vanheeringen-lab/peaksql

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Merge pull request #18 from vanheeringen-lab/develop #198
Maarten-vd-Sande authored 27297c46
complete00:00:10
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I, [2024-10-31T07:01:11.813252 #1]  INFO -- : Skipping file ./peaksql/datasets/narrowpeak.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
    database: str,
            ^
SyntaxError: invalid syntax


I, [2024-10-31T07:01:11.822100 #1]  INFO -- : Skipping file ./peaksql/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 7
    def _nuc_to_onehot_idx(nuc: int) -> int:
                              ^
SyntaxError: invalid syntax


I, [2024-10-31T07:01:11.827346 #1]  INFO -- : Skipping file ./peaksql/datasets/bedregion.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
    database: str,
            ^
SyntaxError: invalid syntax


I, [2024-10-31T07:01:11.836333 #1]  INFO -- : Skipping file ./peaksql/datasets/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 21
    def __init__(self, database: str, where: str = "", seq_length: int = 200, **kwargs):
                               ^
SyntaxError: invalid syntax


I, [2024-10-31T07:01:11.841808 #1]  INFO -- : Skipping file ./peaksql/datasets/bed.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
    SELECT_LABEL: str
                ^
SyntaxError: invalid syntax


I, [2024-10-31T07:01:11.858720 #1]  INFO -- : Skipping file ./peaksql/database.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 __init__(self, db: str = "PeakSQL.sqlite", in_memory: bool = False):
                         ^
SyntaxError: invalid syntax


I, [2024-10-31T07:01:11.870341 #1]  INFO -- : Skipping file ./peaksql/tables.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 49
    f"BedVirtual USING rtree("
                             ^
SyntaxError: invalid syntax