Nothing
R/MzQC_classes.R
In PTXQC: Quality Report Generation for MaxQuant and mzTab Results
Defines functions
NULL_to_NA
NULL_to_charNA
fromDatatoMzQC
isValidMzQC
isUndefined
Documented in
fromDatatoMzQC
isUndefined
isValidMzQC
NULL_to_charNA
NULL_to_NA
## some generic information on why/how/what?? :)
##
## + we provide initialize() functions for all RefClasses to enable unnamed construction (shorter syntax)
##
##
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##
##
##
# Defining this function to enable overload
# e.g. setMethod('asJSON', 'mzQC', function(x, ...) x$toJSON())
# which allows to use
# jsonlite::toJSON(mzQC$new(content))
asJSON <- jsonlite:::asJSON
#'
#' Tell if a string is undefined (NA or NULL); If yes, and its required by the mzQC standard, we can raise an error
#'
#' You can pass multiple strings, which are all checked. If any of them is undefined, the function returns TRUE
#'
#' @param s A string to be checked for NA/NULL
#' @param ... More strings to be checked
#' @param verbose If TRUE and 's' is NULL/NA, will print the name of the variable which was passed in
#'
#' @examples
#' isUndefined(NA) ## TRUE
#' isUndefined(NULL) ## TRUE
#' isUndefined(NA, NULL) ## TRUE
#' isUndefined("") ## FALSE
#' isUndefined("", NA) ## TRUE
#' isUndefined(1) ## FALSE
#' myVar = NA
#' isUndefined(myVar) ## TRUE, with warning "variable 'myVar' is NA/NULL!"
#'
#' @export
#'
isUndefined = function(s, ..., verbose = TRUE)
{
# anchor
if (missing(s)) return(FALSE)
r = (is.na(s) || is.null(s))
name_of_var = deparse(substitute(s))
# omit the '.self' part of the variable's name
name_of_var = gsub("^.self\\$", "", name_of_var)
if (verbose && r) warning(paste0("Variable '", name_of_var, "' is NA/NULL!"), immediate. = TRUE, call. = FALSE)
## check remaining args from ... by using '+' (force evaluation)
return(r + isUndefined(..., verbose = verbose) > 0)
}
#'
#' Checks validity (= completeness) of mzQC objects - or lists (JSON arrays) thereof
#'
#' Note: Returns TRUE for empty lists!
#'
#' You can pass multiple arguments, which are all checked individually.
#' All of them need to be valid, for TRUE to be returned.
#' The reason for combining list support for arguments and ellipsis (...) into this function is that
#' JSON arrays are represented as lists and you can simply pass them as a single argument
#' (without the need for do.call()) and get the indices of invalid objects (if any).
#' The ellipsis is useful to avoid clutter,
#' i.e.
#' if (!isValidMzQC(a) || !isValidMzQC(b)) doStuff()
#' is harder to read than
#' if (!isValidMzQC(a,b)) doStuff()
#'
#' @param x An mzQC refclass (or list of them), each will be subjected to `isValidMzQC()`
#' @param ... Ellipsis, for recursive argument splitting
#'
#' @examples
#' isValidMzQC(MzQCcvParameter$new("QC:4000059")) # FALSE
#' isValidMzQC(MzQCcvParameter$new("QC:4000059", "Number of MS1 spectra")) # TRUE
#' isValidMzQC(list(MzQCcvParameter$new("QC:4000059"))) # FALSE
#' isValidMzQC(list(MzQCcvParameter$new("QC:4000059", "Number of MS1 spectra"))) # TRUE
#' isValidMzQC(list(MzQCcvParameter$new("QC:4000059", "Number of MS1 spectra")),
#' MzQCcvParameter$new()) # FALSE
#'
#' @export
#'
isValidMzQC = function(x, ...)
