refactor all cell types to load in via JS

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

@@ -57,17 +57,5 @@
     id="<%= "metadata-#{header}-column" %>"
     class="dark:bg-slate-700 bg-slate-50"
   >
-    <% samples.each_with_index do |sample, index| %>
-      <div
-        style="content-visibility: auto;"
-        class="border table-td dark:border-slate-600 border-slate-100"
-      >
-        <%= fields_for "workflow_execution[samples_workflow_executions_attributes][#{index}]" do |s| %>
-          <%= s.fields_for "samplesheet_params" do |fields| %>
-            <%= render_cell_type(header, property, sample, fields, index, workflow_params) %>
-          <% end %>
-        <% end %>
-      </div>
-    <% end %>
   </div>
 </div>

app/components/nextflow/samplesheet/column_component.rb

@@ -56,7 +56,7 @@ def filter_files_by_pattern(files, pattern)
       end
 
       def render_sample_cell(sample_identifier)
-        render(Samplesheet::SampleCellComponent.new(sample_identifier:))
+        # render(Samplesheet::SampleCellComponent.new(sample_identifier:))
       end
 
       def render_metadata_cell(sample, name, fields, index)

app/components/nextflow/samplesheet/sample_cell_component.rb

@@ -4,12 +4,6 @@ module Nextflow
   module Samplesheet
     # Render a single cell of a Nextflow samplesheet for a given sample
     class SampleCellComponent < Component
-      erb_template <<~ERB
-              <div class="p-2.5 sticky left-0">
-          <%= @sample_identifier %>
-        </div>
-      ERB
-
       def initialize(sample_identifier:)
         @sample_identifier = sample_identifier
       end

app/components/nextflow/samplesheet_component.html.erb

@@ -2,6 +2,9 @@
   <div class="hidden" data-nextflow--samplesheet-target="workflowAttributes">
     <%= samples_workflow_executions_attributes %>
   </div>
+  <div class="hidden" data-nextflow--samplesheet-target="samplesheetProperties">
+    <%= @properties.to_json %>
+  </div>
   <label class="block mb-2 text-sm font-medium text-slate-900 dark:text-white"><%= t(".label") %></label>
   <div
     role="alert"
@@ -53,5 +56,89 @@
       </div>
     </template>
   </div>
-
 </div>
+
+<template data-nextflow--samplesheet-target="cellContainer">
+  <div
+    style="content-visibility: auto;"
+    class="border table-td dark:border-slate-600 border-slate-100"
+  >
+  </div>
+</template>
+
+<template data-nextflow--samplesheet-target="sampleIdentifierCell">
+  <div class="p-2.5 sticky left-0">
+    CELL_PLACEHOLDER
+  </div>
+</template>
+
+<template data-nextflow--samplesheet-target="dropdownCell">
+  <select
+    aria-label="COLUMN_NAME_PLACEHOLDER"
+    class="
+      w-full focus:ring-primary-500 focus:border-primary-500 p-2.5 dark:bg-slate-700
+      bg-slate-50 border-none dark:border-none dark:placeholder-slate-400 text-inherit
+      text-sm dark:focus:ring-primary-500 dark:focus:border-primary-500 cursor-pointer
+    "
+    data-action="change->nextflow--samplesheet#updateEditableSamplesheetData"
+    name="workflow_execution[samples_workflow_executions_attributes][INDEX_PLACEHOLDER][samplesheet_params][COLUMN_NAME_PLACEHOLDER]"
+    id="workflow_execution_samples_workflow_executions_attributes_INDEX_PLACEHOLDER_samplesheet_params_COLUMN_NAME_PLACEHOLDER"
+  >
+    <option value="" label=" "></option>
+  </select>
+</template>
+
+<template data-nextflow--samplesheet-target="fileCell">
+  <div>
+    <%= link_to new_workflow_executions_file_selector_path(
+  "file_selector[attachable_id]": "ATTACHABLE_ID_PLACEHOLDER",
+  "file_selector[attachable_type]": "ATTACHABLE_TYPE_PLACEHOLDER",
+  "file_selector[index]": "INDEX_PLACEHOLDER",
+  "file_selector[selected_id]": "SELECTED_ID_PLACEHOLDER",
+  "file_selector[property]": "PROPERTY_PLACEHOLDER",
+  "file_selector[required_properties]": @required_properties,
+  "file_selector[file_type]": "FILE_TYPE_PLACEHOLDER",
+  "file_selector[file_selector_arguments]": {workflow_params:, patterns:}
+),
+data: {
+  turbo_stream: "true",
+} do %>
+      <div
+        id="<%="ATTACHABLE_ID_PLACEHOLDER_PROPERTY_PLACEHOLDER" %>"
+        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
+        "
+        <% if @required_properties.present? && @required_properties.include?(@property) %>
+        data-file-missing="<%= @selected.empty? ? "true" : "false" %>"
+        <% end %>
+      >
+        <%# <%= @selected.empty? ? t(".no_selected_file") : @selected[:filename] %>
+        CELL_VALUE_PLACEHOLDER
+      </div>
+    <% end %>
+  </div>
+
+</template>
+
+<template data-nextflow--samplesheet-target="metadataCell">
+  <div class="p-2.5 text-nowrap">
+    <span class="h-3.5 inline-block">METADATA_VALUE_PLACEHOLDER</span>
+  </div>
+</template>
+
+<template data-nextflow--samplesheet-target="textCell">
+  <input
+    class="
+      bg-slate-50 border-0 text-slate-900 text-sm focus:ring-primary-500 block w-full
+      p-2.5 dark:bg-slate-700 dark:border-slate-600 dark:placeholder-slate-400
+      dark:text-white dark:focus:ring-primary-500 dark:focus:border-primary-500
+    "
+    data-action="change->nextflow--samplesheet#updateEditableSamplesheetData"
+    type="text"
+    name="NAME_PLACEHOLDER"
+    id="ID_PLACEHOLDER"
+  >
+</template>

