[ENHC0010042] Add new file format labels for attachments (#663)

* adding new text & spreadsheet pills to attachments

* fixing rubocop error

* fixing test

* adding rtf file extension for labeling text attachments & adding more model tests

* changing the color of text labels

app/components/viral/pill_component.rb

@@ -11,6 +11,7 @@ class PillComponent < Viral::Component
       red: 'bg-red-100 text-red-800 dark:bg-red-900 dark:text-red-300',
       green: 'bg-green-100 text-green-800 dark:bg-green-900 dark:text-green-300',
       yellow: 'bg-yellow-100 text-yellow-800 dark:bg-yellow-900 dark:text-yellow-300',
+      orange: 'bg-orange-100 text-orange-800 dark:bg-orange-900 dark:text-orange-300',
       indigo: 'bg-indigo-100 text-indigo-800 dark:bg-indigo-900 dark:text-indigo-300',
       purple: 'bg-purple-100 text-purple-800 dark:bg-purple-900 dark:text-purple-300',
       pink: 'bg-pink-100 text-pink-800 dark:bg-pink-900 dark:text-pink-300',
@@ -24,6 +25,7 @@ class PillComponent < Viral::Component
       red: 'border border-red-800 dark:border-red-300',
       green: 'border border-green-800 dark:border-green-300',
       yellow: 'border border-yellow-800 dark:border-yellow-300',
+      orange: 'border border-orange-800 dark:border-orange-300',
       indigo: 'border border-indigo-800 dark:border-indigo-300',
       purple: 'border border-purple-800 dark:border-purple-300',
       pink: 'border border-pink-800 dark:border-pink-300',

app/helpers/pill_color_helper.rb

@@ -6,6 +6,8 @@ module PillColorHelper
     format: {
       fasta: 'blue',
       fastq: 'green',
+      text: 'orange',
+      spreadsheet: 'yellow',
       unknown: 'slate'
     },
     type: {

app/models/attachment.rb

@@ -44,7 +44,7 @@ def associated_attachment
 
   private
 
-  def assign_metadata
+  def assign_metadata # rubocop:disable Metrics/AbcSize
     return if metadata.key? 'format'
 
     case filename.to_s
@@ -56,6 +56,12 @@ def assign_metadata
     # Assigns fastq to metadata format for following file types: .fastq, .fastq.gz, .fq, .fq.gz
     when /^\S+\.f(ast)?q(\.gz)?$/
       metadata['format'] = 'fastq'
+    # Assigns text to metadata format for following file types: .txt, .rtf, .csv, .tsv
+    when /^\S+\.(txt|rtf|csv|tsv)?$/
+      metadata['format'] = 'text'
+    # Assigns spreadsheet to metadata format for following file types: .xls, .xlsx
+    when /^\S+\.(xls|xlsx)?$/
+      metadata['format'] = 'spreadsheet'
     # Else assigns unknown to metadata format
     else
       metadata['format'] = 'unknown'

test/models/attachment_test.rb

@@ -101,6 +101,46 @@ def setup
     assert new_fasta_attachment_ext_fna_gz.fasta?
   end
 
+  test 'metadata text file types' do
+    new_text_attachment_ext_txt =
+      @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/test_file_14.txt').open,
+                                        filename: 'test_file_14.txt' })
+    new_text_attachment_ext_txt.save
+    assert_equal 'text', new_text_attachment_ext_txt.metadata['format']
+
+    new_text_attachment_ext_rtf =
+      @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/test_file_13.rtf').open,
+                                        filename: 'test_file_13.rtf' })
+    new_text_attachment_ext_rtf.save
+    assert_equal 'text', new_text_attachment_ext_rtf.metadata['format']
+
+    new_text_attachment_ext_csv =
+      @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/metadata/valid.csv').open,
+                                        filename: 'valid.csv' })
+    new_text_attachment_ext_csv.save
+    assert_equal 'text', new_text_attachment_ext_csv.metadata['format']
+
+    new_text_attachment_ext_tsv =
+      @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/metadata/valid.tsv').open,
+                                        filename: 'valid.tsv' })
+    new_text_attachment_ext_tsv.save
+    assert_equal 'text', new_text_attachment_ext_tsv.metadata['format']
+  end
+
+  test 'metadata spreadsheet file types' do
+    new_spreadsheet_attachment_ext_xls =
+      @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/metadata/valid.xls').open,
+                                        filename: 'valid.xls' })
+    new_spreadsheet_attachment_ext_xls.save
+    assert_equal 'spreadsheet', new_spreadsheet_attachment_ext_xls.metadata['format']
+
+    new_spreadsheet_attachment_ext_xlsx =
+      @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/metadata/valid.xlsx').open,
+                                        filename: 'valid.xlsx' })
+    new_spreadsheet_attachment_ext_xlsx.save
+    assert_equal 'spreadsheet', new_spreadsheet_attachment_ext_xlsx.metadata['format']
+  end
+
   test 'metadata unknown file types' do
     new_unknown_attachment_ext_docx =
       @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/test_file_11.docx').open,
@@ -113,18 +153,6 @@ def setup
                                         filename: 'test_file_12.pdf' })
     new_unknown_attachment_ext_pdf.save
     assert_equal 'unknown', new_unknown_attachment_ext_pdf.metadata['format']
-
-    new_unknown_attachment_ext_rtf =
-      @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/test_file_13.rtf').open,
-                                        filename: 'test_file_13.rtf' })
-    new_unknown_attachment_ext_rtf.save
-    assert_equal 'unknown', new_unknown_attachment_ext_rtf.metadata['format']
-
-    new_unknown_attachment_ext_txt =
-      @sample.attachments.build(file: { io: Rails.root.join('test/fixtures/files/test_file_14.txt').open,
-                                        filename: 'test_file_14.txt' })
-    new_unknown_attachment_ext_txt.save
-    assert_equal 'unknown', new_unknown_attachment_ext_txt.metadata['format']
   end
 
   test '#destroy does not destroy the ActiveStorage::Attachment' do