{
# anchor
if (missing(x)) return(TRUE)
if (inherits(x, "list")) {
idx = sapply(x, isValidMzQC)
if (any(idx == FALSE)) {
warning(paste0("In list of '", class(x[[1]]), "', the element(s) #[", paste(which(idx == FALSE), collapse = ","), "] is/are invalid."), immediate. = TRUE, call. = FALSE)
}
return(all(idx) & isValidMzQC(...))
}
r = x$isValid()
if (r == FALSE)
{
warning(paste0("A field in object of type ", class(x), " is invalid."), immediate. = TRUE, call. = FALSE)
}
return(r & isValidMzQC(...))
}
#'
#' Allow conversion of plain named lists to mzQC objects
#'
#' The plain-R representation of your mzQC objects must be wrapped in an outer list,
#' if your mzQC object representation is already a list
#' because upon detecting lists, this function will call 'class$fromData(element)' for every element.
#'
#' @param mzqc_class Prototype of the class to convert 'data' into
#' @param data A datastructure of R lists/arrays as obtained by 'jsonlite::fromJSON()'
#'
#' @examples
#' data = MzQCcvParameter$new("acc", "myName", "value")
#' data_recovered = fromDatatoMzQC(MzQCcvParameter, list(jsonlite::fromJSON(jsonlite::toJSON(data))))
#' data_recovered
#'
#' @export
#'
fromDatatoMzQC = function(mzqc_class, data)
{
if (inherits(data, "list"))
{
return(sapply(data, function(x) {
obj = mzqc_class$new()
obj$fromData(x)
obj
}))
}
if (is.na(data) || is.null(data)) return(list())
obj = mzqc_class$new()
return(obj$fromData(data))
}
#'
#' converts a NULL to NA_character_; or returns the argument unchanged otherwise
#'
#' This is useful for missing list elements (which returns NULL),
#' but when the missing element in refClass should be NA_character_ (and NULL would return an error)
#'
#' @param char_or_NULL A string or NULL
#'
#' @examples
#' NULL_to_charNA(NA) ## NA
#' NULL_to_charNA(NULL) ## NA_character_
#' NULL_to_charNA("hi") ## "hi"
#'
#' @export
#'
NULL_to_charNA = function(char_or_NULL) {
if (is.null(char_or_NULL)) return(NA_character_)
return(char_or_NULL)
}
#'
#' converts a NULL to NA; or returns the argument unchanged otherwise
#'
#' This is useful for missing list elements (which returns NULL),
#' but when the missing element in refClass should be NA (and NULL would return an error)
#'
#' @param var_or_NULL A variable of any kind or NULL
#'
#' @examples
#' NULL_to_NA(NA) ## NA
#' NULL_to_NA(NULL) ## NA
#' NULL_to_NA("hi") ## "hi"
#'
#' @export
#'
NULL_to_NA = function(var_or_NULL) {
if (is.null(var_or_NULL)) return(NA)
return(var_or_NULL)
}
#'
#' An mzQC-formatted date+time, as required by the mzQC spec doc
#'
#' The format is "%Y-%m-%d %H:%M:%S".
#'
#' @field datetime A correctly formatted date time (use as read-only)
#'
#' @exportClass MzQCDateTime
#' @export MzQCDateTime
#'
#' @examples
#' dt1 = MzQCDateTime$new("1900-01-01")
#' dt2 = MzQCDateTime$new(Sys.time())
#' ## test faulty input
#' ## errors with 'character string is not in a standard unambiguous format'
#' try(MzQCDateTime$new('lala'), silent=TRUE)
#' ## test roundtrip conversion from/to JSON
#' dt2$fromData(jsonlite::fromJSON(jsonlite::toJSON(dt1)))
# dt1$datetime == dt2$datetime ## TRUE
#'
#' @export
#'
MzQCDateTime = setRefClass(
'MzQCDateTime',
fields = list(datetime = 'character'),
methods = list(
initialize = function(date = as.character(Sys.time()))
{
set(date)
},
set = function(.self, date)
{
.self$datetime = format(as.POSIXct(date), "%Y-%m-%dT%H:%M:%S") # using ISO8601 format
},
isValid = function(.self)
{
return(TRUE) ## always valid, because it's designed that way
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
return(jsonlite:::asJSON(.self$datetime, ...))
