protein-translation: sync

exercises/practice/protein-translation/.meta/additional-tests.json

@@ -0,0 +1,182 @@
+[
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "methionine",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "AUG"
+    },
+    "expected": "Some(\"methionine\")"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "cysteine tgt",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "UGU"
+    },
+    "expected": "Some(\"cysteine\")"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "stop",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "UAA"
+    },
+    "expected": "Some(\"stop codon\")"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "valine",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "GUU"
+    },
+    "expected": "Some(\"valine\")"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "isoleucine",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "AUU"
+    },
+    "expected": "Some(\"isoleucine\")"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "arginine cga",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "CGA"
+    },
+    "expected": "Some(\"arginine\")"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "arginine aga",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "AGA"
+    },
+    "expected": "Some(\"arginine\")"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "arginine agg",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "AGG"
+    },
+    "expected": "Some(\"arginine\")"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "empty is invalid",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": ""
+    },
+    "expected": "None"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "x is not shorthand so is invalid",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "VWX"
+    },
+    "expected": "None"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "too short is invalid",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "AU"
+    },
+    "expected": "None"
+  },
+  {
+    "uuid": "ecafab60-89f2-4680-9286-56b423e8a7b9",
+    "description": "too long is invalid",
+    "comments": [
+      "The original design of the exercise deviates from problem-specifications",
+      "by having a name_for function for individual codons.",
+      "Upstreaming is impossible as it would change the design of the exercise.",
+      "Omitting them would leave the function untested, which would be confusing."
+    ],
+    "property": "name_for",
+    "input": {
+      "name": "ATTA"
+    },
+    "expected": "None"
+  }
+]

exercises/practice/protein-translation/.meta/test_template.tera

@@ -0,0 +1,76 @@
+use protein_translation::*;
+
+{% for test in cases %}
+{# custom name_for tests are first, of_rna is supposed to build on it #}
+{% if test.property != "name_for" %}{% continue %}{% endif %}
+#[test]
+#[ignore]
+fn {{ test.description | snake_case }}() {
+    let info = parse(make_pairs());
+    assert_eq!(info.name_for({{ test.input.name | json_encode() }}), {{ test.expected }});
+}
+{% endfor -%}
+
+{% for test in cases %}
+{% if test.property != "proteins" %}{% continue %}{% endif %}
+#[test]
+#[ignore]
+fn {{ test.description | snake_case }}() {
+    let info = parse(make_pairs());
+    assert_eq!(
+        info.of_rna({{ test.input.strand | json_encode() }}),
+        {% if test.expected is object %}
+            None
+        {% else %}
+            Some(vec![
+                {% for s in test.expected %}
+                    "{{ s | lower }}" {% if not loop.last %} , {% endif %}
+                {% endfor %}
+            ])
+        {% endif %},
+    );
+}
+{% endfor -%}
+
+// The input data constructor. Returns a list of codon, name pairs.
+fn make_pairs() -> Vec<(&'static str, &'static str)> {
+    let grouped = vec![
+        ("isoleucine", vec!["AUU", "AUC", "AUA"]),
+        ("valine", vec!["GUU", "GUC", "GUA", "GUG"]),
+        ("phenylalanine", vec!["UUU", "UUC"]),
+        ("methionine", vec!["AUG"]),
+        ("cysteine", vec!["UGU", "UGC"]),
+        ("alanine", vec!["GCU", "GCC", "GCA", "GCG"]),
+        ("glycine", vec!["GGU", "GGC", "GGA", "GGG"]),
+        ("proline", vec!["CCU", "CCC", "CCA", "CCG"]),
+        ("threonine", vec!["ACU", "ACC", "ACA", "ACG"]),
+        ("serine", vec!["UCU", "UCC", "UCA", "UCG"]),
+        ("tyrosine", vec!["UAU", "UAC"]),
+        ("tryptophan", vec!["UGG"]),
+        ("glutamine", vec!["CAA", "CAG"]),
+        ("asparagine", vec!["AAU", "AAC"]),
+        ("histidine", vec!["CAU", "CAC"]),
+        ("glutamic acid", vec!["GAA", "GAG"]),
+        ("aspartic acid", vec!["GAU", "GAC"]),
+        {#
+            ("lysine", vec!["AAA", "AAG"]),
+            Lysine is not listed in the canonical description
+            and there are no tests for it.
+            Unfortunately, problem-specifications has a test against
+            "invalid" codons, where "AAA" is the invalid input.
+            This technically maps to lysine, so we have to exclude it here
+            to pass the test from upstream.
+        #}
+        ("arginine", vec!["CGU", "CGC", "CGA", "CGG", "AGA", "AGG"]),
+        ("leucine", vec!["UUA", "UUG"]),
+        ("stop codon", vec!["UAA", "UAG", "UGA"]),
+    ];
+    let mut pairs = Vec::<(&'static str, &'static str)>::new();
+    for (name, codons) in grouped.into_iter() {
+        for codon in codons {
+            pairs.push((codon, name));
+        }
+    }
+    pairs.sort_by(|&(_, a), &(_, b)| a.cmp(b));
+    pairs
+}

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

@@ -1,3 +1,100 @@
-# 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"
+
+[1b4c56d8-d69f-44eb-be0e-7b17546143d9]
+description = "Phenylalanine RNA sequence 1"
+
+[81b53646-bd57-4732-b2cb-6b1880e36d11]
+description = "Phenylalanine RNA sequence 2"
+
+[42f69d4f-19d2-4d2c-a8b0-f0ae9ee1b6b4]
+description = "Leucine RNA sequence 1"
+
+[ac5edadd-08ed-40a3-b2b9-d82bb50424c4]
+description = "Leucine RNA sequence 2"
+
+[8bc36e22-f984-44c3-9f6b-ee5d4e73f120]
+description = "Serine RNA sequence 1"
+
+[5c3fa5da-4268-44e5-9f4b-f016ccf90131]
+description = "Serine RNA sequence 2"
+
+[00579891-b594-42b4-96dc-7ff8bf519606]
+description = "Serine RNA sequence 3"
+
+[08c61c3b-fa34-4950-8c4a-133945570ef6]
+description = "Serine RNA sequence 4"
+
+[54e1e7d8-63c0-456d-91d2-062c72f8eef5]
+description = "Tyrosine RNA sequence 1"
+
+[47bcfba2-9d72-46ad-bbce-22f7666b7eb1]
+description = "Tyrosine RNA sequence 2"
+
+[3a691829-fe72-43a7-8c8e-1bd083163f72]
+description = "Cysteine RNA sequence 1"
+
+[1b6f8a26-ca2f-43b8-8262-3ee446021767]
+description = "Cysteine RNA sequence 2"
+
+[1e91c1eb-02c0-48a0-9e35-168ad0cb5f39]
+description = "Tryptophan RNA sequence"
+
+[e547af0b-aeab-49c7-9f13-801773a73557]
+description = "STOP codon RNA sequence 1"
+
+[67640947-ff02-4f23-a2ef-816f8a2ba72e]
+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"
+
+[e30e8505-97ec-4e5f-a73e-5726a1faa1f4]
+description = "Translation stops if STOP codon at beginning of sequence"
+
+[5358a20b-6f4c-4893-bce4-f929001710f3]
+description = "Translation stops if STOP codon at end of two-codon sequence"
+
+[ba16703a-1a55-482f-bb07-b21eef5093a3]
+description = "Translation stops if STOP codon at end of three-codon sequence"
+
+[4089bb5a-d5b4-4e71-b79e-b8d1f14a2911]
+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"