Merge pull request #25 from brainglobe/brainmapper-refactor

Add misc functionality from brainmapper

brainglobe_utils/general/list.py

@@ -1,3 +1,6 @@
+from natsort import natsorted
+
+
 def remove_empty_string(str_list):
     """
     Removes any empty strings from a list of strings
@@ -10,3 +13,51 @@ def remove_empty_string(str_list):
 def unique_elements_lists(list_in):
     """return the unique elements in a list"""
     return list(dict.fromkeys(list_in))
+
+
+def check_unique_list(in_list, natural_sort=True):
+    """
+    Checks if all the items in a list are unique or not
+    :param list in_list: Input list
+    :param bool natural_sort: Sort the resulting items naturally
+    (default: True)
+    :return: True/False and a list of any repeated values
+    """
+    unique = set(in_list)
+    repeated_items = []
+
+    for item in unique:
+        count = in_list.count(item)
+        if count > 1:
+            repeated_items.append(item)
+
+    if repeated_items:
+        if natural_sort:
+            repeated_items = natsorted(repeated_items)
+        return False, repeated_items
+    else:
+        return True, []
+
+
+def common_member(a, b, natural_sort=True):
+    """
+    Checks if two lists (or sets) have a common member, and if so, returns
+    the common members.
+    :param a: First list (or set)
+    :param b: Second list (or set)
+    :param bool natural_sort: Sort the resulting items naturally
+    (default: True)
+    :return: True/False and the list of values
+    """
+    a_set = set(a)
+    b_set = set(b)
+    intersection = list(a_set.intersection(b_set))
+    if len(intersection) > 0:
+        result = True
+    else:
+        result = False
+
+    if natural_sort:
+        intersection = natsorted(intersection)
+
+    return result, intersection

brainglobe_utils/general/system.py

@@ -12,6 +12,7 @@
 from slurmio import slurmio
 from tqdm import tqdm
 
+from brainglobe_utils.general.exceptions import CommandLineInputError
 from brainglobe_utils.general.string import get_text_lines
 
 # On Windows, max_workers must be less than or equal to 61
@@ -349,3 +350,32 @@ def delete_directory_contents(directory, progress=False):
     else:
         for f in files:
             os.remove(os.path.join(directory, f))
+
+
+def check_path_exists(file):
+    """
+    Returns True is a file exists, otherwise throws a FileNotFoundError
+    :param file: Input file
+    :return: True, if the file exists
+    """
+    file = Path(file)
+    if file.exists():
+        return True
+    else:
+        raise FileNotFoundError
+
+
+def catch_input_file_error(path):
+    """
+    Catches if an input path doesn't exist, and returns an informative error
+    :param path: Input file path
+    default)
+    """
+    try:
+        check_path_exists(path)
+    except FileNotFoundError:
+        message = (
+            "File path: '{}' cannot be found. Please check your input "
+            "arguments.".format(path)
+        )
+        raise CommandLineInputError(message)

tests/tests/test_general/test_list.py

@@ -1,7 +1,10 @@
 from brainglobe_utils.general import list as list_tools
 
-list_with_empty = ["test1", "test 2", " ", "", "test4", ""]
+a = [1, "a", 10, 30]
+b = [30, 10, "c", "d"]
+
 
+list_with_empty = ["test1", "test 2", " ", "", "test4", ""]
 list_without_empty = ["test1", "test 2", " ", "test4"]
 
 
@@ -15,3 +18,14 @@ def test_unique_elements_list():
     list_in = [1, 2, 2, "a", "b", 1, "a", "dog"]
     unique_list = [1, 2, "a", "b", "dog"]
     assert list_tools.unique_elements_lists(list_in) == unique_list
+
+
+def test_check_unique_list():
+    a = [1, "a", 10, 30]
+    assert (True, []) == list_tools.check_unique_list(a)
+    repeating_list = [1, 2, 3, 3, "dog", "cat", "dog"]
+    assert (False, [3, "dog"]) == list_tools.check_unique_list(repeating_list)
+
+
+def test_common_member():
+    assert (True, [10, 30]) == list_tools.common_member(a, b)

tests/tests/test_general/test_system.py

@@ -8,6 +8,7 @@
 import pytest
 
 from brainglobe_utils.general import system
+from brainglobe_utils.general.exceptions import CommandLineInputError
 from brainglobe_utils.general.string import get_text_lines
 
 data_dir = Path("tests", "data")
@@ -326,3 +327,33 @@ def test_delete_directory_contents(tmp_path):
 
     system.delete_directory_contents(delete_dir, progress=False)
     assert os.listdir(delete_dir) == []
+
+
+def write_file_single_size(directory, file_size):
+    with open(os.path.join(directory, str(file_size)), "wb") as fout:
+        fout.write(os.urandom(file_size))
+
+
+def test_check_path_exists(tmpdir):
+    num = 10
+    tmpdir = str(tmpdir)
+
+    assert system.check_path_exists(os.path.join(tmpdir))
+    no_exist_dir = os.path.join(tmpdir, "i_dont_exist")
+    with pytest.raises(FileNotFoundError):
+        assert system.check_path_exists(no_exist_dir)
+
+    write_file_single_size(tmpdir, num)
+    assert system.check_path_exists(os.path.join(tmpdir, str(num)))
+    with pytest.raises(FileNotFoundError):
+        assert system.check_path_exists(os.path.join(tmpdir, "20"))
+
+
+def test_catch_input_file_error(tmpdir):
+    tmpdir = str(tmpdir)
+    # check no error is raised:
+    system.catch_input_file_error(tmpdir)
+
+    no_exist_dir = os.path.join(tmpdir, "i_dont_exist")
+    with pytest.raises(CommandLineInputError):
+        system.catch_input_file_error(no_exist_dir)