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142 lines
4.2 KiB
Python
142 lines
4.2 KiB
Python
import errno
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import os
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import tempfile
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from io import StringIO
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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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"""
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a
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b
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c
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"""
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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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monkeypatch.setattr(util, "galaxy_root_path", "a/b")
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assert not util.in_packages()
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monkeypatch.setattr(util, "galaxy_root_path", "a/b/packages")
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assert util.in_packages()
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def test_galaxy_directory(monkeypatch):
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monkeypatch.setattr(util, "galaxy_root_path", "a/b") # a/b
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path1 = util.galaxy_directory()
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monkeypatch.setattr(util, "galaxy_root_path", "a/b/c/..") # a/b
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path2 = util.galaxy_directory()
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monkeypatch.setattr(util, "galaxy_root_path", "a/b/packages/c/..") # a/b/packages
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path3 = util.galaxy_directory()
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assert path1 == path2 == path3
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assert os.path.isabs(path1)
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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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assert util.listify([1, 2, 3]) == [1, 2, 3]
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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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