapply:") + #str(dat, max.level=2) } else { showModal( modalDialog( @@ -447,12 +442,15 @@ uploadServer <- function(id, parent, globals) { ) ) v$dataUploaded <- "no" + print("CAMs scheinen fehlerhaft zu sein. (TestifJson)") return(NULL) } CAMfiles <- create_CAMfiles(datCAM = dat, reDeleted = TRUE, verbose = FALSE) + #print("CAMfiles nach create_CAMfiles:") + #str(CAMfiles, max.level=2) # check if parsing CAMs was successful if(is.null(CAMfiles)) { @@ -467,6 +465,7 @@ uploadServer <- function(id, parent, globals) { ) ) v$dataUploaded <- "no" + print("CAM doesn't have a valid Data Collection Tool dataset or it contains only empty CAMS") return(NULL) } @@ -474,6 +473,9 @@ uploadServer <- function(id, parent, globals) { CAMfiles[[1]]$text <- stringr::str_trim(string = CAMfiles[[1]]$text, side = "both") v$dataUploaded <- "yes" + + #print("CAMfiles nach trim:") + #str(CAMfiles, max.level=2) ## if Valence data (checked by .csv ending) } else if (all(stringr::str_detect(string = ext(), pattern = "csv"))) { @@ -491,6 +493,7 @@ uploadServer <- function(id, parent, globals) { ) ) v$dataUploaded <- "no" + print("Not enough csv files") return(NULL) } @@ -498,10 +501,10 @@ uploadServer <- function(id, parent, globals) { ## names for blocks and links files files_blocks <- sort(stringr::str_subset(string = input$upload[, "name"], - pattern = "blocks")) + pattern = "blocks")) files_links <- sort(stringr::str_subset(string = input$upload[, "name"], - pattern = "links")) + pattern = "links")) ## check: equal numbers of blocks and links dataset if (v$boolContinue) { @@ -518,6 +521,7 @@ uploadServer <- function(id, parent, globals) { ) ) v$dataUploaded <- "no" + print("csv files do not have the same number of blocks and links") return(NULL) } } @@ -548,6 +552,7 @@ uploadServer <- function(id, parent, globals) { ) ) v$dataUploaded <- "no" + print("CSV Files do not have identical IDs in the format ID_CAMnumber_links/blocks") return(NULL) } } @@ -611,7 +616,7 @@ uploadServer <- function(id, parent, globals) { CAMfiles <- NULL } - } else{ + }else{ ## if no CAMEL or Valence files have been upload showModal(modalDialog( title = "Wrong files", @@ -631,13 +636,14 @@ uploadServer <- function(id, parent, globals) { # print(head(CAMfiles[[3]])) if(v$protocol){ - # print(globals$protocol) + #Possible error, if protocol()$software is NULL! globals$protocol$software <- protocol()$software - globals$protocol$cleanValence <- protocol()$cleanValence + ## keep only CAMs which have not been deleted if(length(protocol()$currentCAMs) > 0){ + print("tries to ony keep CAMs which have not been deleted?") # if participants IDs have been used in the draw CAM step if(all(unlist(protocol()$currentCAMs) %in% CAMfiles[[1]]$CAM)){ CAMfiles[[1]] <- CAMfiles[[1]][CAMfiles[[1]]$CAM %in% unlist(protocol()$currentCAMs), ] @@ -660,9 +666,10 @@ uploadServer <- function(id, parent, globals) { } if(length(protocol()$approximateMatching) > 0 - || length(protocol()$searchTerms) > 0 - || length(protocol()$findSynonyms) > 0 - || length(protocol()$modelwordVec) > 0){ + || length(protocol()$searchTerms) > 0 + || length(protocol()$findSynonyms) > 0 + || length(protocol()$modelwordVec) > 0){ + print("tries to overwrite protocol, if apporximate Matching has been done") CAMfiles[[1]]$text_summarized <- CAMfiles[[1]]$text tmp_out <- overwriteTextNodes(protocolDat = protocol(), nodesDat = CAMfiles[[1]]) CAMfiles[[1]] <- tmp_out[[1]] @@ -679,9 +686,9 @@ uploadServer <- function(id, parent, globals) { # print("globals$protocol:") # print(globals$protocol) } - ## save