def handle_include(context, phenotype: PhenotypeModel):
print('include')
# ohdsi_helpers = PhenotypeDefine('OHDSIHelpers', 'include', version='1.0', alias='OHDSI')
# include OHDSIHelpers version "1.0" called OHDSI;
phenotype_def = None
previous = ''
for c in context.getChildren():
if previous == 'include':
desc = c.getText()
phenotype_def = PhenotypeDefine(desc, previous)
elif previous == 'called':
alias = c.getText()
phenotype_def['alias'] = alias
elif type(c) == nlpql_parserParser.VersionContext:
version = c.getChild(1).getText().strip('"')
phenotype_def['version'] = version
previous = c.getText()
if not phenotype.includes:
phenotype.includes = list()
phenotype.includes.append(phenotype_def)
def handle_code_system(context, phenotype: PhenotypeModel):
print('code system')
# codesystem OMOP: "http://omop.org";
# omop = PhenotypeDefine('OMOP', 'codesystem', values=['http://omop.org'])
identifier = context.getChild(1)
kv = get_identifier_pair(identifier)
if type(kv['value']) == list:
phenotype_def = PhenotypeDefine(kv['name'], 'codesystem', values=kv['value'])
else:
vals = list()
vals.append(kv['value'])
phenotype_def = PhenotypeDefine(kv['name'], 'codesystem', values=vals)
if not phenotype.code_systems:
phenotype.code_systems = list()
phenotype.code_systems.append(phenotype_def)
def handle_phenotype_name(context, phenotype: PhenotypeModel):
print('phenotype_name')
previous = ''
phenotype_def = None
for c in context.getChildren():
if previous == 'phenotype':
desc = c.getText()
phenotype_def = PhenotypeDefine(desc, previous)
elif type(c) == nlpql_parserParser.VersionContext:
version = c.getChild(1).getText().strip('"')
phenotype_def['version'] = version
previous = c.getText()
phenotype.phenotype = phenotype_def
def handle_cohort(context, phenotype: PhenotypeModel):
print('cohort')
call = get_pair_method(context.getChild(1))
name = call["name"]
library = call["method"]["library"]
funct = call["method"]["funct"]
arguments = call["method"]["arguments"]
named_arguments = call["method"]["named_arguments"]
phenotype_def = PhenotypeDefine(name, 'cohort', library=library,
funct=funct, arguments=arguments,
named_arguments=named_arguments)
if not phenotype.cohorts:
phenotype.cohorts = list()
phenotype.cohorts.append(phenotype_def)
def handle_data_model(context, phenotype: PhenotypeModel):
print('data model')
previous = ''
phenotype_def = None
for c in context.getChildren():
if previous == 'datamodel':
desc = c.getText()
phenotype_def = PhenotypeDefine(desc, previous)
elif type(c) == nlpql_parserParser.VersionContext:
version = c.getChild(1).getText().strip('"')
phenotype_def['version'] = version
previous = c.getText()
if not phenotype.data_models:
phenotype.data_models = list()
phenotype.data_models.append(phenotype_def)
def handle_document_set(context, phenotype: PhenotypeModel):
print('document set')
# documentset ProviderNotes: Clarity.createDocumentList("'Physician' OR 'Nurse' OR 'Note' OR 'Discharge Summary'");
call = get_pair_method(context.getChild(1))
name = call["name"]
library = call["method"]["library"]
funct = call["method"]["funct"]
arguments = call["method"]["arguments"]
named_arguments = call["method"]["named_arguments"]
phenotype_def = PhenotypeDefine(name, 'documentset', library=library,
funct=funct, arguments=arguments, named_arguments=named_arguments)
if not phenotype.document_sets:
phenotype.document_sets = list()
phenotype.document_sets.append(phenotype_def)
def handle_term_set(context, phenotype: PhenotypeModel):
print('term set')
# termset RigorsTerms: ["Rigors",
# "Rigoring",
# "Rigours",
# "Rigouring",
# "Chill",
# "Chills",
# "Shivers",
# "Shivering",
# "Teeth chattering"];
# Sepsis = PhenotypeDefine("Sepsis", "termset", values=['Sepsis', 'Systemic infection'])
ts = get_pair_array(context.getChild(1))
pd = PhenotypeDefine(ts["name"], "termset", values=ts["array"])
if not phenotype.term_sets:
phenotype.term_sets = list()
phenotype.term_sets.append(pd)
def handle_value_set(context, phenotype: PhenotypeModel):
print('value set')
# Sepsis = PhenotypeDefine('Sepsis', 'valueset', library='OHDSI',
# funct='getConceptSet',
# arguments=['assets/Sepsis.json'])
# valueset RigorsConcepts:OHDSI.getConceptSet("assets/RigorsConcepts.json");
call = get_pair_method(context.getChild(1))
name = call["name"]
library = call["method"]["library"]
funct = call["method"]["funct"]
arguments = call["method"]["arguments"]
phenotype_def = PhenotypeDefine(name, 'valueset', library=library,
funct=funct, arguments=arguments)
if not phenotype.value_sets:
phenotype.value_sets = list()
phenotype.value_sets.append(phenotype_def)
