def test_no_updated_date(self):
format = 'https://spec-url-for-format'
content = data_model.CombineArchiveContent('1.txt', format, False)
archive = data_model.CombineArchive([content])
archive_file = os.path.join(self.temp_dir, 'test.omex')
in_dir = os.path.join(self.temp_dir, 'in')
out_dir = os.path.join(self.temp_dir, 'out')
os.mkdir(in_dir)
os.mkdir(out_dir)
with open(os.path.join(in_dir, content.location), 'w') as file:
file.write('a')
io.CombineArchiveWriter().run(archive, in_dir, archive_file)
archive_b = io.CombineArchiveReader().run(archive_file, out_dir)
archive_b.contents = list(
filter(
lambda content: content.format != data_model.
CombineArchiveContentFormat.OMEX_METADATA, archive_b.contents))
self.assertTrue(archive.is_equal(archive_b))
self.assertEqual(sorted(os.listdir(out_dir)),
sorted([
content.location,
'manifest.xml',
]))
with open(os.path.join(out_dir, content.location), 'r') as file:
self.assertEqual('a', file.read())
def test_write_read_manifest_with_manifest(self):
manifest_filename = os.path.join(self.temp_dir, 'test.xml')
contents = [
data_model.CombineArchiveContent(
location='1.txt',
format='http://purl.org/NET/mediatypes/plain/text',
master=False,
),
data_model.CombineArchiveContent(
location='2.jpg',
format='http://purl.org/NET/mediatypes/image/jpeg',
master=True,
),
data_model.CombineArchiveContent(
location='manifest.xml',
format=data_model.CombineArchiveContentFormat.OMEX_MANIFEST,
master=False,
),
]
io.CombineArchiveWriter().write_manifest(contents, manifest_filename)
contents_2 = io.CombineArchiveReader().read_manifest(manifest_filename)
archive = data_model.CombineArchive(contents=contents)
archive_2 = data_model.CombineArchive(contents=contents_2)
self.assertTrue(archive_2.is_equal(archive))
def test(self):
format = 'https://spec-url-for-format'
content1 = data_model.CombineArchiveContent('1.txt', format, False)
content2 = data_model.CombineArchiveContent('2/2.txt', format, True)
archive1 = data_model.CombineArchive([content1, content2])
archive2 = data_model.CombineArchive([content1, content1])
archive_file = os.path.join(self.temp_dir, 'test.omex')
in_dir = os.path.join(self.temp_dir, 'in')
out_dir = os.path.join(self.temp_dir, 'out')
out_dir2 = os.path.join(self.temp_dir, 'out2')
os.mkdir(in_dir)
os.mkdir(os.path.join(in_dir, '2'))
os.mkdir(out_dir)
with open(os.path.join(in_dir, content1.location), 'w') as file:
file.write('a')
with open(os.path.join(in_dir, content2.location), 'w') as file:
file.write('b')
io.CombineArchiveWriter().run(archive1, in_dir, archive_file)
archive1b = io.CombineArchiveReader().run(
archive_file, out_dir, include_omex_metadata_files=False)
self.assertTrue(archive1.is_equal(archive1b))
archive1b = io.CombineArchiveReader().run(
archive_file, out_dir, include_omex_metadata_files=True)
metadata_contents = [
content.location for content in archive1b.contents if re.match(
data_model.CombineArchiveContentFormatPattern.OMEX_METADATA.
value, content.format)
]
self.assertEqual(metadata_contents, [])
self.assertEqual(
sorted(os.listdir(out_dir)),
sorted([
content1.location,
os.path.dirname(content2.location),
'manifest.xml',
]))
with open(os.path.join(out_dir, content1.location), 'r') as file:
self.assertEqual('a', file.read())
with open(os.path.join(out_dir, content2.location), 'r') as file:
self.assertEqual('b', file.read())
io.CombineArchiveWriter().run(archive2, in_dir, archive_file)
archive2b = io.CombineArchiveReader().run(
archive_file, out_dir2, include_omex_metadata_files=False)
self.assertTrue(archive2.is_equal(archive2b))
self.assertEqual(sorted(os.listdir(out_dir2)),
sorted([
content1.location,
'manifest.xml',
]))
with open(os.path.join(out_dir2, content1.location), 'r') as file:
self.assertEqual('a', file.read())
with self.assertRaisesRegex(ValueError, 'is not a file'):
io.CombineArchiveReader().run(
os.path.join(self.temp_dir, 'test2.omex'), out_dir)
def test_write_error_handling(self):
now = datetime.datetime(2020,
1,
2,
1,
2,
3,
tzinfo=dateutil.tz.tzutc())
content = data_model.CombineArchiveContent('1.txt', 'plain/text',
False)
with open(os.path.join(self.temp_dir, content.location), 'w') as file:
pass
archive = data_model.CombineArchive([content])
archive_file = os.path.join(self.temp_dir, 'archive.omex')
with self.assertRaisesRegex(Exception, 'could not be saved'):
with mock.patch.object(libcombine.CombineArchive,
'writeToFile',
return_value=False):
io.CombineArchiveWriter().run(archive, self.temp_dir,
archive_file)
with self.assertRaisesRegex(Exception,
'could not be added to the archive'):
with mock.patch.object(libcombine.CombineArchive,
'addFile',
return_value=False):
io.CombineArchiveWriter().run(archive, self.temp_dir,
archive_file)
with self.assertRaisesRegex(ValueError, 'my error'):
with mock.patch(
'biosimulators_utils.combine.io.get_combine_errors_warnings',
return_value=([['my error']], [])):
io.CombineArchiveWriter().run(archive, self.temp_dir,
archive_file)
with self.assertWarnsRegex(BioSimulatorsWarning, 'my warning'):
with mock.patch(
'biosimulators_utils.combine.io.get_combine_errors_warnings',
return_value=([], [['my warning']])):
io.CombineArchiveWriter().run(archive, self.temp_dir,
archive_file)
archive_file = os.path.join(os.path.dirname(__file__), '..',
'fixtures',
'invalid-parent-format-in-manifest.omex')
out_dir = os.path.join(self.temp_dir, 'out-1')
with self.assertRaisesRegex(ValueError,
'format of the archive must be'):
io.CombineArchiveReader().run(archive_file,
out_dir,
include_omex_metadata_files=False)
archive_file = os.path.join(os.path.dirname(__file__), '..',
'fixtures',
'missing-parent-in-manifest.omex')
out_dir = os.path.join(self.temp_dir, 'out-2')
with self.assertWarnsRegex(
BioSimulatorsWarning,
'Manifests should include their parent COMBINE/OMEX archives'):
io.CombineArchiveReader().run(archive_file,
out_dir,
include_omex_metadata_files=False)