rmzTabM object creation.R

library(httr)
library(rmzTabM)
library(xcms)
library(faahKO)
data(faahko3)

faahkoMzTab <- rmzTabM::MzTab$new(
  metadata=Metadata$new(
    'mzTab-version' = "2.2.0-M",
    'mzTab-ID' = "faahKO",
    # title = "faahKO",
    # description = "faahKO",
    # sample_processing = "Just do it",
    # instrument = "Some TripleQ",
    software=list(Software$new(id=1, parameter=Parameter$new(id=1, cv_label="MS", cv_accession="MS:4711", name="xcms", value="3.1.1"), setting = "bla")),
    assay=mapply(function(id, name) Assay$new(id=id, name=name), seq(1,nrow(pData(faahko3))), pData(faahko3)$sample_name),
    sample=mapply(function(id, name) Sample$new(id=id, name=name), seq(1,nrow(pData(faahko3))), pData(faahko3)$sample_name),
    ms_run=mapply(function(id, location) MsRun$new(id=id, location=location), seq(1,nrow(pData(faahko3))), processingData(faahko3)@files),
    study_variable = mapply(function(id, level, assays) StudyVariable$new(id=id, name=level, description=level, assays=assays),
                            seq(1:length(unique(phenoData(faahko3)$sample_group))),
                            unique(phenoData(faahko3)$sample_group),
                            sapply(unique(phenoData(faahko3)$sample_group), 
                                   function(group) paste("assay[", which(phenoData(faahko3)$sample_group==group), "]", sep="", collapse=" | ")) 
                            ),
    cv=list(CV$new(label="MS", full_name="PSI-MS controlled vocabulary", version="4.0.9", uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"))
  )
)

cat(faahkoMzTab$toJSONString(), file="/tmp/faahko3.mzTab.json")

url <- ("https://apps.lifs.isas.de/mztabvalidator/rest/v2/validate?level=info&maxErrors=100&semanticValidation=true")
resp <- POST(url, body = faahkoMzTab$toJSONString(), content_type_json())
content(resp)$message


## Results in: 
# [1] "JSON parse error: Missing type id when trying to resolve 
# subtype of [simple type, class de.isas.mztab2.model.Software]: 
# missing type id property 'elementType' (for POJO property 'software'); 

What happens if you use
SoftwareAllOf$new instead of Software$new? I think SoftwareAllOf is needed, because it is the specialization class of Software and IndexedElement.
https://gist.github.com/sneumann/0f0d22027eda4db8ab28175de06b77f2#file-rmztabm-object-creation-r-L15

Same would apply to Assay -> AssayAllOf, Sample -> SampleAllOf, MsRun -> MsRunAllOf, StudyVariable -> StudyVariableAllOf, CV -> CVAllOf