mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
dcb6f061f6
When enabling the `warn_unused_ignores = True` option of mypy, this
was making the `test_galaxy_packages` tests fail with:
```
mypy .
Traceback (most recent call last):
File "/tmp/gxpkgtestenvu3fgDr/bin/mypy", line 8, in <module>
sys.exit(console_entry())
File "/tmp/gxpkgtestenvu3fgDr/lib/python3.10/site-packages/mypy/__main__.py", line 15, in console_entry
main()
File "mypy/main.py", line 100, in main
File "mypy/main.py", line 182, in run_build
File "mypy/build.py", line 192, in build
File "mypy/build.py", line 266, in _build
File "mypy/build.py", line 2942, in dispatch
File "mypy/build.py", line 3333, in process_graph
File "mypy/build.py", line 3414, in process_fresh_modules
File "mypy/build.py", line 2110, in fix_cross_refs
File "mypy/fixup.py", line 52, in fixup_module
File "mypy/fixup.py", line 127, in visit_symbol_table
File "mypy/lookup.py", line 49, in lookup_fully_qualified
AssertionError: Cannot find component 'util' for 'galaxy.util'
make: *** [Makefile:96: mypy] Error 1
```
Moreover, installing packages in editable mode was hiding some issues
with how files from other packages were accessed.
142 lines
4.0 KiB
Python
142 lines
4.0 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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"""
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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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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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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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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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