Merge pull request #1069 from sanger/sh/remove-spec-puts

Tidy rspec output

spec/lib/tasks_spec.rb

@@ -13,19 +13,76 @@
 
   describe 'create tags' do
     it 'creates all of the pacbio tag sets' do
-      Rake::Task['tags:create:pacbio_all'].invoke
+      expect { Rake::Task['tags:create:pacbio_all'].invoke }.to output(
+        <<~HEREDOC
+          -> Creating Sequel_16_barcodes_v3 tag set and tags
+          -> Tag Set successfully created
+          -> Sequel_16_barcodes_v3 tags successfully created
+          -> Creating Sequel_48_Microbial_Barcoded_OHA_v1tag set and tags
+          -> Tag Set successfully created
+          -> Sequel_48_Microbial_Barcoded_OHA_v1 tags successfully created
+          -> Creating TruSeq_CD_i7_i5_D0x_8mer tag set and tags
+          -> Tag Set successfully created
+          -> TruSeq_CD_i7_i5_D0x_8mer tags successfully created
+          -> Creating Sequel_96_Barcoded_OHA_v1 tag set and tags
+          -> Tag Set successfully created
+          -> Sequel_96_Barcoded_OHA_v1 tags successfully created
+          -> Creating Pacbio IsoSeq tag set and tags
+          -> Tag Set successfully created
+          -> IsoSeq_Primers_12_Barcodes_v1 created
+          -> Creating Nextera UD tag set and tags
+          -> Tag Set successfully created
+          -> Nextera_UD_Index_PlateA tags successfully created
+          -> Creating Pacbio_96_barcode_plate_v3 tag set and tags
+          -> Tag Set successfully created
+          -> Pacbio_96_barcode_plate_v3 tags successfully created
+        HEREDOC
+      ).to_stdout
       expect(TagSet.count).to eq(7)
     end
 
     it 'creates all of the ont tag sets' do
-      Rake::Task['tags:create:ont_all'].invoke
+      expect { Rake::Task['tags:create:ont_all'].invoke }.to output(
+        <<~HEREDOC
+          -> Creating SQK-NBD114.96 tag set and tags
+          -> Tag Set successfully created
+          -> SQK-NBD114.96 tags successfully created
+        HEREDOC
+      ).to_stdout
       expect(TagSet.count).to eq(1)
     end
 
