mirror of
https://github.com/galaxyproject/galaxy.git
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mvdbeek
b997b31849
Strip whitespace from target filename before building the Content-Disposition header to prevent h11 LocalProtocolError when dataset names contain trailing spaces. Fixes GALAXY-MAIN-4KSCZZZ0015E3
223 lines
6.5 KiB
Python
223 lines
6.5 KiB
Python
import errno
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import os
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import tempfile
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from enum import Enum
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from io import StringIO
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from pathlib import Path
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from typing import Dict
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import pytest
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from galaxy import util
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from galaxy.util.json import safe_loads
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SECTION_XML = """<?xml version="1.0" ?>
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<section id="fasta_fastq_manipulation" name="Fasta Fastq Manipulation" version="">
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<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">
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<tool_shed>
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toolshed.g2.bx.psu.edu
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</tool_shed>
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</tool>
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</section>
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"""
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def test_strip_control_characters():
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s = "\x00bla"
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assert util.strip_control_characters(s) == "bla"
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def test_parse_xml_string():
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section = util.parse_xml_string(SECTION_XML)
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_verify_section(section)
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def test_parse_xml_file():
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with tempfile.NamedTemporaryFile(mode="w") as tmp:
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tmp.write(SECTION_XML)
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tmp.flush()
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section = util.parse_xml(tmp.name).getroot()
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_verify_section(section)
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def _verify_section(section):
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tool = next(iter(section))
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assert sorted(tool.items()) == [
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(
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"file",
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"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",
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),
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("guid", "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.5"),
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]
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assert next(iter(tool)).text == "toolshed.g2.bx.psu.edu"
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def test_xml_to_string():
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section = util.parse_xml_string(SECTION_XML)
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s = util.xml_to_string(section)
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assert len(s.split("\n")) == 1
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def test_xml_to_string_pretty():
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section = util.parse_xml_string(SECTION_XML)
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s = util.xml_to_string(section, pretty=True)
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PRETTY = """<?xml version="1.0" ?>
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<section id="fasta_fastq_manipulation" name="Fasta Fastq Manipulation" version="">
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<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">
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<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
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</tool>
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</section>"""
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assert s == PRETTY
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def test_parse_xml_enoent():
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with tempfile.NamedTemporaryFile() as temp:
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path = temp.name
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with pytest.raises(IOError) as excinfo:
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util.parse_xml(path)
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assert excinfo.value.errno == errno.ENOENT
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def test_clean_multiline_string():
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x = util.clean_multiline_string("""
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a
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b
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c
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""")
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assert x == "a\nb\nc\n"
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def test_iter_start_of_lines():
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assert list(util.iter_start_of_line(StringIO("\n1\n\n12\n123\n1234\n"), 1)) == ["\n", "1", "\n", "1", "1", "1"]
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def test_safe_loads():
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d: Dict[str, str] = {}
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rval = safe_loads(d)
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assert rval == d
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assert rval is not d
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rval["foo"] = "bar"
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assert "foo" not in d
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s = '{"foo": "bar"}'
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assert safe_loads(s) == {"foo": "bar"}
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def test_in_packages(monkeypatch):
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util_path = Path(util.__file__).parent
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assert util.in_packages() == (not str(util_path).endswith("lib/galaxy/util"))
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def test_galaxy_directory(monkeypatch):
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galaxy_dir = util.galaxy_directory()
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assert os.path.isabs(galaxy_dir)
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assert os.path.isfile(os.path.join(galaxy_dir, "run.sh"))
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def test_listify() -> None:
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assert util.listify(None) == []
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assert util.listify(False) == []
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assert util.listify(True) == [True]
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assert util.listify("foo") == ["foo"]
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assert util.listify("foo, bar") == ["foo", " bar"]
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assert util.listify("foo, bar", do_strip=True) == ["foo", "bar"]
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list_ = [1, 2, 3]
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assert util.listify(list_) is list_
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assert util.listify((1, 2, 3)) == [1, 2, 3]
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s = {1, 2, 3}
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assert util.listify(s) == [s]
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d = {"a": 1, "b": 2, "c": 3}
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assert util.listify(d) == [d]
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o = object()
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assert util.listify(o) == [o]
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def test_enum_values():
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class Stuff(str, Enum):
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A = "a"
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C = "c"
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B = "b"
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assert util.enum_values(Stuff) == ["a", "c", "b"]
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DOI_VALID_VALUES = [
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"https://doi.org/10.1234/42",
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"doi.org/10.1234/42",
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"doi:10.1234/42",
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"doi:10.1234567890/42", # longer prefix
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"doi:10.1234/42ab:%&*$//crazy-suffix/%/&/",
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"doi:10.1234/aa",
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]
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@pytest.mark.parametrize("input", DOI_VALID_VALUES)
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def test_validate_doi_pass(input):
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assert util.validate_doi(input)
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DOI_INVALID_VALUES = [
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"http://doi.org/10.1234/42",
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"invalid:10.1234/42",
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"doi:11.1234/42",
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"doi:101234/42",
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"doi:10. 1234/42",
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"doi:10.abc/42",
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"doi:10.1234/ 42",
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"doi:10.1234/42/a b",
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]
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@pytest.mark.parametrize("input", DOI_INVALID_VALUES)
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def test_validate_doi_fail(input):
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assert not util.validate_doi(input)
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def test_validate_doi_fail_too_long():
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long_suffix = "a" * (util.DOI_MAX_LENGTH - 12)
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doi = f"doi:10.1000/{long_suffix}"
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assert util.validate_doi(doi)
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assert not util.validate_doi(doi + "a") # Increase length by 1 past max limit
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@pytest.mark.parametrize(
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"input_name,expected_output",
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[
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# Existing documented behavior
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("My Cool Object", "My-Cool-Object"),
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("!My Cool Object!", "My-Cool-Object"),
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("Hello\u20a9\u25ce\u0491\u029f\u217e", "Hello"),
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# Additional edge cases
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("simple", "simple"),
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("UPPERCASE", "UPPERCASE"), # Note: lowercase applied separately
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("with-dash", "with-dash"),
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("with spaces", "with-spaces"),
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(" multiple spaces ", "-multiple-spaces"),
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("trailing!", "trailing"),
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("!leading", "leading"),
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("special@#$chars", "specialchars"),
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("parentheses(test)", "parenthesestest"),
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("Rincewind (Ankh-Morpork)", "Rincewind-Ankh-Morpork"),
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],
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)
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def test_ready_name_for_url(input_name, expected_output):
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"""Test that ready_name_for_url correctly sanitizes names for URL use."""
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assert util.ready_name_for_url(input_name) == expected_output
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@pytest.mark.parametrize(
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"target,expected_substring",
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[
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("normal.txt", 'filename="normal.txt"'),
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("file.gz ", 'filename="file.gz"'),
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(" file.gz", 'filename="file.gz"'),
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(" file.gz ", 'filename="file.gz"'),
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("Galaxy102-[name].fastqsanger.gz ", 'filename="Galaxy102-[name].fastqsanger.gz"'),
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],
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)
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def test_to_content_disposition(target, expected_substring):
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result = util.to_content_disposition(target)
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assert result.startswith("attachment; ")
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assert expected_substring in result
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# Ensure no trailing whitespace in the header value
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assert result == result.strip()
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