Working with healthcare datasets often involves addressing missing values, as lab results may be incomplete due to a variety of reasons. Handling these gaps is essential before any analysis or modeling. Suppose you receive a DataFrame containing patient lab results, and you notice that some entries in the `cholesterol` column are missing. Your task is to prepare this data for further analysis by following a standard cleaning procedure.

import pandas as pd

# Sample DataFrame representing patient lab results
data = {
    "patient_id": [101, 102, 103, 104, 105],
    "cholesterol": [180, None, 210, None, 190]
}
df = pd.DataFrame(data)

# 1. Identify the number of missing values in 'cholesterol'
missing_count = df["cholesterol"].isnull().sum()
print("Number of missing values in 'cholesterol':", missing_count)

# 2. Fill missing values with the median cholesterol value
median_chol = df["cholesterol"].median()
df["cholesterol"].fillna(median_chol, inplace=True)

# 3. Output the cleaned DataFrame
print("\nCleaned DataFrame:")
print(df)

By identifying and filling missing values with the **median**, you ensure that the dataset remains representative of the typical patient and is less skewed by outliers than if you used the **mean**. This approach is especially relevant in healthcare, where preserving the integrity of clinical data is crucial for accurate downstream analysis.


import unittest
import user_code
import ast
import re   
import importlib
import csv
import unittest
import importlib
import sys
import io
from contextlib import redirect_stdout
import pandas as pd

class TestTask(unittest.TestCase):
    def test_missing_count_var(self):
        import user_code
        importlib.reload(user_code)
        missing_count = getattr(user_code, 'missing_count', None)
        _dynamic_test(
            self,
            missing_count == 2,
            "Variable 'missing_count' is correctly set to 2.",
            f"Expected 'missing_count' to be 2, got {missing_count}"
        )

    def test_fill_with_median_df(self):
        import user_code
        importlib.reload(user_code)
        df = getattr(user_code, 'df', None)
        _dynamic_test(
            self,
            isinstance(df, pd.DataFrame),
            "Variable 'df' exists and is a pandas DataFrame.",
            "Variable 'df' is missing or not a DataFrame."
        )
        # Check that all cholesterol values are filled and correct
        expected = [205, 205.0, 187, 205.0, 220]
        actual = df["cholesterol"].tolist() if df is not None else None
        _dynamic_test(
            self,
            actual is not None and all(abs(a - e) < 1e-6 for a, e in zip(actual, expected)),
            "Missing values in 'cholesterol' are filled with median correctly.",
            f"Expected cholesterol column {expected}, got {actual}"
        )

    def test_output_content(self):
        import importlib
        import sys
        import io
        from contextlib import redirect_stdout
        import user_code
        importlib.reload(user_code)
        f = io.StringIO()
        with redirect_stdout(f):
            importlib.reload(user_code)
        output = normalize_text(f.getvalue())
        # Check missing count is printed
        _dynamic_test(
            self,
            "2" in output,
            "Output includes correct missing value count.",
            f"Expected missing value count '2' in output, got: {output}"
        )
        # Check cleaned DataFrame is printed
        expected_lines = [
            "201",
            "202",
            "203",
            "204",
            "205",
            "205.0",
            "205.0",
            "187.0",
            "205.0",
            "220.0"
        ]
        for line in expected_lines:
            _dynamic_test(
                self,
                line in output,
                f"Output includes line: {line}",
                f"Expected line '{line}' not found in output: {output}"
            )

def _dynamic_test(test_case, condition, success_message, failure_message):
    if condition:
        test_case._testMethodName = success_message
        test_case.assertTrue(True, success_message)
    else:
        test_case._testMethodName = failure_message
        test_case.fail(failure_message)

def normalize_text(text):
    text = text.lower()
    text = re.sub(r"\\s{2,}", " ", text)
    text = re.sub(r"\\s*([,:?])\\s*", r"\\1 ", text)
    return text.strip()

def change_var(code: str, var_name: str, value: str) -> str:
    tree = ast.parse(code)
    lines = code.splitlines()
    changed = False
    # Collect all assignment nodes to modify
    assign_nodes = [
        (i, node)
        for i, node in enumerate(tree.body)
        if isinstance(node, ast.Assign)
        and any(isinstance(target, ast.Name) and target.id == var_name for target in node.targets)
    ]

    # If nothing to change, return unmodified code
    if not assign_nodes:
        return code

    # Perform replacements for all matching assignments (from last to first to not break line offsets)
    for i, node in reversed(assign_nodes):
        start_line = node.lineno - 1
        line = lines[start_line]
        indent = ' ' * (len(line) - len(line.lstrip()))
        lines[start_line] = f"{indent}{var_name} = {value}"
        next_line = len(lines)
        for next_node in tree.body[i+1:]:
            if hasattr(next_node, 'lineno'):
                next_line = next_node.lineno - 1
                break
        if next_line > start_line + 1:
            lines[start_line+1:next_line] = []
        changed = True

    return '\\n'.join(lines) if changed else code

if __name__ == "__main__":
    unittest.main()


test_main.py

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Explore the essentials of working with healthcare data in Python, including data structures, importing datasets, and basic data cleaning tailored to medical records.

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Challenge: Clean Lab Results

Oplossing

patient_id	cholesterol
201	205
202
203	187
204
205	220