wfcommons.wfchef
wfcommons.wfchef.recipes.blast.recipe
- class wfcommons.wfchef.recipes.blast.recipe.BlastRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Blast workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]
wfcommons.wfchef.recipes.bwa.recipe
- class wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Bwa workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]
wfcommons.wfchef.recipes.cycles.recipe
- class wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Cycles workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]
wfcommons.wfchef.recipes.epigenomics.recipe
- class wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Epigenomics workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]
wfcommons.wfchef.recipes.genome.recipe
- class wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Genome workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]
wfcommons.wfchef.recipes.montage.recipe
- class wfcommons.wfchef.recipes.montage.recipe.MontageRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Montage workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]
wfcommons.wfchef.recipes.seismology.recipe
- class wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Seismology workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]
wfcommons.wfchef.recipes.soykb.recipe
- class wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Soykb workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]
wfcommons.wfchef.recipes.srasearch.recipe
- class wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe(data_footprint: Optional[int] = 0, num_tasks: Optional[int] = 3, exclude_graphs: Set[str] = {}, runtime_factor: Optional[float] = 1.0, input_file_size_factor: Optional[float] = 1.0, output_file_size_factor: Optional[float] = 1.0, logger: Optional[logging.Logger] = None, base_method: wfcommons.wfchef.wfchef_abstract_recipe.BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)
Bases:
wfcommons.wfchef.wfchef_abstract_recipe.WfChefWorkflowRecipe
A Srasearch workflow recipe class for creating synthetic workflow instances.
- Parameters
data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).
num_tasks (int) – The upper bound for the total number of tasks in the workflow.
exclude_graphs (Set) –
runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.
input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.
output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.
logger (Logger) – The logger where to log information/warning or errors (optional).
- data_footprint: Optional[int]
- input_file_size_factor: Optional[float]
- logger: Optional[Logger]
- num_tasks: Optional[int]
- output_file_size_factor: Optional[float]
- runtime_factor: Optional[float]
- task_id_counter: int
- tasks_files_names: Dict[str, List[str]]