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migraf/fhir-kindling

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bump version #249
Michael Graf authored ebad3bfe
complete00:00:13
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1
git clone
2
codeclimate validate-config
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codeclimate validate-config
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3
codeclimate prepare
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codeclimate prepare
4
builder pull-engines
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determining required images
5
structure
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12
Parser process id: 12
codeclimate-parser socket not present
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6
duplication
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12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
I, [2024-10-27T23:58:40.006779 #1]  INFO -- : Skipping file ./benchmarks/benchmark_clients.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 18
    def generate_data(server_address: str, n_patients: int, results: dict):
                                    ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.022464 #1]  INFO -- : Skipping file ./benchmarks/benchmark_servers.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 21
    print(f"initializing Server {s['name']} -- {s['api_address']}")
                                                                 ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.036261 #1]  INFO -- : Skipping file ./testing/prefill.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 18
    server_1: str,
            ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.049720 #1]  INFO -- : Skipping file ./fhir_kindling/figures/summary.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 6
    def server_summary_plot(server_summary: ServerSummary, show: bool = True) -> dict:
                                          ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.059717 #1]  INFO -- : Skipping file ./fhir_kindling/figures/resource_plots.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 9
    resources: List[Resource],
             ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.070988 #1]  INFO -- : Skipping file ./fhir_kindling/generators/patient.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 22
    n: int,
     ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.073234 #1]  INFO -- : Skipping file ./fhir_kindling/generators/field_generator.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 8
    field: str
         ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.082879 #1]  INFO -- : Skipping file ./fhir_kindling/generators/time_series_generator.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 35
    resource_generator: ResourceGenerator
                      ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.084538 #1]  INFO -- : Skipping file ./fhir_kindling/generators/base.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 7
    resource: Resource
            ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.094339 #1]  INFO -- : Skipping file ./fhir_kindling/generators/resource_generator.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 14
    field: str
         ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.106450 #1]  INFO -- : Skipping file ./fhir_kindling/generators/dataset.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 28
    name: str
        ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.108535 #1]  INFO -- : Skipping file ./fhir_kindling/util/date_utils.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 5
    def format_date(date: datetime) -> str:
                        ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.118037 #1]  INFO -- : Skipping file ./fhir_kindling/util/resources.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 10
    resource: Union[Resource, ResourceType, str, Type[FHIRAbstractModel]]
            ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.120259 #1]  INFO -- : Skipping file ./fhir_kindling/util/references.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 11
    def extract_references(resource: Resource) -> List[Tuple[str, str, str, bool]]:
                                   ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.132169 #1]  INFO -- : Skipping file ./fhir_kindling/util/retry_transport.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 19
    wrapped_transport: Union[httpx.BaseTransport, httpx.AsyncBaseTransport],
                     ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.141273 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_server/server_responses.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 12
    def _process_location_header(server_create_response: dict):
                                                       ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.144093 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_server/fhir_server.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 41
    api_address: str,
               ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.153205 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_server/summary.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 16
    resource: str
            ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.156048 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_server/transactions.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 23
    transaction_type: TransactionType = TransactionType.TRANSACTION,
                    ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.165709 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_server/transfer.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 24
    source: "FhirServer",
          ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.169968 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_server/auth.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 8
    def load_environment_auth_vars() -> tuple:
                                     ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.181479 #1]  INFO -- : Skipping file ./fhir_kindling/privacy/k_anonymity.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 9
    df: pd.DataFrame,
      ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.193005 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_query/query_async.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 24
    base_url: str,
            ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.200729 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_query/query_parameters.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 34
    def check_url_param_primitives(value: str) -> Union[int, float, bool, str]:
                                        ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.204431 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_query/base.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 27
    base_url: str,
            ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.215826 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_query/query_response.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 33
    resource_type: str
                 ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.223753 #1]  INFO -- : Skipping file ./fhir_kindling/fhir_query/query_sync.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 24
    base_url: str,
            ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.234939 #1]  INFO -- : Skipping file ./fhir_kindling/serde/flatten.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 12
    resources: Union[List[FHIRResourceModel], List[FHIRAbstractModel]] = None,
             ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.238347 #1]  INFO -- : Skipping file ./fhir_kindling/serde/json.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 9
    resource: Union[Resource, FHIRAbstractModel] = None, json_dict: dict = None
            ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.249715 #1]  INFO -- : Skipping file ./fhir_kindling/benchmark/data.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 22
    def generate_benchmark_data(n_patients: int = N_BASE_RESOURCES) -> DatasetGenerator:
                                          ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.258414 #1]  INFO -- : Skipping file ./fhir_kindling/benchmark/bench.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 31
    steps: List[BenchmarkOperations]
         ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.261051 #1]  INFO -- : Skipping file ./fhir_kindling/benchmark/figures.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 10
    def plot_benchmark_results(results: "BenchmarkResults") -> go.Figure:
                                      ^
SyntaxError: invalid syntax


I, [2024-10-27T23:58:40.272513 #1]  INFO -- : Skipping file ./fhir_kindling/benchmark/results.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 20
    def set_completed(self, completed: bool):
                                     ^
SyntaxError: invalid syntax