as global variable - else triggered to early + ## save as global variable - else triggered to early - # print(globals$protocol$cleanValence) + # print(globals$protocol$cleanValence) if(!globals$protocol$cleanValence[[1]]){ v$df <- CAMfiles @@ -691,21 +698,37 @@ uploadServer <- function(id, parent, globals) { dat_merged = CAMfiles[[3]], verbose = FALSE) message("successfully cleaned Valence data!") - } # nodes_raw$text_summarized <- nodes_raw$text - + print("End of uploadedData, v$df:") + print(str(v$df, max.level=1)) return(v$df) ### ??? CAMfiles }) - + ## SAVE to globals ## observeEvent(input$upload, { + print("Input upload:") + print(input$upload) + print("ext:") + print(ext()) + if (!exists("uploadedData") || is.null(uploadedData)){ + print("uploadedData ist NULL!") + return(NULL) + } + + dat <- tryCatch(uploadedData(), error = function(e) NULL) + if (is.null(dat)) { + print("uploadedData() ist NULL!") + return(NULL) + } + req(dat) + req(ext()) - req(data()) + req(uploadedData()) message("uploaded file(s) - extensions:", ext()) - if (!is.null(v$df)) { + if (v$dataUploaded == "yes" && !is.null(v$df)) { message("successfully uploaded data!") #> change condition globals$condition <- @@ -727,6 +750,7 @@ uploadServer <- function(id, parent, globals) { tmp_list } } else{ + print("Fehler beim Data-Upload") #> avoid error in download function globals$condition <- str_replace_all( @@ -738,7 +762,7 @@ uploadServer <- function(id, parent, globals) { globals$protocol$software[[length(globals$protocol$software) + 1]] <- c("unknown", as.character(as.POSIXct(Sys.time()))) } - }) + }, ignoreNULL = TRUE) #### @@ -940,6 +964,7 @@ uploadServer <- function(id, parent, globals) { if(length(list_summarizeTerms) == 0){ + print("Länge der list_summarizeTerms ist Null)") return(NULL) } @@ -1193,105 +1218,101 @@ uploadServer <- function(id, parent, globals) { ) }) -#> Server -split_data <- reactive({ - - tmp_extensions <- tools::file_ext(input$split_uploadCAMfiles$name) - print(tmp_extensions) - - ## if CAMEL data (checked by .txt ending) - - if (all(stringr::str_detect(string = tmp_extensions, pattern = "txt")) && length(tmp_extensions) == 3 && all(stringr::str_detect(string = input$split_uploadCAMfiles$name, pattern = "nodes|connectors|merged"))){ - - -tmp_names <- input$split_uploadCAMfiles$name -tmp_datapat <- input$split_uploadCAMfiles$datapath - -CAMfiles <- list() -CAMfiles[[1]] <- vroom::vroom( - file = tmp_datapat[stringr::str_detect(string = tmp_names, pattern = "nodes")], - delim = "\t", - show_col_types = FALSE, - col_names = TRUE -) -## trim whitespace -CAMfiles[[1]]$text <- - stringr::str_trim(string = CAMfiles[[1]]$text, side = "both") + #> Server + split_data <- reactive({ + + tmp_extensions <- tools::file_ext(input$split_uploadCAMfiles$name) + print(tmp_extensions) + + ## if CAMEL data (checked by .txt ending) - if(any(colnames(CAMfiles[[1]]) == "text_summarized")){ -## trim whitespace -CAMfiles[[1]]$text_summarized <- - stringr::str_trim(string = CAMfiles[[1]]$text_summarized, side = "both") + if (all(stringr::str_detect(string = tmp_extensions, pattern = "txt")) && length(tmp_extensions) == 3 && all(stringr::str_detect(string = input$split_uploadCAMfiles$name, pattern = "nodes|connectors|merged"))){ - ## remove white spaces before suffixes - CAMfiles[[1]]$text_summarized <- str_remove_all(string = CAMfiles[[1]]$text_summarized, pattern = "\\s(?