Feature/basic tests

.Rbuildignore

@@ -0,0 +1,5 @@
+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/actions/renv-plus/LICENSE

@@ -0,0 +1,25 @@
+The MIT License (MIT)
+=====================
+
+Copyright © 2021 RStudio and others.
+
+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.

.github/actions/renv-plus/README.md

@@ -0,0 +1,32 @@
+# setup-renv
+
+[![RStudio community](https://img.shields.io/badge/community-github--actions-blue?style=social&logo=rstudio&logoColor=75AADB)](https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions)
+
+This action installs dependencies for the current R environment based on the renv lockfile in the repository by:
+
+- Installing [renv](https://rstudio.github.io/renv/articles/renv.html)
+- Setting up a dependency cache using [actions/cache](https://github.com/actions/cache).
+
+# Usage
+
+Inputs available
+
+- `cache-version` - default `1`. If you need to invalidate the existing cache pass any other number and a new cache will be used.
+
+Basic:
+```yaml
+steps:
+- uses: actions/checkout@v2
+- uses: r-lib/actions/setup-r@v2
+- uses: r-lib/actions/setup-renv@v2
+  with:
+    cache-version: 2
+```
+
+# License
+
+The scripts and documentation in this project are released under the [MIT License](LICENSE)
+
+# Contributions
+
+Contributions are welcome!

.github/actions/renv-plus/action.yaml

@@ -0,0 +1,48 @@
+name: 'setup-renv'
+description: 'Action to setup renv and install R dependencies in the lockfile'
+author: 'Jim Hester'
+inputs:
+  restore-args:
+    description: 'Arguments passed to renv::restore()'
+    default: ''
+  cache-version:
+    description: 'The version of the cache, change this from the default (1) to start over with a fresh cache'
+    required: true
+    default: 1
+runs:
+  using: "composite"
+  steps:
+      - name: Set RENV_PATHS_ROOT
+        shell: bash
+        run: |
+          echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV
+      - name: Install and activate renv
+        run: |
+          install.packages("renv")
+          renv::activate()
+        shell: Rscript {0}
+
+      - name: Get R and OS version
+        id: get-version
+        run: |
+          cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "")
+          cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "")
+        shell: Rscript {0}
+
+      - name: Restore Renv package cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.RENV_PATHS_ROOT }}
+          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-${{ hashFiles('renv.lock') }}
+          restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-
+
+      - name: Install renv dependencies
+        run: renv::restore(${{ inputs.restore-args }})
+        shell: Rscript {0}
+
+      - name: Don't use tar 1.30 from Rtools35 to store the cache
+        shell: bash
+        run: |
+          if command -v /c/Rtools/bin/tar && /c/Rtools/bin/tar --version | grep -q 'tar (GNU tar) 1.30'
+            then echo 'C:/Program Files/Git/usr/bin' >> $GITHUB_PATH
+          fi

.github/workflows/test-app.yaml

@@ -0,0 +1,57 @@
+
+
+# Workflow derived from https://github.com/rstudio/shinytest2/tree/main/actions/test-app/example-test-app-description.yaml
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: Test app w/ DESCRIPTION
+
+jobs:
+  test-app:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: release}
+
+    env:
+      GITHUB_PAT: ${{ secrets.EXTERNAL_GITHUB_TOKEN }}
+      GITLAB_PAT: ${{ secrets.GITLAB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install libcurl4-openssl-dev libv8-dev
+
+      - uses: ./.github/actions/renv-plus
+        with:
+          cache-version: 2
+          restore-args: 'exclude = "mapDataAccess"'
+
+      - name: Install extra dependencies
+        run: |
+          install.packages("shinytest2")
+        shell: Rscript {0}
+
+      - uses: rstudio/shinytest2/actions/test-app@v1
+        with:
+          path: "."

