galaxy/test/unit/util/test_utils.py

import errno
import os
import tempfile
from enum import Enum
from io import StringIO
from pathlib import Path

import pytest

from galaxy import util
from galaxy.util.json import safe_loads

SECTION_XML = """<?xml version="1.0" ?>
<section id="fasta_fastq_manipulation" name="Fasta Fastq Manipulation" version="">
    <tool file="toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/fb1313d79396/seq_filter_by_id/tools/seq_filter_by_id/seq_filter_by_id.xml" guid="toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.5">
        <tool_shed>
            toolshed.g2.bx.psu.edu
        </tool_shed>
    </tool>
</section>
"""


def test_strip_control_characters():
    s = "\x00bla"
    assert util.strip_control_characters(s) == "bla"


def test_parse_xml_string():
    section = util.parse_xml_string(SECTION_XML)
    _verify_section(section)


def test_parse_xml_file():
    with tempfile.NamedTemporaryFile(mode="w") as tmp:
        tmp.write(SECTION_XML)
        tmp.flush()
        section = util.parse_xml(tmp.name).getroot()
    _verify_section(section)


def _verify_section(section):
    tool = next(iter(section))
    assert sorted(tool.items()) == [
        (
            "file",
            "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/fb1313d79396/seq_filter_by_id/tools/seq_filter_by_id/seq_filter_by_id.xml",
        ),
        ("guid", "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.5"),
    ]
    assert next(iter(tool)).text == "toolshed.g2.bx.psu.edu"


def test_xml_to_string():
    section = util.parse_xml_string(SECTION_XML)
    s = util.xml_to_string(section)
    assert len(s.split("\n")) == 1


def test_xml_to_string_pretty():
    section = util.parse_xml_string(SECTION_XML)
    s = util.xml_to_string(section, pretty=True)
    PRETTY = """<?xml version="1.0" ?>
<section id="fasta_fastq_manipulation" name="Fasta Fastq Manipulation" version="">
    <tool file="toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/fb1313d79396/seq_filter_by_id/tools/seq_filter_by_id/seq_filter_by_id.xml" guid="toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.5">
        <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
    </tool>
</section>"""
    assert s == PRETTY


def test_parse_xml_enoent():
    with tempfile.NamedTemporaryFile() as temp:
        path = temp.name
    with pytest.raises(IOError) as excinfo:
        util.parse_xml(path)
    assert excinfo.value.errno == errno.ENOENT


def test_clean_multiline_string():
    x = util.clean_multiline_string("""
        a
        b
        c
""")
    assert x == "a\nb\nc\n"


def test_iter_start_of_lines():
    assert list(util.iter_start_of_line(StringIO("\n1\n\n12\n123\n1234\n"), 1)) == ["\n", "1", "\n", "1", "1", "1"]


def test_safe_loads():
    d: dict[str, str] = {}
    rval = safe_loads(d)
    assert rval == d
    assert rval is not d
    rval["foo"] = "bar"
    assert "foo" not in d
    s = '{"foo": "bar"}'
    assert safe_loads(s) == {"foo": "bar"}


def test_in_packages(monkeypatch):
    util_path = Path(util.__file__).parent
    assert util.in_packages() == (not str(util_path).endswith("lib/galaxy/util"))


def test_galaxy_directory(monkeypatch):
    galaxy_dir = util.galaxy_directory()
    assert os.path.isabs(galaxy_dir)
    assert os.path.isfile(os.path.join(galaxy_dir, "run.sh"))


def test_listify() -> None:
    assert util.listify(None) == []
    assert util.listify(False) == []
    assert util.listify(True) == [True]
    assert util.listify("foo") == ["foo"]
    assert util.listify("foo, bar") == ["foo", " bar"]
    assert util.listify("foo, bar", do_strip=True) == ["foo", "bar"]
    list_ = [1, 2, 3]
    assert util.listify(list_) is list_
    assert util.listify((1, 2, 3)) == [1, 2, 3]
    s = {1, 2, 3}
    assert util.listify(s) == [s]
    d = {"a": 1, "b": 2, "c": 3}
    assert util.listify(d) == [d]
    o = object()
    assert util.listify(o) == [o]


def test_enum_values():
    class Stuff(str, Enum):
        A = "a"
        C = "c"
        B = "b"

    assert util.enum_values(Stuff) == ["a", "c", "b"]


DOI_VALID_VALUES = [
    "https://doi.org/10.1234/42",
    "doi.org/10.1234/42",
    "doi:10.1234/42",
    "doi:10.1234567890/42",  # longer prefix
    "doi:10.1234/42ab:%&*$//crazy-suffix/%/&/",
    "doi:10.1234/aa",
]


@pytest.mark.parametrize("input", DOI_VALID_VALUES)
def test_validate_doi_pass(input):
    assert util.validate_doi(input)


DOI_INVALID_VALUES = [
    "http://doi.org/10.1234/42",
    "invalid:10.1234/42",
    "doi:11.1234/42",
    "doi:101234/42",
    "doi:10. 1234/42",
    "doi:10.abc/42",
    "doi:10.1234/ 42",
    "doi:10.1234/42/a b",
]


@pytest.mark.parametrize("input", DOI_INVALID_VALUES)
def test_validate_doi_fail(input):
    assert not util.validate_doi(input)


def test_validate_doi_fail_too_long():
    long_suffix = "a" * (util.DOI_MAX_LENGTH - 12)
    doi = f"doi:10.1000/{long_suffix}"
    assert util.validate_doi(doi)
    assert not util.validate_doi(doi + "a")  # Increase length by 1 past max limit


@pytest.mark.parametrize(
    "input_name,expected_output",
    [
        # Existing documented behavior
        ("My Cool Object", "My-Cool-Object"),
        ("!My Cool Object!", "My-Cool-Object"),
        ("Hello\u20a9\u25ce\u0491\u029f\u217e", "Hello"),
        # Additional edge cases
        ("simple", "simple"),
        ("UPPERCASE", "UPPERCASE"),  # Note: lowercase applied separately
        ("with-dash", "with-dash"),
        ("with spaces", "with-spaces"),
        ("  multiple   spaces  ", "-multiple-spaces"),
        ("trailing!", "trailing"),
        ("!leading", "leading"),
        ("special@#$chars", "specialchars"),
        ("parentheses(test)", "parenthesestest"),
        ("Rincewind (Ankh-Morpork)", "Rincewind-Ankh-Morpork"),
    ],
)
def test_ready_name_for_url(input_name, expected_output):
    """Test that ready_name_for_url correctly sanitizes names for URL use."""
    assert util.ready_name_for_url(input_name) == expected_output


@pytest.mark.parametrize(
    "target,expected_substring",
    [
        ("normal.txt", 'filename="normal.txt"'),
        ("file.gz ", 'filename="file.gz"'),
        (" file.gz", 'filename="file.gz"'),
        (" file.gz ", 'filename="file.gz"'),
        ("Galaxy102-[name].fastqsanger.gz ", 'filename="Galaxy102-[name].fastqsanger.gz"'),
    ],
)
def test_to_content_disposition(target, expected_substring):
    result = util.to_content_disposition(target)
    assert result.startswith("attachment; ")
    assert expected_substring in result
    # Ensure no trailing whitespace in the header value
    assert result == result.strip()