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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.blast.recipe.BlastRecipe

Instantiate a Blast workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Blast workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

BlastRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]

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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe

Instantiate a Bwa workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Bwa workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

BwaRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]

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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe

Instantiate a Cycles workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Cycles workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

CyclesRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]

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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe

Instantiate a Epigenomics workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Epigenomics workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

EpigenomicsRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]

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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe

Instantiate a Genome workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Genome workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

GenomeRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]

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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.montage.recipe.MontageRecipe

Instantiate a Montage workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Montage workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

MontageRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]

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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe

Instantiate a Seismology workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Seismology workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

SeismologyRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]

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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe

Instantiate a Soykb workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Soykb workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

SoykbRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]

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, **kwargs)

Bases: wfcommons.wfgen.abstract_recipe.WorkflowRecipe

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).

classmethod from_num_tasks(num_tasks: int, 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)wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe

Instantiate a Srasearch workflow recipe that will generate synthetic workflows up to the total number of tasks provided.

Parameters
  • num_tasks (int) – The upper bound for the total number of tasks in the workflow (at least 3).

  • 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.

Returns

A Srasearch workflow recipe object that will generate synthetic workflows up to the total number of tasks provided.

Return type

SrasearchRecipe

tasks_files: Dict[str, List[File]]
workflows: List[Workflow]