FREDA.Rproj

@@ -11,3 +11,7 @@ Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

Observers/groups_observers.R

@@ -8,7 +8,8 @@ observeEvent(input$add_group, {
 
   updateTextInput(session, "group_name", value = "")
   updatePickerInput(session, "group_samples", selected = setdiff(sample_names(), c(unlist(revals$groups_list), input$group_samples)))
-
+
+  exportTestValues(groups_list = revals$groups_list)
 })
 
 # shinyjs observer which disables input if selection is not valid

Observers/preprocess_observers.R

@@ -53,7 +53,6 @@ observeEvent(input$preprocess_click, {
             for(i in 1:length(valence_list)){
               V <- valence_list[[i]]
               for(name in names(V)){
-                print(V[[name]])
                 valence_df[i,name] <- V[[name]]
               }
             }
@@ -93,50 +92,41 @@ observeEvent(input$preprocess_click, {
       revals$warningmessage_preprocess$makeobject_error <<- sprintf("<p style = 'color:red'>%s</p>", msg)
     })
 
-    if(!exists('msg')) revals$uploaded_data <- temp
+    if(!exists('msg')) {
+      revals$uploaded_data <- temp
+      exportTestValues(uploaded_data_processed = revals$uploaded_data)
+    }
   })
 
-  # post mortem test object
-  # test_uploaded_data <<- revals$peakData2 
-
-  if (isTRUE(getOption("shiny.testmode"))) {
-    exportTestValues(peakData2 = revals$peakData2)
-  }
-
 }, priority = 10) # End action button event
 
 # Creates two reactive variables for continuous and categorical variables which are used to display separate tables
 # Note: dependent on preprocess click and the user-specified calculations
 observeEvent(input$preprocess_click, {
-  # Error handling: revals$uploaded_data must have a non-NULL Kendrick Mass column name
-  #req(!is.null(attr(revals$uploaded_data, 'cnames')$kmass_cname))
   req(input$tests)
 
-  # Get csv file of all possible calculation column names
-  possible_calc_cnames <- read_csv("calculation_variables.csv") %>% as.data.frame(stringsAsFactors = FALSE)
-
   # Get column names from revals$uploaded_data's e_meta
   actual_cnames <- colnames(revals$uploaded_data$e_meta)
 
   # Find all columns with names that match names for calculated columns
-  v_index <- which(possible_calc_cnames[,1] %in% actual_cnames)
+  v_index <- which(names(PREPROCESS_CALC_VARS) %in% actual_cnames)
 
   # Save calculation column names from above and their display names 
-  intersect <- possible_calc_cnames[v_index,]
+  present_vars <- PREPROCESS_CALC_VARS[v_index]
 
   # get numeric columns
   numeric_cols <- revals$uploaded_data$e_meta %>% 
-    dplyr::select(which(sapply(.[intersect[,1]], is.numeric))) %>% 
+    dplyr::select(which(sapply(.[,names(present_vars)], is.numeric))) %>% 
     names()
 
   # get categorical columns
   categorical_cols <- revals$uploaded_data$e_meta %>% 
-    dplyr::select(which(!sapply(.[intersect[,1]], is.numeric))) %>%
+    dplyr::select(which(!sapply(.[names(present_vars)], is.numeric))) %>%
     names() 
 
   #set reactive variables for observers
-  revals$numeric_cols <- intersect %>% filter(ColumnName %in% numeric_cols)
-  revals$categorical_cols <- intersect %>% filter(ColumnName %in% categorical_cols)
+  revals$numeric_cols <- present_vars[names(present_vars) %in% numeric_cols]
+  revals$categorical_cols <- present_vars[names(present_vars) %in% categorical_cols]
 
 }) 
 
@@ -164,18 +154,24 @@ observeEvent(input$preprocess_dismiss,{
 
   req(c(revals$numeric_cols, revals$categorical_cols))
 
-  if(isTRUE(nrow(revals$numeric_cols) > 0)){
-    columns <- summaryPreprocess(isolate(revals$uploaded_data), revals$numeric_cols) %>% colnames()
+  if(isTRUE(length(revals$numeric_cols) > 0)){
+    tmp_num_table <- summaryPreprocess(isolate(revals$uploaded_data), revals$numeric_cols)
 
-    revals$preprocess_tables$numeric <- summaryPreprocess(isolate(revals$uploaded_data), revals$numeric_cols) %>%
+    revals$preprocess_tables$numeric <- tmp_num_table %>%
                                           datatable(options = list(dom = "t", pageLength = nrow(.))) %>% 
-                                          formatRound(columns, digits = 2)
+                                          formatRound(colnames(tmp_num_table), digits = 2)
+
+    # __SHINYTEST__
+    exportTestValues(numeric_table = tmp_num_table)
   }
 
-  if(isTRUE(nrow(revals$categorical_cols) > 0)){
+  if(isTRUE(length(revals$categorical_cols) > 0)){
     revals$preprocess_tables$categorical <- summaryPreprocess(revals$uploaded_data, revals$categorical_cols, categorical = TRUE)
+
+    # __SHINYTEST__
+    exportTestValues(categorical_table = revals$preprocess_tables$categorical)
   }
-  
+
 })
 
