- fix merge confilicts

Merge branch 'main' into dev # Conflicts: # .github/workflows/docker-publish.yml # Dockerfile # components/mainpanel.R # components/server.R # functions/plotFunctions.R # install_packages.R # req.txt # tests/testthat/test_loadData_bruker.R # tests/testthat/test_loadData_mzML.R
CeMOS-Mannheim · Jul 1, 2024 · 6a5b8e4 · 6a5b8e4
2 parents 8fa3ee7 + 4c26569
commit 6a5b8e4
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diff --git a/Dockerfile b/Dockerfile
@@ -16,6 +16,7 @@ RUN R -e "packages <- readLines('/req.txt'); install.packages(packages)"
 # Install the MALDIcellassay from GitHub
 RUN R -e "pak::pkg_install('CeMOS-Mannheim/MALDIcellassay')"
 
+
 ## copy app folder into container
 COPY ./ ./app
 

diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Thomas Enzlein
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/components/server.R b/components/server.R
@@ -9,6 +9,42 @@ server <- function(input, output, session) {
 
   ## main ####
   appData <<- emptyAppDataObject()
+<<<<<<< HEAD
+=======
+  vol <- getVolumes()
+
+  # check if "dir" is set in defaults
+  if (!is.null(defaults$dir)) {
+    appData$selected_dir <- defaults$dir
+    message("Dir set from loaded default value.\n")
+    appData$info_state <- "dir_set"
+  }
+
+  ### choose dir ####
+  shinyDirChoose(input,
+                 "dir",
+                 roots = vol,
+                 allowDirCreate = FALSE,
+                 defaultRoot = names(vol)[1])
+
+  observeEvent(input$dir, {
+    # check if folder was selected
+    # prepare info massage
+    appData$selected_dir <- parseDirPath(vol, input$dir)
+    if (length(appData$selected_dir) > 0) {
+      appData$info_state <- "dir_set"
+    }
+  })
+
+  observeEvent(input$preproc_settings, {
+    appData$preprocessing$smooth <-
+      handlePreprocSettings(input$preproc_settings,
+                            "smooth")
+
+    appData$preprocessing$rmBl <-
+      handlePreprocSettings(input$preproc_settings,
+                            "rmBl")
+>>>>>>> main
 
   appData <- selectDir(appData, input)
 
@@ -188,6 +224,10 @@ server <- function(input, output, session) {
       ggplotly(p)
     } else {
       dummyPlot()
+<<<<<<< HEAD
+=======
+
+>>>>>>> main
     }
   })
 
@@ -253,10 +293,19 @@ server <- function(input, output, session) {
       p <- loadingsPlot(appData$pca,
                         pc = input$pcaX,
                         simple = input$simpleLoadings)
+<<<<<<< HEAD
+=======
+
+      return(p)
+>>>>>>> main
 
       return(p)
     } else {
       dummyPlot()
+<<<<<<< HEAD
+=======
+
+>>>>>>> main
     }
   })
 
@@ -285,6 +334,7 @@ server <- function(input, output, session) {
     }
   })
 
+<<<<<<< HEAD
   ### clustering tab #####
   observeEvent(input$doClust, {
     if (appData$show_plot) {
@@ -298,15 +348,38 @@ server <- function(input, output, session) {
     if (appData$show_plot & !is.null(appData$clust)) {
       show_spinner()
       p <- plotClusters(appData$clust, k = input$num_cluster)
+=======
+  #### HClust tab #####
+  observeEvent(input$doHC, {
+    if (appData$show_plot) {
+      show_spinner()
+
+      appData$hc <- clusterCurves(appData$res, nClusters = 15)
+>>>>>>> main
       hide_spinner()
       return(p)
     }
   })
+<<<<<<< HEAD
+=======
+  output$hclustPlot <- renderPlotly({
+    if (appData$show_plot & !is.null(appData$hc)) {
+      plotClusters(appData$hc, k = input$num_cluster)
+
+    }
+  })
+>>>>>>> main
 
   output$clustCurvesPlot <- renderPlotly({
     if (appData$show_plot & !is.null(appData$clust)) {
       show_spinner()
+<<<<<<< HEAD
       p <- plotTraj(appData$clust, k = input$num_cluster)
+=======
+
+      p <- plotTraj(appData$hc, k = input$num_cluster)
+
+>>>>>>> main
       hide_spinner()
       return(p)
     }
@@ -315,7 +388,12 @@ server <- function(input, output, session) {
   output$optNumClust <- renderPlotly({
     if (appData$show_plot & !is.null(appData$clust)) {
       show_spinner()
+<<<<<<< HEAD
       p <- plotClusterMetrics(appData$clust)
+=======
+      p <- plotClusterMetrics(appData$hc)
+
+>>>>>>> main
       hide_spinner()
       return(p)
     }
@@ -324,7 +402,14 @@ server <- function(input, output, session) {
   observeEvent(input$clust2peaksTable, {
     if (appData$show_plot & !is.null(appData$clust)) {
 
