Sync tests for practice exercise protein translation (#2617)

exercises/practice/protein-translation/.meta/src/reference/java/ProteinTranslator.java

@@ -1,45 +1,52 @@
-import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
+import java.util.ArrayList;
+import java.util.Map;
+import java.util.HashMap;
 
 class ProteinTranslator {
 
-    private static final String[] METHIONINE = {"AUG"};
-    private static final String[] PHENYLALANINE = {"UUU", "UUC"};
-    private static final String[] LEUCINE = {"UUA", "UUG"};
-    private static final String[] SERINE = {"UCU", "UCC", "UCA", "UCG"};
-    private static final String[] TYROSINE = {"UAU", "UAC"};
-    private static final String[] CYSTEINE = {"UGU", "UGC"};
-    private static final String[] TRYPTOPHAN = {"UGG"};
-    private static final String[] STOP = {"UAA", "UAG", "UGA"};
+    private final Map<String, String> aminoAcidsMap = new HashMap<>() {
+        {
+            put("AUG", "Methionine");
+            put("UUU", "Phenylalanine");
+            put("UUC", "Phenylalanine");
+            put("UUA", "Leucine");
+            put("UUG", "Leucine");
+            put("UCU", "Serine");
+            put("UCC", "Serine");
+            put("UCA", "Serine");
+            put("UCG", "Serine");
+            put("UAU", "Tyrosine");
+            put("UAC", "Tyrosine");
+            put("UGU", "Cysteine");
+            put("UGC", "Cysteine");
+            put("UGG", "Tryptophan");
+            put("UAA", "STOP");
+            put("UAG", "STOP");
+            put("UGA", "STOP");
+        }
+    };
 
     List<String> translate(String rnaSequence) {
+        List<String> proteinList = new ArrayList<>();
 
-        List<String> proteinList = new ArrayList<String>();
+        if (rnaSequence.length() % 3 != 0
+                && !(rnaSequence.contains("UAA") || rnaSequence.contains("UAG") || rnaSequence.contains("UGA"))) {
+            throw new IllegalArgumentException("Invalid codon");
+        }
 
         for (int i = 0; i < rnaSequence.length(); i += 3) {
-            String codon = rnaSequence.substring(i, i + 3);
-
-            if (Arrays.asList(METHIONINE).contains(codon)) {
-                proteinList.add("Methionine");
-            } else if (Arrays.asList(PHENYLALANINE).contains(codon)) {
-                proteinList.add("Phenylalanine");
-            } else if (Arrays.asList(LEUCINE).contains(codon)) {
-                proteinList.add("Leucine");
-            } else if (Arrays.asList(SERINE).contains(codon)) {
-                proteinList.add("Serine");
-            } else if (Arrays.asList(TYROSINE).contains(codon)) {
-                proteinList.add("Tyrosine");
-            } else if (Arrays.asList(CYSTEINE).contains(codon)) {
-                proteinList.add("Cysteine");
-            } else if (Arrays.asList(TRYPTOPHAN).contains(codon)) {
-                proteinList.add("Tryptophan");
-            } else if (Arrays.asList(STOP).contains(codon)) {
-                break;
+            String currentSequence = rnaSequence.substring(i, i + 3);
+
+            if (aminoAcidsMap.containsKey(currentSequence)) {
+                if (aminoAcidsMap.get(currentSequence).equals("STOP")) {
+                    return proteinList;
+                }
+
+                proteinList.add(aminoAcidsMap.get(currentSequence));
             } else {
-                throw new IllegalArgumentException("Invalid input");
+                throw new IllegalArgumentException("Invalid codon");
             }
-
         }
 
         return proteinList;

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 +86,15 @@ 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"
+
+[1e75ea2a-f907-4994-ae5c-118632a1cb0f]
+description = "Non-existing codon can't translate"
+
+[9eac93f3-627a-4c90-8653-6d0a0595bc6f]
+description = "Unknown amino acids, not part of a codon, can't translate"
+
+[9d73899f-e68e-4291-b1e2-7bf87c00f024]
+description = "Incomplete RNA sequence can't translate"
+
+[43945cf7-9968-402d-ab9f-b8a28750b050]
+description = "Incomplete RNA sequence can translate if valid until a STOP codon"

exercises/practice/protein-translation/src/test/java/ProteinTranslatorTest.java

@@ -3,6 +3,7 @@
 import org.junit.Test;
 
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.assertThatExceptionOfType;
 
 public class ProteinTranslatorTest {
 
@@ -13,6 +14,12 @@ public void setUp() {
         proteinTranslator = new ProteinTranslator();
     }
 
+    @Test
+    public void testEmptyRnaSequenceResultInNoproteins() {
+        assertThat(proteinTranslator.translate("")).isEmpty();
+    }
+
+    @Ignore("Remove to run test")
     @Test
     public void testMethionineRnaSequence() {
         assertThat(proteinTranslator.translate("AUG")).containsExactly("Methionine");
@@ -114,11 +121,23 @@ public void testStopRnaSequence3() {
         assertThat(proteinTranslator.translate("UGA")).isEmpty();
     }
 
+    @Ignore("Remove to run test")
+    @Test
+    public void testSequenceOfTwoProteinCodonsTranslatesIntoProteins() {
+        assertThat(proteinTranslator.translate("UUUUUU")).containsExactly("Phenylalanine", "Phenylalanine");
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testSequenceOfTwoDifferentProteinCodonsTranslatesIntoProteins() {
+        assertThat(proteinTranslator.translate("UUAUUG")).containsExactly("Leucine", "Leucine");
+    }
+
     @Ignore("Remove to run test")
     @Test
     public void testTranslationOfRnaToProteinList() {
         assertThat(proteinTranslator.translate("AUGUUUUGG"))
-            .containsExactly("Methionine", "Phenylalanine", "Tryptophan");
+                .containsExactly("Methionine", "Phenylalanine", "Tryptophan");
     }
 
     @Ignore("Remove to run test")
@@ -149,7 +168,36 @@ public void testTranslationStopsIfStopCodonInMiddle1() {
     @Test
     public void testTranslationStopsIfStopCodonInMiddle2() {
         assertThat(proteinTranslator.translate("UGGUGUUAUUAAUGGUUU"))
-            .containsExactly("Tryptophan", "Cysteine", "Tyrosine");
+                .containsExactly("Tryptophan", "Cysteine", "Tyrosine");
     }
 
+    @Ignore("Remove to run test")
+    @Test
+    public void testNonExistingCodonCantTranslate() {
+        assertThatExceptionOfType(IllegalArgumentException.class)
+                .isThrownBy(() -> proteinTranslator.translate("AAA"))
+                .withMessage("Invalid codon");
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testUnknownAminoAcidsNotPartOfACodonCantTranslate() {
+        assertThatExceptionOfType(IllegalArgumentException.class)
+                .isThrownBy(() -> proteinTranslator.translate("XYZ"))
+                .withMessage("Invalid codon");
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testIncompleteRnaSequenceCantTranslate() {
+        assertThatExceptionOfType(IllegalArgumentException.class)
+                .isThrownBy(() -> proteinTranslator.translate("AUGU"))
+                .withMessage("Invalid codon");
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testIncompleteRnaSequenceCanTranslateIfValidUntilAStopCodon() {
+        assertThat(proteinTranslator.translate("UUCUUCUAAUGGU")).containsExactly("Phenylalanine", "Phenylalanine");
+    }
 }