Add new practice exercise: hamming

config.json

@@ -258,6 +258,14 @@
         "prerequisites": [],
         "difficulty": 8
       },
+      {
+        "slug": "hamming",
+        "name": "Hamming",
+        "uuid": "d1ea133e-1d3f-4894-975e-6ab91aa33a35",
+        "practices": [],
+        "prerequisites": [],
+        "difficulty": 8
+      },
       {
         "slug": "high-scores",
         "name": "High Scores",

exercises/practice/hamming/.docs/instructions.md

@@ -0,0 +1,16 @@
+# Instructions
+
+Calculate the Hamming distance between two DNA strands.
+
+We read DNA using the letters C, A, G and T.
+Two strands might look like this:
+
+    GAGCCTACTAACGGGAT
+    CATCGTAATGACGGCCT
+    ^ ^ ^  ^ ^    ^^
+
+They have 7 differences, and therefore the Hamming distance is 7.
+
+## Implementation notes
+
+The Hamming distance is only defined for sequences of equal length, so an attempt to calculate it between sequences of different lengths should not work.

exercises/practice/hamming/.docs/introduction.md

@@ -0,0 +1,12 @@
+# Introduction
+
+Your body is made up of cells that contain DNA.
+Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells.
+In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!
+
+When cells divide, their DNA replicates too.
+Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information.
+If we compare two strands of DNA and count the differences between them, we can see how many mistakes occurred.
+This is known as the "Hamming distance".
+
+The Hamming distance is useful in many areas of science, not just biology, so it's a nice phrase to be familiar with :)

exercises/practice/hamming/.meta/config.json

@@ -0,0 +1,19 @@
+{
+  "authors": [
+    "jimmytty"
+  ],
+  "files": {
+    "solution": [
+      "hamming.sql"
+    ],
+    "test": [
+      "hamming_test.sql"
+    ],
+    "example": [
+      ".meta/example.sql"
+    ]
+  },
+  "blurb": "Calculate the Hamming distance between two DNA strands.",
+  "source": "The Calculating Point Mutations problem at Rosalind",
+  "source_url": "https://rosalind.info/problems/hamm/"
+}

exercises/practice/hamming/.meta/example.sql

@@ -0,0 +1,21 @@
+UPDATE hamming
+   SET error = 'strands must be of equal length'
+ WHERE LENGTH(strand1) != LENGTH(strand2)
+;
+
+UPDATE hamming
+   SET result = (
+     WITH RECURSIVE rcte(string1, string2, char1, char2) AS (
+       VALUES(strand1, strand2, '', '')
+       UNION ALL
+       SELECT SUBSTRING(string1, 2),    SUBSTRING(string2, 2),
+              SUBSTRING(string1, 1, 1), SUBSTRING(string2, 1, 1)
+         FROM rcte
+        WHERE string1 <> ''
+     )
+     SELECT COUNT(*)
+       FROM rcte
+      WHERE char1 != char2
+   )
+ WHERE LENGTH(strand1) = LENGTH(strand2)
+;

exercises/practice/hamming/.meta/tests.toml

@@ -0,0 +1,67 @@
+# 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.
+
+[f6dcb64f-03b0-4b60-81b1-3c9dbf47e887]
+description = "empty strands"
+
+[54681314-eee2-439a-9db0-b0636c656156]
+description = "single letter identical strands"
+
+[294479a3-a4c8-478f-8d63-6209815a827b]
+description = "single letter different strands"
+
+[9aed5f34-5693-4344-9b31-40c692fb5592]
+description = "long identical strands"
+
+[cd2273a5-c576-46c8-a52b-dee251c3e6e5]
+description = "long different strands"
+
+[919f8ef0-b767-4d1b-8516-6379d07fcb28]
+description = "disallow first strand longer"
+include = false
+
+[b9228bb1-465f-4141-b40f-1f99812de5a8]
+description = "disallow first strand longer"
+reimplements = "919f8ef0-b767-4d1b-8516-6379d07fcb28"
+
+[8a2d4ed0-ead5-4fdd-924d-27c4cf56e60e]
+description = "disallow second strand longer"
+include = false
+
+[dab38838-26bb-4fff-acbe-3b0a9bfeba2d]
+description = "disallow second strand longer"
+reimplements = "8a2d4ed0-ead5-4fdd-924d-27c4cf56e60e"
+
+[5dce058b-28d4-4ca7-aa64-adfe4e17784c]
+description = "disallow left empty strand"
+include = false
+
+[db92e77e-7c72-499d-8fe6-9354d2bfd504]
+description = "disallow left empty strand"
+include = false
+reimplements = "5dce058b-28d4-4ca7-aa64-adfe4e17784c"
+
+[b764d47c-83ff-4de2-ab10-6cfe4b15c0f3]
+description = "disallow empty first strand"
+reimplements = "db92e77e-7c72-499d-8fe6-9354d2bfd504"
+
+[38826d4b-16fb-4639-ac3e-ba027dec8b5f]
+description = "disallow right empty strand"
+include = false
+
+[920cd6e3-18f4-4143-b6b8-74270bb8f8a3]
+description = "disallow right empty strand"
+include = false
+reimplements = "38826d4b-16fb-4639-ac3e-ba027dec8b5f"
+
+[9ab9262f-3521-4191-81f5-0ed184a5aa89]
+description = "disallow empty second strand"
+reimplements = "920cd6e3-18f4-4143-b6b8-74270bb8f8a3"