},
fromData = function(.self, data)
{
.self$set(data)
}
)
)
setMethod('asJSON', 'MzQCDateTime', function(x, ...) x$toJSON(...))
#'
#' An controlled vocabulary document, usually pointing to an .obo file
#'
#' @field name Full name of the controlled vocabulary.
#' @field uri Publicly accessible URI of the controlled vocabulary.
#' @field version [optional] Version of the controlled vocabulary.
#'
#' @export MzQCcontrolledVocabulary
#'
#' @examples
#' MzQCcontrolledVocabulary$new(
#' "Proteomics Standards Initiative Quality Control Ontology",
#' "https://github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo",
#' "1.2.0")
#'
#' @export
#'
MzQCcontrolledVocabulary = setRefClass(
'MzQCcontrolledVocabulary',
fields = list(name = 'character',
uri = 'character',
version = 'character' # optional
),
methods = list(
initialize = function(name = NA_character_, uri = NA_character_, version = NA_character_)
{
.self$name = name
.self$uri = uri
.self$version = version
},
isValid = function(.self) {
if (isUndefined(.self$name, .self$uri)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("name" = .self$name,
"uri" = .self$uri,
"version" = .self$version)
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$name = data$name
.self$uri = data$uri
.self$version = NULL_to_charNA(data$version)
}
)
)
setMethod('asJSON', 'MzQCcontrolledVocabulary', function(x, ...) x$toJSON(...))
#'
#' An controlled vocabulary parameter, as detailed in the OBO file
#'
#' @field accession Accession number identifying the term within its controlled vocabulary (pattern: ^[A-Z]+:[A-Z0-9]+$).
#' @field name Name of the controlled vocabulary term describing the parameter.
#' @field value [optional] Value of the parameter.
#' @field description [optional] Definition of the controlled vocabulary term.
#'
#' @export MzQCcvParameter
#'
#' @examples
#' MzQCcvParameter$new("QC:4000139",
#' "RT acquisition range",
#' c(0.2959, 5969.8172))
#' isValidMzQC(MzQCcvParameter$new("MS:0000000"))
#'
#' @export
#'
MzQCcvParameter = setRefClass(
'MzQCcvParameter',
fields = list(accession = 'character',
name = 'character',
value = 'ANY', # optional
description = 'character' # optional
),
methods = list(
initialize = function(accession = NA_character_, name = NA_character_, value = NA, description = NA_character_)
{
.self$accession = accession
.self$name = name
.self$value = value
.self$description = description
},
isValid = function(.self) {
if (isUndefined(.self$accession, .self$name)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("accession" = .self$accession,
"name" = .self$name)
if (!is.na(.self$description)) r["description"] = .self$description
if (!is.na(.self$value)) r["value"] = .self$value
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$accession = data$accession
.self$name = data$name
.self$description = NULL_to_charNA(data$description)
.self$value = NULL_to_NA(data$value)
}
)
)
setMethod('asJSON', 'MzQCcvParameter', function(x, ...) x$toJSON(...))
#'
#' An inputfile within metadata for a run/setQuality
#'
#' @field name The name MUST uniquely match to a location (specified below) listed in the mzQC file.
#' @field location Unique file location, REQUIRED to be specified as a URI. The file URI is RECOMMENDED to be publicly accessible.
#' @field fileFormat A MzQCcvParameter with 'accession' and 'name'.
#' @field fileProperties An array of MzQCcvParameter, usually with 'accession', 'name' and 'value'. Recommended are at least two entries:
#' a) Completion time of the input file (MS:1000747) and b) Checksum of the input file (any child of: MS:1000561 ! data file checksum type).
