fix some older arguments

phac-nml · Jan 6, 2025 · e7e565b · e7e565b
1 parent 0962c31
commit e7e565b
Show file tree

Hide file tree

Showing 9 changed files with 23 additions and 12 deletions.
diff --git a/app/components/nextflow/samplesheet/column_component.rb b/app/components/nextflow/samplesheet/column_component.rb
@@ -4,10 +4,12 @@ module Nextflow
   module Samplesheet
     # Renders a column in the sample sheet table
     class ColumnComponent < Component
-      attr_reader :header, :property, :samples, :workflow_params
+      attr_reader :namespace_id, :header, :property, :samples, :workflow_params
 
       # rubocop:disable Metrics/ParameterLists
-      def initialize(header:, property:, samples:, metadata_fields:, required_properties:, workflow_params:)
+      def initialize(namespace_id:, header:, property:, samples:, metadata_fields:, required_properties:,
+                     workflow_params:)
+        @namespace_id = namespace_id
         @header = header
         @property = property
         @samples = samples

diff --git a/app/components/nextflow/samplesheet/file_cell_component.html.erb b/app/components/nextflow/samplesheet/file_cell_component.html.erb
@@ -28,6 +28,6 @@
       value= <%= @selected[:global_id]%>
     >
   <% end %>
-  <%= @selected.empty? ? t(".select_attachment") : @selected[:filename] %>
+  <%= @selected.empty? ? t(".select_file") : @selected[:filename] %>
 </div>
 <% end %>
diff --git a/app/components/nextflow/samplesheet_component.html.erb b/app/components/nextflow/samplesheet_component.html.erb
@@ -25,6 +25,7 @@
   >
     <% properties.each do |header, property| %>
       <%= render Nextflow::Samplesheet::ColumnComponent.new(
+        namespace_id:,
         header:,
         property:,
         samples: @samples,

diff --git a/app/components/nextflow/samplesheet_component.rb b/app/components/nextflow/samplesheet_component.rb
@@ -3,7 +3,7 @@
 module Nextflow
   # Render the contents of a Nextflow samplesheet to a table
   class SamplesheetComponent < Component
-    attr_reader :properties, :samples, :required_properties, :metadata_fields, :workflow_params
+    attr_reader :properties, :samples, :required_properties, :metadata_fields, :namespace_id, :workflow_params
 
     FILE_CELL_TYPES = %w[fastq_cell file_cell].freeze
 

diff --git a/app/controllers/file_selector_controller.rb b/app/controllers/file_selector_controller.rb
@@ -24,7 +24,8 @@ def create
 
   def file_selector_params
     params.require(:file_selector).permit(
-      :attachable, :index, :property, :selected_id, :file_type, required_properties: [], file_selector_arguments: [:pattern, workflow_params: [:name, :version]]
+      :attachable, :index, :property, :selected_id, :file_type, required_properties: [],
+      file_selector_arguments: [:pattern, workflow_params: [:name, :version]]
     )
   end
 
@@ -49,14 +50,16 @@ def attachable
   def attachments
     @attachment_params = {}
     return if params[:attachment_id] == 'no_attachment'
+
     attachment = Attachment.find(params[:attachment_id])
     @attachment_params = { filename: attachment.file.filename.to_s,
     global_id: attachment.to_global_id,
     id: attachment.id,
     byte_size: attachment.byte_size,
     created_at: attachment.created_at
   }
-    return unless attachment.associated_attachment && (file_selector_params["property"] == 'fastq_1' || file_selector_params["property"] == 'fastq_2')
+    return unless attachment.associated_attachment &&
+    (file_selector_params["property"] == 'fastq_1' || file_selector_params["property"] == 'fastq_2')
 
     assign_associated_attachment_params(attachment)
   end

diff --git a/app/models/sample.rb b/app/models/sample.rb
@@ -139,8 +139,7 @@ def sort_files
 
   def samplesheet_fastq_files(property, workflow_params)
     direction = get_fastq_direction(property)
-    pattern = Irida::Pipelines.instance.find_pipeline_by(workflow_params[:name], workflow_params[:version])
-    .property_pattern(property)
+    pattern = Irida::Pipelines.instance.find_pipeline_by(workflow_params[:name], workflow_params[:version]).property_pattern(property)
     singles = filter_files_by_pattern(sorted_files[:singles] || [],
                                         pattern || "/^\S+.f(ast)?q(.gz)?$/")
     files = []

diff --git a/config/locales/en.yml b/config/locales/en.yml
@@ -949,7 +949,7 @@ en:
         default: "%{label} (default)"
         required: Required
       file_cell_component:
-        select_attachment: Select Attachment
+        select_file: Select File
     samplesheet_component:
       attachments_error: The highlighted file cells below require a selection.
       label: Samples

diff --git a/config/locales/fr.yml b/config/locales/fr.yml
@@ -948,6 +948,8 @@ fr:
       column_component:
         default: "%{label} (default)"
         required: Required
+      file_cell_component:
+        select_file: Select File
     samplesheet_component:
       attachments_error: The highlighted file cells below require a selection.
       label: Samples

diff --git a/test/components/previews/nextflow_samplesheet_component_preview/default.html.erb b/test/components/previews/nextflow_samplesheet_component_preview/default.html.erb
@@ -2,10 +2,14 @@
   schema:
     JSON.parse(
       File.read(
-        Rails.root.join("test", "fixtures", "files", "nextflow", schema_file)
-      )
+        Rails.root.join("test", "fixtures", "files", "nextflow", schema_file),
+      ),
     ),
   samples:,
   fields:,
-  namespace_id: "SDFSDFSDF"
+  namespace_id: "SDFSDFSDF",
+  workflow_params: {
+    name: "workflow-name",
+    version: "workflow-version",
+  },
 ) %>