cwl_utils.cwl_v1_2_expression_refactor
======================================
.. py:module:: cwl_utils.cwl_v1_2_expression_refactor
.. autoapi-nested-parse::
CWL Expression refactoring tool for CWL v1.2 .
Attributes
----------
.. autoapisummary::
cwl_utils.cwl_v1_2_expression_refactor.EMPTY_FILE
cwl_utils.cwl_v1_2_expression_refactor.TOPLEVEL_SF_EXPR_ERROR
cwl_utils.cwl_v1_2_expression_refactor.TOPLEVEL_FORMAT_EXPR_ERROR
cwl_utils.cwl_v1_2_expression_refactor.PICKVALUE_FIRST_NON_NULL_EXPR
cwl_utils.cwl_v1_2_expression_refactor.PICKVALUE_THE_ONLY_NON_NULL_EXPR
cwl_utils.cwl_v1_2_expression_refactor.PICKVALUE_ALL_NON_NULL_EXPR
cwl_utils.cwl_v1_2_expression_refactor.PICKVALUE_ERROR
Functions
---------
.. autoapisummary::
cwl_utils.cwl_v1_2_expression_refactor.expand_stream_shortcuts
cwl_utils.cwl_v1_2_expression_refactor.escape_expression_field
cwl_utils.cwl_v1_2_expression_refactor.clean_type_ids
cwl_utils.cwl_v1_2_expression_refactor.get_expression
cwl_utils.cwl_v1_2_expression_refactor.etool_to_cltool
cwl_utils.cwl_v1_2_expression_refactor.traverse
cwl_utils.cwl_v1_2_expression_refactor.load_step
cwl_utils.cwl_v1_2_expression_refactor.generate_etool_from_expr
cwl_utils.cwl_v1_2_expression_refactor.get_input_for_id
cwl_utils.cwl_v1_2_expression_refactor.find_expressionLib
cwl_utils.cwl_v1_2_expression_refactor.replace_expr_with_etool
cwl_utils.cwl_v1_2_expression_refactor.replace_wf_input_ref_with_step_output
cwl_utils.cwl_v1_2_expression_refactor.empty_inputs
cwl_utils.cwl_v1_2_expression_refactor.example_input
cwl_utils.cwl_v1_2_expression_refactor.process_workflow_inputs_and_outputs
cwl_utils.cwl_v1_2_expression_refactor.process_workflow_reqs_and_hints
cwl_utils.cwl_v1_2_expression_refactor.process_level_reqs
cwl_utils.cwl_v1_2_expression_refactor.add_input_to_process
cwl_utils.cwl_v1_2_expression_refactor.traverse_CommandLineTool
cwl_utils.cwl_v1_2_expression_refactor.rename_step_source
cwl_utils.cwl_v1_2_expression_refactor.remove_JSReq
cwl_utils.cwl_v1_2_expression_refactor.replace_step_clt_expr_with_etool
cwl_utils.cwl_v1_2_expression_refactor.replace_clt_hintreq_expr_with_etool
cwl_utils.cwl_v1_2_expression_refactor.cltool_inputs_to_etool_inputs
cwl_utils.cwl_v1_2_expression_refactor.cltool_step_outputs_to_workflow_outputs
cwl_utils.cwl_v1_2_expression_refactor.generate_etool_from_expr2
cwl_utils.cwl_v1_2_expression_refactor.traverse_step
cwl_utils.cwl_v1_2_expression_refactor.workflow_step_to_WorkflowInputParameters
cwl_utils.cwl_v1_2_expression_refactor.replace_step_valueFrom_expr_with_etool
cwl_utils.cwl_v1_2_expression_refactor.replace_step_when_expr_with_etool
cwl_utils.cwl_v1_2_expression_refactor.traverse_workflow
Module Contents
---------------
.. py:function:: expand_stream_shortcuts(process)
Rewrite the "type: stdout" shortcut to use an explicit random filename.
.. py:function:: escape_expression_field(contents)
Escape sequences similar to CWL expressions or param references.
.. py:function:: clean_type_ids(cwltype)
Simplify type identifiers.
.. py:function:: get_expression(string, inputs, self)
Find and return a normalized CWL expression, if any.
CWL expressions in the $() form are converted to the ${} form.
.. py:function:: etool_to_cltool(etool, expressionLib = None)
Convert a ExpressionTool to a CommandLineTool.
.. py:function:: traverse(process, replace_etool, inside, skip_command_line1, skip_command_line2)
Convert the given process and any subprocesses.
.. py:function:: load_step(step, replace_etool, skip_command_line1, skip_command_line2)
If the step's Process is not inline, load and process it.
.. py:function:: generate_etool_from_expr(expr, target, no_inputs = False, self_type = None, extra_processes = None)
Convert a CWL Expression into an ExpressionTool.
.. py:function:: get_input_for_id(name, tool)
Determine the CommandInputParameter for the given input name.
.. py:function:: find_expressionLib(processes)
Return the expressionLib from the highest priority InlineJavascriptRequirement.
processes: should be in order of least important to most important
(Workflow, WorkflowStep, ... CommandLineTool/ExpressionTool)
.. py:function:: replace_expr_with_etool(expr, name, workflow, target, source, replace_etool = False, extra_process = None, source_type = None)
Modify the given workflow, replacing the expr with an standalone ExpressionTool.
.. py:function:: replace_wf_input_ref_with_step_output(workflow, name, target)
Refactor all reference to a workflow input to the specified step output.
.. py:function:: empty_inputs(process_or_step, parent = None)
Produce a mock input object for the given inputs.
.. py:function:: example_input(some_type)
Produce a fake input for the given type.
.. py:data:: EMPTY_FILE
.. py:data:: TOPLEVEL_SF_EXPR_ERROR
:value: "Input '{}'. Sorry, CWL Expressions as part of a secondaryFiles specification in a Workflow...
.. py:data:: TOPLEVEL_FORMAT_EXPR_ERROR
:value: "Input '{}'. Sorry, CWL Expressions as part of a format specification in a Workflow level input...
.. py:data:: PICKVALUE_FIRST_NON_NULL_EXPR
:value: Multiline-String
.. raw:: html
Show Value
.. code-block:: python
"""${
for (let i = 0; i < self.length; i++) {
if (self[i] !== null){
return self[i];
}
}
throw 'pickValue=first_non_null, but no non-null value found: ' + self;
}
"""
.. raw:: html
Show Value
.. code-block:: python
"""${
var found = null;
self.forEach(function(item) {
if (item !== null) {
if (found !== null) {
throw 'pickValue=the_only_non_null, but multiple non-null values found: ' + self;
} else {
found = item;
}
}
})
if (found !== null) {
return found;
}
throw 'pickValue=the_only_non_null, but no non-null value found: ' + self;
}
"""
.. raw:: html
Show Value
.. code-block:: python
"""${
var results = [];
self.forEach(function(item) {
if (item !== null){
results.push(item);
}
})
return results;
}
"""
.. raw:: html