plugin_input_output_processing#

Classes:

`Generate_Template_Input_File`(...[, origin, ...])	Generate input file template from a minimal input file.
`Template_File`(inp)	Generate input file from inp dictionary.

Functions:

`convert_inp_to_requirements`(dictionary[, path])	Convert inp dictionary structure to requirements dictionary structure.
`extract_input_output_from_docstring`(target, ...)	Convert docstring to structured dictionary.
`is_parameter_or_output`(line[, ...])	Detection of parameters and output values in line based on presence of more than spaces_cuttoff spaces (tabs are converted to four spaces).
`process_single_line`(line, output_dict, ...)	Process single line to extract parameter/output information and comments

class pyH2A.Utilities.plugin_input_output_processing.Generate_Template_Input_File(input_file_stub, output_file, origin=False, comment=False)[source]#

Generate input file template from a minimal input file.

Parameters

input_file_stubstr: Path to input file containing workflow and analysis specifications.
output_filestr: Path to file where input template is to be written.
originbool, optional: Include origin of each requested input parameter in input template file (“requested by” information).
commentbool, optional: Include comments for each requested input parameter (additional information on parameter).

Returns

Templateobject: Template object which contains information on requirements and output. Input template is written to specified output file.

Methods:

`check_parameters`(data, output)	Check if needed parameter is in output.
`convert_requirements_to_inp`([insert_origin, ...])	Convert dictionary of requirements to formatted self.inp
`generate_requirements`()	Generate dictionary with input requirements.
`get_analysis_modules`(post_workflow_position)	Get analysis modules from input stub.
`get_docstring_data`(target_name, target_type)	Get parameter requirements and outputs from docstrings.

check_parameters(data, output)[source]#: Check if needed parameter is in output.

convert_requirements_to_inp(insert_origin=False, insert_comment=False)[source]#: Convert dictionary of requirements to formatted self.inp

generate_requirements()[source]#: Generate dictionary with input requirements.

get_analysis_modules(post_workflow_position)[source]#: Get analysis modules from input stub.

get_docstring_data(target_name, target_type)[source]#: Get parameter requirements and outputs from docstrings.

class pyH2A.Utilities.plugin_input_output_processing.Template_File(inp)[source]#

Generate input file from inp dictionary.

Parameters

inpdict: Dictionary containing information on requested input (generated by Generate_Template_Input_File)

Returns

Template_Fileobject: Object containing formatted string for output file.

Methods:

`convert_column_names_to_string`(names)	Convert list of names to markdown style table string.
`convert_inp_to_string`()	Convert inp to string.
`get_column_names`(dictionary)	Get names of table columns.
`get_row_entries`(columns, column_names, ...)	Get entries for each row of table.
`get_single_row`(column_names, column, dictionary)	Get entries for a single row.
`write_template_file`(file_name)	Write output string to file.

convert_column_names_to_string(names)[source]#: Convert list of names to markdown style table string.

convert_inp_to_string()[source]#: Convert inp to string.

get_column_names(dictionary)[source]#: Get names of table columns.

get_row_entries(columns, column_names, dictionary)[source]#: Get entries for each row of table.

get_single_row(column_names, column, dictionary)[source]#: Get entries for a single row.

write_template_file(file_name)[source]#: Write output string to file.

pyH2A.Utilities.plugin_input_output_processing.convert_inp_to_requirements(dictionary, path=None)[source]#: Convert inp dictionary structure to requirements dictionary structure.

pyH2A.Utilities.plugin_input_output_processing.extract_input_output_from_docstring(target, **kwargs)[source]#: Convert docstring to structured dictionary.

pyH2A.Utilities.plugin_input_output_processing.is_parameter_or_output(line, spaces_for_tab=4, spaces_cutoff=5)[source]#: Detection of parameters and output values in line based on presence of more than spaces_cuttoff spaces (tabs are converted to four spaces).

pyH2A.Utilities.plugin_input_output_processing.process_single_line(line, output_dict, origin, variable_string, **kwargs)[source]#: Process single line to extract parameter/output information and comments