#'
#' @export MzQCinputFile
#'
#'
#' @export
#'
MzQCinputFile = setRefClass(
'MzQCinputFile',
fields = list(name = 'character',
location = 'character',
fileFormat = 'MzQCcvParameter',
fileProperties = 'list' # array of MzQCcvParameter, optional
),
methods = list(
# defaults are required, otherwise refClasses do not work.
initialize = function(name = NA_character_, location = NA_character_, fileFormat = MzQCcvParameter$new(), fileProperties = list())
{
.self$name = name
.self$location = location
.self$fileFormat = fileFormat
.self$fileProperties = fileProperties
},
isValid = function(.self)
{
# force evaluation of all fields by '+'
if (isUndefined(.self$name, .self$location) + !.self$fileFormat$isValid()) return(FALSE)
return(isValidMzQC(.self$fileProperties)) ## TRUE for empty list, which is ok
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list(name = .self$name, location = .self$location, fileFormat = .self$fileFormat)
if (length(.self$fileProperties) > 0) r$fileProperties = .self$fileProperties
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$name = data$name
.self$location = data$location
.self$fileFormat$fromData(data$fileFormat)
.self$fileProperties = fromDatatoMzQC(MzQCcvParameter, data$fileProperties) ## for lists, call the free function
}
)
)
setMethod('asJSON', 'MzQCinputFile', function(x, ...) x$toJSON(...))
#
# file_format = MzQCcvParameter$new("MS:1000584", "mzML format")
# nif = MzQCinputFile$new("tmp.mzML", "c:\\", file_format)
# nif
# nif2 = nif
# l2 = list(file_format, file_format)
# nif2$fileProperties = l2
# x = jsonlite::toJSON(nif, pretty = TRUE)
# x
# x2 = jsonlite::toJSON(nif2)
# xdata = jsonlite::fromJSON(x, simplifyDataFrame = FALSE)
# xdata
# inherits(fromDatatoMzQC(MzQCcvParameter, xdata$fileProperties), "list")
# jsonlite::toJSON(xdata, pretty = TRUE, auto_unbox = T)
# isValidMzQC(l2)
# nif$fromData(xdata)
#'
#' Details of the software used to create the QC metrics
#'
#' @field accession Accession number identifying the term within its controlled vocabulary (pattern: ^[A-Z]+:[A-Z0-9]+$).
#' @field name Name of the controlled vocabulary term describing the software tool.
#' @field version Version number of the software tool.
#' @field uri Publicly accessible URI of the software tool or documentation.
#' @field description [optional] Definition of the controlled vocabulary term.
#' @field value [optional] Value of the software tool.
#'
#' @export MzQCanalysisSoftware
#'
#'
#' @export
#'
MzQCanalysisSoftware = setRefClass(
'MzQCanalysisSoftware',
fields = list(accession = 'character',
name = 'character',
version = 'character',
uri = 'character',
description = 'character', # optional
value = 'character' # optional
),
methods = list(
# defaults are required, otherwise refClasses do not work.
initialize = function(accession = NA_character_,
name = NA_character_,
version = NA_character_,
uri = NA_character_,
description = NA_character_, ## optional
value = NA_character_ ## optional
)
{
.self$accession = accession
.self$name = name
.self$version = version
.self$uri = uri
.self$description = description
.self$value = value
},
isValid = function(.self)
{
if (isUndefined(.self$accession, .self$name, .self$version, .self$uri)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("accession" = .self$accession,
"name" = .self$name,
"version" = .self$version,
"uri" = .self$uri)
if (!isUndefined(.self$description)) r$description = .self$description
if (!isUndefined(.self$value)) r$value = .self$value
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$accession = data$accession
.self$name = data$name
.self$version = data$version
.self$uri = data$uri
.self$description = NULL_to_charNA(data$description)
.self$value = NULL_to_charNA(data$value)
}
)
)
setMethod('asJSON', 'MzQCanalysisSoftware', function(x, ...) x$toJSON(...))
