def test_TriplesOmexMetaWriter_run(self):
triples, errors, _ = io.TriplesOmexMetaReader().run(self.FIXTURE)
self.assertEqual(errors, [])
filename2 = os.path.join(self.dir_name, 'md2.rdf')
filename3 = os.path.join(self.dir_name, 'md3.rdf')
io.TriplesOmexMetaWriter().run(
triples, filename2,
config=Config(OMEX_METADATA_OUTPUT_FORMAT=data_model.OmexMetadataOutputFormat.rdfxml),
)
io.TriplesOmexMetaWriter().run(triples, filename3)
md, errors, _ = io.BiosimulationsOmexMetaReader().run(self.FIXTURE)
self.assertEqual(errors, [])
md2, errors, _ = io.BiosimulationsOmexMetaReader().run(filename2)
self.assertEqual(errors, [])
md3, errors, _ = io.BiosimulationsOmexMetaReader().run(filename3)
self.assertEqual(errors, [])
for key in md[0].keys():
if isinstance(md[0][key], list) and md[0][key]:
if isinstance(md[0][key][0], str):
md2[0][key].sort()
md[0][key].sort()
elif isinstance(md[0][key][0], dict) and 'uri' in md[0][key][0]:
md2[0][key].sort(key=lambda obj: (obj['uri'], obj['label']))
md[0][key].sort(key=lambda obj: (obj['uri'], obj['label']))
self.assertEqual(md2[0][key], md[0][key], key)
self.assertEqual(md2, md)
self.assertEqual(md3, md)
filename = os.path.join(self.dir_name, 'md')
io.TriplesOmexMetaWriter().run(triples, filename,
config=Config(OMEX_METADATA_OUTPUT_FORMAT=data_model.OmexMetadataOutputFormat.turtle)
)
filename = os.path.join(self.dir_name, 'md.xml')
io.TriplesOmexMetaWriter().run(triples, filename,
config=Config(OMEX_METADATA_OUTPUT_FORMAT=data_model.OmexMetadataOutputFormat.rdfxml_abbrev)
)
md2, errors, _ = io.BiosimulationsOmexMetaReader().run(filename)
self.assertEqual(errors, [])
for key in md[0].keys():
if isinstance(md[0][key], list) and md[0][key]:
if isinstance(md[0][key][0], str):
md2[0][key].sort()
md[0][key].sort()
elif isinstance(md[0][key][0], dict) and 'uri' in md[0][key][0]:
md2[0][key].sort(key=lambda obj: (obj['uri'], obj['label']))
md[0][key].sort(key=lambda obj: (obj['uri'], obj['label']))
self.assertEqual(md2[0][key], md[0][key], key)
self.assertEqual(md2, md)
def test_BiosimulationsOmexMetaReader_get_combine_archive_uri_multiple_root(self):
rdf, errors, warnings = io.BiosimulationsOmexMetaReader.read_rdf(self.MULTIPLE_ROOTS_FIXTURE)
triples = io.BiosimulationsOmexMetaReader.get_rdf_triples(rdf)
root_uri, errors, warnings = io.BiosimulationsOmexMetaReader.get_combine_archive_uri(triples)
self.assertEqual(root_uri, None)
self.assertIn('metadata about multiple', flatten_nested_list_of_strings(errors))
self.assertEqual(warnings, [])
_, errors, warnings = io.BiosimulationsOmexMetaReader().run(self.MULTIPLE_ROOTS_FIXTURE)
self.assertIn('metadata about multiple OMEX archives', flatten_nested_list_of_strings(errors))
def test_BiosimulationsOmexMetaReader_get_combine_archive_uri_no_root(self):
rdf, errors, warnings = io.BiosimulationsOmexMetaReader.read_rdf(self.NO_ROOT_FIXTURE)
triples = io.BiosimulationsOmexMetaReader.get_rdf_triples(rdf)
root_uri, errors, warnings = io.BiosimulationsOmexMetaReader.get_combine_archive_uri(triples)
self.assertEqual(root_uri, '.')
