ParamCWLFile Class Reference

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

#include <OpenMS/FORMAT/ParamCWLFile.h>

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