#'
#'The metadata for a run/setQuality
#'
#' @field label Unique name for the run (for runQuality) or set (for setQuality).
#' @field inputFiles Array/list of MzQCinputFile objects
#' @field analysisSoftware Array/list of MzQCanalysisSoftware objects
#' @field cvParameters [optional] Array of cvParameters objects
#'
#' @export MzQCmetadata
#'
#' @export
#'
MzQCmetadata = setRefClass(
'MzQCmetadata',
fields = list(label = 'character',
inputFiles = 'list', # array of MzQCinputFile
analysisSoftware = 'list', # array of MzQCanalysisSoftware
cvParameters = 'list' # optional array of MzQCcvParameter
),
methods = list(
initialize = function(label = NA_character_, inputFiles =list(), analysisSoftware = list(), cvParameters = list())
{
.self$label = label
.self$inputFiles = inputFiles
.self$analysisSoftware = analysisSoftware
.self$cvParameters = cvParameters
},
isValid = function(.self)
{
# force evaluation of all fields by '+'
if (isUndefined(.self$label) + !isValidMzQC(.self$inputFiles, .self$analysisSoftware, .self$cvParameters)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("label" = .self$label,
"inputFiles" = .self$inputFiles,
"analysisSoftware" = .self$analysisSoftware)
## only add if present (otherwise leads to 'cvParameters = []')
if (length(.self$cvParameters) > 0 ) r$cvParameters = list(.self$cvParameters) ## extra list for the enclosing '[ ... ]'
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$label = data$label
.self$inputFiles = fromDatatoMzQC(MzQCinputFile, data$inputFiles)
.self$analysisSoftware = fromDatatoMzQC(MzQCanalysisSoftware, data$analysisSoftware)
.self$cvParameters = fromDatatoMzQC(MzQCcvParameter, data$cvParameters)
}
)
)
setMethod('asJSON', 'MzQCmetadata', function(x, ...) x$toJSON(...))
################################################################################################################################
#################################################################################################################################'
#' The central class to store QC information
#'
#' @field accession Accession number identifying the term within its controlled vocabulary (pattern: ^[A-Z]+:[A-Z0-9]+$).
#' @field name Name of the controlled vocabulary element describing the metric.
#' @field description [optional] Definition of the controlled vocabulary term.
#' @field value [optional] Value of the metric (single value, n-tuple, table, matrix).
#' The structure is not checked by our mzQC implementation and must be handled by the caller
#' @field unit [optional] Array of unit(s), stored as MzQcvParameter
#'
#' @export MzQCqualityMetric
#'
MzQCqualityMetric = setRefClass(
'MzQCqualityMetric',
fields = list(accession = 'character',
name = 'character',
description = 'character', # optional
value = 'ANY', # optional value of unspecified type
unit = 'list' # optional array of MzQCcvParameter
),
methods = list(
initialize = function(accession = NA_character_, name = NA_character_, description = NA_character_, value = NA, unit = list())
{
.self$accession = accession
.self$name = name
.self$description = description
if (!missing(value)) .self$value = value else .self$value = NA ## need to set as NA explicitly, because the default value 'uninitialized class ANY' cannot be converted to JSON
.self$unit = unit
},
isValid = function(.self)
{
if (isUndefined(.self$accession, .self$name)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("accession" = .self$accession,
"name" = .self$name,
"description" = .self$description,
"value" = .self$value ## NA is written as "value": [null] and read back as NA
)
if (length(.self$unit) > 0) r$unit = .self$unit ## optional
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$accession = data$accession
.self$name = data$name
.self$description = NULL_to_charNA(data$description)
if (!is.na(data$value)) .self$value = data$value
.self$unit = fromDatatoMzQC(MzQCcvParameter, data$unit) ## if data$unit is empty, or NA, the empty list will be returned
}
)
)
setMethod('asJSON', 'MzQCqualityMetric', function(x, ...) x$toJSON(...))