 # For numeric columns:

Observers/startup_observers.R

@@ -5,6 +5,7 @@ observe({
 
   # establish minio connection if we are pulling cloud resources
   if(any(names(query) %in% VALID_MINIO_HEADER_PARAMS)) {
+    library(mapDataAccess)
     minio_con <<- mapDataAccess::map_data_connection("./cfg/minio_config.yml")
   }
 

Observers/upload_observers.R

@@ -158,6 +158,8 @@ observeEvent(input$upload_click, {
     shinyjs::show('ok_idcols')
 
     revals$uploaded_data <- res
+
+    exportTestValues(uploaded_data = res)
   }
 
 }) # End peakData creation

README.md

@@ -1,4 +1,7 @@
 # FREDA
+<!-- badges: start -->
+[![tests](https://github.com/EMSL-computing/FREDA/actions/workflows/test-app.yaml/badge.svg)](https://github.com/EMSL-computing/FREDA/actions/workflows/test-app.yaml)
+<!-- badges: end -->
 
 ***
 

global.R

@@ -18,7 +18,6 @@ library(readr)
 library(plotly)
 library(DT)
 library(shinycssloaders)
-library(mapDataAccess)
 
 # uncomment either library() or load_all() if you need to load kegg
 library(KeggData)
@@ -36,7 +35,11 @@ kendrick_opts_info <- 'The base compound(s) used to calculate the Kendrick Mass.
 dt_checkmark <- '<span class="glyphicon glyphicon-ok" style="color:deepskyblue"></span>'
 dt_minus <- '<span class="glyphicon glyphicon-minus"></span>'
 
-ttip_text = list("plot_save"="Save the last created plot", "plot_review"="Review saved plots", "page_help"="How do I use this page?")
+ttip_text = list(
+  "plot_save"="Save the last created plot", 
+  "plot_review"="Review saved plots", 
+  "page_help"="How do I use this page?"
+)
 
 #------ Download Example Data ---------#
 example_edata <- read_csv('Data/example12T_edata.csv') %>% as.data.frame(stringsAsFactors = FALSE)
@@ -46,6 +49,37 @@ calc_vars <- read_csv('calculation_variables.csv') %>% as.data.frame(stringsAsFa
 # determines when 'large data' options are triggered
 max_cells <- 2000000
 
+PREPROCESS_CALC_VARS <- list(
+  "ColumnName" = "DisplayName",
+  "OtoC_ratio" = "O:C Ratio",
+  "HtoC_ratio" = "H:C Ratio",
+  "NtoC_ratio" = "N:C Ratio",
+  "PtoC_ratio" = "P:C Ratio",
+  "NtoP_ratio" = "N:P Ratio",
+  "NOSC" = "NOSC",
+  "GFE" = "Gibbs Free Energy",
+  "AI" = "Aromaticity",
+  "AI_Mod" = "Modified Aromaticity",
+  "DBE" = "DBE",
+  "DBE_O" = "DBE - O",
+  "DBE_AI" = "DBE - AI",
+  "ElComposition" = "Elemental Composition",
+  "bs1_class" = "Compound Classes Using bs1",
+  "bs2_class" = "Compound Classes Using bs2",
+  "bs3_class" = "Compound Classes Using bs3"
+) 
+
+BASE_COMPS <- c("CH2", "CO2", "H2", "H2O", "CHO")
+
+.extra_kmass <- lapply(BASE_COMPS, function(x) sprintf("Kendrick Mass (Base %s)", x))
+names(.extra_kmass) <- paste0("kmass.", BASE_COMPS)
+
+.extra_kdefect <- lapply(BASE_COMPS, function(x) sprintf("Kendrick Defect (Base %s)", x))
+names(.extra_kdefect) <- paste0("kdefect.", BASE_COMPS)
+
+PREPROCESS_CALC_VARS <- c(PREPROCESS_CALC_VARS, .extra_kmass, .extra_kdefect)
+
+# Info text for things such as warnings
 info_text = list(
   COREMS_UPLOAD_ERROR = "There was an error retrieving your Core-MS files: %s",
   COREMS_UPLOAD_NOSAMPS = "No files found in the cloud location specified by 'corems-prefix' in the URL.",