Feature/minio connection

.dockerignore

@@ -3,6 +3,7 @@
 !calculation_options.csv
 !calculation_variables.csv
 !processedCols.csv
+!isotopes.json
 !DataRequirements.md
 !Docker_instructions.md
 !peakData_Report.Rmd

.gitignore

@@ -36,3 +36,9 @@ tests/test_*/
 script_dump.R
 packrat/lib*/
 Data/
+untracked_resources
+cfg
+!cfg/minio_config_example.yml
+!cfg/minio_config_corems.yml
+renv
+!renv/settings.json

.renvignore

@@ -0,0 +1,3 @@
+untracked_resources
+.git
+tests/

DESCRIPTION

@@ -0,0 +1,51 @@
+Package: FREDA
+Title: An app for the processing and visualization of Fourier-transform mass spectrometry data.
+Version: 1.7
+Authors@R: c(person("Lisa", "Bramer", "[email protected]", role = "aut", "cre"),
+    person("Daniel", "Claborne", "[email protected]", role = c("aut")))
+Description: A frontend application which exposes functionality of the ftmsRanalysis R package.  See 
+License: GPL (>= 3) + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.1
+Depends:
+    R (>= 4.1.0)
+Imports:
+    dplyr, 
+    DT, 
+    ggplot2, 
+    htmlwidgets, 
+    jsonlite, 
+    kableExtra, 
+    KeggData, 
+    knitr,
+    markdown, 
+    pander, 
+    plotly, 
+    purrr, 
+    raster, 
+    RColorBrewer, 
+    readr, 
+    reshape2, 
+    reticulate, 
+    rlang, 
+    rmarkdown, 
+    scales, 
+    shiny, 
+    shinyBS, 
+    shinycssloaders, 
+    shinyjs, 
+    shinyWidgets, 
+    sp, 
+    stringr, 
+    tibble, 
+    tidyr, 
+    viridis,
+    webshot, 
+    withr, 
+    xfun,
+    MetaCycData, 
+    mapDataAccess,
+    ftmsRanalysis,
+    datadr
+

Dockerfile

@@ -15,4 +15,4 @@ COPY . /srv/shiny-server/FREDA
 COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
 
 # App is run as user shiny, need to change ownership
-RUN chown -R shiny:shiny /srv/shiny-server/FREDA /opt/orca/squashfs-root
+RUN chown -R shiny:shiny /srv/shiny-server/FREDA

Dockerfile-base

@@ -1,52 +1,31 @@
-FROM rocker/shiny:4.1.1
+FROM rocker/shiny:4.2.3
 
 RUN apt-get update -qq && apt-get install -y \
   git-core \
   libssl-dev \
   libcurl4-gnutls-dev \
   libmagick++-dev \
   libv8-dev \
-  vim python3-venv
+  vim python3-venv \
+  libgdal-dev
 
 WORKDIR /srv/shiny-server/
-COPY renv.lock .
 
 # pre-install renv
-RUN R -e "install.packages('renv', repos = 'https://cran.rstudio.com')"
+ENV RENV_VERSION 1.0.3
+RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
+RUN R -e "options('repos'=c(CRAN = 'https://cloud.r-project.org'));remotes::install_version('renv', version = '${RENV_VERSION}')"
 
 # install all packages listed in renv.lock
+COPY renv.lock .
 RUN --mount=type=secret,id=access_tokens set -a \
 && . /run/secrets/access_tokens && set +a \
-&& R -e 'renv::restore()'
+&& R -e 'options(renv.config.connect.timeout=300);options(timeout=300);renv::restore()'
 
 ## Setup Python venv ##
 USER root
 COPY python_requirements.txt .
 RUN python3 -m venv /venv
 RUN /venv/bin/pip install --upgrade pip
 RUN /venv/bin/pip install -r python_requirements.txt
-
-# Install all plotly's dependencies
-RUN R -e "install.packages('plotly', dependencies = T)"
-
-# Download orca binary and make it executable under xvfb
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-        xvfb \
-        xauth \
-        libgtk2.0-0 \
-        libxtst6 \
-        libxss1 \
-        libgconf-2-4 \
-        libnss3 \
-        libasound2 && \
-    mkdir -p /opt/orca && \
-    cd /opt/orca && \
-    wget https://github.com/plotly/orca/releases/download/v1.2.1/orca-1.2.1-x86_64.AppImage && \
-    chmod +x orca-1.2.1-x86_64.AppImage && \
-    ./orca-1.2.1-x86_64.AppImage --appimage-extract && \
-    rm orca-1.2.1-x86_64.AppImage && \
-    printf '#!/bin/bash \nxvfb-run --auto-servernum --server-args "-screen 0 640x480x24" /opt/orca/squashfs-root/app/orca "$@"' > /usr/bin/orca && \
-    chmod +x /usr/bin/orca && \
-    apt-get remove -y libnode-dev
 