     it 'creates all of the tag sets' do
       # We need to reenable all tag tasks because they have all already been invoked by this point
       Rake.application.in_namespace(:tags) { |namespace| namespace.tasks.each(&:reenable) }
-      Rake::Task['tags:create:traction_all'].invoke
+      expect { Rake::Task['tags:create:traction_all'].invoke }.to output(
+        <<~HEREDOC
+          -> Creating Sequel_16_barcodes_v3 tag set and tags
+          -> Tag Set successfully created
+          -> Sequel_16_barcodes_v3 tags successfully created
+          -> Creating Sequel_48_Microbial_Barcoded_OHA_v1tag set and tags
+          -> Tag Set successfully created
+          -> Sequel_48_Microbial_Barcoded_OHA_v1 tags successfully created
+          -> Creating TruSeq_CD_i7_i5_D0x_8mer tag set and tags
+          -> Tag Set successfully created
+          -> TruSeq_CD_i7_i5_D0x_8mer tags successfully created
+          -> Creating Sequel_96_Barcoded_OHA_v1 tag set and tags
+          -> Tag Set successfully created
+          -> Sequel_96_Barcoded_OHA_v1 tags successfully created
+          -> Creating Pacbio IsoSeq tag set and tags
+          -> Tag Set successfully created
+          -> IsoSeq_Primers_12_Barcodes_v1 created
+          -> Creating Nextera UD tag set and tags
+          -> Tag Set successfully created
+          -> Nextera_UD_Index_PlateA tags successfully created
+          -> Creating Pacbio_96_barcode_plate_v3 tag set and tags
+          -> Tag Set successfully created
+          -> Pacbio_96_barcode_plate_v3 tags successfully created
+          -> Creating SQK-NBD114.96 tag set and tags
+          -> Tag Set successfully created
+          -> SQK-NBD114.96 tags successfully created
+        HEREDOC
+      ).to_stdout
       expect(TagSet.count).to eq(8)
     end
   end
@@ -40,19 +97,21 @@
       Rake::Task['tags:create:pacbio_isoseq'].reenable
       expect { Rake::Task['pacbio_data:create'].invoke }
         .to output(
-          "-> Creating Sequel_16_barcodes_v3 tag set and tags\n" \
-          "-> Tag Set successfully created\n" \
-          "-> Sequel_16_barcodes_v3 tags successfully created\n" \
-          "-> Creating Pacbio IsoSeq tag set and tags\n" \
-          "-> Tag Set successfully created\n" \
-          "-> IsoSeq_Primers_12_Barcodes_v1 created\n" \
-          "-> Creating pacbio plates and tubes...\b\b\b √ \n" \
-          "-> Creating pacbio libraries...\b\b\b √ \n" \
-          "-> Finding Pacbio SMRT Link versions...\b\b\b √ \n" \
-          "-> Creating pacbio runs:\n   " \
-          "-> Creating runs for v11...\b\b\b √ \n   " \
-          "-> Creating runs for v12_revio...\b\b\b √ \n" \
-          "-> Pacbio runs successfully created\n"
+          <<~HEREDOC
+            -> Creating Sequel_16_barcodes_v3 tag set and tags
+            -> Tag Set successfully created
+            -> Sequel_16_barcodes_v3 tags successfully created
+            -> Creating Pacbio IsoSeq tag set and tags
+            -> Tag Set successfully created
+            -> IsoSeq_Primers_12_Barcodes_v1 created
+            -> Creating pacbio plates and tubes...\b\b\b √#{' '}
+            -> Creating pacbio libraries...\b\b\b √#{' '}
+            -> Finding Pacbio SMRT Link versions...\b\b\b √#{' '}
+            -> Creating pacbio runs:
+               -> Creating runs for v11...\b\b\b √#{' '}
+               -> Creating runs for v12_revio...\b\b\b √#{' '}
+            -> Pacbio runs successfully created
+          HEREDOC
         ).to_stdout
       expect(Pacbio::Run.count)
         .to eq(12)
@@ -61,26 +120,42 @@
 
   describe 'library_types:create' do
     it 'creates the library types' do
-      expect { Rake::Task['library_types:create'].invoke }.to change(LibraryType, :count).by(15).and output("-> Library types updated\n").to_stdout
+      expect { Rake::Task['library_types:create'].invoke }.to change(LibraryType, :count).by(15).and output(
+        <<~HEREDOC
+          -> Library types updated
+        HEREDOC
+      ).to_stdout
     end
   end
 
   describe 'data_types:create' do
     it 'creates the data types' do
-      expect { Rake::Task['data_types:create'].invoke }.to change(DataType, :count).by(2).and output("-> Data types updated\n").to_stdout
+      expect { Rake::Task['data_types:create'].invoke }.to change(DataType, :count).by(2).and output(
+        <<~HEREDOC
+          -> Data types updated
+        HEREDOC
+      ).to_stdout
     end
   end
 
   describe 'ont_instruments:create' do
     it 'creates the correct instrument data' do
       Rake::Task['ont_instruments:create'].reenable
-      expect { Rake::Task['ont_instruments:create'].invoke }.to change(Ont::Instrument, :count).and output("-> ONT Instruments successfully created\n").to_stdout
+      expect { Rake::Task['ont_instruments:create'].invoke }.to change(Ont::Instrument, :count).and output(
+        <<~HEREDOC
+          -> ONT Instruments successfully created
+        HEREDOC
+      ).to_stdout
     end
   end
 
   describe 'min_know_versions:create' do
     it 'creates the correct MinKnowVersion data' do
-      expect { Rake::Task['min_know_versions:create'].invoke }.to change(Ont::MinKnowVersion, :count).and output("-> ONT MinKnow versions successfully created\n").to_stdout
+      expect { Rake::Task['min_know_versions:create'].invoke }.to change(Ont::MinKnowVersion, :count).and output(
+        <<~HEREDOC
+          -> ONT MinKnow versions successfully created
+        HEREDOC
+      ).to_stdout
     end
   end
 
