def handle_tuple(context, phenotype: PhenotypeModel, define_name, final): log('tuple') obj = get_obj_context(context.getChild(0).getChild(1), to_string=True) num_children = len(context.children) op_raw_text = '' tuple_name = '{}_Step1'.format(define_name) if num_children == 2: operation = parse_operation(context.getChild(1), tuple_name, final) if operation: if not phenotype.operations: phenotype.operations = list() phenotype.operations.append(operation) op_raw_text = operation.get('raw_text') else: operation = None raw_text = ''' Tuple {} {} ''' if not operation: where = '' else: where = 'where {}'.format(op_raw_text) tuple_str = json.dumps(obj, indent=4) pe = PhenotypeEntity(tuple_name, 'define', final=final, tuple_=True, tuple_object=obj, tuple_predicate=operation, raw_text=raw_text.format(tuple_str, where), tuple_raw_text='Tuple {}'.format(tuple_str)) if not phenotype.tuples: phenotype.tuples = list() phenotype.tuples.append(pe)
def handle_operation(context, phenotype: PhenotypeModel, define_name, final): print('operation') # SepsisState = PhenotypeOperations('SepsisState', 'OR', ['onVentilator', 'hasSepsis'], final=True) # : notOperator=(NOT | BANG) expression # | expression logicalOperator expression # | predicate IS NOT? BOOL expression_context = context.getChild(1) first = expression_context.getChild(0) res = None if type(first) == nlpql_parserParser.NotOperatorContext: res = get_not_expression(expression_context, define_name, final) elif type(first) == nlpql_parserParser.ExpressionContext: res = get_logical_expression(expression_context, define_name, final) elif type(first) == nlpql_parserParser.PredicateBooleanContext: res = get_predicate_boolean(expression_context, define_name, final) elif type(first) == nlpql_parserParser.PredicateContext: res = get_predicate_expression(expression_context.getChild(0), define_name, final) if not phenotype.operations: phenotype.operations = list() if res: phenotype.operations.append(res)
def handle_operation(context, phenotype: PhenotypeModel, define_name, final): print('operation') # SepsisState = PhenotypeOperations('SepsisState', 'OR', ['onVentilator', 'hasSepsis'], final=True) # : notOperator=(NOT | BANG) expression # | expression logicalOperator expression # | predicate IS NOT? BOOL expression_context = context.getChild(1) first = expression_context.getChild(0) res = None if type(first) == nlpql_parserParser.NotOperatorContext: res = get_not_expression(expression_context, define_name, final) elif type(first) == nlpql_parserParser.ExpressionContext: res = get_logical_expression(expression_context, define_name, final) elif type(first) == nlpql_parserParser.PredicateBooleanContext: res = get_predicate_boolean(expression_context, define_name, final) elif type(first) == nlpql_parserParser.PredicateContext: res = get_predicate_expression(expression_context.getChild(0), define_name, final) if not phenotype.operations: phenotype.operations = list() if res: phenotype.operations.append(res)
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_data_entity(context, phenotype: PhenotypeModel, define_name, final): print('data entity') pe = PhenotypeEntity(define_name, 'define', final=final) call = get_method_call(context.getChild(0)) # hasSepsis = PhenotypeEntity('hasSepsis', 'define', # library='ClarityNLP', # funct='ProviderAssertion', # named_arguments={ # "termsets": ['Sepsis'], # "documentsets": [ # 'ProviderNotes', # "Radiology" # ] # }) pe["funct"] = call["funct"] pe["library"] = call["library"] named_args = call["named_arguments"] args = call["arguments"] if named_args: pe["named_arguments"] = named_args if args and len(args) > 0: pe["arguments"] = args if not phenotype.data_entities: phenotype.data_entities = list() phenotype.data_entities.append(pe)
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_data_entity(context, phenotype: PhenotypeModel, define_name, final): print('data entity') pe = PhenotypeEntity(define_name, 'define', final=final) call = get_method_call(context.getChild(0)) # hasSepsis = PhenotypeEntity('hasSepsis', 'define', # library='ClarityNLP', # funct='ProviderAssertion', # named_arguments={ # "termsets": ['Sepsis'], # "documentsets": [ # 'ProviderNotes', # "Radiology" # ] # }) pe["funct"] = call["funct"] pe["library"] = call["library"] named_args = call["named_arguments"] args = call["arguments"] if named_args: pe["named_arguments"] = named_args if args and len(args) > 0: pe["arguments"] = args if not phenotype.data_entities: phenotype.data_entities = list() phenotype.data_entities.append(pe)
def handle_phenotype_name(context, phenotype: PhenotypeModel): print('phenotype_name') previous = '' phenotype_def = None name = '' for c in context.getChildren(): if previous == 'phenotype': desc = c.getText().replace('"', '').strip() phenotype_def = PhenotypeDefine(desc, previous) name = desc elif type(c) == nlpql_parserParser.VersionContext: version = c.getChild(1).getText().strip('"') phenotype_def['version'] = version previous = c.getText() phenotype.name = name phenotype.phenotype = phenotype_def
