Module eoap_cwlwrap

EOAP CWLWrap is a command-line utility that composes a CWL Workflow from a series of Workflow/CommandLineTool steps, defined according to Application package patterns based on data stage-in and stage-out behaviors commonly used in EO workflows, and packs it into a single self-contained CWL document.

EOAP CWLWrap is licensed under Creative Commons Attribution-ShareAlike 4.0 International.

You should have received a copy of the license along with this work. If not, see https://creativecommons.org/licenses/by-sa/4.0/.

Sub-modules

Variables

URL_SCHEMA

Functions

wrap

def wrap(
    workflows: Union[cwl_utils.parser.cwl_v1_0.Workflow, cwl_utils.parser.cwl_v1_1.Workflow, cwl_utils.parser.cwl_v1_2.Workflow, cwl_utils.parser.cwl_v1_0.CommandLineTool, cwl_utils.parser.cwl_v1_1.CommandLineTool, cwl_utils.parser.cwl_v1_2.CommandLineTool, cwl_utils.parser.cwl_v1_0.ExpressionTool, cwl_utils.parser.cwl_v1_1.ExpressionTool, cwl_utils.parser.cwl_v1_2.ExpressionTool, cwl_utils.parser.cwl_v1_2.Operation, List[Union[cwl_utils.parser.cwl_v1_0.Workflow, cwl_utils.parser.cwl_v1_1.Workflow, cwl_utils.parser.cwl_v1_2.Workflow, cwl_utils.parser.cwl_v1_0.CommandLineTool, cwl_utils.parser.cwl_v1_1.CommandLineTool, cwl_utils.parser.cwl_v1_2.CommandLineTool, cwl_utils.parser.cwl_v1_0.ExpressionTool, cwl_utils.parser.cwl_v1_1.ExpressionTool, cwl_utils.parser.cwl_v1_2.ExpressionTool, cwl_utils.parser.cwl_v1_2.Operation]]],
    workflow_id: str,
    stage_out: Union[cwl_utils.parser.cwl_v1_0.Workflow, cwl_utils.parser.cwl_v1_1.Workflow, cwl_utils.parser.cwl_v1_2.Workflow, cwl_utils.parser.cwl_v1_0.CommandLineTool, cwl_utils.parser.cwl_v1_1.CommandLineTool, cwl_utils.parser.cwl_v1_2.CommandLineTool, cwl_utils.parser.cwl_v1_0.ExpressionTool, cwl_utils.parser.cwl_v1_1.ExpressionTool, cwl_utils.parser.cwl_v1_2.ExpressionTool, cwl_utils.parser.cwl_v1_2.Operation],
    directory_stage_in: Union[cwl_utils.parser.cwl_v1_0.Workflow, cwl_utils.parser.cwl_v1_1.Workflow, cwl_utils.parser.cwl_v1_2.Workflow, cwl_utils.parser.cwl_v1_0.CommandLineTool, cwl_utils.parser.cwl_v1_1.CommandLineTool, cwl_utils.parser.cwl_v1_2.CommandLineTool, cwl_utils.parser.cwl_v1_0.ExpressionTool, cwl_utils.parser.cwl_v1_1.ExpressionTool, cwl_utils.parser.cwl_v1_2.ExpressionTool, cwl_utils.parser.cwl_v1_2.Operation, NoneType] = None,
    file_stage_in: Union[cwl_utils.parser.cwl_v1_0.Workflow, cwl_utils.parser.cwl_v1_1.Workflow, cwl_utils.parser.cwl_v1_2.Workflow, cwl_utils.parser.cwl_v1_0.CommandLineTool, cwl_utils.parser.cwl_v1_1.CommandLineTool, cwl_utils.parser.cwl_v1_2.CommandLineTool, cwl_utils.parser.cwl_v1_0.ExpressionTool, cwl_utils.parser.cwl_v1_1.ExpressionTool, cwl_utils.parser.cwl_v1_2.ExpressionTool, cwl_utils.parser.cwl_v1_2.Operation, NoneType] = None
) -> List[Union[cwl_utils.parser.cwl_v1_0.Workflow, cwl_utils.parser.cwl_v1_1.Workflow, cwl_utils.parser.cwl_v1_2.Workflow, cwl_utils.parser.cwl_v1_0.CommandLineTool, cwl_utils.parser.cwl_v1_1.CommandLineTool, cwl_utils.parser.cwl_v1_2.CommandLineTool, cwl_utils.parser.cwl_v1_0.ExpressionTool, cwl_utils.parser.cwl_v1_1.ExpressionTool, cwl_utils.parser.cwl_v1_2.ExpressionTool, cwl_utils.parser.cwl_v1_2.Operation]]

Composes a CWL Workflow from a series of Workflow/CommandLineTool steps, defined according to Application package patterns based on data stage-in and stage-out behaviors commonly used in EO workflows, and packs it into a single self-contained CWL document.

