Add data tool for colon data. (#100)

* base functions

* add full function

* add doc

* add api doc

Makefile

@@ -20,5 +20,8 @@ test:
 sphinx:
 	poetry run make -C docs clean html
 
+open-sphinx:
+	open docs/build/html/index.html
+
 install:
 	poetry lock && poetry install --all-extras

docs/source/api-reference/data.rst

@@ -0,0 +1,6 @@
+.. _data_code_doc:
+
+:mod:`~mltb2.data`
+==================
+
+.. automodule:: mltb2.data

mltb2/data.py

@@ -0,0 +1,111 @@
+# Copyright (c) 2020 - 2023 Philip May
+# Copyright (c) 2021 Sigrun May, Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
+# Copyright (c) 2021 Sigrun May, Ostfalia Hochschule für angewandte Wissenschaften
+# This software is distributed under the terms of the MIT license
+# which is available at https://opensource.org/licenses/MIT
+
+"""Data loading functionality."""
+
+import os
+from hashlib import sha256
+from typing import Tuple
+
+import joblib
+import numpy as np
+import pandas as pd
+import requests
+from bs4 import BeautifulSoup
+
+from mltb2.files import get_and_create_mltb2_data_dir
+
+
+def _load_colon_data() -> pd.DataFrame:
+    """Load colon data (not the labels).
+
+    The data is loaded and parsed from the internet.
+    Also see `colon tissues probed by oligonucleotide arrays
+    <http://genomics-pubs.princeton.edu/oncology/affydata/index.html>`_.
+
+    Returns:
+        data as pandas DataFrame
+    """
+    # download data file
+    url = "http://genomics-pubs.princeton.edu/oncology/affydata/I2000.html"
+    page = requests.get(url, timeout=10)
+
+    # check checksum of data file
+    page_hash = sha256(page.content).hexdigest()
+    assert page_hash == "74cc7b47d40a0fbca8dde05f42bcb799b7babad29ea634139a221bb4386b1c3d", page_hash
+
+    soup = BeautifulSoup(page.content, "html.parser")
+    page_text = soup.get_text()
+
+    page_text_lines = page_text.splitlines()
+    assert len(page_text_lines) >= 2000
+    page_text_lines = [[float(s) for s in line.split()] for line in page_text_lines if len(line) > 20]
+    assert len(page_text_lines) == 2000
+    assert len(page_text_lines[0]) == 62
+
+    data = np.array(page_text_lines).T
+    data_df = pd.DataFrame(data)
+    return data_df
+
+
+def _load_colon_label() -> pd.Series:
+    """Load colon label (not the data).
+
+    The data is loaded and parsed from the internet.
+    Also see `colon tissues probed by oligonucleotide arrays
+    <http://genomics-pubs.princeton.edu/oncology/affydata/index.html>`_.
+
+    Returns:
+        labels as pandas Series
+    """
+    # download data file
+    url = "http://genomics-pubs.princeton.edu/oncology/affydata/tissues.html"
+    page = requests.get(url, timeout=10)
+
+    # check checksum of data file
+    page_hash = sha256(page.content).hexdigest()
+    assert page_hash == "0c5b377c5dd5544d015bff479a4260d5ccf0bcf98657f600a1d37e34193e0f52", page_hash
+
+    soup = BeautifulSoup(page.content, "html.parser")
+    page_text = soup.get_text()
+    page_text_lines = page_text.splitlines()
+
+    label = []
+
+    for line in page_text_lines:
+        try:
+            i = int(line)
+            label.append(0 if i > 0 else 1)
+        except ValueError:
+            pass  # we ignore this
+
+    assert len(label) == 62
+    label_series = pd.Series(label)
+    return label_series
+
+
+def load_colon() -> Tuple[pd.Series, pd.DataFrame]:
+    """Load colon data.
+
+    The data is loaded and parsed from the internet.
+    Also see `colon tissues probed by oligonucleotide arrays
+    <http://genomics-pubs.princeton.edu/oncology/affydata/index.html>`_.
+
+    Returns:
+        Tuple containing labels and data.
+    """
+    filename = "colon.pkl.gz"
+    mltb2_data_home = get_and_create_mltb2_data_dir()
+    full_path = os.path.join(mltb2_data_home, filename)
+    if not os.path.exists(full_path):
+        data_df = _load_colon_data()
+        label_series = _load_colon_label()
+        result = (label_series, data_df)
+        joblib.dump(result, full_path, compress=("gzip", 3))
+    else:
+        result = joblib.load(full_path)
+
+    return result

pyproject.toml

@@ -68,10 +68,14 @@ tiktoken = {version = "*", optional = true}
 safetensors = {version = "!=0.3.2", optional = true}  # version 0.3.2 has poetry issues
 openai = {version = "^0", optional = true}
 pyyaml = {version = "*", optional = true}
+pandas = {version = "*", optional = true}
+beautifulsoup4 = {version = "*", optional = true}
+joblib = {version = "*", optional = true}
 
 [tool.poetry.extras]
 files = ["platformdirs", "scikit-learn"]
 fasttext = ["fasttext-wheel"]
+data = ["platformdirs", "scikit-learn", "pandas", "beautifulsoup4", "joblib"]
 optuna = ["optuna"]
 plot = ["matplotlib"]
 somajo = ["SoMaJo"]
@@ -131,6 +135,8 @@ ignore = [
   "PLR0913",  # Too many arguments to function call ({c_args} > {max_args})
   "S106",  # Possible hardcoded password assigned to argument: "{}"
   "COM812",  # Trailing comma missing
+  "S101",  # Use of `assert` detected
+  "PLR2004",  # Magic value used in comparison,
 ]
 
 [tool.ruff.per-file-ignores]

tests/test_data.py

@@ -0,0 +1,32 @@
+# Copyright (c) 2023 Philip May
+# This software is distributed under the terms of the MIT license
+# which is available at https://opensource.org/licenses/MIT
+
+import pandas as pd
+
+from mltb2.data import _load_colon_data, _load_colon_label, load_colon
+
+
+def test_load_colon_data():
+    result = _load_colon_data()
+    assert result is not None
+    assert isinstance(result, pd.DataFrame)
+    assert result.shape == (62, 2000)
+
+
+def test_load_colon_label():
+    result = _load_colon_label()
+    assert result is not None
+    assert isinstance(result, pd.Series)
+    assert len(result) == 62
+
+
+def test_load_colon():
+    result = load_colon()
+    assert result is not None
+    assert isinstance(result, tuple)
+    assert len(result) == 2
+    assert isinstance(result[0], pd.Series)
+    assert isinstance(result[1], pd.DataFrame)
+    assert result[0].shape == (62,)
+    assert result[1].shape == (62, 2000)