def handle_phenotype_name(context, phenotype: PhenotypeModel): print('phenotype_name') previous = '' phenotype_def = None name = '' for c in context.getChildren(): if previous == 'phenotype': desc = c.getText().replace('"', '').strip() phenotype_def = PhenotypeDefine(desc, previous) name = desc elif type(c) == nlpql_parserParser.VersionContext: version = c.getChild(1).getText().strip('"') phenotype_def['version'] = version previous = c.getText() phenotype.name = name phenotype.phenotype = phenotype_def
def handle_operation(context, phenotype: PhenotypeModel, define_name, final): log('operation') # SepsisState = PhenotypeOperations('SepsisState', 'OR', ['onVentilator', 'hasSepsis'], final=True) # : notOperator=(NOT | BANG) expression # | expression logicalOperator expression # | predicate IS NOT? BOOL res = parse_operation(context, define_name, final) if not phenotype.operations: phenotype.operations = list() if res: phenotype.operations.append(res)
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_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_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_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_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 validate_phenotype(p_cfg: PhenotypeModel): error = None try: if not error: if not p_cfg: error = "Empty phenotype object" if not error and len(p_cfg.data_entities) == 0: error = "Must have at least one data entity (define)" if not error and len(p_cfg.operations) > 0 and len( p_cfg.data_entities) == 0: error = "Operations (define) require at least one data entity (define)" except Exception as ex: log(ex) error = ''.join(traceback.format_stack()) # Run validity and syntax checks on all expressions, ensure that only # defined names are used as variables, etc. name_list = get_all_names(p_cfg) # get raw text of all expressions KEY_RAW = 'raw_text' expression_list = [] for i, op in enumerate(p_cfg.operations): if KEY_RAW in op: # save expression index and raw text expression_list.append((i, op[KEY_RAW])) for i, expr in expression_list: # The 'parse_result' is a string of whitespace-separated expression # tokens. Invalid expressions cause an empty string to be returned. parse_result = expr_eval.parse_expression(expr, name_list) if 0 == len(parse_result): error = 'Invalid expression: {0}'.format(expr) break else: # saved the parse result for later use p_cfg.operations[i]['normalized_expr'] = parse_result if not error: return {"success": True} else: return {"success": False, "error": error}
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_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)
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)
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_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_expression(expr): has_errors = False has_warnings = False errors = [] unknown = [] p = PhenotypeModel() for child in expr.getChildren(): if type(child) == nlpql_parserParser.StatementContext: statement_members = child.getChildren() for stmt in statement_members: stmt_type = type(stmt) if not stmt_type == antlr4.tree.Tree.TerminalNodeImpl: if stmt_type == antlr4.tree.Tree.ErrorNodeImpl: has_errors = True errors.append(stmt) elif stmt_type in handlers: try: handlers[stmt_type](stmt, p) except Exception as ex: has_errors = True print(ex) traceback.print_exc(file=sys.stderr) error = ''.join(traceback.format_stack()) errors.append(error) else: has_warnings = True unknown.append(child) print('UNKNOWN child: ' + child.getText()) return { "has_warnings": has_warnings, "has_errors": has_errors, "errors": errors, "warnings": unknown, "phenotype": p, "valid": not has_errors and not has_warnings }
def handle_context(context, phenotype: PhenotypeModel): phenotype.context = context.getChild(1).getText()
def handle_description(context, phenotype: PhenotypeModel): phenotype.description = context.getChild(1).getText()
def handle_limit(context, phenotype: PhenotypeModel): limit = context.getChild(1).getText() if len(limit) > 0: phenotype.limit = int(limit)
def handle_debug(context, phenotype: PhenotypeModel): phenotype.debug = True
def handle_debug(context, phenotype: PhenotypeModel): phenotype.debug = True
def handle_limit(context, phenotype: PhenotypeModel): limit = context.getChild(1).getText() if len(limit) > 0: phenotype.limit = int(limit)
def handle_context(context, phenotype: PhenotypeModel): phenotype.context = context.getChild(1).getText()
def handle_description(context, phenotype: PhenotypeModel): phenotype.description = context.getChild(1).getText()