def __init__(self, text=None, coding=None, block=None):
self.text = text
self.coding = None
if coding:
self.coding = Coding(block=coding)
if block:
if "coding" in block:
self.coding = Coding(block=block.get('coding'))
self.text = block.get('text')
def __init__(self,
value=None,
unit=None,
system=None,
code=None,
block=None):
self.value = value
self.unit = unit
self.system = system
self.code = code
if block is not None:
self.value = block.get('value')
self.unit = block.get('unit')
self.system = block.get('system')
if 'code' in block:
self.code = Coding(block.get('code'))
def test_coding_block_init_multi():
c1 = Coding(block=[{
'code': 'A1',
'system': 'sys1',
'display': 'A1 Something'
}, {
'code': 'B10',
'system': 'sysL',
'display': 'Burritos'
}])
c2 = Coding(code='A1', system='sys1', display='A1 Some Other')
c3 = Coding(code='A2', system='sys1', display='A2 something')
c4 = Coding(code='A1', system='sys2', display='A1 something')
assert (c1 == 'A1')
assert (c1 == 'B10')
assert (c1 != 'A2')
assert (c1 == c2)
assert (c1 != c3)
assert (c1 != c4)
obj = c1.as_obj()
assert (len(obj) == 2)
assert (obj[0]['code'] == 'A1')
assert (obj[0]['system'] == 'sys1')
assert (obj[1]['code'] == 'B10')
assert (obj[1]['system'] == 'sysL')
def __init__(self, block):
assert block['name'] == "match"
self.equivalence = None
self.concept = None
self.source = ""
for part in block['part']:
if part['name'] == "equivalence":
self.equivalence = part['valueCode']
elif part['name'] == "concept":
self.concept = Coding(block=part['valueCoding'])
elif part['name'] == "source":
self.source = part['valueUri']
class SimpleQuantity(FhirBase):
def __init__(self,
value=None,
unit=None,
system=None,
code=None,
block=None):
self.value = value
self.unit = unit
self.system = system
self.code = code
if block is not None:
self.value = block.get('value')
self.unit = block.get('unit')
self.system = block.get('system')
if 'code' in block:
self.code = Coding(block.get('code'))
def __eq__(self, value):
"Check to see if this matches the string or another text object"
if value is None:
return False
# This is a bit more complicated. Let's assume that a real range
# can be separated by a "-"
if type(value) is str:
return self.value == float(value)
if type(value) in [int, float]:
return self.value == value
return self.value == value.value
def as_obj(self):
"Convert to generic object"
repr = {"value": self.value}
self.add_kv(repr, 'unit')
self.add_kv(repr, 'system')
if self.code:
repr['code'] = self.code.as_obj()
return repr
def test_coding_param_init():
c1 = Coding(code='A1', system='sys1', display='A1 Something')
c2 = Coding(code='A1', system='sys1', display='A1 Some Other')
c3 = Coding(code='A2', system='sys1', display='A2 something')
c4 = Coding(code='A1', system='sys2', display='A1 something')
assert (c1 == 'A1')
assert (c1 != 'A2')
assert (c1 == c2)
assert (c1 != c3)
assert (c1 != c4)
obj = c1.as_obj()
assert (obj['code'] == 'A1')
assert (obj['system'] == 'sys1')
def test_coding_param_init_as_array():
c1 = Coding(code='A1', system='sys1', display='A1 Something', is_list=True)
c2 = Coding(code='A1', system='sys1', display='A1 Some Other')
c3 = Coding(code='A2', system='sys1', display='A2 something')
c4 = Coding(code='A1', system='sys2', display='A1 something')
assert (c1 == 'A1')
assert (c1 != 'A2')
assert (c1 == c2)
assert (c1 != c3)
assert (c1 != c4)
obj = c1.as_obj()
assert (obj[0]['code'] == 'A1')
assert (obj[0]['system'] == 'sys1')
assert (len(obj) == 1)
class CodeableConcept(FhirBase):
def __init__(self, text=None, coding=None, block=None):
self.text = text
self.coding = None
if coding:
self.coding = Coding(block=coding)
if block:
if "coding" in block:
self.coding = Coding(block=block.get('coding'))
self.text = block.get('text')
def to_str(self):
if self.text:
return self.text
return self.coding.display
def __eq__(self, cc):
if self.coding:
if type(cc) is str:
return self.coding == cc
if cc.coding:
return cc.coding == self.coding
if type(cc) is str:
return self.text == cc
return self.text == cc.text
def as_obj(self):
obj = {}
self.add_kv(obj, 'text')
if self.coding:
obj['coding'] = self.coding.as_obj()
return obj
def build_entity(cls, record, get_target_id_from_record):
key = cls.get_key_components(record,
get_target_id_from_record)['identifier']
study_id = record[CONCEPT.STUDY.NAME]
biospecimen_id = get_target_id_from_record(Specimen, record)
subject_id = record[CONCEPT.PARTICIPANT.ID]
variant_id = record[CONCEPT.DISCOVERY.VARIANT.ID]
inheritance = record[CONCEPT.DISCOVERY.VARIANT.INHERITANCE]
signif = record[CONCEPT.DISCOVERY.VARIANT.SIGNIFICANCE]
entity = {
"resourceType":
DiscoveryImplication.resource_type,
"id":
get_target_id_from_record(DiscoveryImplication, record),
"meta": {
"profile": [
f"http://hl7.org/fhir/StructureDefinition/{DiscoveryImplication.resource_type}"
]
},
"identifier":
Identifier(system=cls.identifier_system, value=key,
is_list=True).as_obj(),
"status":
"final",
"category": [{
"coding":
Coding(
system=
"http://terminology.hl7.org/CodeSystem/observation-category",
code="laboratory",
is_list=True).as_obj()
}],
"code": {
"coding":
Coding(
system=
"http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
code="diagnostic-implication",
display="Diagnostic Implication",
is_list=True).as_obj()
},
"specimen":
Reference(ref=f"{Specimen.resource_type}/{biospecimen_id}",
display="Specimen").as_obj(),
"derivedFrom": [
Reference(
ref=
f"{DiscoveryVariant.resource_type}/{get_target_id_from_record(DiscoveryVariant, record)}"
).as_obj()
],
"component": []
}
if inheritance:
entity['component'].append({
"code": {
"coding":
Coding(
system=
"http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
code="mode-of-inheritance",
display="mode-of-inheritance",
is_list=True).as_obj()
},
"valueCodeableConcept": {
"coding":
Coding(
system=
"http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns",
code=inheritance,
display=inheritance,
is_list=True).as_obj()
}
})
if signif:
entity['component'].append({
"code": {
"coding":
Coding(
system="http://loinc.org",
code="53037-8",
display="Genetic variation clinical significance [Imp]",
is_list=True).as_obj()
},
"valueCodeableConcept":
add_loinc_coding(signif)
})
# If we end up wanting to apply the clinvar url as an extension, it would be like this:
# https://www.ncbi.nlm.nih.gov/clinvar/variation/{cvid}/#clinical-assertions
# cvid is what we get when we probed the NIH for the hgsvc match
return entity