Adding demo files download to the app

taxonomicallyinformedannotation · Aug 16, 2024 · e7174ea · e7174ea
1 parent 143fab0
commit e7174ea
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Showing 3 changed files with 41 additions and 13 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,7 @@
 
 # tima 2.11.0
 
+* Added demo files download to the app
 * Better packaging
 * Improved documentation
 * Fixed all CRAN warnings

diff --git a/codemeta.json b/codemeta.json
@@ -506,7 +506,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "3284.67KB",
+ "fileSize": "3298.849KB",
  "citation": [
  {
  "@type": "SoftwareSourceCode",

diff --git a/inst/app.R b/inst/app.R
@@ -61,13 +61,13 @@ ui <- shiny::fluidPage(
  shiny::tabPanel(
  title = "Files",
  shiny::h3("Required files"),
- shiny::h5("They SHOULD be located in `data/source`"),
  shiny::div(
  shiny::fileInput(
  inputId = "fil_spe_raw",
  label = .label_mandatory("MGF file"),
  accept = ".mgf"
- )
+ ),
+ shiny::downloadButton(outputId = "demo_spe", "Download example spectra")
  ) |>
  shinyhelper::helper(
  type = "inline",
@@ -78,10 +78,13 @@ ui <- shiny::fluidPage(
  # "If you have a GNPS job ID, the spectra will be stored there."
  )
  ),
- shiny::fileInput(
- inputId = "fil_fea_raw",
- label = .label_mandatory("Features table"),
- accept = c(".csv", ".tsv", ".csv.gz", ".tsv.gz", ".csv.zip", ".tsv.zip")
+ shiny::div(
+ shiny::fileInput(
+ inputId = "fil_fea_raw",
+ label = .label_mandatory("Features table"),
+ accept = c(".csv", ".tsv", ".csv.gz", ".tsv.gz", ".csv.zip", ".tsv.zip")
+ ),
+ shiny::downloadButton(outputId = "demo_fea", "Download example features")
  ) |>
  shinyhelper::helper(
  type = "inline",
@@ -92,10 +95,13 @@ ui <- shiny::fluidPage(
  # "If you have a GNPS job ID, the spectra will be stored there."
  )
  ),
- shiny::fileInput(
- inputId = "fil_met_raw",
- label = "Metadata table (mandatory if no taxon name)",
- accept = c(".csv", ".tsv", ".csv.gz", ".tsv.gz", ".csv.zip", ".tsv.zip")
+ shiny::div(
+ shiny::fileInput(
+ inputId = "fil_met_raw",
+ label = "Metadata table (mandatory if no taxon name)",
+ accept = c(".csv", ".tsv", ".csv.gz", ".tsv.gz", ".csv.zip", ".tsv.zip")
+ ),
+ shiny::downloadButton(outputId = "demo_met", "Download example metadata")
  ) |>
  shinyhelper::helper(
  type = "inline",
@@ -1787,8 +1793,8 @@ ui <- shiny::fluidPage(
  yaml_small$organisms$taxon <- org_tax
  yaml_small$options$high_confidence <- hig_con
  yaml_small$options$summarise <- summarise
- create_dir("params")
- yaml::write_yaml(x = yaml_small, file = get_default_paths()$params$prepare_params)
+ tima:::create_dir("params")
+ yaml::write_yaml(x = yaml_small, file = tima:::get_default_paths()$params$prepare_params)
 
  message(x = "... Advanced")
  yaml_advanced <- yamls_params[["params/prepare_params_advanced"]]
@@ -2111,6 +2117,27 @@ server <- function(input, output, session) {
  ## Observe helpers
  shinyhelper::observe_helpers()
 
+ output$demo_spe <- downloadHandler(
+ filename = basename(tima:::get_default_paths()$urls$examples$spectra),
+ content = function(file) {
+ writeLines(readLines(tima:::get_default_paths()$urls$examples$spectra_mini), file)
+ }
+ )
+
+ output$demo_fea <- downloadHandler(
+ filename = basename(tima:::get_default_paths()$urls$examples$features),
+ content = function(file) {
+ writeLines(readLines(tima:::get_default_paths()$urls$examples$features), file)
+ }
+ )
+
+ output$demo_met <- downloadHandler(
+ filename = basename(tima:::get_default_paths()$urls$examples$metadata),
+ content = function(file) {
+ writeLines(readLines(tima:::get_default_paths()$urls$examples$metadata), file)
+ }
+ )
+
  ## Mandatory fields
  fields_mandatory <- c("fil_fea_raw", "fil_spe_raw", "fil_pat")