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CIMAC-CIDC/cidc-schemas

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Merge pull request #581 from CIMAC-CIDC/add-rna-enrichment-method #1776
crouchcd authored 24dbb928
complete00:00:13
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Your first build completed successfully!

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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
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duplication
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12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
I, [2024-04-15T11:24:22.571473 #1]  INFO -- : Skipping file ./cidc_schemas/prism/pipelines.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 RNA_GOOGLE_BUCKET_PATH_FN(trial_id: str, batch_num: int) -> str:
                                          ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.572515 #1]  INFO -- : Skipping file ./cidc_schemas/template.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 66
    target_dir: str = ANALYSIS_TEMPLATE_DIR,
              ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.583616 #1]  INFO -- : Skipping file ./cidc_schemas/prism/merger.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
    ct: dict,
      ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.584153 #1]  INFO -- : Skipping file ./cidc_schemas/prism/constants.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 59
    ASSAY_TO_FILEPATH: Dict[str, str] = {
                     ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.595935 #1]  INFO -- : Skipping file ./cidc_schemas/prism/core.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
    pointer: str,
           ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.606365 #1]  INFO -- : Skipping file ./cidc_schemas/prism/extra_metadata.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 25
    def parse_elisa(xlsx: BinaryIO) -> dict:
                        ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.607014 #1]  INFO -- : Skipping file ./cidc_schemas/util.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 load_pipeline_config_template(name: str) -> jinja2.Template:
                                          ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.617230 #1]  INFO -- : Skipping file ./cidc_schemas/json_validation.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 30
    f"Ref {schema_prop_value.split('/')[-1]}: {ref_value!r} not found within {schema_prop_value!r}"
                                                                                                  ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.617790 #1]  INFO -- : Skipping file ./cidc_schemas/utils/template_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 13
    output_folder: str,
                 ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.628378 #1]  INFO -- : Skipping file ./cidc_schemas/migrations.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
    def _follow_path(d: dict, *keys):
                      ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.629768 #1]  INFO -- : Skipping file ./cidc_schemas/cli.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
    def interface() -> argparse.Namespace:
                    ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.640686 #1]  INFO -- : Skipping file ./cidc_schemas/template_reader.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
    row_num: int
           ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.643959 #1]  INFO -- : Skipping file ./cidc_schemas/unprism.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
    trial_metadata: dict
                  ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.651930 #1]  INFO -- : Skipping file ./cidc_schemas/constants.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 17
    f"{d}/{f}".replace(f"{SCHEMA_DIR}/", "")
             ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.663139 #1]  INFO -- : Skipping file ./cidc_schemas/template_writer.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
    def row_type_from_string(maybe_type: str) -> Optional[RowType]:
                                       ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.670180 #1]  INFO -- : Skipping file ./docs/generate_docs.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 25
    root_object_pointer: str, sheet: dict
                       ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.680971 #1]  INFO -- : Skipping file ./docs/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 9
    SCHEMA_STORE: Dict[Tuple[str, bool], dict] = dict()
                ^
SyntaxError: invalid syntax


I, [2024-04-15T11:24:22.685603 #1]  INFO -- : Skipping file benchmark.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
    def profiling(run_name: str, outdir: str = "benchmark"):
                          ^
SyntaxError: invalid syntax