self.assertIn('does not contain metadata', flatten_nested_list_of_strings(errors))
self.assertEqual(warnings, [])
_, errors, warnings = io.BiosimulationsOmexMetaReader().run(self.NO_ROOT_FIXTURE)
self.assertIn('does not contain metadata', flatten_nested_list_of_strings(errors))
def test_write_omex_meta_file(self):
config = Config(
OMEX_METADATA_SCHEMA=data_model.OmexMetadataSchema.rdf_triples,
)
triples, errors, _ = io.read_omex_meta_file(self.FIXTURE, config=config)
self.assertEqual(errors, [])
filename = os.path.join(self.dir_name, 'md.rdf')
io.write_omex_meta_file(triples, filename, config=config)
md, errors, _ = io.BiosimulationsOmexMetaReader().run(self.FIXTURE)
self.assertEqual(errors, [])
filename = os.path.join(self.dir_name, 'md.rdf')
config.OMEX_METADATA_SCHEMA = data_model.OmexMetadataSchema.biosimulations
io.write_omex_meta_file(md, filename, config=config)
io.write_omex_meta_file(md, filename)
config.OMEX_METADATA_SCHEMA = None
with self.assertRaises(NotImplementedError):
io.write_omex_meta_file(triples, filename, config=config)
def test_BiosimulationsOmexMetaWriter_run(self):
md, errors, _ = io.BiosimulationsOmexMetaReader().run(self.FIXTURE)
self.assertEqual(errors, [])
filename2 = os.path.join(self.dir_name, 'md2.rdf')
filename3 = os.path.join(self.dir_name, 'md3.rdf')
io.BiosimulationsOmexMetaWriter().run(md, filename2,
config=Config(OMEX_METADATA_OUTPUT_FORMAT=data_model.OmexMetadataOutputFormat.rdfxml)
)
io.BiosimulationsOmexMetaWriter().run(md, filename3)
md2, errors, _ = io.BiosimulationsOmexMetaReader().run(filename2)
md3, errors, _ = io.BiosimulationsOmexMetaReader().run(filename3)
self.assertEqual(errors, [])
for key in md[0].keys():
if isinstance(md[0][key], list) and md[0][key]:
if isinstance(md[0][key][0], str):
md2[0][key].sort()
md[0][key].sort()
elif isinstance(md[0][key][0], dict) and 'uri' in md[0][key][0]:
md2[0][key].sort(key=lambda obj: (obj['uri'], obj['label']))
md[0][key].sort(key=lambda obj: (obj['uri'], obj['label']))
self.assertEqual(md2[0][key], md[0][key], key)
self.assertEqual(md2, md)
self.assertEqual(md3, md)
filename = os.path.join(self.dir_name, 'md.rdf')
md[0]['title'] = None
md[0]['other'].append({
'attribute': {
'uri': 'http://www.collex.org/schema#thumbnail',
'label': 'Image',
},
'value': {
'uri': 'https://website.com/image.png',
'label': 'Big image',
},
})
io.BiosimulationsOmexMetaWriter().run(md, filename,
config=Config(OMEX_METADATA_OUTPUT_FORMAT=data_model.OmexMetadataOutputFormat.rdfxml))
md, errors, _ = io.BiosimulationsOmexMetaReader().run(
os.path.join(self.FIXTURE_DIR, 'biosimulations-with-file-annotations.rdf'))
self.assertEqual(errors, [])
filename = os.path.join(self.dir_name, 'md.rdf')
io.BiosimulationsOmexMetaWriter().run(md, filename,
config=Config(OMEX_METADATA_OUTPUT_FORMAT=data_model.OmexMetadataOutputFormat.rdfxml))
