Nextflow Samplesheet: File Selector (#879)

* start file selector

* tie in params for selector dialog and rendering file cell

* streamline param passing between actions, add paired attachment auto selection

* add ability to handle no attachment selection

* fix regex filtering, more cleanup

* move filtering to sample rather than samplesheet

* rework logic to use pipeline for pattern

* streamline params, fix ordering

* start migrating logic to accept non-fastq files as well

* make other file types useable with file selector

* start adding translations, add empty state for file selector

* add frontend validation for samplesheet file cells

* make full div clickable on samplesheet, add hover state

* fix tailwind classes for error submission state

* fix some older arguments

* cleanup

* further cleanup, fixing styling

* add ui tests

* some cleanup

* cleanup

* fix tests, fix required headers, move file selector under WE module

* generalize nextflow component error

* cleanup

* run normalize

* add controller tests

* fix translation in test

* fix translations, move file filtering methods to concern, add unrelated asserts for flakes

* change required_properties default value

* run normalize

* fix test

* cleanup

* rework some of the required_properties logic

* add wrapper for file selector dialog

* further fix file selector dialog

* make submit btn of file selector dialog part of dialog, add stimulus logic, make radio buttons sticky for horizontal scrolling

* fix dialog id ambiguity, fix tests with now moved submit button out of original selector

* add type and format to file selector, add non-pe selection autopopulate fastq_2 to no file

* revert form button changes

app/components/nextflow/samplesheet/column_component.html.erb

@@ -1,9 +1,15 @@
 <div
-  class="table-column flex-grow text-sm text-left  whitespace-nowrap bg-slate-50 text-slate-500 dark:text-white"
+  class="
+    table-column flex-grow text-sm text-left whitespace-nowrap bg-slate-50
+    text-slate-500 dark:text-white
+  "
 >
   <% if property["cell_type"] == "metadata_cell" %>
     <div
-      class="sticky top-0 z-10 border  table-header dark:border-slate-600 border-slate-100 dark:bg-slate-700 bg-slate-50"
+      class="
+        sticky top-0 z-10 border table-header dark:border-slate-600 border-slate-100
+        dark:bg-slate-700 bg-slate-50
+      "
     >
       <%= form_with url: fields_workflow_executions_metadata_path do |f| %>
         <%= f.hidden_field :format, value: "turbo_stream", id: "field_#{header}_turbo" %>
@@ -21,7 +27,7 @@
         <% end %>
         <%= f.select :field,
                  options_for_select(metadata_fields_for_field(header), header),
-                 { include_blank: !@required },
+                 { include_blank: !@required_properties.include?(header) },
                  {
                    id: "field-#{header}",
                    "aria-label": header,
@@ -40,7 +46,7 @@
     >
       <div class="flex items-center space-x-2 uppercase">
         <%= header %>
-        <% if @required %>
+        <% if @required_properties.include?(header) %>
           <span class="ml-1 text-red-600 dark:text-red-300">(<%= t(".required") %>)</span>
         <% end %>
       </div>
@@ -61,7 +67,7 @@
             <%= s.hidden_field :sample_id, value: sample.id %>
           <% end %>
           <%= s.fields_for "samplesheet_params" do |fields| %>
-            <%= render_cell_type(header, property, sample, fields, index) %>
+            <%= render_cell_type(header, property, sample, fields, index, workflow_params) %>
           <% end %>
         <% end %>
       </div>

app/components/nextflow/samplesheet/column_component.rb

@@ -4,30 +4,32 @@ module Nextflow
   module Samplesheet
     # Renders a column in the sample sheet table
     class ColumnComponent < Component
-      attr_reader :namespace_id, :header, :property, :samples
+      attr_reader :namespace_id, :header, :property, :samples, :metadata_fields, :required_properties, :workflow_params
 
       # rubocop:disable Metrics/ParameterLists
-      def initialize(namespace_id:, header:, property:, samples:, metadata_fields:, required:)
+      def initialize(namespace_id:, header:, property:, samples:, metadata_fields:, required_properties:,
+                     workflow_params:)
         @namespace_id = namespace_id
         @header = header
         @property = property
         @samples = samples
         @metadata_fields = metadata_fields
-        @required = required
+        @required_properties = required_properties
+        @workflow_params = workflow_params
       end
 
       # rubocop:enable Metrics/ParameterLists
 
-      def render_cell_type(property, entry, sample, fields, index) # rubocop:disable Metrics/MethodLength, Metrics/CyclomaticComplexity
+      def render_cell_type(property, entry, sample, fields, index, workflow_params) # rubocop:disable Metrics/MethodLength, Metrics/CyclomaticComplexity, Metrics/ParameterLists
         case entry['cell_type']
         when 'sample_cell'
           render_sample_cell(sample, fields)
         when 'sample_name_cell'
           render_sample_name_cell(sample, fields)
         when 'fastq_cell'
-          render_fastq_cell(sample, property, entry, fields, index)
+          render_fastq_cell(sample, property, index, workflow_params)
         when 'file_cell'
-          render_other_file_cell(sample, property, entry, fields)
+          render_other_file_cell(sample, property, index, entry)
         when 'metadata_cell'
           render_metadata_cell(sample, property, fields)
         when 'dropdown_cell'
@@ -37,56 +39,20 @@ def render_cell_type(property, entry, sample, fields, index) # rubocop:disable M
         end
       end
 
