Load from JSON (in a Common Workflow Language (CWL) compatible way) into the Param class. More...

#include <OpenMS/FORMAT/ParamJSONFile.h>

Collaboration diagram for ParamJSONFile:

Public Member Functions
void	store (const std::string &filename, const Param &param, const ToolInfo &tool_info) const
	Write Json file with set values. More...

void	writeToStream (std::ostream *os_ptr, const Param &param) const

Static Public Member Functions
static bool	load (const std::string &filename, Param &param)
	Read JSON file that is formatted in CWL conforming style. More...

Public Attributes
bool	flatHierarchy {}
	If set to true, all parameters will be listed on when writing the JSON file. The names will be expanded to include the nesting hierarchy. More...

Detailed Description

Load from JSON (in a Common Workflow Language (CWL) compatible way) into the Param class.

The JSON file must contain one top level mapping of param value names to actual values.
These values can be one of the following types:
    - null
    - boolean
    - int
    - long
    - float
    - double
    - string
    - a CWL style file path ({ "class": "File", "path": "./myFolder/myFile.txt" })
    - an array of these

param value names match the command line option without the leading '-'. Optionally the ':'
can be replaced with a double underscore "__".

{
    "in": {
        "class": "File",
        "path": "./myFolder/myFile.txt"
    },
    "out_prefix": "test_cwl_",
    "algorithm:threshold": 5,
    "algorithm:score_type": "ID"
}

Same file with "__" instead of ':' as the section separator.

{
    "in": {
        "class": "File",
        "path": "./myFolder/myFile.txt"
    },
    "out_prefix": "test_cwl_",
    "algorithm__threshold": 5,
    "algorithm__score_type": "ID"
}

Member Function Documentation

◆ load()

static bool load	(	const std::string &	filename,
		Param &	param
	)

static

Read JSON file that is formatted in CWL conforming style.

Parameters

filename	The file from where to read the Param object.
param	A param object with pre-filled defaults, which are updated by the values in the JSON file

Returns: returns true if file was successfully loaded; false if an unknown (non-default) parameter name was encountered in the JSON file

Exceptions

Exception::FileNotFound	is thrown if the file could not be found
Exception::ParseError	is thrown if an error occurs during parsing

◆ store()

void store	(	const std::string &	filename,
		const Param &	param,
		const ToolInfo &	tool_info
	)		const

Write Json file with set values.

Parameters

filename	The name of the file the param data structure should be stored in.
param	The param data structure that should be stored.
tool_info	unused, required for compatiblity with ParamCWLFile

Exceptions

std::ios::failure is thrown if the file could not be created

◆ writeToStream()

void writeToStream	(	std::ostream *	os_ptr,
		const Param &	param
	)		const

Member Data Documentation

◆ flatHierarchy

bool flatHierarchy {}

If set to true, all parameters will be listed on when writing the JSON file. The names will be expanded to include the nesting hierarchy.

Public Member Functions

Static Public Member Functions