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https://github.com/galaxyproject/galaxy.git
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John Chilton
22ddea4337
clean_multiline_string was used in multiple places across modules in different packages so I simply refactored it into galaxy.util and added a test case (used in multiple places and has tests a lower bar then some other code in galaxy.util). The tempfilecache abstraction was only used in one place, so I've refactored it right into that file. Together these should simplify the package tests for galaxy-data (and hopefully other packages also).
94 lines
2.8 KiB
Python
94 lines
2.8 KiB
Python
import errno
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import os
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import tempfile
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import pytest
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from galaxy import util
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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_strip_control_characters_nested():
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s = '\x00bla'
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stripped_s = 'bla'
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l = [s]
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t = (s, 'blub')
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d = {42: s}
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assert util.strip_control_characters_nested(l)[0] == stripped_s
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assert util.strip_control_characters_nested(t)[0] == stripped_s
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assert util.strip_control_characters_nested(d)[42] == stripped_s
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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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('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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('guid',
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'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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fd, path = tempfile.mkstemp()
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os.close(fd)
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os.remove(path)
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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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