-      def render_fastq_cell(sample, property, entry, fields, index)
-        direction = get_fastq_direction(property)
-        files = get_fastq_files(entry, sample, direction, pe_only: property['pe_only'].present?)
-        data = get_fastq_data(files, direction, index, property)
-        render_file_cell(property, entry, fields, files, @required, data, files&.first)
+      def render_fastq_cell(sample, property, index, workflow_params)
+        selected_file = sample.most_recent_file('fastq', property:, workflow_params:)
+        render_file_cell(sample, property, index, selected_file, 'fastq', workflow_params:)
       end
 
       private
 
-      def get_fastq_direction(property)
-        property.match(/fastq_(\d+)/)[1].to_i == 1 ? :pe_forward : :pe_reverse
-      end
-
-      def get_fastq_files(entry, sample, direction, pe_only: false)
-        singles = filter_files_by_pattern(sample.sorted_files[:singles] || [],
-                                          entry['pattern'] || "/^\S+.f(ast)?q(.gz)?$/")
-
-        files = []
-        if sample.sorted_files[direction].present?
-          files = sample.sorted_files[direction] || []
-          files.concat(singles) unless pe_only
-        else
-          files = singles
-        end
-        files
-      end
-
-      def get_fastq_data(files, direction, index, property)
-        return {} if files.empty? && property == 'fastq_2'
-
-        {
-          'data-action' => 'change->nextflow--samplesheet#file_selected',
-          'data-nextflow--samplesheet-target' => "select#{direction.to_s.sub!('pe_', '').capitalize}",
-          'data-direction' => direction.to_s,
-          'data-index' => index
-        }
-      end
-
-      def render_other_file_cell(sample, property, entry, fields)
-        files = if entry['pattern']
-                  filter_files_by_pattern(sample.sorted_files[:singles] || [], entry['pattern'])
-                else
-                  sample.sorted_files[:singles] || []
-                end
-        render_file_cell(property, entry, fields,
-                         files, @required, {}, nil)
+      def render_other_file_cell(sample, property, index, entry)
+        selected_file = sample.most_recent_file('other', autopopulate: entry['autopopulate'], pattern: entry['pattern'])
+        render_file_cell(sample, property, index, selected_file, 'other', pattern: entry['pattern'])
       end
 
       def filter_files_by_pattern(files, pattern)
-        files.select { |file| file.first[Regexp.new(pattern)] }
+        files.select { |file| file[:filename] =~ Regexp.new(pattern) }
       end
 
       def render_sample_cell(sample, fields)
@@ -98,24 +64,20 @@ def render_sample_name_cell(sample, fields)
       end
 
       def render_metadata_cell(sample, name, fields)
-        render(Samplesheet::MetadataCellComponent.new(sample:, name:, form: fields, required: @required))
+        render(Samplesheet::MetadataCellComponent.new(sample:, name:, form: fields, required: required?))
       end
 
       # rubocop:disable Metrics/ParameterLists
-      def render_file_cell(property, entry, fields, files, is_required, data, selected)
-        selected_item = if selected.present?
-                          selected
-                        else
-                          entry['autopopulate'] && files.present? ? files[0] : nil
-                        end
 
-        render(Samplesheet::DropdownCellComponent.new(
+      def render_file_cell(sample, property, index, selected, file_type, **file_selector_arguments)
+        render(Samplesheet::FileCellComponent.new(
+                 sample,
                  property,
-                 files,
-                 selected_item,
-                 fields,
-                 is_required,
-                 data
+                 selected,
+                 index,
+                 @required_properties,
+                 file_type,
+                 **file_selector_arguments
                ))
       end
 
@@ -127,15 +89,15 @@ def render_dropdown_cell(property, entry, fields)
                  entry['enum'],
                  nil,
                  fields,
-                 @required
+                 required?
                ))
       end
 
       def render_input_cell(property, fields)
         render(Samplesheet::TextCellComponent.new(
                  property,
                  fields:,
-                 required: @required
+                 required: required?
                ))
       end
 