md2, errors, _ = io.BiosimulationsOmexMetaReader().run(filename)
self.assertEqual(errors, [])
md.sort(key=lambda file: file['uri'])
md2.sort(key=lambda file: file['uri'])
for i in range(len(md)):
for key in md[i].keys():
if isinstance(md[i][key], list) and md[i][key]:
if isinstance(md[i][key][0], str):
md2[i][key].sort()
md[i][key].sort()
elif isinstance(md[i][key][0], dict) and 'uri' in md[i][key][0]:
md2[i][key].sort(key=lambda obj: (obj['uri'], obj['label']))
md[i][key].sort(key=lambda obj: (obj['uri'], obj['label']))
self.assertEqual(md2, md)
def test_read_omex_meta_file_no_root(self):
filename = self.NO_ROOT_FIXTURE
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertEqual(metadata, None)
self.assertIn('does not contain metadata', flatten_nested_list_of_strings(errors))
self.assertEqual(warnings, [])
def test_BiosimulationsOmexMetaReader_run(self):
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(self.FIXTURE, working_dir=self.dir_name)
expected = [{
'uri': '.',
'combine_archive_uri': 'http://omex-library.org/BioSim0001.omex',
'title': 'Name',
'abstract': 'Short summary',
'keywords': ['tag 1', 'tag 2'],
'thumbnails': ['./thumbnail.png'],
'description': 'Description',
'taxa': [
{
'uri': 'http://identifiers.org/taxonomy/9606',
'label': 'H**o sapiens',
}
],
'encodes': [
{
'uri': 'http://identifiers.org/CL:0001057',
'label': 'myeloid dendritic cell, human',
}
],
'sources': [
{
'uri': 'http://identifiers.org/github:lab/project',
'label': 'Tsur 2019 model source code',
}
],
'predecessors': [
{
'uri': 'http://identifiers.org/biomodels.db:BIOMD0000000837',
'label': 'Hanson2016 - Toxicity Management in CAR T cell therapy for B-ALL',
}
],
'references': [
{
'uri': 'http://identifiers.org/pubmed:1234',
'label': 'D Nadeau, C Marchand. Change in the kinetics of sulphacetamide tissue distribution in Walker tumor-bearing rats. Drug Metab Dispos 3(6): 565-76 (1975).',
},
],
'successors': [
{
'uri': 'http://identifiers.org/biomodels.db:BIOMD0000000839',
'label': 'Almeida2019 - Transcription-based circadian ...',
}
],
'see_also': [
{
'uri': 'http://identifiers.org/biomodels.db:BIOMD0000000836',
'label': 'Radosavljevic2009_BioterroristAttack_PanicProtection_1',
}
],
'identifiers': [
{
'uri': 'http://identifiers.org/biomodels.db:BIOMD0000000838',
'label': 'biomodels.db:BIOMD0000000838',
}
],
'citations': [
{
'uri': 'http://identifiers.org/doi:10.1016/j.copbio.2017.12.013',
'label': (
'Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD & Karr JR. '
'Emerging whole-cell modeling principles and methods. '
'Curr Opin Biotechnol 2018, 51:97-102.'
),
},
{
'uri': 'http://identifiers.org/pubmed:29275251',
'label': (
'Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD & Karr JR. '
'Emerging whole-cell modeling principles and methods. '
'Curr Opin Biotechnol 2018, 51:97-102.'