app/components/nextflow/samplesheet_component.rb

@@ -3,7 +3,8 @@
 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, :workflow_params
+    attr_reader :properties, :samples, :required_properties, :metadata_fields, :namespace_id, :workflow_params,
+                :patterns
 
     FILE_CELL_TYPES = %w[fastq_cell file_cell].freeze
 
@@ -13,6 +14,7 @@ def initialize(schema:, samples:, fields:, namespace_id:, workflow_params:)
       @metadata_fields = fields
       @required_properties = schema['items']['required'] || []
       @workflow_params = workflow_params
+      @patterns = {}
       extract_properties(schema)
     end
 
@@ -28,34 +30,62 @@ def samples_workflow_executions_attributes
     def samples_workflow_execution_attributes(sample)
       {
         'sample_id' => sample.id,
-        'samplesheet_params' => sample_samplesheet_params(sample)
+        'samplesheet_params' => sample_samplesheet_params(sample),
+        'patterns' => {}
       }
     end
 
     def sample_samplesheet_params(sample) # rubocop:disable Metrics/CyclomaticComplexity,Metrics/MethodLength
       @properties.to_h do |name, property|
         case property['cell_type']
         when 'sample_cell'
-          [name, sample.puid]
+          [name, { form_value: sample.puid, cell_type: 'sample_cell', cell_value: sample.puid }]
         when 'sample_name_cell'
-          [name, sample.name]
+          [name, { form_value: sample.name, cell_type: 'sample_name_cell', cell_value: sample.name }]
         when 'fastq_cell'
-          [name, sample.attachments.empty? ? '' : sample.most_recent_fastq_file(name, @workflow_params)[:global_id]]
+          [name,
+           file_samplesheet_values(sample.attachments.empty? ? nil : sample.most_recent_fastq_file(name,
+                                                                                                   @workflow_params))]
         when 'file_cell'
-          [name, sample.most_recent_other_file(property['autopopulate'], property['pattern'])[:global_id]]
+          [name,
+           file_samplesheet_values(sample.most_recent_other_file(property['autopopulate'], property['pattern']))]
         when 'metadata_cell'
-          [name, sample.metadata.fetch(name, '')]
+          [name, metadata_samplesheet_values(sample, name)]
         when 'dropdown_cell' || 'input_cell'
-          [name, '']
+          [name, { form_value: '', cell_type: property['cell_type'], cell_value: '' }]
         end
       end
     end
 