exercises/practice/hamming/create_fixture.sql

@@ -0,0 +1,12 @@
+DROP TABLE IF EXISTS hamming;
+CREATE TABLE hamming (
+    strand1 TEXT NOT NULL,
+    strand2 TEXT NOT NULL,
+    result  INTEGER,
+    error   TEXT
+);
+
+.mode csv
+.import ./data.csv hamming
+
+UPDATE hamming SET result = NULL, error = NULL;

exercises/practice/hamming/create_test_table.sql

@@ -0,0 +1,29 @@
+DROP TABLE IF EXISTS tests;
+CREATE TABLE IF NOT EXISTS tests (
+    -- uuid and description are taken from the test.toml file
+    uuid TEXT PRIMARY KEY,
+    description TEXT NOT NULL,
+    -- The following section is needed by the online test-runner
+    status TEXT DEFAULT 'fail',
+    message TEXT,
+    output TEXT,
+    test_code TEXT,
+    task_id INTEGER DEFAULT NULL,
+    -- Here are columns for the actual tests
+    strand1 TEXT NOT NULL,
+    strand2 TEXT NOT NULL,
+    expected_result INTEGER,
+    expected_error TEXT
+);
+
+INSERT INTO tests (uuid, description, strand1, strand2, expected_result, expected_error)
+    VALUES
+        ('f6dcb64f-03b0-4b60-81b1-3c9dbf47e887', 'empty strands', '', '', 0, null),
+        ('54681314-eee2-439a-9db0-b0636c656156', 'single letter identical strands', 'A', 'A', 0, null),
+        ('294479a3-a4c8-478f-8d63-6209815a827b', 'single letter different strands', 'G', 'T', 1, null),
+        ('9aed5f34-5693-4344-9b31-40c692fb5592', 'long identical strands', 'GGACTGAAATCTG', 'GGACTGAAATCTG', 0, null),
+        ('cd2273a5-c576-46c8-a52b-dee251c3e6e5', 'long different strands', 'GGACGGATTCTG', 'AGGACGGATTCT', 9, null),
+        ('b9228bb1-465f-4141-b40f-1f99812de5a8', 'disallow first strand longer', 'AATG', 'AAA', null, 'strands must be of equal length'),
+        ('dab38838-26bb-4fff-acbe-3b0a9bfeba2d', 'disallow second strand longer', 'ATA', 'AGTG', null, 'strands must be of equal length'),
+        ('b764d47c-83ff-4de2-ab10-6cfe4b15c0f3', 'disallow empty first strand', '', 'G', null, 'strands must be of equal length'),
+        ('9ab9262f-3521-4191-81f5-0ed184a5aa89', 'disallow empty second strand', 'G', '', null, 'strands must be of equal length');

exercises/practice/hamming/data.csv

@@ -0,0 +1,9 @@
+"","","",""
+"A","A","",""
+"G","T","",""
+"GGACTGAAATCTG","GGACTGAAATCTG","",""
+"GGACGGATTCTG","AGGACGGATTCT","",""
+"AATG","AAA","",""
+"ATA","AGTG","",""
+"","G","",""
+"G","","",""

exercises/practice/hamming/hamming.sql

@@ -0,0 +1,9 @@
+-- Schema:
+-- CREATE TABLE hamming (
+--     strand1 TEXT NOT NULL,
+--     strand2 TEXT NOT NULL,
+--     result  INTEGER,
+--     error   TEXT
+-- );
+--
+-- Task: update the hamming table and set the result column or the error column based on the comparison between strand1 and strand2.

exercises/practice/hamming/hamming_test.sql

@@ -0,0 +1,40 @@
+-- Create database:
+.read ./create_fixture.sql
+
+-- Read user student solution and save any output as markdown in user_output.md:
+.mode markdown
+.output user_output.md
+.read ./hamming.sql
+.output
+
+-- Create a clean testing environment:
+.read ./create_test_table.sql
+
+-- Comparison of user input and the tests updates the status for each test:
+UPDATE tests
+SET status = 'pass'
+FROM (SELECT strand1, strand2, result, error FROM hamming) AS actual
+WHERE (actual.strand1, actual.strand2) = (tests.strand1, tests.strand2) AND (actual.result = tests.expected_result OR COALESCE(actual.result, tests.expected_result) ISNULL) AND (actual.error = tests.expected_error OR COALESCE(actual.error, tests.expected_error) ISNULL);
+
+-- Update message for failed tests to give helpful information:
+UPDATE tests
+SET message = (
+    'Result for "'
+    || PRINTF('strand1=''%s'' and strand2=''%s''', actual.strand1, actual.strand2)
+    || '"'
+    || ' is <' || PRINTF('result=%s and error="%s"', COALESCE(actual.result, 'NULL'), COALESCE(actual.error, 'NULL'))
+    || '> but should be <' || PRINTF('result=%s and error="%s"', COALESCE(tests.expected_result, '"NULL"'), COALESCE(tests.expected_error, 'NULL')) || '>'
+)
+FROM (SELECT strand1, strand2, result, error FROM hamming) AS actual
+WHERE (actual.strand1, actual.strand2) = (tests.strand1, tests.strand2) AND tests.status = 'fail';
+
+-- Save results to ./output.json (needed by the online test-runner)
+.mode json
+.once './output.json'
+SELECT description, status, message, output, test_code, task_id
+FROM tests;
+
+-- Display test results in readable form for the student:
+.mode table
+SELECT description, status, message
+FROM tests;