Export Service - add simple manifest file, manifest.txt (#700)

* first cut, working functionality

* Fix existing tests, add comments

* simplify recursive function

* fix folder line formatting

* Add test for output of simple manifest file

* fix test case failing from mismatched date

app/jobs/data_exports/create_job.rb

@@ -72,6 +72,66 @@ def write_manifest(zip)
       manifest_file.unlink
     end
 
+    def write_simple_manifest(data_export_id:, zip:)
+      output_lines = simple_manifest_begin(data_export_id:)
+
+      simple_manifest_file = Tempfile.new
+      File.open(simple_manifest_file, 'a+') { |f| f.puts(output_lines) }
+      zip.write_file('manifest.txt') { |writer_for_file| IO.copy_stream(simple_manifest_file.open, writer_for_file) }
+
+      simple_manifest_file.close
+      simple_manifest_file.unlink
+    end
+
+    def simple_manifest_begin(data_export_id:)
+      output_lines = [
+        @manifest['type'],
+        @manifest['date'],
+        '',
+        'contents:',
+        "#{data_export_id}/"
+      ]
+
+      child_count = @manifest['children'].count
+      (@manifest['children']).each_with_index do |child, index|
+        # push with * is used to flatten array without creating a new array
+        output_lines.push(*simple_manifest_gen_lines_recursive(
+          cursor: child, prefix: '', final_child: child_count == index + 1
+        ))
+      end
+
+      output_lines
+    end
+
+    def simple_manifest_gen_lines_recursive(cursor:, prefix: '', final_child: false) # rubocop:disable Metrics/MethodLength
+      output = []
+
+      # when the current cursor is the final child of the parent, we change which symbols are used to generate the lines
+      if final_child
+        line = "#{prefix}└─ #{cursor['name']}"
+        child_prefix = "#{prefix}   "
+      else
+        line = "#{prefix}├─ #{cursor['name']}"
+        child_prefix = "#{prefix}│  "
+      end
+
+      line += '/' if cursor['type'] == 'folder'
+      line += " (#{cursor['irida-next-name']})" if cursor.key?('irida-next-name')
+      output.append(line)
+
+      if cursor['type'] == 'folder'
+        child_count = cursor['children'].count
+        (cursor['children']).each_with_index do |child, index|
+          # push with * is used to flatten array without creating a new array
+          output.push(*simple_manifest_gen_lines_recursive(
+            cursor: child, prefix: child_prefix, final_child: child_count == index + 1
+          ))
+        end
+      end
+
+      output # array of lines
+    end
+
     # Sample export specific functions------------------------------------------------------------------
     def create_sample_zip(data_export)
       Tempfile.new(binmode: true).tap do |tempfile|
@@ -92,6 +152,7 @@ def create_sample_zip(data_export)
           end
 
           write_manifest(zip)
+          write_simple_manifest(data_export_id: data_export.id.to_s, zip:)
         end
       end
     end
@@ -167,6 +228,7 @@ def create_analysis_zip(data_export)
           end
 
           write_manifest(zip)
+          write_simple_manifest(data_export_id: data_export.id.to_s, zip:)
         end
       end
     end

test/jobs/data_exports/create_job_test.rb

@@ -28,7 +28,8 @@ def setup
       attachment2 = attachments(:attachment2)
       expected_files_in_zip = ["#{project.puid}/#{sample.puid}/#{attachment1.puid}/#{attachment1.file.filename}",
                                "#{project.puid}/#{sample.puid}/#{attachment2.puid}/#{attachment2.file.filename}",
-                               'manifest.json']
+                               'manifest.json',
+                               'manifest.txt']
       DataExports::CreateJob.perform_now(@data_export2)
       export_file = ActiveStorage::Blob.service.path_for(@data_export2.file.key)
       Zip::File.open(export_file) do |zip_file|
@@ -82,6 +83,46 @@ def setup
       assert_equal expected_manifest.to_json, @data_export2.manifest
     end
 
+    test 'content of sample export simple manifest' do
+      sample = samples(:sample1)
+      project = projects(:project1)
+      attachment1 = attachments(:attachment1)
+      attachment2 = attachments(:attachment2)
+      expected_files_in_zip = ["#{project.puid}/#{sample.puid}/#{attachment1.puid}/#{attachment1.file.filename}",
+                               "#{project.puid}/#{sample.puid}/#{attachment2.puid}/#{attachment2.file.filename}",
+                               'manifest.json',
+                               'manifest.txt']
+      actual_simple_manifest = ''
+
+      DataExports::CreateJob.perform_now(@data_export2)
+      export_file = ActiveStorage::Blob.service.path_for(@data_export2.file.key)
+      Zip::File.open(export_file) do |zip_file|
+        zip_file.each do |entry|
+          assert expected_files_in_zip.include?(entry.to_s)
+          actual_simple_manifest = entry.get_input_stream.read.force_encoding('utf-8') if entry.to_s == 'manifest.txt'
+          expected_files_in_zip.delete(entry.to_s)
+        end
+      end
+      assert expected_files_in_zip.empty?
+
+      expected_simple_manifest = [
+        'Samples Export',
+        Date.current.strftime('%Y-%m-%d').to_s,
+        '',
+        'contents:',
+        '9eb3e2b7-6e20-5324-b6a3-49f44dc33fd8/',
+        '└─ INXT_PRJ_AAAAAAAAAA/ (Project 1)',
+        '   └─ INXT_SAM_AAAAAAAAAA/ (Project 1 Sample 1)',
+        '      ├─ INXT_ATT_AAAAAAAAAA/',
+        '      │  └─ test_file.fastq',
+        '      └─ INXT_ATT_AAAAAAAAAB/',
+        '         └─ test_file_A.fastq',
+        ''
+      ].join("\n")
+
+      assert_equal expected_simple_manifest, actual_simple_manifest
+    end
+
     test 'content of sample export including paired files' do
       sample_b = samples(:sampleB)
 
@@ -108,7 +149,8 @@ def setup
           "#{project.puid}/#{sample_b.puid}/#{attachment_d.puid}/#{attachment_d.file.filename}",
           "#{project.puid}/#{sample_b.puid}/#{attachment_e.puid}/#{attachment_e.file.filename}",
           "#{project.puid}/#{sample_b.puid}/#{attachment_f.puid}/#{attachment_f.file.filename}",
-          'manifest.json'
+          'manifest.json',
+          'manifest.txt'
         ]
 
       expected_manifest = {
@@ -257,6 +299,7 @@ def setup
 
       expected_files_in_zip = ["#{sample.puid}/#{samples_workflow_execution.outputs[0].filename}",
                                'manifest.json',
+                               'manifest.txt',
                                workflow_execution.outputs[0].filename.to_s]
       DataExports::CreateJob.perform_now(@data_export6)
       export_file = ActiveStorage::Blob.service.path_for(@data_export6.file.key)
@@ -367,7 +410,8 @@ def setup
         [
           "#{project.puid}/#{sample22.puid}/#{text_attachment.puid}/#{text_attachment.file.filename}",
           "#{project.puid}/#{sample22.puid}/#{fasta_attachment.puid}/#{fasta_attachment.file.filename}",
-          'manifest.json'
+          'manifest.json',
+          'manifest.txt'
         ]
 
       expected_manifest = {