Parameters

Parameters are in JSON format and have following structure:

filesystem

Describes the virtual filesystem that is used by the MISA++ application.

source

Determines how MISA++ imports the filesystem.

Following values are valid:

• json imports the filesystem from json-data
• directories imports the filesystem from input-directory and output-directory

input-directory

If source is directories, input data is imported from the provided directory. The folder structure must be consistent with the filesystem structure expected by the MISA++ application (see Parameter schema).

Each data folder can contain a file misa-metadata.json in JSON format that has equivalent effects to the metadata property in json-data (see below).

output-directory

If source is directories, output data is exported to the provided directory.

json-data

Imports the filesystem via the json-data property. It should be consistent with the filesystem parameter schema (see Parameter schema).

The json-data property has following structure:

imported

An object of type filesystem-entry. The external-path property must be set to a valid path.

exported

An object of type filesystem-entry. The external-path property must be set to a valid path.

filesystem-entry

external-path

Links the virtual filesystem entry to a physical filesystem location. Required for imported and exported.

Entries in children automatically link to corresponding sub-folders in the path unless external-path of the child overrides the previous definition.

children

Map from directory name to a filesystem-entry type.

metadata

Optional metadata for data import. The Parameter schema contains information about the structure of metadata.

algorithm

Parameters that are independent from sample. The structure depends on the MISA++ application. See Parameter schema for more information.

sample

Map from sample name to sample parameters. The structure of sample parameters depends on the MISA++ application. See Parameter schema for more information.

runtime

Global parameter for the MISA++ runtime. The structure of sample parameters depends on the MISA++ application. See Parameter schema for more information.

Following parameters are defined by MISA++ Core itself and are always present:

num-threads

Number of threads. Must be at least 1.

full-runtime-log

If true, a fully detailed runtime log (see Runtime log) is created. If false, only an overview is generated. Defaults to false.

request-skipping

If true, algorithms are informated that existing results should be re-used and not overwritten. Depends on the algorithm implementation. Defaults to false.