Updated protein-translation-tests (#590)

Author: ryanplusplus

exercises/practice/protein-translation/.meta/example.lua

@@ -18,16 +18,16 @@ local codon_to_protein = {
   UGA = 'STOP'
 }
 
-local function translate_codon(codon)
+local function protein_for_codon(codon)
   local protein = codon_to_protein[codon]
   assert(protein ~= nil, 'Unknown codon')
   return protein
 end
 
-local function translate_rna_strand(rna_strand)
+local function proteins(strand)
   local proteins = {}
-  for codon in rna_strand:gmatch('...') do
-    local protein = translate_codon(codon)
+  for codon in strand:gmatch('...') do
+    local protein = protein_for_codon(codon)
     if protein == 'STOP' then
       break
     end
@@ -36,4 +36,4 @@ local function translate_rna_strand(rna_strand)
   return proteins
 end
 
-return { codon = translate_codon, rna_strand = translate_rna_strand }
+return { proteins = proteins }

exercises/practice/protein-translation/.meta/spec_generator.lua

@@ -0,0 +1,31 @@
+local map = function(t, f)
+  local mapped = {}
+  for i, v in ipairs(t) do
+    mapped[i] = f(v)
+  end
+  return mapped
+end
+
+local function stringify(v)
+  return ("'%s'"):format(tostring(v))
+end
+
+return {
+  module_name = 'protein_translation',
+
+  generate_test = function(case)
+    if case.expected.error then
+      local template = [[
+        assert.has_error(function()
+          protein_translation.%s('%s')
+        end)]]
+
+      return template:format(case.property, case.input.strand)
+    else
+      local template = [[
+        assert.are.same({ %s }, protein_translation.%s('%s'))]]
+
+      return template:format(table.concat(map(case.expected, stringify), ', '), case.property, case.input.strand)
+    end
+  end
+}

exercises/practice/protein-translation/.meta/tests.toml

@@ -1,6 +1,16 @@
-# This is an auto-generated file. Regular comments will be removed when this
-# file is regenerated. Regenerating will not touch any manually added keys,
-# so comments can be added in a "comment" key.
+# This is an auto-generated file.
+#
+# Regenerating this file via `configlet sync` will:
+# - Recreate every `description` key/value pair
+# - Recreate every `reimplements` key/value pair, where they exist in problem-specifications
+# - Remove any `include = true` key/value pair (an omitted `include` key implies inclusion)
+# - Preserve any other key/value pair
+#
+# As user-added comments (using the # character) will be removed when this file
+# is regenerated, comments can be added via a `comment` key.
+
+[2c44f7bf-ba20-43f7-a3bf-f2219c0c3f98]
+description = "Empty RNA sequence results in no proteins"
 
 [96d3d44f-34a2-4db4-84cd-fff523e069be]
 description = "Methionine RNA sequence"
@@ -53,6 +63,12 @@ description = "STOP codon RNA sequence 2"
 [9c2ad527-ebc9-4ace-808b-2b6447cb54cb]
 description = "STOP codon RNA sequence 3"
 
+[f4d9d8ee-00a8-47bf-a1e3-1641d4428e54]
+description = "Sequence of two protein codons translates into proteins"
+
+[dd22eef3-b4f1-4ad6-bb0b-27093c090a9d]
+description = "Sequence of two different protein codons translates into proteins"
+
 [d0f295df-fb70-425c-946c-ec2ec185388e]
 description = "Translate RNA strand into correct protein list"
 
@@ -70,3 +86,21 @@ description = "Translation stops if STOP codon in middle of three-codon sequence
 
 [2c2a2a60-401f-4a80-b977-e0715b23b93d]
 description = "Translation stops if STOP codon in middle of six-codon sequence"
+
+[f6f92714-769f-4187-9524-e353e8a41a80]
+description = "Sequence of two non-STOP codons does not translate to a STOP codon"
+
+[1e75ea2a-f907-4994-ae5c-118632a1cb0f]
+description = "Non-existing codon can't translate"
+include = false
+
+[9eac93f3-627a-4c90-8653-6d0a0595bc6f]
+description = "Unknown amino acids, not part of a codon, can't translate"
+reimplements = "1e75ea2a-f907-4994-ae5c-118632a1cb0f"
+
+[9d73899f-e68e-4291-b1e2-7bf87c00f024]
+description = "Incomplete RNA sequence can't translate"
+include = false
+
+[43945cf7-9968-402d-ab9f-b8a28750b050]
+description = "Incomplete RNA sequence can translate if valid until a STOP codon"

exercises/practice/protein-translation/protein-translation.lua

@@ -1,7 +1,5 @@
-local function translate_codon(codon)
-end
+local function proteins(strand)
 