),
}
],
'creators': [
{
'uri': 'http://identifiers.org/orcid:0000-0001-8254-4958',
'label': 'Jonathan Karr',
}
],
'contributors': [
{
'uri': None,
'label': 'Name of person with no ORCID account',
}
],
'license': {
'uri': 'http://identifiers.org/spdx:MIT',
'label': 'MIT',
},
'funders': [
{
'uri': 'http://identifiers.org/doi:10.13039/100000001',
'label': 'National Science Foundation',
},
],
'created': '2020-06-18',
'modified': ['2021-06-18'],
'other': [
{
'attribute': {
'uri': 'http://ontology.eil.utoronto.ca/icity/OM/temporalUnit',
'label': 'Temporal unit',
},
'value': {
'uri': 'http://www.w3.org/2006/time#second',
'label': 'second',
},
},
],
}]
for key in expected[0].keys():
self.assertEqual(metadata[0][key], expected[0][key], key)
self.assertEqual(metadata, expected)
self.assertEqual(errors, [])
self.assertEqual(warnings, [])
filename = os.path.join(self.FIXTURE_DIR, 'biosimulations-abbrev.rdf')
metadata2, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertEqual(metadata2, metadata)
filename = os.path.join(self.FIXTURE_DIR, 'abbrev.rdf')
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertEqual(metadata[0]['title'], 'Name')
self.assertEqual(metadata[0]['funders'], [
{
'uri': 'http://identifiers.org/doi:10.13039/100000001',
'label': 'National Science Foundation',
},
])
self.assertEqual(errors, [])
self.assertEqual(warnings, [])
md, errors, warnings = io.BiosimulationsOmexMetaReader().run(
os.path.join(self.FIXTURE_DIR, 'biosimulations-with-file-annotations.rdf'),
working_dir=self.dir_name)
self.assertEqual(errors, [])
self.assertEqual(warnings, [])
self.assertEqual(len(md), 2)
self.assertEqual(set(m['uri'] for m in md), set(['.', './sim.sedml/figure1']))
m = next(m for m in md if m['uri'] == './sim.sedml/figure1')
self.assertEqual(m, {
'uri': './sim.sedml/figure1',
'combine_archive_uri': 'http://omex-library.org/BioSim0001.omex',
'title': None,
'abstract': None,
'keywords': [],
'thumbnails': [],
'description': None,
'taxa': [],
'encodes': [],
'sources': [],
'predecessors': [],
'references': [],
'successors': [],
'see_also': [],
'identifiers': [{
'uri': 'http://identifiers.org/doi:10.1371/journal.pcbi.1008379.g001',
'label': 'Figure 1a',
}],
'citations': [],
'creators': [],
'contributors': [],
'license': None,
'funders': [],
'created': None,
'modified': [],
'other': [
],
})
filename = os.path.join(self.FIXTURE_DIR, 'missing-required.rdf')
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertIn('is required', flatten_nested_list_of_strings(errors))
self.assertEqual(warnings, [])
filename = os.path.join(self.FIXTURE_DIR, 'missing-label.rdf')
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertEqual(errors, [])
self.assertIn('does not contain an rdf:label', flatten_nested_list_of_strings(warnings))
filename = os.path.join(self.FIXTURE_DIR, 'invalid-thumbnail-uri.rdf')
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertIn('must begin with the URI', flatten_nested_list_of_strings(errors))
self.assertEqual(warnings, [])
filename = os.path.join(self.FIXTURE_DIR, 'missing-thumbnail-uri.rdf')
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertEqual(errors, [])
self.assertIn('does not contain an URI', flatten_nested_list_of_strings(warnings))
filename = os.path.join(self.FIXTURE_DIR, 'missing-uri.rdf')
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertEqual(errors, [])
self.assertEqual(warnings, [])
filename = os.path.join(self.FIXTURE_DIR, 'missing-label-2.rdf')
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertEqual(errors, [])
self.assertIn('does not contain an rdf:label', flatten_nested_list_of_strings(warnings))
filename = os.path.join(self.FIXTURE_DIR, 'too-many-objects.rdf')
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertIn('should only contain one instance of predicate', flatten_nested_list_of_strings(errors))
self.assertEqual(warnings, [])
filename = 'does not exist'
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertEqual(metadata, None)
self.assertIn('is not a file', flatten_nested_list_of_strings(errors))
self.assertEqual(warnings, [])
filename = self.NO_ROOT_FIXTURE
metadata, errors, warnings = io.BiosimulationsOmexMetaReader().run(filename, working_dir=self.dir_name)
self.assertNotEqual(metadata, None)
self.assertIn('Thumbnail URIs must begin with', flatten_nested_list_of_strings(errors))
self.assertEqual(warnings, [])