@@ -150,7 +225,11 @@
 
     it 'modifies the data correctly' do
       expect(Pacbio::Well.count).to eq(6) # create(:pacbio_plate) also creates a well
-      Rake::Task['pacbio_wells:migrate_smrt_link_options'].invoke
+      expect { Rake::Task['pacbio_wells:migrate_smrt_link_options'].invoke }.to output(
+        <<~HEREDOC
+          -> 6 instances of pacbio well updated.
+        HEREDOC
+      ).to_stdout
       [well1, well2, well3, well4, well5].collect(&:reload)
       expect(well1.generate_hifi).to eq('In SMRT Link')
       expect(well2.generate_hifi).to eq('On Instrument')
@@ -162,7 +241,11 @@
 
   describe 'qc_assay_types:create' do
     it 'creates the correct number of qc assay types' do
-      expect { Rake::Task['qc_assay_types:create'].invoke }.to change(QcAssayType, :count).by(10).and output("-> QC Assay Types updated\n").to_stdout
+      expect { Rake::Task['qc_assay_types:create'].invoke }.to change(QcAssayType, :count).by(10).and output(
+        <<~HEREDOC
+          -> QC Assay Types updated
+        HEREDOC
+      ).to_stdout
     end
   end
 
@@ -191,7 +274,11 @@
       # Reenabling the task makes it possible to invoke again.
       # Invoke the data migration task for smrt_link options.
       Rake::Task['pacbio_wells:migrate_smrt_link_options'].reenable
-      Rake::Task['pacbio_wells:migrate_smrt_link_options'].invoke
+      expect { Rake::Task['pacbio_wells:migrate_smrt_link_options'].invoke }.to output(
+        <<~HEREDOC
+          -> 2 instances of pacbio well updated.
+        HEREDOC
+      ).to_stdout
 
       # Reload the attributes of the record from the database.
       # We want to see what was saved by the task.
@@ -208,7 +295,13 @@
   describe 'migrate_pacbio_run_smrt_link_versions' do
     it 'creates smrt link version and options for v10' do
       Rake::Task['pacbio_runs:migrate_pacbio_run_smrt_link_versions'].reenable
-      Rake::Task['pacbio_runs:migrate_pacbio_run_smrt_link_versions'].invoke
+      expect do
+        Rake::Task['pacbio_runs:migrate_pacbio_run_smrt_link_versions'].invoke
+      end.to output(
+        <<~HEREDOC
+          -> Pacbio SMRT Link versions and options successfully created
+        HEREDOC
+      ).to_stdout
 
       version = Pacbio::SmrtLinkVersion.find_by(name: 'v10', default: true, active: true)
       expect(version).not_to be_nil
@@ -294,7 +387,11 @@
 
       Rake::Task['smrt_link_versions:create'].reenable
       Rake::Task['pacbio_runs:migrate_pacbio_run_smrt_link_versions'].reenable
-      Rake::Task['pacbio_runs:migrate_pacbio_run_smrt_link_versions'].invoke
+      expect { Rake::Task['pacbio_runs:migrate_pacbio_run_smrt_link_versions'].invoke }.to output(
+        <<~HEREDOC
+          -> Pacbio SMRT Link versions and options successfully created
+        HEREDOC
+      ).to_stdout
 
       run10.reload
       run11.reload

spec/spec_helper.rb

@@ -88,10 +88,10 @@
   #     config.default_formatter = "doc"
   #   end
   #
-  # Print the 10 slowest examples and example groups at the
+  # Print the 1 slowest examples and example groups at the
   # end of the spec run, to help surface which specs are running
   # particularly slow.
-  config.profile_examples = 10
+  config.profile_examples = 1
   #
   #   # Run specs in random order to surface order dependencies. If you find an
   #   # order dependency and want to debug it, you can fix the order by providing