def _to_json(rec: etl.Record):
"""Converts a record to a formatted `Relationship` in JSON form.
Args:
rec: A table record
Returns:
A new record containing a single field, which is the JSON object
"""
coding = Coding(
system=_SYSTEM,
code=rec['source.CODE'],
display=rec['source.CODE_TEXT'],
version=rec.get('version')
)
parent = Coding(
system=_SYSTEM,
code=rec['source.IMMEDIATE_PARENT'],
display=rec['target.CODE_TEXT'],
version=rec.get('version')
)
relationships = [
Relationship('subsumes', coding, parent),
Relationship('specializes', parent, coding)
]
schema = RelationshipSchema()
return map(lambda relationship: [json.dumps(schema.dump(relationship))], relationships)
def _to_json(rec):
"""
Convert record in table to Relationship as a JSON object
Record is expected to have the following fields: [ source.CODE, source.STR, target.CODE, target.STR]
Args:
rec: A table record
Returns:
A new record containing a single field, which is the JSON object
"""
source = Coding(system="http://snomed.info/sct",
code=rec['sourceId'],
display=rec['source.term'],
version=rec['effectiveTime'] if rec['versioned'] else None)
target = Coding(system="http://snomed.info/sct",
code=rec['destinationId'],
display=rec['target.term'],
version=rec['effectiveTime'] if rec['versioned'] else None)
relationship = Relationship('subsumes', source, target)
schema = RelationshipSchema()
return [json.dumps(schema.dump(relationship))]
def test_to_relationship():
"A record is converted to an index"
rec = ['target', 'source']
idx = 1
relationship = _to_relationship(rec, idx, equivalence='subsumes')
eq_(
relationship,
Relationship(
equivalence='subsumes',
source=Coding(system="http://www.broadinstitute.org/gsea/msigdb",
code='source',
display='source'),
target=Coding(system="http://www.broadinstitute.org/gsea/msigdb",
code='target',
display='target')))
def _to_coding(term, system):
"""Converts a term into a `Coding`.
Args:
term: A `pronto.Term`
Returns:
a `termlink.models.Coding`
"""
_id = term.id
if ':' in _id:
if _id.endswith(':') and validators.url(_id[:-1]):
system = _id[:-1]
code = None
else:
parts = _id.rsplit(':', 1)
if validators.url(parts[0]):
system = parts[0]
code = parts[1]
else:
system = system
code = parts[1]
else:
system = system
code = _id
return Coding(system=system, code=code, display=term.name)
def test_to_json():
"""Checks that a source, equivalence and target and properly converted"""
system = "http://snomed.info/sct"
source = Term(id='SNOMEDCT_US:735938006', name='Acute headache')
equivalence = 'subsumes'
target = Term(id='SNOMEDCT_US:25064002', name='Headache')
res = _to_relationship(source, equivalence, target, system)
exp = Relationship(equivalence='subsumes',
source=Coding(system=system,
code='735938006',
display='Acute headache'),
target=Coding(system=system,
code='25064002',
display='Headache'))
eq_(exp, res)
def test_to_relationship():
"""Checks that a source, equivalence and target and properly converted"""
source = Term(id='HP:0000107', name='Renal cyst')
equivalence = 'subsumes'
target = Term(id='HP:0000003', name='Multicystic kidney dysplasia')
res = _to_relationship(source, equivalence, target)
exp = Relationship(
equivalence='subsumes',
source=Coding(system='http://www.human-phenotype-ontology.org/',
code='0000107',
display='Renal cyst'),
target=Coding(system='http://www.human-phenotype-ontology.org/',
code='0000003',
display='Multicystic kidney dysplasia'))
eq_(exp, res)
def test_to_coding_without_colon():
"""Checks that a term without a ':' is properly converted"""
system = "http://snomed.info/sct"
term = Term(id='25064002', name='Headache')
res = _to_coding(term, system)
exp = Coding(system=system, code='25064002', display='Headache')
eq_(exp, res)
def test_to_coding_with_system_and_code():
"""Checks that a term with a system and code identifier is properly converted"""
system = "http://snomed.info/sct"
term = Term(id='http://snomed.info/sct:25064002', name='Headache')
res = _to_coding(term, system)
exp = Coding(system=system, code='25064002', display='Headache')
eq_(exp, res)
def test_to_coding_with_system():
"""Checks that a term with a system identifier is properly converted"""
system = "http://snomed.info/sct"
term = Term(id='http://snomed.info/sct:', name='SNOMED-CT')
res = _to_coding(term, system)
exp = Coding(system=system, display='SNOMED-CT')
eq_(exp, res)
def test_to_coding():
"""Checks that a term is properly converted to a coding"""
term = Term(id='HP:0000001', name='All')
res = _to_coding(term)
exp = Coding(system='http://www.human-phenotype-ontology.org/',
code='0000001',
display='All')
ok_(exp == res)
def _to_coding(term):
"""Converts a term into a `Coding`.
