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Runner

Runners Module

DefaultPhEvalRunner dataclass

Bases: PhEvalRunner

DefaultPhEvalRunner

Parameters:

Name Type Description Default
PhEvalRunner PhEvalRunner

Abstract PhEvalRunnerClass

 required
Source code in src/pheval/runners/runner.py 
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class DefaultPhEvalRunner(PhEvalRunner):
    """DefaultPhEvalRunner

    Args:
        PhEvalRunner (PhEvalRunner): Abstract PhEvalRunnerClass
    """

    input_dir: Path
    testdata_dir: Path
    tmp_dir: Path
    output_dir: Path
    config_file: Path
    version: str

    def prepare(self):
        print("preparing")

    def run(self):
        print("running")

    def post_process(self):
        print("post processing")

PhEvalRunner dataclass

Bases: ABC

PhEvalRunner Class

Source code in src/pheval/runners/runner.py 
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@dataclass
class PhEvalRunner(ABC):
    """PhEvalRunner Class"""

    input_dir: Path
    testdata_dir: Path
    tmp_dir: Path
    output_dir: Path
    config_file: Path
    version: str
    directory_path = None
    input_dir_config = None
    _meta_data = None
    __raw_results_dir = "raw_results/"
    __pheval_gene_results_dir = "pheval_gene_results/"
    __pheval_variant_results_dir = "pheval_variant_results/"
    __pheval_disease_results_dir = "pheval_disease_results/"
    __tool_input_commands_dir = "tool_input_commands/"
    __run_meta_data_file = "results.yml"

    def __post_init__(self):
        self.input_dir_config = parse_input_dir_config(self.input_dir)

    def _get_tool(self):
        return self.input_dir_config.tool

    def _get_variant_analysis(self):
        return self.input_dir_config.variant_analysis

    def _get_gene_analysis(self):
        return self.input_dir_config.gene_analysis

    def _get_disease_analysis(self):
        return self.input_dir_config.disease_analysis

    @property
    def tool_input_commands_dir(self):
        return Path(self.output_dir).joinpath(self.__tool_input_commands_dir)

    @tool_input_commands_dir.setter
    def tool_input_commands_dir(self, directory_path):
        self.directory_path = Path(directory_path)

    @property
    def raw_results_dir(self):
        return Path(self.output_dir).joinpath(self.__raw_results_dir)

    @raw_results_dir.setter
    def raw_results_dir(self, directory_path):
        self.directory_path = Path(directory_path)

    @property
    def pheval_gene_results_dir(self):
        return Path(self.output_dir).joinpath(self.__pheval_gene_results_dir)

    @pheval_gene_results_dir.setter
    def pheval_gene_results_dir(self, directory_path):
        self.directory_path = Path(directory_path)

    @property
    def pheval_variant_results_dir(self):
        return Path(self.output_dir).joinpath(self.__pheval_variant_results_dir)

    @pheval_variant_results_dir.setter
    def pheval_variant_results_dir(self, directory_path):
        self.directory_path = Path(directory_path)

    @property
    def pheval_disease_results_dir(self):
        return Path(self.output_dir).joinpath(self.__pheval_disease_results_dir)

    @pheval_disease_results_dir.setter
    def pheval_disease_results_dir(self, directory_path):
        self.directory_path = Path(directory_path)

    def build_output_directory_structure(self):
        """build output directory structure"""
        logger.info(
            f"Building output directory structure for {self.input_dir_config.tool} "
            f"version {self.input_dir_config.tool_version}"
        )
        self.tool_input_commands_dir.mkdir(exist_ok=True)
        self.raw_results_dir.mkdir(exist_ok=True)
        if self._get_variant_analysis():
            self.pheval_variant_results_dir.mkdir(exist_ok=True)
        if self._get_gene_analysis():
            self.pheval_gene_results_dir.mkdir(exist_ok=True)
        if self._get_disease_analysis():
            self.pheval_disease_results_dir.mkdir(exist_ok=True)

    @property
    def meta_data(self):
        self._meta_data = BasicOutputRunMetaData(
            tool=self.input_dir_config.tool,
            tool_version=self.version,
            config=f"{Path(self.input_dir).parent.name}/{Path(self.input_dir).name}",
            run_timestamp=datetime.now().timestamp(),
            corpus=f"{Path(self.testdata_dir).parent.name}/{Path(self.testdata_dir).name}",
            mondo_download_date=get_resource_timestamp("mondo.sssom.tsv"),
            hgnc_download_date=get_resource_timestamp("hgnc_complete_set.txt"),
        )
        return self._meta_data

    @meta_data.setter
    def meta_data(self, meta_data):
        self._meta_data = meta_data

    @abstractmethod
    def prepare(self) -> str:
        """prepare"""

    @abstractmethod
    def run(self):
        """run"""

    @abstractmethod
    def post_process(self):
        """post_process"""

    def construct_meta_data(self):
        """Construct run output meta data"""
        return self.meta_data

build_output_directory_structure()

build output directory structure

Source code in src/pheval/runners/runner.py 
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def build_output_directory_structure(self):
    """build output directory structure"""
    logger.info(
        f"Building output directory structure for {self.input_dir_config.tool} "
        f"version {self.input_dir_config.tool_version}"
    )
    self.tool_input_commands_dir.mkdir(exist_ok=True)
    self.raw_results_dir.mkdir(exist_ok=True)
    if self._get_variant_analysis():
        self.pheval_variant_results_dir.mkdir(exist_ok=True)
    if self._get_gene_analysis():
        self.pheval_gene_results_dir.mkdir(exist_ok=True)
    if self._get_disease_analysis():
        self.pheval_disease_results_dir.mkdir(exist_ok=True)

construct_meta_data()

Construct run output meta data

Source code in src/pheval/runners/runner.py 
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def construct_meta_data(self):
    """Construct run output meta data"""
    return self.meta_data

post_process() abstractmethod

post_process

Source code in src/pheval/runners/runner.py 
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@abstractmethod
def post_process(self):
    """post_process"""

prepare() abstractmethod

prepare

Source code in src/pheval/runners/runner.py 
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@abstractmethod
def prepare(self) -> str:
    """prepare"""

run() abstractmethod

run

Source code in src/pheval/runners/runner.py 
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@abstractmethod
def run(self):
    """run"""