def test_read_files():
"Test that the system can read files."
db = get_db_with_content()
# Create the test files.
test_file_fmt = 'test_reading_input.%s'
example_files = []
for fmt in [formats.TEXT, formats.XML]:
tc = db.select_one(db.TextContent, db.TextContent.format == fmt)
if tc is None:
print("Could not find %s content for testing." % fmt)
continue
suffix = fmt
if fmt is formats.XML:
suffix = 'n' + fmt
with open(test_file_fmt % suffix, 'wb') as f:
f.write(zlib.decompress(tc.content, 16 + zlib.MAX_WBITS))
example_files.append(test_file_fmt % suffix)
# Now read them.
readers = get_readers()
outputs = read_files(example_files, readers)
N_out = len(outputs)
N_exp = len(example_files)
assert N_out == N_exp, "Expected %d outputs, got %d." % (N_exp, N_out)
def test_read_files():
"Test that the system can read files."
# Create the test files.
example_files = []
# Get txt content
abstract_txt = ("This is a paper that contains the phrase: MEK "
"phosphorylates ERK.")
with open('test_abstract.txt', 'w') as f:
f.write(abstract_txt)
example_files.append('test_abstract.txt')
# Get nxml content
pmc_test_fpath = path.join(path.dirname(path.abspath(__file__)),
'pmc_cont_example.nxml')
if path.exists(pmc_test_fpath):
example_files.append(pmc_test_fpath)
assert len(example_files), "No content available to test."
# Now read them.
reader_classes = get_reader_classes()
readers = []
for rc in reader_classes:
readers.append(rc())
outputs = read_files(example_files, readers)
N_out = len(outputs)
proper_readers = [r for r in readers if not isinstance(r, EmptyReader)]
N_exp = len(proper_readers) * len(example_files)
assert N_out == N_exp, "Expected %d outputs, got %d." % (N_exp, N_out)
def test_read_files():
"Test that the system can read files."
# Create the test files.
example_files = []
# Get txt content
abstract_txt = ("This is a paper that contains the phrase: MEK "
"phosphorylates ERK.")
with open('test_abstract.txt', 'w') as f:
f.write(abstract_txt)
example_files.append('test_abstract.txt')
# Get nxml content
pmc_test_fpath = path.join(path.dirname(path.abspath(__file__)),
'pmc_cont_example.nxml')
if path.exists(pmc_test_fpath):
example_files.append(pmc_test_fpath)
assert len(example_files), "No content available to test."
# Now read them.
reader_classes = get_reader_classes()
readers = []
for rc in reader_classes:
readers.append(rc())
outputs = read_files(example_files, readers)
N_out = len(outputs)
proper_readers = [r for r in readers if not isinstance(r, EmptyReader)]
N_exp = len(proper_readers)*len(example_files)
assert N_out == N_exp, "Expected %d outputs, got %d." % (N_exp, N_out)