=(_neutral$|_positive$|_negative$|_ambivalent$))") - } - + tmp_names <- input$split_uploadCAMfiles$name + tmp_datapat <- input$split_uploadCAMfiles$datapath + CAMfiles <- list() + CAMfiles[[1]] <- vroom::vroom( + file = tmp_datapat[stringr::str_detect(string = tmp_names, pattern = "nodes")], + delim = "\t", + show_col_types = FALSE, + col_names = TRUE + ) + ## trim whitespace + CAMfiles[[1]]$text <- + stringr::str_trim(string = CAMfiles[[1]]$text, side = "both") -CAMfiles[[2]] <- vroom::vroom( - file = tmp_datapat[stringr::str_detect(string = tmp_names, pattern = "connectors")], - delim = "\t", - show_col_types = FALSE, - col_names = TRUE -) + if(any(colnames(CAMfiles[[1]]) == "text_summarized")){ + ## trim whitespace + CAMfiles[[1]]$text_summarized <- + stringr::str_trim(string = CAMfiles[[1]]$text_summarized, side = "both") -CAMfiles[[3]] <- vroom::vroom( - file = tmp_datapat[stringr::str_detect(string = tmp_names, pattern = "merged")], - delim = "\t", - show_col_types = FALSE, - col_names = TRUE -) + ## remove white spaces before suffixes + CAMfiles[[1]]$text_summarized <- str_remove_all(string = CAMfiles[[1]]$text_summarized, pattern = "\\s(?=(_neutral$|_positive$|_negative$|_ambivalent$))") + } + + CAMfiles[[2]] <- vroom::vroom( + file = tmp_datapat[stringr::str_detect(string = tmp_names, pattern = "connectors")], + delim = "\t", + show_col_types = FALSE, + col_names = TRUE + ) + CAMfiles[[3]] <- vroom::vroom( + file = tmp_datapat[stringr::str_detect(string = tmp_names, pattern = "merged")], + delim = "\t", + show_col_types = FALSE, + col_names = TRUE + ) - ## continue analysis - v$df <- CAMfiles - v$dataUploaded <- "yes" + ## continue analysis + v$df <- CAMfiles + v$dataUploaded <- "yes" - } else { - if(!all(stringr::str_detect(string = tmp_extensions, pattern = "txt")) || length(tmp_extensions) != 3){ - showModal( - modalDialog( - title = "Invalid raw data", - paste0( - "You have uploaded ", length(tmp_extensions), " files. Please upload exactly three files .txt files." - ), - easyClose = TRUE, - footer = tagList(modalButton("Ok")) - ) - ) - }else if(!all(stringr::str_detect(string = input$split_uploadCAMfiles$name, pattern = "nodes|connectors|merged"))){ - showModal( - modalDialog( - title = "Invalid raw data", - paste0( - "You have uploaded files with the following names: ", paste0(input$split_uploadCAMfiles$name, collapse = ", ")," files. Please upload exactly three .txt files containing the names nodes, connectors, merged." - ), - easyClose = TRUE, - footer = tagList(modalButton("Ok")) - ) - ) - } - } - }) + } else { + if(!all(stringr::str_detect(string = tmp_extensions, pattern = "txt")) || length(tmp_extensions) != 3){ + showModal( + modalDialog( + title = "Invalid raw data", + paste0( + "You have uploaded ", length(tmp_extensions), " files. Please upload exactly three files .txt files." + ), + easyClose = TRUE, + footer = tagList(modalButton("Ok")) + ) + ) + }else if(!all(stringr::str_detect(string = input$split_uploadCAMfiles$name, pattern = "nodes|connectors|merged"))){ + showModal( + modalDialog( + title = "Invalid raw data", + paste0( + "You have uploaded files with the following names: ", paste0(input$split_uploadCAMfiles$name, collapse = ", ")," files. Please upload exactly three .txt files containing the names nodes, connectors, merged." + ), + easyClose = TRUE, + footer = tagList(modalButton("Ok")) + ) + ) + } + } + }) -observeEvent(input$split_uploadExcel, { - showModal( - modalDialog( - title = "Will be implemented soon", - paste0( - "Just wait for it." - ), - easyClose = TRUE, - footer = tagList(modalButton("Ok")) - ) - ) -}) + observeEvent(input$split_uploadExcel, { + showModal( + modalDialog( + title = "Will be implemented soon", + paste0( + "Just wait for it." + ), + easyClose = TRUE, + footer = tagList(modalButton("Ok")) + ) + ) + }) ## wait for uploaded files ## observeEvent(input$split_uploadCAMfiles, { @@ -1320,11 +1341,11 @@ observeEvent(input$split_uploadExcel, { tags$br(), HTML( 'The tool is a shiny-App programmed in the R environment. Every time you have finished the central step of - the module (here the Upload step) you can click "continue" in the bottom right to jump to the next - module. This is just a recommended procedure, whereby the first two steps - uploading your data and draw your CAMs - is mandatory. Feel free to skip every other module. - The central step within each module is depicted in bold. -
- The application is divided in two central parts, whereby for the first part a protocol is generated, which should be uploaded together with the raw dataset(s).' + the module (here the Upload step) you can click "continue" in the bottom right to jump to the next + module. This is just a recommended procedure, whereby the first two steps - uploading your data and draw your CAMs - is mandatory. Feel free to skip every other module. + The central step within each module is depicted in bold. +
+ The application is divided in two central parts, whereby for the first part a protocol is generated, which should be uploaded together with the raw dataset(s).' ), tags$ol(tags$li( HTML('Prep-rocessing Part: using multiple modules it is possible to summarize the CAM data semi-automatically') From 1cf64f712021346ed677c4dd8705d6ca3a5694f5 Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Tue, 30 Sep 2025 20:56:18 +0200 Subject: [PATCH 8/9] small error catch --- www/modules/uploadServer.R | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/www/modules/uploadServer.R b/www/modules/uploadServer.R index 5581972..9c9b897 100644 --- a/www/modules/uploadServer.R +++ b/www/modules/uploadServer.R @@ -635,8 +635,11 @@ uploadServer <- function(id, parent, globals) { # print(head(CAMfiles[[2]])) # print(head(CAMfiles[[3]])) - if(v$protocol){ + print("Starting protocol-section") + tryCatch({ + if(v$protocol){ #Possible error, if protocol()$software is NULL! + req(protocol()) globals$protocol$software <- protocol()$software globals$protocol$cleanValence <- protocol()$cleanValence @@ -685,7 +688,8 @@ uploadServer <- function(id, parent, globals) { # print("globals$protocol:") # print(globals$protocol) - } + }}, error = function(e) { + print(paste("error in protocol section:", e$message))}) ## save as global variable - else triggered to early # print(globals$protocol$cleanValence) From e07c776f0dcc4568f5c083e398ecd33482ac69ce Mon Sep 17 00:00:00 2001 From: moritzoc <93144026+moritzoc@users.noreply.github.com> Date: Wed, 1 Oct 2025 09:47:16 +0200 Subject: [PATCH 9/9] typo: comment --- www/modules/uploadServer.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/www/modules/uploadServer.R b/www/modules/uploadServer.R index 9c9b897..8f16f2c 100644 --- a/www/modules/uploadServer.R +++ b/www/modules/uploadServer.R @@ -646,7 +646,7 @@ uploadServer <- function(id, parent, globals) { ## keep only CAMs which have not been deleted if(length(protocol()$currentCAMs) > 0){ - print("tries to ony keep CAMs which have not been deleted?") + print("tries to only keep CAMs which have not been deleted") # if participants IDs have been used in the draw CAM step if(all(unlist(protocol()$currentCAMs) %in% CAMfiles[[1]]$CAM)){ CAMfiles[[1]] <- CAMfiles[[1]][CAMfiles[[1]]$CAM %in% unlist(protocol()$currentCAMs), ]