Allow files outside data/source (#89)

taxonomicallyinformedannotation · Aug 30, 2023 · 49ec2f0 · 49ec2f0
1 parent d4e15e7
commit 49ec2f0
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Showing 3 changed files with 41 additions and 28 deletions.
diff --git a/inst/app/R/save_input.R b/inst/app/R/save_input.R
@@ -15,9 +15,28 @@ save_input <- function(input) {
   timaR::load_yaml_files()
 
   ## Params occurring more than once
-  fil_fea_raw <<- shiny::isolate(input$fil_fea_raw)[[1]]
-  fil_spe_raw <<- shiny::isolate(input$fil_spe_raw)[[1]]
-  fil_tax_raw <<- shiny::isolate(input$fil_tax_raw)[[1]]
+  ## This allows to keep files correctly placed in `data/source` clean
+  prefil_fea_raw <- shiny::isolate(input$fil_fea_raw)
+  prefil_spe_raw <- shiny::isolate(input$fil_spe_raw)
+  prefil_tax_raw <- shiny::isolate(input$fil_tax_raw)
+  prefil_fea_raw_1 <- file.path(paths_data_source,prefil_fea_raw[[1]])
+  prefil_spe_raw_1 <- file.path(paths_data_source,prefil_spe_raw[[1]])
+  prefil_tax_raw_1 <- file.path(paths_data_source,prefil_tax_raw[[1]])
+  if (file.exists(prefil_fea_raw_1)) {
+    fil_fea_raw <<- prefil_fea_raw_1
+  } else {
+    fil_fea_raw <<- prefil_fea_raw[[4]]
+  }
+  if (file.exists(prefil_spe_raw_1)) {
+    fil_spe_raw <<- prefil_spe_raw_1
+  } else {
+    fil_fea_raw <<- prefil_spe_raw[[4]]
+  }
+  if (file.exists(prefil_tax_raw_1)) {
+    fil_tax_raw <<- prefil_tax_raw_1
+  } else {
+    fil_tax_raw <<- prefil_tax_raw[[4]]
+  }
 
   filename <<- shiny::isolate(input$fil_pat)
   gnps_job_id <<- shiny::isolate(input$gnps_id)
@@ -48,14 +67,12 @@ save_input <- function(input) {
     `inst/params/prepare_params`$
     files$
     features$
-    raw <-
-    file.path(paths_data_source, fil_fea_raw)
+    raw <- fil_fea_raw
   yamls_params$
     `inst/params/prepare_params`$
     files$
     spectral$
-    raw <-
-    file.path(paths_data_source, fil_spe_raw)
+    raw <- fil_spe_raw
   yamls_params$`inst/params/prepare_params`$gnps$id <- gnps_job_id
   yamls_params$
     `inst/params/prepare_params`$
@@ -120,8 +137,7 @@ save_input <- function(input) {
   yamls_params$annotate_masses$names$target <- names_target
   yamls_params$annotate_masses$options$force <- forceps
 
-  yamls_params$annotate_spectra$files$spectral$raw <-
-    file.path(paths_data_source, fil_spe_raw)
+  yamls_params$annotate_spectra$files$spectral$raw <- fil_spe_raw
   yamls_params$
     annotate_spectra$
     annotations$
@@ -164,8 +180,7 @@ save_input <- function(input) {
     create_edges_spectra$
     files$
     spectral$
-    raw <-
-    file.path(paths_data_source, fil_spe_raw)
+    raw <- fil_spe_raw
   yamls_params$
     create_edges_spectra$
     annotations$
@@ -244,8 +259,7 @@ save_input <- function(input) {
     prepare_features_tables$
     files$
     features$
-    raw <-
-    file.path(paths_data_source, fil_fea_raw)
+    raw <- fil_fea_raw
   yamls_params$
     prepare_features_tables$
     names$
@@ -286,10 +300,8 @@ save_input <- function(input) {
     ms$
     polarity <- ms_mode
 
-  yamls_params$prepare_taxa$files$features$raw <-
-    file.path(paths_data_source, fil_fea_raw)
-  yamls_params$prepare_taxa$files$taxa$raw <-
-    file.path(paths_data_source, fil_tax_raw)
+  yamls_params$prepare_taxa$files$features$raw <- fil_fea_raw
+  yamls_params$prepare_taxa$files$taxa$raw <- fil_tax_raw
   if (!is.null(gnps_job_id)) {
     yamls_params$prepare_taxa$files$taxa$raw <-
       file.path(paths_data_source, paste0(gnps_job_id, "_metadata.tsv"))

diff --git a/inst/app/server.R b/inst/app/server.R
@@ -160,7 +160,8 @@ server <- function(input, output, session) {
           )
         )
         targets::tar_make(
-          names = matches("ann_pre$"),
+          names = matches("^ann_pre$"),
+          garbage_collection = TRUE,
           reporter = "verbose_positives"
         )
       }, finally = {

diff --git a/inst/app/ui.R b/inst/app/ui.R
@@ -32,12 +32,12 @@ ui <- fluidPage(
   fluidPage(div(
     id = "params",
     navlistPanel(
-      widths = c(4, 4),
+      widths = c(4, 5),
       "Parameters",
       tabPanel(
         title = "Files",
         h3("Required files"),
-        h5("They MUST be located in `data/source`"),
+        h5("They SHOULD be located in `data/source`"),
         div(
           fileInput(
             inputId = "fil_spe_raw",
@@ -49,7 +49,7 @@ ui <- fluidPage(
             type = "inline",
             content = c(
               "The MGF file containing your spectra.",
-              "Must be located in `data/source`.",
+              "Should be located in `data/source`.",
               "Reason therefore is to find it in the future.",
               "If you have a GNPS job ID, the spectra will be stored there."
             )
@@ -70,7 +70,7 @@ ui <- fluidPage(
             type = "inline",
             content = c(
               "The csv or tsv file containing your features",
-              "Must be located in `data/source`.",
+              "Should be located in `data/source`.",
               "Reason therefore is to find it in the future.",
               "If you have a GNPS job ID, the spectra will be stored there."
             )
@@ -91,7 +91,7 @@ ui <- fluidPage(
             type = "inline",
             content = c(
               "The csv or tsv file containing the metadata of your experiment.",
-              "Must be located in `data/source`.",
+              "Should be located in `data/source`.",
               "Reason therefore is to find it in the future.",
               "If you have a GNPS job ID, the spectra will be stored there.",
               "Do not forget to change the `name` in the corresponding tab."
@@ -136,8 +136,8 @@ ui <- fluidPage(
           label = "Number of final candidates",
           min = 1,
           max = 500,
-          step = 1,
           value = 3,
+          step = 1,
           ticks = FALSE
         ) |>
           shinyhelper::helper(
@@ -176,8 +176,8 @@ ui <- fluidPage(
           label = "Minimal biological score to keep MS1 only annotation",
           min = 0,
           max = 1,
-          value = 0.5,
-          step = 0.1,
+          value = 0.6,
+          step = 0.05,
           ticks = FALSE
         ) |>
           shinyhelper::helper(
@@ -193,7 +193,7 @@ ui <- fluidPage(
           label = "Minimal chemical score to keep MS1 only annotation",
           min = 0,
           max = 1,
-          value = 0.5,
+          value = 0.6,
           step = 0.1,
           ticks = FALSE
         ) |>
@@ -239,7 +239,7 @@ ui <- fluidPage(
           min = 0,
           max = 1,
           step = 0.05,
-          value = 0.1,
+          value = 0.0,
           ticks = FALSE
         ) |>
           shinyhelper::helper(