Missing addParameterValue in Assay

[feserm]

When building samples for the assay file, there is not option to add Parameter Values. Instead you are able to add Factor Values.

https://ipk-bit.github.io/isa4j/javadoc/de/ipk_gatersleben/bit/bi/isa4j/components/Sample.html
https://isa-specs.readthedocs.io/en/latest/isatab.html#assay-table-file

[Thyra]

Hey, Parameters are only ever attached to Processes, not Process Inputs or Outputs like Sources or Samples. Samples instead can carry Characteristics and Factors. From the link you provided:

A Sample MUST be provided as the first node in the experimental graph, indicated with the column heading Sample Name.

Protocol REF columns MUST be used to indicate Process nodes, with values referencing protocols declared in the Investigation file. The Protocol REF column MAY be qualified with Parameter Value [<parameter term>]

It is even more clear from the JSON schemas (https://isa-specs.readthedocs.io/en/latest/isajson.html#sample-schema-json):

{
    "$schema": "http://json-schema.org/draft-04/schema",
    "title" : "ISA sample schema",
    "description" : "JSON-schema representing a sample in the ISA model. A sample represents a major output resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.",
    "type": "object",
    "properties" : {
        "@id": { "type": "string", "format": "uri" },
        "name" : { "type" : "string" },
        "characteristics" : {
            "type" : "array",
            "items" :  {
                "$ref": "material_attribute_value_schema.json#"
            }
        },
        "factorValues" : {
            "type" : "array",
            "items" : {
                "$ref" : "factor_value_schema.json#"
            }
        },
        "derivesFrom": {
            "type" : "array",
            "items" : {
                "$ref": "source_schema.json#"
            }
        }
    },
    "additionalProperties": false
}

Please reopen the issue if I misunderstood you.