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PLOS
test error in Debian fresh install
The package was installed with pip install allofplos (not by cloning the repo)
Also installed the test part with:
pip install -U allofplos[test]
root@7881ab553829:~# python -c "from allofplos import get_corpus_dir; print(get_corpus_dir())" /usr/local/lib/python3.6/site-packages/allofplos/allofplos_xml
When I try to run the tests I get:
root@7881ab553829:~# pytest --pyargs allofplos
========================================================= test session starts =========================================================
platform linux -- Python 3.6.5, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /root, inifile:
collected 20 items
allofplos/tests/test_corpus.py .FFLocal article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pbio.2002354.xml
FLocal article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pbio.2002354.xml
FLocal article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pbio.2002354.xml
FLocal article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pbio.2002354.xml
FFFFFF [ 60%]
allofplos/tests/test_unittests.py ...Local article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pone.0185809.xml
FLocal article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pbio.2001413.xml
FLocal article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/plos.correction.3155a3e9-5fbe-435c-a07a-e9a4846ec0b6.xml
FLocal article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pbio.2002399.xml
F. [100%]
============================================================== FAILURES ===============================================================
___________________________________________________________ test_corpus_len ___________________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f60581bd9e8>
def test_corpus_len(corpus):
> assert len(corpus) == 5
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:33: in __len__
return len(self.dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:115: in dois
return list(self.iter_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:98: in iter_dois
return (x[1] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f60581bd9e8>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
__________________________________________________________ test_corpus_iter_ __________________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efbe208>
def test_corpus_iter_(corpus):
> article_dois = {article.doi for article in corpus}
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:29:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:36: in __iter__
return (article for article in self.random_article_generator)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:132: in random_article_generator
for doi in self.iter_random_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:152: in iter_random_dois
return (doi for doi in self.random.sample(self.dois, len(self)))
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:115: in dois
return list(self.iter_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:98: in iter_dois
return (x[1] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efbe208>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
____________________________________________________ test_corpus_contains_article _____________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efb2668>
no_article = DOI: 10.1371/journal.pmed.0030132
Title: Bigger and Better: How Pfizer Redefined Erectile Dysfunction
yes_article = <[AttributeError("'NoneType' object has no attribute 'getroot'") raised in repr()] Article object at 0x7f604efb2b38>
def test_corpus_contains_article(corpus, no_article, yes_article):
> assert yes_article in corpus
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:39:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:62: in __contains__
is_in = value.doi in self.dois and value.directory == self.directory
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:115: in dois
return list(self.iter_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:98: in iter_dois
return (x[1] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efb2668>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
______________________________________________________ test_corpus_contains_doi _______________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efaf208>
no_article = DOI: 10.1371/journal.pmed.0030132
Title: Bigger and Better: How Pfizer Redefined Erectile Dysfunction
yes_article = <[AttributeError("'NoneType' object has no attribute 'getroot'") raised in repr()] Article object at 0x7f604efaf2e8>
def test_corpus_contains_doi(corpus, no_article, yes_article):
> assert yes_article.doi in corpus
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:43:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:64: in __contains__
doi_in = value in self.dois
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:115: in dois
return list(self.iter_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:98: in iter_dois
return (x[1] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efaf208>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
____________________________________________________ test_corpus_contains_filepath ____________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efcc0f0>
no_article = DOI: 10.1371/journal.pmed.0030132
Title: Bigger and Better: How Pfizer Redefined Erectile Dysfunction
yes_article = <[AttributeError("'NoneType' object has no attribute 'getroot'") raised in repr()] Article object at 0x7f604efcc1d0>
def test_corpus_contains_filepath(corpus, no_article, yes_article):
## check for filepath, which is currently called filename on Article
> assert yes_article.filename in corpus
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:48:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:64: in __contains__
doi_in = value in self.dois
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:115: in dois
return list(self.iter_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:98: in iter_dois
return (x[1] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efcc0f0>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
______________________________________________________ test_corpus_contains_file ______________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efe04a8>
no_article = DOI: 10.1371/journal.pmed.0030132
Title: Bigger and Better: How Pfizer Redefined Erectile Dysfunction
yes_article = <[AttributeError("'NoneType' object has no attribute 'getroot'") raised in repr()] Article object at 0x7f604efe0ba8>
def test_corpus_contains_file(corpus, no_article, yes_article):