@@ -144,6 +106,10 @@ def metadata_fields_for_field(field)
         label = t('.default', label: field)
         options.map { |f| [f.eql?(field) ? label : f, f] }
       end
+
+      def required?
+        @required_properties.include?(@header)
+      end
     end
   end
 end

app/components/nextflow/samplesheet/file_cell_component.html.erb

@@ -0,0 +1,33 @@
+<%= link_to new_workflow_executions_file_selector_path(
+  "file_selector[attachable_id]": @attachable.id,
+  "file_selector[attachable_type]": @attachable.class.to_s,
+  "file_selector[index]": @index,
+  "file_selector[selected_id]": @selected.empty? ? nil : @selected[:id],
+  "file_selector[property]": @property,
+  "file_selector[required_properties]": @required_properties,
+  "file_selector[file_type]": @file_type,
+  "file_selector[file_selector_arguments]": @file_selector_arguments
+),
+data: {
+  turbo_stream: "true",
+} do %>
+  <div
+    id="<%="#{@attachable.id}_#{@property}" %>"
+    class="
+      w-full focus:ring-primary-500 focus:border-primary-500 p-2 dark:bg-inherit
+      bg-inherit dark:placeholder-slate-400 text-inherit
+      text-sm dark:focus:ring-primary-500 dark:focus:border-primary-500 cursor-pointer
+      hover:border-slate-300 border-transparent border-2
+    "
+    data-file-cell-required="<%= @required_properties.present? && @required_properties.include?(@property) ? "true" : "false" %>"
+  >
+    <% unless @selected.empty? %>
+      <input
+      type="hidden"
+        name="workflow_execution[samples_workflow_executions_attributes][<%= @index%>][samplesheet_params][<%= @property %>]"
+        value= <%= @selected[:global_id]%>
+      >
+    <% end %>
+    <%= @selected.empty? ? t(".no_selected_file") : @selected[:filename] %>
+  </div>
+<% end %>

app/components/nextflow/samplesheet/file_cell_component.rb

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+module Nextflow
+  module Samplesheet
+    # Render a single cell of a Nextflow samplesheet for a property that requires a file
+    class FileCellComponent < Component
+      attr_reader :attachable, :property, :selected, :index, :required_properties, :file_type, :file_selector_arguments
+
+      # rubocop: disable Metrics/ParameterLists
+      def initialize(attachable, property, selected, index, required_properties, file_type, **file_selector_arguments)
+        @attachable = attachable
+        @property = property
+        @selected = selected
+        @index = index
+        @required_properties = required_properties
+        @file_type = file_type
+        @file_selector_arguments = file_selector_arguments
+      end
+      # rubocop: enable Metrics/ParameterLists
+    end
+  end
+end

app/components/nextflow/samplesheet_component.html.erb

@@ -1,18 +1,26 @@
 <div class="sample-sheet">
 
   <label class="block mb-2 text-sm font-medium text-slate-900 dark:text-white"><%= t(".label") %></label>
-
+  <div
+    role="alert"
+    class="
+      hidden flex items-center p-4 border-l-4 text-red-800 border-red-300 bg-red-50
+      dark:text-red-400 dark:bg-slate-800 dark:border-red-800 mb-2
+    "
+    data-nextflow--samplesheet-target="error"
+  >
+    <span class="flex-shrink-0 inline">
+      <%= viral_icon(name: "exclamation_circle", classes: "w-5 h-5 mr-3 stroke-2") %>
+    </span>
+    <div>
+      <div class="font-medium" data-nextflow--samplesheet-target="errorMessage"></div>
+    </div>
+  </div>
   <div
     data-nextflow--samplesheet-target="table"
     class="
-      samplesheet-table
-      flex
-      border
-      dark:border-slate-600
-      border-slate-100
-      max-h-72
-      overflow-y-auto
-      relative
+      samplesheet-table flex border dark:border-slate-600 border-slate-100 max-h-72
+      overflow-y-auto relative
     "
   >
     <% properties.each do |header, property| %>
@@ -22,23 +30,16 @@
         property:,
         samples: @samples,
         metadata_fields:,
-        required: required_properties.include?(header)
+        required_properties:,
+        workflow_params:,
       ) %>
     <% end %>
     <template data-nextflow--samplesheet-target="loading">
       <div
         role="status"
         class="
-          absolute
-          h-full
-          w-full
-          text-black
-          dark:text-white
-          backdrop-blur-sm
-          flex
-          items-center
-          justify-center
-          z-20
+          absolute h-full w-full text-black dark:text-white backdrop-blur-sm flex
+          items-center justify-center z-20
         "
       >
         <span class="flex items-center p-4 space-x-4">

app/components/nextflow/samplesheet_component.rb

@@ -3,15 +3,16 @@
 module Nextflow
   # Render the contents of a Nextflow samplesheet to a table
   class SamplesheetComponent < Component
-    attr_reader :properties, :samples, :required_properties, :metadata_fields, :namespace_id
+    attr_reader :properties, :samples, :required_properties, :metadata_fields, :namespace_id, :workflow_params
 
     FILE_CELL_TYPES = %w[fastq_cell file_cell].freeze
 
-    def initialize(schema:, samples:, fields:, namespace_id:)
+    def initialize(schema:, samples:, fields:, namespace_id:, workflow_params:)
       @samples = samples
       @namespace_id = namespace_id
       @metadata_fields = fields
-      @required_properties = schema['items']['required']
+      @required_properties = schema['items']['required'] || []
+      @workflow_params = workflow_params
       extract_properties(schema)
     end