#a_qc_metric = MzQCqualityMetric$new("acc", "nnam")
#xq = jsonlite::toJSON(a_qc_metric)
#jsonlite::fromJSON(xq)
#'
#' Base class of runQuality/setQuality
#'
#' @field metadata The metadata for this run/setQuality
#' @field qualityMetrics Array of MzQCqualityMetric objects
#'
#' @export MzQCbaseQuality
#'
#'
MzQCbaseQuality = setRefClass(
'MzQCbaseQuality',
fields = list(metadata = 'MzQCmetadata',
qualityMetrics = 'list'), # array of MzQCqualityMetric
methods = list(
initialize = function(metadata = MzQCmetadata$new(), qualityMetrics = list())
{
.self$metadata = metadata
.self$qualityMetrics = qualityMetrics
},
isValid = function(.self)
{
if (!isValidMzQC(.self$metadata, .self$qualityMetrics)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("metadata" = .self$metadata,
"qualityMetrics" = .self$qualityMetrics)
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$metadata = data$metadata
.self$qualityMetrics = fromDatatoMzQC(MzQCbaseQuality, data$qualityMetrics) ## if data$qualityMetrics is empty, or NA, the empty list will be returned
}
)
)
setMethod('asJSON', 'MzQCbaseQuality', function(x, ...) x$toJSON(...))
MzQCrunQuality = setRefClass(
"MzQCrunQuality",
contains = "MzQCbaseQuality"
)
MzQCsetQuality = setRefClass(
"MzQCsetQuality",
contains = "MzQCbaseQuality"
)
###########################################################################
#' Root element of an mzQC document
#'
#' At least one of runQualities or setQualities MUST be present.
#'
#' @field version Version of the mzQC format.
#' @field creationDate Creation date of the mzQC file.
#' @field contactName Name of the operator/creator of this mzQC file.
#' @field contactAddress Contact address (mail/e-mail or phone)
#' @field description Description and comments about the mzQC file contents.
#' @field runQualities Array of MzQCrunQuality;
#' @field setQualities Array of MzQCsetQuality
#' @field controlledVocabularies Array of CV domains used (obo files)
#'
#' @export MzQCmzQC
#'
#'
MzQCmzQC = setRefClass(
'MzQCmzQC',
fields = list(version = 'character',
creationDate = 'MzQCDateTime',
contactName = 'character', # optional
contactAddress = 'character', # optional
description = 'character', # optional
runQualities = 'list', # array of MzQCrunQuality # hint: at least runQuality or a setQuality must be present
setQualities = 'list', # array of MzQCsetQuality
controlledVocabularies = 'list'), # array of MzQCcontrolledVocabulary
methods = list(
initialize = function(version = NA_character_,
creationDate = MzQCDateTime$new(),
contactName = NA_character_,
contactAddress = NA_character_,
description = NA_character_,
runQualities = list(),
setQualities = list(),
controlledVocabularies = list())
{
.self$version = version
.self$creationDate = creationDate
.self$contactName = contactName
.self$contactAddress = contactAddress
.self$description = description
.self$runQualities = runQualities
.self$setQualities = setQualities
.self$controlledVocabularies = controlledVocabularies
},
isValid = function(.self)
{
# force evaluation using '+'
if (isUndefined(.self$version) +
!isValidMzQC(.self$creationDate, .self$runQualities, .self$setQualities, .self$controlledVocabularies)) return(FALSE)
# at least one must be present
if (length(.self$runQualities) + length(.self$setQualities) == 0)
{
warning("At least one runQuality or setQuality must be present! (currently all empty)", immediate. = TRUE, call. = FALSE)
return(FALSE)
}
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("version" = .self$version,
"creationDate" = .self$creationDate)
if (!isUndefined(.self$contactName)) r$contactName = .self$contactName
if (!isUndefined(.self$contactAddress)) r$contactAddress = .self$contactAddress
if (!isUndefined(.self$description)) r$description = .self$description
## do not write them out if they are empty (leads to 'runQuality: []', which is invalid)
if (length(.self$runQualities) > 0) r$runQualities = list(.self$runQualities) ## wrap in extra list for the enclosing '[ { ...} ]'
if (length(.self$setQualities) > 0) r$setQualities = list(.self$setQualities) ## wrap in extra list for the enclosing '[ { ...} ]'
r$controlledVocabularies = .self$controlledVocabularies
return (jsonlite:::asJSON(list("mzQC" = r), ...))
