add exp name pattern and apply button

example/config_file.yaml

@@ -36,6 +36,10 @@ exclude_files: '180614_S_A'
 # %e -- raw file name
 exp_name_format: 'Exp %f %i'
 
+# optional regular expression pattern to extract
+# from the experiment names after applying the format string
+exp_name_pattern: '[0-9]{6}'
+
 # custom names for files
 exp_names:
   - Control

server.R

@@ -474,7 +474,17 @@ shinyServer(function(input, output, session) {
     file_levels(.file_levels)
   })
 
-  exp_name_format <- debounce(reactive({ input$exp_name_format }), 1000)
+  exp_name_format <- reactiveVal(config[['exp_name_format']])
+  # only change the exp_name_pattern when the apply button is pressed
+  observeEvent(input$exp_name_format_apply, {
+    exp_name_format(input$exp_name_format)
+  })
+
+  exp_name_pattern <- reactiveVal(config[['exp_name_pattern']])
+  # only change the exp_name_pattern when the apply button is pressed
+  observeEvent(input$exp_name_pattern_apply, {
+    exp_name_pattern(input$exp_name_pattern)
+  })
 
   file_levels <- reactiveVal()
 
@@ -490,6 +500,7 @@ shinyServer(function(input, output, session) {
 
     # load naming format
     .format <- exp_name_format()
+    .pattern <- exp_name_pattern()
     .file_levels <- rep(.format, length(.raw_files))
 
     # replace flags in the format
@@ -505,6 +516,13 @@ shinyServer(function(input, output, session) {
     # replace %e with the raw file name
     .file_levels <- str_replace(.file_levels, '\\%e', .raw_files)
 
+    # apply custom string extraction expression to file levels
+    if(!is.null(.pattern) & length(.pattern) > 0 & nchar(.pattern) > 0) {
+      .file_levels <- str_extract(.file_levels, .pattern)
+      # if string extraction failed, then will return NA. set NAs to "default"
+      .file_levels[is.na(.file_levels)] <- 'default'
+    }
+
     file_levels(.file_levels)
   })
 

settings.yaml

@@ -53,6 +53,7 @@ remove_decoy: REV_
 remove_contam: CON_
 
 exp_name_format: 'Exp %f %i'
+exp_name_pattern: ''
 
 ## Figure rendering options
 

ui/import_tab.R

@@ -133,8 +133,22 @@ import_tab <- tabItem(tabName='import', fluidPage(
       tags$li(tags$b('%e'), tags$span('  Name of the experiment raw file.'))
     ),
     p('For example, "file_%f-%i" would render to "file_SCOPE-3" given the folder "SCOPE" and the index 3'),
-    textInput('exp_name_format', 'Experiment Label Format', value=config[['exp_name_format']],
-              width=NULL, placeholder='Experiment naming format'),
+    fixedRow(style='display:flex;flex-direction:row;align-items:center;',
+      column(9,
+        textInput('exp_name_format', 'Experiment Label Format', value=config[['exp_name_format']],
+                  width=NULL, placeholder='Experiment naming format')),
+      column(3,
+        actionButton('exp_name_format_apply', 'Apply', width=100))
+    ),
+    p('Further process file names after applying the format string with a string extraction pattern'),
+    p('For example, a pattern "[0-9]{6}" would extract the first 6 sequential numbers in the experiment name.'),
+    fixedRow(style='display:flex;flex-direction:row;align-items:center;',
+      column(9,
+        textInput('exp_name_pattern', 'Experiment Extraction Pattern', value=config[['exp_name_pattern']],
+                  width=NULL, placeholder='Regular expression. e.g., [0-9]{6}')),
+      column(3,
+        actionButton('exp_name_pattern_apply', 'Apply', width=100))
+    ),
     p('Or, use the table below to manually rename experiments'),
     p('Double click on an entry in the "Label" column to begin editing. Press enter or click outside of the table to finish editing and confirm the changes.'),
     DT::dataTableOutput('exp_name_table'),