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test-report.xml
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<?xml version="1.0" encoding="utf-8"?><testsuite errors="0" failures="2" name="pytest" skips="0" tests="2" time="0.606"><testcase classname="src.toil_topmed.test.test_topmed_cgl" file="src/toil_topmed/test/test_topmed_cgl.py" line="12" name="test_parse_samples_valid_cases" time="0.00337100028992"><failure message="TypeError: unhashable type: 'list'">tmpdir = local('/tmp/pytest-of-trevorp/pytest-4/test_parse_samples_valid_cases0')
def test_parse_samples_valid_cases(tmpdir):
# fq validation
out1 = _test_successful_parse_sample(tmpdir, "uuid", "fq", "single",
["file:///file.fq", "http://host/file.fastq", "s3:///bucket/file.fq.gz", "ftp://host/file.fastq.gz"])
out2 = _test_successful_parse_sample(tmpdir, "uuid", "fq", "paired",
> ["file:///file_1.fq", "file:///file_2.fq", "file:///fileR1.fq", "file:///fileR2.fq"])
src/toil_topmed/test/test_topmed_cgl.py:19:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src/toil_topmed/test/test_topmed_cgl.py:100: in _test_successful_parse_sample
output = parse_samples(manifest_location)
src/toil_topmed/topmed_cgl_pipeline.py:113: in parse_samples
require(file_count_with_suffix(url, "R1") == file_count_with_suffix(url, "R2"),
src/toil_topmed/topmed_cgl_pipeline.py:112: in file_count_with_suffix
lambda x: os.path.splitext(os.path.basename(urlparse(url).path))[0].endswith(suffix), urls))
src/toil_topmed/topmed_cgl_pipeline.py:112: in <lambda>
lambda x: os.path.splitext(os.path.basename(urlparse(url).path))[0].endswith(suffix), urls))
/usr/lib/python2.7/urlparse.py:143: in urlparse
tuple = urlsplit(url, scheme, allow_fragments)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
url = ['file:///file_1.fq', 'file:///file_2.fq', 'file:///fileR1.fq', 'file:///fileR2.fq'], scheme = '', allow_fragments = True
def urlsplit(url, scheme='', allow_fragments=True):
"""Parse a URL into 5 components:
<scheme>://<netloc>/<path>?<query>#<fragment>
Return a 5-tuple: (scheme, netloc, path, query, fragment).
Note that we don't break the components up in smaller bits
(e.g. netloc is a single string) and we don't expand % escapes."""
allow_fragments = bool(allow_fragments)
key = url, scheme, allow_fragments, type(url), type(scheme)
> cached = _parse_cache.get(key, None)
E TypeError: unhashable type: 'list'
/usr/lib/python2.7/urlparse.py:176: TypeError</failure></testcase><testcase classname="src.toil_topmed.test.test_topmed_cgl" file="src/toil_topmed/test/test_topmed_cgl.py" line="51" name="test_parse_samples_error_cases" time="0.00308990478516"><failure message="TypeError: unhashable type: 'list'">tmpdir = local('/tmp/pytest-of-trevorp/pytest-4/test_parse_samples_error_cases0')
def test_parse_samples_error_cases(tmpdir):
# scheme issues
_test_failed_parse_sample(tmpdir, "uuid", "fq", "single", ["badscheme:///file.fq"],
"expected error for bad scheme")
_test_failed_parse_sample(tmpdir, "uuid", "bam", "single", ["badscheme:///file.bam"],
"expected error for bad scheme")
_test_failed_parse_sample(tmpdir, "uuid", "tar", "single", ["badscheme:///file.tar"],
"expected error for bad scheme")
# extension issues
_test_failed_parse_sample(tmpdir, "uuid", "fq", "single", ["file:///file.badextension"],
"expected error for bad extension")
_test_failed_parse_sample(tmpdir, "uuid", "bam", "single", ["file:///file.badextension"],
"expected error for bad extension")
_test_failed_parse_sample(tmpdir, "uuid", "tar", "single", ["file:///file.badextension"],
"expected error for bad extension")
# paired issues
_test_failed_parse_sample(tmpdir, "uuid", "fq", "paired", ["file:///file.fq", "file:///anotherfile.fq"],
> "expected error for inconsistent file pairs")
src/toil_topmed/test/test_topmed_cgl.py:72:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src/toil_topmed/test/test_topmed_cgl.py:120: in _test_failed_parse_sample
parse_samples(manifest_location)
src/toil_topmed/topmed_cgl_pipeline.py:113: in parse_samples
require(file_count_with_suffix(url, "R1") == file_count_with_suffix(url, "R2"),
src/toil_topmed/topmed_cgl_pipeline.py:112: in file_count_with_suffix
lambda x: os.path.splitext(os.path.basename(urlparse(url).path))[0].endswith(suffix), urls))
src/toil_topmed/topmed_cgl_pipeline.py:112: in <lambda>
lambda x: os.path.splitext(os.path.basename(urlparse(url).path))[0].endswith(suffix), urls))
/usr/lib/python2.7/urlparse.py:143: in urlparse
tuple = urlsplit(url, scheme, allow_fragments)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
url = ['file:///file.fq', 'file:///anotherfile.fq'], scheme = '', allow_fragments = True
def urlsplit(url, scheme='', allow_fragments=True):
"""Parse a URL into 5 components:
<scheme>://<netloc>/<path>?<query>#<fragment>
Return a 5-tuple: (scheme, netloc, path, query, fragment).
Note that we don't break the components up in smaller bits
(e.g. netloc is a single string) and we don't expand % escapes."""
allow_fragments = bool(allow_fragments)
key = url, scheme, allow_fragments, type(url), type(scheme)
> cached = _parse_cache.get(key, None)
E TypeError: unhashable type: 'list'
/usr/lib/python2.7/urlparse.py:176: TypeError</failure></testcase></testsuite>