## check for filename, which is currently unavailable on Article
> assert os.path.basename(yes_article.filename) in corpus
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:53:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:64: in __contains__
doi_in = value in self.dois
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:115: in dois
return list(self.iter_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:98: in iter_dois
return (x[1] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efe04a8>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
_____________________________________________________ test_corpus_random_article ______________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efd8f28>
def test_corpus_random_article(corpus):
> article = corpus.random_article
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:57:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:136: in random_article
return next(self.random_article_generator)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:132: in random_article_generator
for doi in self.iter_random_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:152: in iter_random_dois
return (doi for doi in self.random.sample(self.dois, len(self)))
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:115: in dois
return list(self.iter_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:98: in iter_dois
return (x[1] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efd8f28>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
________________________________________________________ test_corpus_indexing _________________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efe0400>
def test_corpus_indexing(corpus):
> assert corpus["10.1371/journal.pbio.2001413"] == corpus[0]
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:61:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:45: in __getitem__
elif key not in self.dois:
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:115: in dois
return list(self.iter_dois)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:98: in iter_dois
return (x[1] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efe0400>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
_________________________________________________________ test_iter_file_doi __________________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efabf28>
def test_iter_file_doi(corpus):
expected = {
'journal.pbio.2001413.xml': '10.1371/journal.pbio.2001413',
'journal.pbio.2002354.xml': '10.1371/journal.pbio.2002354',
'journal.pbio.2002399.xml': '10.1371/journal.pbio.2002399',
'journal.pone.0185809.xml': '10.1371/journal.pone.0185809',
'plos.correction.3155a3e9-5fbe-435c-a07a-e9a4846ec0b6.xml':
'10.1371/annotation/3155a3e9-5fbe-435c-a07a-e9a4846ec0b6',
}
> assert expected == {f:doi for f, doi in corpus.iter_file_doi}
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:74:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efabf28>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
___________________________________________________________ test_filepaths ____________________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efd8240>
def test_filepaths(corpus):
> assert set(corpus.filepaths) == set(listdir_nohidden(TESTDATADIR))
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:78:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:120: in filepaths
return list(self.iter_filepaths)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:103: in iter_filepaths
return (os.path.join(self.directory, fname) for fname in self.iter_files)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:89: in iter_files
return (x[0] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efd8240>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
_____________________________________________________________ test_files ______________________________________________________________
corpus = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efd0a20>
def test_files(corpus):
annote_file = 'plos.correction.3155a3e9-5fbe-435c-a07a-e9a4846ec0b6.xml'
> assert annote_file in corpus.files
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_corpus.py:82:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:109: in files
return list(self.iter_files)
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:89: in iter_files
return (x[0] for x in self.iter_file_doi)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[FileNotFoundError("[Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'") raised in repr()] Corpus object at 0x7f604efd0a20>
@property
def iter_file_doi(self):
"""Generator that returns filename, doi tuples for every file in the corpus.
Used to generate both DOI and file generators for the corpus.
"""
return ((file_, filename_to_doi(file_))
> for file_ in sorted(os.listdir(self.directory))
if file_.endswith(self.extension) and 'DS_Store' not in file_)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/site-packages/allofplos/tests/testdata'
/usr/local/lib/python3.6/site-packages/allofplos/corpus/corpus.py:77: FileNotFoundError
__________________________________________________ TestArticleClass.test_class_doi1 ___________________________________________________
self = <allofplos.tests.test_unittests.TestArticleClass testMethod=test_class_doi1>
def test_class_doi1(self):
"""Tests the methods and properties of the Article class
Test article DOI: 10.1371/journal.pone.0185809
TODO: there is a socket warning from requests module. See https://github.com/requests/requests/issues/3912
XML file is in test directory
"""
article = Article(class_doi, directory=TESTDATADIR)
# self.assertEqual(article.check_if_doi_resolves(), "works", 'check_if_doi_resolves does not transform correctly for {}'.format(article.doi))
# self.assertEqual(article.check_if_link_works(), True, 'check_if_link_works does not transform correctly for {}'.format(article.doi))
> self.assertEqual(article.amendment, False, 'amendment does not transform correctly for {}'.format(article.doi))
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_unittests.py:77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:1180: in amendment
if self.type_ in ['correction', 'retraction', 'expression-of-concern']:
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:1095: in type_
"article"])
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:201: in get_element_xpath
root = self.root
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'NoneType' object has no attribute 'getroot'") raised in repr()] Article object at 0x7f604efe8438>
@property
def root(self):
"""Get the root (base) element of an article.