},
fromData = function(.self, data)
{
.self$version = data$version
.self$creationDate = fromDatatoMzQC(MzQCDateTime, data$creationDate)
.self$contactName = NULL_to_charNA(data$contactName)
.self$contactAddress = NULL_to_charNA(data$contactAddress)
.self$description = NULL_to_charNA(data$description)
.self$runQualities = fromDatatoMzQC(MzQCrunQuality, data$runQualities) ## if data$runQualities is empty, or NA, the empty list will be returned
.self$setQualities = fromDatatoMzQC(MzQCsetQuality, data$setQualities) ## if data$setQualities is empty, or NA, the empty list will be returned
.self$controlledVocabularies = fromDatatoMzQC(MzQCcontrolledVocabulary, data$controlledVocabularies) ## if data$controlledVocabularies is empty, or NA, the empty list will be returned
}
)
)
setMethod('asJSON', 'MzQCmzQC', function(x, ...) x$toJSON(...))
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Defines functions NULL_to_NA NULL_to_charNA fromDatatoMzQC isValidMzQC isUndefined
Documented in fromDatatoMzQC isUndefined isValidMzQC NULL_to_charNA NULL_to_NA
## some generic information on why/how/what?? :)
##
## + we provide initialize() functions for all RefClasses to enable unnamed construction (shorter syntax)
##
##
##
##
##
##
# Defining this function to enable overload
# e.g. setMethod('asJSON', 'mzQC', function(x, ...) x$toJSON())
# which allows to use
# jsonlite::toJSON(mzQC$new(content))
asJSON <- jsonlite:::asJSON
#'
#' Tell if a string is undefined (NA or NULL); If yes, and its required by the mzQC standard, we can raise an error
#'
#' You can pass multiple strings, which are all checked. If any of them is undefined, the function returns TRUE
#'
#' @param s A string to be checked for NA/NULL
#' @param ... More strings to be checked
#' @param verbose If TRUE and 's' is NULL/NA, will print the name of the variable which was passed in
#'
#' @examples
#' isUndefined(NA) ## TRUE
#' isUndefined(NULL) ## TRUE
#' isUndefined(NA, NULL) ## TRUE
#' isUndefined("") ## FALSE
#' isUndefined("", NA) ## TRUE
#' isUndefined(1) ## FALSE
#' myVar = NA
#' isUndefined(myVar) ## TRUE, with warning "variable 'myVar' is NA/NULL!"
#'
#' @export
#'
isUndefined = function(s, ..., verbose = TRUE)
{
# anchor
if (missing(s)) return(FALSE)
r = (is.na(s) || is.null(s))
name_of_var = deparse(substitute(s))
# omit the '.self' part of the variable's name
name_of_var = gsub("^.self\\$", "", name_of_var)
if (verbose && r) warning(paste0("Variable '", name_of_var, "' is NA/NULL!"), immediate. = TRUE, call. = FALSE)
## check remaining args from ... by using '+' (force evaluation)
return(r + isUndefined(..., verbose = verbose) > 0)
}
#'
#' Checks validity (= completeness) of mzQC objects - or lists (JSON arrays) thereof
#'
#' Note: Returns TRUE for empty lists!
#'
#' You can pass multiple arguments, which are all checked individually.