-local function translate_rna_strand(rna_strand)
 end
 
-return { codon = translate_codon, rna_strand = translate_rna_strand }
+return { proteins = proteins }

exercises/practice/protein-translation/protein-translation_spec.lua

@@ -1,73 +1,121 @@
-local translate = require('protein-translation')
+local protein_translation = require('protein-translation')
 
 describe('protein-translation', function()
-  describe('translate.codon', function()
-    it('should translate AUG to Methionine', function()
-      assert.equal('Methionine', translate.codon('AUG'))
-    end)
+  it('empty rna sequence results in no proteins', function()
+    assert.are.same({}, protein_translation.proteins(''))
+  end)
 
-    it('should translate UUU and UUC to Phenylalanine', function()
-      assert.equal('Phenylalanine', translate.codon('UUU'))
-      assert.equal('Phenylalanine', translate.codon('UUC'))
-    end)
+  it('methionine rna sequence', function()
+    assert.are.same({ 'Methionine' }, protein_translation.proteins('AUG'))
+  end)
 
-    it('should translate UUA and UUG to Leucine', function()
-      assert.equal('Leucine', translate.codon('UUA'))
-      assert.equal('Leucine', translate.codon('UUG'))
-    end)
+  it('phenylalanine rna sequence 1', function()
+    assert.are.same({ 'Phenylalanine' }, protein_translation.proteins('UUU'))
+  end)
 
-    it('should translate UCU, UCC, UCA, and UCG to Serine', function()
-      assert.equal('Serine', translate.codon('UCU'))
-      assert.equal('Serine', translate.codon('UCC'))
-      assert.equal('Serine', translate.codon('UCA'))
-      assert.equal('Serine', translate.codon('UCG'))
-    end)
+  it('phenylalanine rna sequence 2', function()
+    assert.are.same({ 'Phenylalanine' }, protein_translation.proteins('UUC'))
+  end)
 
-    it('should translate UAU and UAC to Tyrosine', function()
-      assert.equal('Tyrosine', translate.codon('UAU'))
-      assert.equal('Tyrosine', translate.codon('UAC'))
-    end)
+  it('leucine rna sequence 1', function()
+    assert.are.same({ 'Leucine' }, protein_translation.proteins('UUA'))
+  end)
 
-    it('should translate UGU and UGC to Cysteine', function()
-      assert.equal('Cysteine', translate.codon('UGU'))
-      assert.equal('Cysteine', translate.codon('UGC'))
-    end)
+  it('leucine rna sequence 2', function()
+    assert.are.same({ 'Leucine' }, protein_translation.proteins('UUG'))
+  end)
 
-    it('should translate UGG to Tryptophan', function()
-      assert.equal('Tryptophan', translate.codon('UGG'))
-    end)
+  it('serine rna sequence 1', function()
+    assert.are.same({ 'Serine' }, protein_translation.proteins('UCU'))
+  end)
 
-    it('should translate UAA, UAG, and UGA to STOP codons', function()
-      assert.equal('STOP', translate.codon('UAA'))
-      assert.equal('STOP', translate.codon('UAG'))
-      assert.equal('STOP', translate.codon('UGA'))
-    end)
+  it('serine rna sequence 2', function()
+    assert.are.same({ 'Serine' }, protein_translation.proteins('UCC'))
+  end)
 
-    it('should raise an error when an unknown codon is translated', function()
-      assert.has_error(function()
-        translate.codon('MIA')
-      end)
-    end)
+  it('serine rna sequence 3', function()
+    assert.are.same({ 'Serine' }, protein_translation.proteins('UCA'))
   end)
 
-  describe('translate.rna_strand', function()
-    it('should translate each codon in a strand into the corresponding protein', function()
-      assert.same({ 'Methionine', 'Phenylalanine', 'Tryptophan' }, translate.rna_strand('AUGUUUUGG'))
-    end)
+  it('serine rna sequence 4', function()
+    assert.are.same({ 'Serine' }, protein_translation.proteins('UCG'))
+  end)
 