Parameters:

Name	Type	Description	Default
`workflows`	`Process \| List[Process]`	The CWL document object model (or models, if the CWl is a `$graph`)	None
`workflow_id`	`str`	ID of the workflow	None
`stage_out`	`Workflow`	The CWL stage-out document object model	None
`directory_stage_in`	`Optional[Workflow]`	The CWL stage-in file for `Directory` derived types	None
`file_stage_in`	`Optional[Workflow]`	The CWL stage-in file for `File` derived types	None

Returns:

Type	Description
`list[Workflow]`	The composed CWL `$graph`.

wrap_locations

def wrap_locations(
    workflows: str,
    workflow_id: str,
    stage_out: str,
    directory_stage_in: Optional[str] = None,
    file_stage_in: Optional[str] = None
) -> List[Union[cwl_utils.parser.cwl_v1_0.Workflow, cwl_utils.parser.cwl_v1_1.Workflow, cwl_utils.parser.cwl_v1_2.Workflow, cwl_utils.parser.cwl_v1_0.CommandLineTool, cwl_utils.parser.cwl_v1_1.CommandLineTool, cwl_utils.parser.cwl_v1_2.CommandLineTool, cwl_utils.parser.cwl_v1_0.ExpressionTool, cwl_utils.parser.cwl_v1_1.ExpressionTool, cwl_utils.parser.cwl_v1_2.ExpressionTool, cwl_utils.parser.cwl_v1_2.Operation]]

Composes a CWL Workflow from a series of Workflow/CommandLineTool steps, defined according to Application package patterns based on data stage-in and stage-out behaviors commonly used in EO workflows, and packs it into a single self-contained CWL document.

Parameters:

Name	Type	Description	Default
`workflows`	`str`	The CWL document object model (or models, if the CWl is a `$graph`)	None
`workflow_id`	`str`	ID of the workflow	None
`stage_out`	`str`	The CWL stage-out document object model	None
`directory_stage_in`	`Optional[str]`	The CWL stage-in file for `Directory` derived types	None
`file_stage_in`	`Optional[str]`	The CWL stage-in file for `File` derived types	None

Returns:

Type	Description
`List[Process]`	The composed CWL `$graph`.

wrap_raw

def wrap_raw(
    workflows: Mapping[str, Any],
    workflow_id: str,
    stage_out: Mapping[str, Any],
    directory_stage_in: Optional[Mapping[str, Any]] = None,
    file_stage_in: Optional[Mapping[str, Any]] = None
) -> List[Union[cwl_utils.parser.cwl_v1_0.Workflow, cwl_utils.parser.cwl_v1_1.Workflow, cwl_utils.parser.cwl_v1_2.Workflow, cwl_utils.parser.cwl_v1_0.CommandLineTool, cwl_utils.parser.cwl_v1_1.CommandLineTool, cwl_utils.parser.cwl_v1_2.CommandLineTool, cwl_utils.parser.cwl_v1_0.ExpressionTool, cwl_utils.parser.cwl_v1_1.ExpressionTool, cwl_utils.parser.cwl_v1_2.ExpressionTool, cwl_utils.parser.cwl_v1_2.Operation]]

Composes a CWL Workflow from a series of Workflow/CommandLineTool steps, defined according to Application package patterns based on data stage-in and stage-out behaviors commonly used in EO workflows, and packs it into a single self-contained CWL document.

Parameters:

Name	Type	Description	Default
`workflows`	`Mapping[str, Any]`	The CWL document object model (or models, if the CWl is a `$graph`)	None
`workflow_id`	`str`	ID of the workflow	None
`stage_out`	`Mapping[str, Any]`	The CWL stage-out document object model	None
`directory_stage_in`	`Optional[Mapping[str, Any]]`	The CWL stage-in file for `Directory` derived types	None
`file_stage_in`	`Optional[Mapping[str, Any]]`	The CWL stage-in file for `File` derived types	None

Returns:

Type	Description
`List[Process]`	The composed CWL `$graph`.