+    def file_samplesheet_values(file)
+      { form_value: file.empty? ? '' : file[:global_id],
+        cell_type: 'file_cell',
+        cell_value: file.empty? ? I18n.t('nextflow.samplesheet.file_cell_component.no_selected_file') : file[:filename],
+        attachment_id: file.empty? ? '' : file[:id] }
+    end
+
+    def metadata_samplesheet_values(sample, name)
+      metadata = sample.metadata.fetch(name, '')
+      if metadata.empty?
+        { form_value: '',
+          cell_type: 'text',
+          cell_value: nil }
+      else
+        { form_value: metadata,
+          cell_type: 'metadata_cell',
+          cell_value: metadata }
+      end
+    end
+
     def extract_properties(schema)
       @properties = schema['items']['properties']
       @properties.each do |property, entry|
         @properties[property]['required'] = schema['items']['required'].include?(property)
         @properties[property]['cell_type'] = identify_cell_type(property, entry)
+        if @properties[property]['pattern'] && %w[fastq_cell
+                                                  file_cell].include?(@properties[property]['cell_type'])
+          @patterns[property] = @properties[property]['pattern']
+        end
       end
 
       if @required_properties.include?('fastq_1') && @required_properties.include?('fastq_2')

app/components/nextflow_component.html.erb

@@ -3,6 +3,7 @@
   data-nextflow--samplesheet-attachments-error-value="<%= t(".attachments_error") %>"
   data-nextflow--samplesheet-submission-error-value="<%= t(".submission_error") %>"
   data-nextflow--samplesheet-url-value="<%= url %>"
+  data-nextflow--samplesheet-workflow-value="<%= {name: @workflow.name, version: @workflow.version }.to_json%>"
   data-action="
     nextflow--autofilled-cell:sendAutofilledInputData->nextflow--samplesheet#updateAutofilledSamplesheetData
   "

app/controllers/workflow_executions/file_selector_controller.rb

@@ -8,6 +8,8 @@ class FileSelectorController < ApplicationController
     before_action :listing_attachments, only: %i[new create]
 
     def new
+      puts 'hihihhihi'
+      puts file_selector_params
       render turbo_stream: turbo_stream.update('file_selector_dialog',
                                                partial: 'file_selector_dialog',
                                                locals: { file_selector_params:, open: true }), status: :ok
@@ -33,7 +35,7 @@ def file_selector_params
         :file_type,
         required_properties: [],
         file_selector_arguments: [
-          :pattern, { workflow_params: %i[name version] }
+          { patterns: {} }, { workflow_params: %i[name version] }
         ]
       )
     end
@@ -45,10 +47,10 @@ def listing_attachments # rubocop:disable Metrics/AbcSize
           file_selector_params['property'], file_selector_params['file_selector_arguments']['workflow_params']
         )
       when 'other'
-        @listing_attachments = if file_selector_params['file_selector_arguments']['pattern']
+        @listing_attachments = if file_selector_params['file_selector_arguments']['patterns'][file_selector_params['property']]
                                  @attachable.filter_files_by_pattern(
                                    @attachable.sorted_files[:singles] || [],
-                                   file_selector_params['file_selector_arguments']['pattern']
+                                   file_selector_params['file_selector_arguments']['patterns'][file_selector_params['property']]
                                  )
                                else
                                  sample.sorted_files[:singles] || []
@@ -77,7 +79,7 @@ def attachments
                              byte_size: attachment.byte_size,
                              created_at: attachment.created_at,
                              metadata: attachment.metadata }
-      return unless file_selector_params['property'] == 'fastq_1' || file_selector_params['property'] == 'fastq_2'
+      return unless %w[fastq_1 fastq_2].include?(file_selector_params['property'])
 
       assign_associated_attachment_params(attachment)
     end

app/javascript/controllers/nextflow/autofilled_cell_controller.js

@@ -5,6 +5,7 @@ export default class extends Controller {
   static values = { inputName: { type: String }, inputValue: { type: String } };
 
   connect() {
+    console.log("autofilled");
     this.sendAutofilledInputData();
   }