"""
> return self.tree.getroot()
E AttributeError: 'NoneType' object has no attribute 'getroot'
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:807: AttributeError
-------------------------------------------------------- Captured stdout call ---------------------------------------------------------
Local article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pone.0185809.xml
__________________________________________________ TestArticleClass.test_example_doi __________________________________________________
self = <allofplos.tests.test_unittests.TestArticleClass testMethod=test_example_doi>
def test_example_doi(self):
"""Tests the methods and properties of the Article class
Test article DOI: 10.1371/journal.pbio.2001413
XML file is in test directory
"""
article = Article(example_doi, directory=TESTDATADIR)
# self.assertEqual(article.check_if_doi_resolves(), "works", 'check_if_doi_resolves does not transform correctly for {}'.format(article.doi))
# self.assertEqual(article.check_if_link_works(), True, 'check_if_link_works does not transform correctly for {}'.format(article.doi))
> self.assertEqual(article.amendment, False, 'amendment does not transform correctly for {}'.format(article.doi))
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_unittests.py:118:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:1180: in amendment
if self.type_ in ['correction', 'retraction', 'expression-of-concern']:
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:1095: in type_
"article"])
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:201: in get_element_xpath
root = self.root
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'NoneType' object has no attribute 'getroot'") raised in repr()] Article object at 0x7f604eee9208>
@property
def root(self):
"""Get the root (base) element of an article.
"""
> return self.tree.getroot()
E AttributeError: 'NoneType' object has no attribute 'getroot'
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:807: AttributeError
-------------------------------------------------------- Captured stdout call ---------------------------------------------------------
Local article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pbio.2001413.xml
_________________________________________________ TestArticleClass.test_example_doi2 __________________________________________________
self = <allofplos.tests.test_unittests.TestArticleClass testMethod=test_example_doi2>
def test_example_doi2(self):
"""Tests the methods and properties of the Article class
Test article DOI: 10.1371/annotation/3155a3e9-5fbe-435c-a07a-e9a4846ec0b6
XML file is in test directory
"""
article = Article(example_doi2, directory=TESTDATADIR)
# self.assertEqual(article.check_if_doi_resolves(), "works", 'check_if_doi_resolves does not transform correctly for {}'.format(article.doi))
# self.assertEqual(article.check_if_link_works(), True, 'check_if_link_works does not transform correctly for {}'.format(article.doi))
> self.assertEqual(article.amendment, True, 'amendment does not transform correctly for {}'.format(article.doi))
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_unittests.py:157:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:1180: in amendment
if self.type_ in ['correction', 'retraction', 'expression-of-concern']:
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:1095: in type_
"article"])
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:201: in get_element_xpath
root = self.root
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'NoneType' object has no attribute 'getroot'") raised in repr()] Article object at 0x7f604eeeb908>
@property
def root(self):
"""Get the root (base) element of an article.
"""
> return self.tree.getroot()
E AttributeError: 'NoneType' object has no attribute 'getroot'
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:807: AttributeError
-------------------------------------------------------- Captured stdout call ---------------------------------------------------------
Local article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/plos.correction.3155a3e9-5fbe-435c-a07a-e9a4846ec0b6.xml
____________________________________________________ TestArticleClass.test_proofs _____________________________________________________
self = <allofplos.tests.test_unittests.TestArticleClass testMethod=test_proofs>
def test_proofs(self):
"""Tests whether uncorrected proofs and VOR updates are being detected correctly."""
os.environ['PLOS_CORPUS'] = TESTDATADIR
article = Article(example_uncorrected_doi)
> self.assertTrue(article.proof == 'uncorrected_proof')
/usr/local/lib/python3.6/site-packages/allofplos/tests/test_unittests.py:193:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:897: in proof
xpath_results = self.get_element_xpath()
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:201: in get_element_xpath
root = self.root
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'NoneType' object has no attribute 'getroot'") raised in repr()] Article object at 0x7f604ebc84a8>
@property
def root(self):
"""Get the root (base) element of an article.
"""
> return self.tree.getroot()
E AttributeError: 'NoneType' object has no attribute 'getroot'
/usr/local/lib/python3.6/site-packages/allofplos/article_class.py:807: AttributeError
-------------------------------------------------------- Captured stdout call ---------------------------------------------------------
Local article file not found: /usr/local/lib/python3.6/site-packages/allofplos/tests/testdata/journal.pbio.2002399.xml
================================================ 15 failed, 5 passed in 26.18 seconds =================================================
root@7881ab553829:~#
The problem is that the testdata directory is not installed. Maybe it is because there is no __init__.py file inside?
