10179980459

Committed 31 Jul 2024 12:14PM UTC coverage: 83.284%. First build

Build # 10179980459

Build Type

Pull #3487

github

Committed by

web-flow

Commit Message

Merge 2a64a106f into eec50e6da

Pull Request Pull Request #3487: add error handlers pacbio flow

Run Details

54 of 59 new or added lines in 10 files covered. (91.53%)

16766 of 20131 relevant lines covered (83.28%)

1.05 hits per line

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90.91

/cg/services/post_processing/validators.py

from pathlib import Path


def validate_name_pre_fix(run_name: str, pre_fix: str) -> None:
    if not run_name.startswith(pre_fix):
        raise ValueError(f"Run name does not start with {pre_fix}")


def validate_has_expected_parts(run_name: str, expected_parts: int) -> None:
    if len(run_name.split("/")) != expected_parts:
        raise ValueError(f"Run name does not have number of expected parts {expected_parts}.")


def validate_files_exist(files: list[Path]) -> None:
    """Validate that all files in the list exist."""
    for file in files:
        if not file.exists():
            raise FileNotFoundError(f"File {file.as_posix()} does not exist")

1	from pathlib import Path	1✔
2
3
4	def validate_name_pre_fix(run_name: str, pre_fix: str) -> None:	1✔
5	if not run_name.startswith(pre_fix):	1✔
6	raise ValueError(f"Run name does not start with {pre_fix}")	1✔
7
8
9	def validate_has_expected_parts(run_name: str, expected_parts: int) -> None:	1✔
10	if len(run_name.split("/")) != expected_parts:	1✔
11	raise ValueError(f"Run name does not have number of expected parts {expected_parts}.")	1✔
12
13
14	def validate_files_exist(files: list[Path]) -> None:	1✔
15	"""Validate that all files in the list exist."""
16	for file in files:	1✔
17	if not file.exists():	1✔
NEW 18	raise FileNotFoundError(f"File {file.as_posix()} does not exist")	×

Clinical-Genomics / cg / 10179980459

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