Observers/corems_observers.R

@@ -0,0 +1,123 @@
+#' @details Convert the filtered corems data to peakData
+#' cms_dat_unq_mf() is converted into peakData using CoreMSData_to_ftmsData and
+#' the result is stored in revals$uploaded_data
+observeEvent(
+  c(
+    input$corems_to_peakdata,
+    input$corems_to_peakdata_modal
+  ), {
+
+    req(cms_dat_unq_mf())
+    req(isTruthy(input$corems_to_peakdata > 0) | isTruthy(input$corems_to_peakdata_modal > 0))
+
+    revals$uploaded_data <- revals$peakData2 <- NULL
+
+    res <- tryCatch({
+      ftmsRanalysis::coreMSDataToFtmsData(cms_dat_unq_mf())
+    },
+    error = function(e) {
+      msg = paste0('Error converting your coreMS data to peakData: \n System error: ', e)
+      revals$warningmessage_corems$corems_to_peakdata <<- sprintf("<p style = 'color:red'>%s</p>", msg)
+      revals$warningmessage_corems$corems_to_peakdata
+    })
+
+    if (inherits(res, "peakData")) {
+      # need a fake f_data column.
+      if (ncol(res$f_data) == 1) {
+        res$f_data[, 2] <- NA
+      }
+
+      revals$uploaded_data <- res
+    } else {
+      if (inherits(res, "character")) {
+        msg = res
+      } else {
+        msg = "Error converting your coreMS data to peakData"
+      }
+
+      showNotification(
+        HTML(msg),
+        duration = NULL,
+        type = "error"
+      )
+    }
+}, ignoreInit = T)
+
+#' @details Show a modal for the completion of corems data
+observeEvent(cms_data(), {
+  req(cms_data(), input$top_page == "CoreMS-create")
+
+  updateCollapse(session, id = "corems-upload-summary-collapse",
+    open = c("corems-upload-visualize"), close = c("corems-upload-table"))
+
+  showModal(
+    # defined in srv_ui_elements/corems_UI.R
+    corems_obj_creation_modal()
+  )
+})
+
+#' @details Go to the corems filter tab from the object creation success tab.
+observeEvent(input$goto_corems_filter, {
+  req(input$top_page == "CoreMS-create")
+  updateTabsetPanel(inputId = "top_page", selected = "CoreMS-conf-filter")
+  removeModal()
+})
+
+#' @details Move the user to the create CoreMSData tab after successful upload
+observeEvent(input$goto_corems_creation, {
+  updateTabsetPanel(inputId = "top_page", selected = "CoreMS-create")
+  removeModal()
+})
+
+#' @details (CoreMS filter tab) Show summary plot and show progression modal
+observeEvent(cms_data_filtered(), {
+  req(cms_data_filtered())
+  updateCollapse(session, id = "corems-filter-summary-collapse",
+    open = c("viz"))
+  updateTabsetPanel(inputId = "corems-viz-tabset", selected = "filt_summary_plot")
+
+  showModal(corems_filter_modal())
+})
+
+#' @details Move user to the formula assignment tab after successful filtering
+observeEvent(input$goto_corems_formula, {
+  updateTabsetPanel(inputId = "top_page", selected = "CoreMS-formula-assign")
+  removeModal()
+})
+
+#' @details display table visualization panels and prompt user for next steps
+#' when unique molecular formula are assigned.
+observeEvent(cms_dat_unq_mf(), {
+  hide("corems_to_peakdata_toggle")
+  req(cms_dat_unq_mf())
+  updateCollapse(session, id = "corems-assign-formula", open = c("viz", "tables"))
+  showModal(corems_unq_mf_modal())
+  show("corems_to_peakdata_toggle")
+})
+
+#' @details disable functionality and helper css for arguments required for corems
+observe({
+  req(input$top_page == "CoreMS-create")
+  fields_filled = TRUE
+
+  for(arg in COREMSDATA_REQ_ARGS) {
+    is_selected = isTruthy(input[[arg]] != NULLSELECT__)
+    toggleCssClass(sprintf("%s_UI", arg), "attention", !is_selected)
+    if(!is_selected) {
+      fields_filled = FALSE
+    }
+  }
+
+  toggleState("make_cmsdata", condition = fields_filled)
+
+  if (!fields_filled) {
+    showNotification(
+      ui = "One or more required fields for making your coreMS data object are not specified",
+      type = "warning",
+      id = "as-corems-args-notification"
+    )
+  } else {
+    removeNotification("as-corems-args-notification")
+  }
+
+})