-    it('should stop translation when a STOP codon is encountered', function()
-      assert.same({ 'Methionine', 'Phenylalanine' }, translate.rna_strand('AUGUUUUAA'))
-      assert.same({ 'Tryptophan', 'Cysteine', 'Tyrosine' }, translate.rna_strand('UGGUGUUAUUAAUGGUUU'))
-    end)
+  it('tyrosine rna sequence 1', function()
+    assert.are.same({ 'Tyrosine' }, protein_translation.proteins('UAU'))
+  end)
 
-    it('should raise an error when an unknown codon is encountered', function()
-      assert.has_error(function()
-        translate.rna_strand('UGUCARROT')
-      end)
-    end)
+  it('tyrosine rna sequence 2', function()
+    assert.are.same({ 'Tyrosine' }, protein_translation.proteins('UAC'))
+  end)
+
+  it('cysteine rna sequence 1', function()
+    assert.are.same({ 'Cysteine' }, protein_translation.proteins('UGU'))
+  end)
 
-    it('should not raise an error when an unknown codon occurs after a STOP codon', function()
-      assert.same({ 'Cysteine' }, translate.rna_strand('UGUUGACARROT'))
+  it('cysteine rna sequence 2', function()
+    assert.are.same({ 'Cysteine' }, protein_translation.proteins('UGC'))
+  end)
+
+  it('tryptophan rna sequence', function()
+    assert.are.same({ 'Tryptophan' }, protein_translation.proteins('UGG'))
+  end)
+
+  it('stop codon rna sequence 1', function()
+    assert.are.same({}, protein_translation.proteins('UAA'))
+  end)
+
+  it('stop codon rna sequence 2', function()
+    assert.are.same({}, protein_translation.proteins('UAG'))
+  end)
+
+  it('stop codon rna sequence 3', function()
+    assert.are.same({}, protein_translation.proteins('UGA'))
+  end)
+
+  it('sequence of two protein codons translates into proteins', function()
+    assert.are.same({ 'Phenylalanine', 'Phenylalanine' }, protein_translation.proteins('UUUUUU'))
+  end)
+
+  it('sequence of two different protein codons translates into proteins', function()
+    assert.are.same({ 'Leucine', 'Leucine' }, protein_translation.proteins('UUAUUG'))
+  end)
+
+  it('translate rna strand into correct protein list', function()
+    assert.are.same({ 'Methionine', 'Phenylalanine', 'Tryptophan' }, protein_translation.proteins('AUGUUUUGG'))
+  end)
+
+  it('translation stops if stop codon at beginning of sequence', function()
+    assert.are.same({}, protein_translation.proteins('UAGUGG'))
+  end)
+
+  it('translation stops if stop codon at end of two-codon sequence', function()
+    assert.are.same({ 'Tryptophan' }, protein_translation.proteins('UGGUAG'))
+  end)
+
+  it('translation stops if stop codon at end of three-codon sequence', function()
+    assert.are.same({ 'Methionine', 'Phenylalanine' }, protein_translation.proteins('AUGUUUUAA'))
+  end)
+
+  it('translation stops if stop codon in middle of three-codon sequence', function()
+    assert.are.same({ 'Tryptophan' }, protein_translation.proteins('UGGUAGUGG'))
+  end)
+
+  it('translation stops if stop codon in middle of six-codon sequence', function()
+    assert.are.same({ 'Tryptophan', 'Cysteine', 'Tyrosine' }, protein_translation.proteins('UGGUGUUAUUAAUGGUUU'))
+  end)
+
+  it('sequence of two non-stop codons does not translate to a stop codon', function()
+    assert.are.same({ 'Methionine', 'Methionine' }, protein_translation.proteins('AUGAUG'))
+  end)
+
+  it('unknown amino acids, not part of a codon, can\'t translate', function()
+    assert.has_error(function()
+      protein_translation.proteins('XYZ')
     end)
   end)
+
+  it('incomplete rna sequence can translate if valid until a stop codon', function()
+    assert.are.same({ 'Phenylalanine', 'Phenylalanine' }, protein_translation.proteins('UUCUUCUAAUGGU'))
+  end)
 end)