+<<<<<<< HEAD
       clusters <- extractLaClusters(appData$clust, k = input$num_cluster)
+=======
+  observeEvent(input$hc2peaksTable, {
+    if (appData$show_plot & !is.null(appData$hc)) {
+
+      clusters <- extractLaClusters(appData$hc, k = input$num_cluster)
+>>>>>>> main
       appData$stats <- appData$stats_original %>%
         left_join(clusters, by = join_by(mzIdx))
       message("Updated peak table with clustering data.\n")
@@ -350,12 +435,15 @@ server <- function(input, output, session) {
 
   exportTestValues(numSpec = length(appData$spec_all),
                    isSpectrumList = MALDIquant::isMassSpectrumList(appData$spec_all),
+<<<<<<< HEAD
                    infoState =  appData$info_state,
                    pca =  appData$pca,
                    clust = appData$clust)
+=======
+                   infoState =  appData$info_state)
+>>>>>>> main
 
   session$onSessionEnded(function() {
     stopApp()
   })
-
 }
diff --git a/functions/plotFunctions.R b/functions/plotFunctions.R
@@ -73,6 +73,7 @@ loadingsPlot <- function(pca, pc, simple = TRUE, n = 10) {
       theme(legend.position = "none")
   }
   p <- ggplotly(p)
+
   return(p)
 }
 

diff --git a/install_packages.R b/install_packages.R
@@ -30,5 +30,6 @@ options(dplyr.summarise.inform = FALSE)
 # special case for packages not on CRAN
 if (!require("MALDIcellassay", character.only = TRUE)) {
   pak::pkg_install("CeMOS-Mannheim/MALDIcellassay")
+
   library(MALDIcellassay, character.only = TRUE)
 }
diff --git a/req.txt b/req.txt
@@ -4,19 +4,39 @@ dplyr
 tibble
 tidyr
 ggplot2
+<<<<<<< HEAD
 forcats
+=======
+purrr
+readr
+stringr
+forcats
+shinyFiles
+>>>>>>> main
 MALDIquant
 MALDIquantForeign
 DT
 plotly
 shiny
+<<<<<<< HEAD
 shinyFiles
 shinycssloaders
 shinyhelper
 shinybusy
 shinytest2
 common
 knitr
+=======
+shinycssloaders
+shinyhelper
+shinybusy
+shinythemes
+shinyWidgets
+shinytest2
+common
+knitr
+devtools
+>>>>>>> main
 sparsepca
 platetools
 fs

diff --git a/tests/testthat/test_loadData_bruker.R b/tests/testthat/test_loadData_bruker.R
@@ -5,9 +5,18 @@ test_that("data can be loaded and processed from Bruker Flex",
               format(Sys.time(), "%H:%M:%OS")
             }
             setwd(dirname(common::file.find(pattern = "req.txt")))
+<<<<<<< HEAD
 
             # download test data and unzip
             curl::curl_download("https://figshare.com/ndownloader/files/46156791", "testdata_bruker.zip")
+=======
+            cat("Working directory is ", getwd(), "\n")
+
+            # download test data and unzip
+            cat(timeNow(), "downloading Bruker Flex test data...\n")
+            curl::curl_download("https://figshare.com/ndownloader/files/46156791", "testdata_bruker.zip")
+            cat(timeNow(), "unzip Bruker test data...\n")
+>>>>>>> main
             unzip("testdata_bruker.zip")
 
             # overwrite settings
@@ -20,19 +29,39 @@ test_that("data can be loaded and processed from Bruker Flex",
 
             library(shinytest2)
             options(shiny.testmode = TRUE)
+<<<<<<< HEAD
 
+=======
+            cat(timeNow(), "Starting app...\n")
+>>>>>>> main
             app <- AppDriver$new(app_dir = getwd(),
                                  name = "M2ara_bruker load test",
                                  seed = 42,
                                  timeout = 4.5*1e5)
 
+<<<<<<< HEAD
             app$click("load")
             Sys.sleep(120)
             app$click("process")
             exp <-app$get_values(export = TRUE)
 
             expect_equal(exp$export$isSpectrumList, TRUE)
             expect_equal(exp$export$numSpec, 88)
+=======
+            cat(timeNow(), "loading spectra...\n")
+            app$click("load")
+            Sys.sleep(120)
+            cat(timeNow(), "processing...\n")
+            app$click("process")
+            cat(timeNow(), "done!\n")
+            exp <-app$get_values(export = TRUE)
+
+            cat(timeNow(), "running tests...\n")
+            expect_equal(exp$export$isSpectrumList, TRUE)
+            expect_equal(exp$export$numSpec, 88)
+
+            cat(timeNow(), "Sucess! Cleaning up...\n")
+>>>>>>> main
             fs::dir_delete("Curve")
             fs::file_delete("settings.csv")
             fs::file_delete("testdata_bruker.zip")

diff --git a/tests/testthat/test_loadData_mzML.R b/tests/testthat/test_loadData_mzML.R
@@ -20,6 +20,8 @@ test_that("data can be loaded and processed from mzML",
 
             library(shinytest2)
             options(shiny.testmode = TRUE)
+
+            cat(timeNow(), "Starting app...\n")
             app <- AppDriver$new(app_dir = getwd(),
                                  name = "M2ara_mzML load test",
                                  seed = 42,