Args:
term: A `pronto.Term`
Returns:
a `termlink.models.Coding`
"""
(abbreviation, code) = term.id.split(':')
return Coding(system=_to_system(abbreviation),
code=code,
display=term.name)
def _to_relationship(rec, index, equivalence='subsumes'):
"""
Convert record in table to Relationship as a JSON object
Record is expected to have the following fields: [ source.CODE, source.STR,
target.CODE, target.STR]
Args:
rec: A table record
Returns:
A new record containing a single field, which is the JSON object
"""
source = Coding(system="http://www.broadinstitute.org/gsea/msigdb",
code=rec[index],
display=rec[index])
target = Coding(system="http://www.broadinstitute.org/gsea/msigdb",
code=rec[0],
display=rec[0])
return Relationship(equivalence, source, target)
def _to_relationship(rec):
"""Convert record in table to `Relationship`
Record is expected to have the following fields: [source.CODE, source.STR, source.SAB, target.CODE, target.STR, target.SAB]
Args:
rec: A table record
Returns:
A `Relationship`
"""
equivalence = _to_equivalence(rec['REL'])
source = Coding(system=_to_system(rec['source.SAB']),
code=rec['source.CODE'],
display=rec['source.STR'])
target = Coding(system=_to_system(rec['target.SAB']),
code=rec['target.CODE'],
display=rec['target.STR'])
return Relationship(equivalence, source, target)
def test_convert_relationship_to_json():
"""Checks converting `Relationship` to JSON"""
equivalence = 'equivalence'
system = 'system'
version = 'version'
code = 'code'
display = 'display'
source = Coding(system=system, version=version, code=code, display=display)
target = Coding(system=system, version=version, code=code, display=display)
relationship = Relationship(equivalence, source, target)
exp = {
'equivalence': equivalence,
'source': {
'type': 'coding',
system: system,
version: version,
code: code,
display: display
},
'target': {
'type': 'coding',
system: system,
version: version,
code: code,
display: display
}
}
schema = RelationshipSchema()
res = schema.dump(relationship)
eq_(exp, res)
def test_convert_empty_coding_to_json():
"""Checks converting `Coding` with no values to JSON"""
coding = Coding()
exp = {
'type': 'coding',
'system': None,
'version': None,
'code': None,
'display': None
}
schema = CodingSchema()
res = schema.dump(coding)
eq_(exp, res)
def test_convert_partial_coding_to_json():
"""Checks converting `Coding` with some values to JSON"""
system = 'system'
coding = Coding(system=system)
exp = {
'type': 'coding',
'system': system,
'version': None,
'code': None,
'display': None
}
schema = CodingSchema()
res = schema.dump(coding)
eq_(exp, res)
def test_convert_coding_to_json():
"""Checks converting `Coding` to JSON"""
system = 'system'
version = 'version'
code = 'code'
display = 'display'
coding = Coding(system=system, version=version, code=code, display=display)
exp = {
'type': 'coding',
'system': system,
'version': version,
'code': code,
'display': display
}
schema = CodingSchema()
res = schema.dump(coding)
eq_(exp, res)