#' All of them need to be valid, for TRUE to be returned.
#' The reason for combining list support for arguments and ellipsis (...) into this function is that
#' JSON arrays are represented as lists and you can simply pass them as a single argument
#' (without the need for do.call()) and get the indices of invalid objects (if any).
#' The ellipsis is useful to avoid clutter,
#' i.e.
#' if (!isValidMzQC(a) || !isValidMzQC(b)) doStuff()
#' is harder to read than
#' if (!isValidMzQC(a,b)) doStuff()
#'
#' @param x An mzQC refclass (or list of them), each will be subjected to `isValidMzQC()`
#' @param ... Ellipsis, for recursive argument splitting
#'
#' @examples
#' isValidMzQC(MzQCcvParameter$new("QC:4000059")) # FALSE
#' isValidMzQC(MzQCcvParameter$new("QC:4000059", "Number of MS1 spectra")) # TRUE
#' isValidMzQC(list(MzQCcvParameter$new("QC:4000059"))) # FALSE
#' isValidMzQC(list(MzQCcvParameter$new("QC:4000059", "Number of MS1 spectra"))) # TRUE
#' isValidMzQC(list(MzQCcvParameter$new("QC:4000059", "Number of MS1 spectra")),
#' MzQCcvParameter$new()) # FALSE
#'
#' @export
#'
isValidMzQC = function(x, ...)
{
# anchor
if (missing(x)) return(TRUE)
if (inherits(x, "list")) {
idx = sapply(x, isValidMzQC)
if (any(idx == FALSE)) {
warning(paste0("In list of '", class(x[[1]]), "', the element(s) #[", paste(which(idx == FALSE), collapse = ","), "] is/are invalid."), immediate. = TRUE, call. = FALSE)
}
return(all(idx) & isValidMzQC(...))
}
r = x$isValid()
if (r == FALSE)
{
warning(paste0("A field in object of type ", class(x), " is invalid."), immediate. = TRUE, call. = FALSE)
}
return(r & isValidMzQC(...))
}
#'
#' Allow conversion of plain named lists to mzQC objects
#'
#' The plain-R representation of your mzQC objects must be wrapped in an outer list,
#' if your mzQC object representation is already a list
#' because upon detecting lists, this function will call 'class$fromData(element)' for every element.
#'
#' @param mzqc_class Prototype of the class to convert 'data' into
#' @param data A datastructure of R lists/arrays as obtained by 'jsonlite::fromJSON()'
#'
#' @examples
#' data = MzQCcvParameter$new("acc", "myName", "value")
#' data_recovered = fromDatatoMzQC(MzQCcvParameter, list(jsonlite::fromJSON(jsonlite::toJSON(data))))
#' data_recovered
#'
#' @export
#'
fromDatatoMzQC = function(mzqc_class, data)
{
if (inherits(data, "list"))
{
return(sapply(data, function(x) {
obj = mzqc_class$new()
obj$fromData(x)
obj
}))
}
if (is.na(data) || is.null(data)) return(list())
obj = mzqc_class$new()
return(obj$fromData(data))
}
#'
#' converts a NULL to NA_character_; or returns the argument unchanged otherwise
#'
#' This is useful for missing list elements (which returns NULL),
#' but when the missing element in refClass should be NA_character_ (and NULL would return an error)
#'
#' @param char_or_NULL A string or NULL
#'
#' @examples
#' NULL_to_charNA(NA) ## NA
#' NULL_to_charNA(NULL) ## NA_character_
#' NULL_to_charNA("hi") ## "hi"
#'
#' @export
#'
NULL_to_charNA = function(char_or_NULL) {
if (is.null(char_or_NULL)) return(NA_character_)
return(char_or_NULL)
}
#'
#' converts a NULL to NA; or returns the argument unchanged otherwise
#'
#' This is useful for missing list elements (which returns NULL),
#' but when the missing element in refClass should be NA (and NULL would return an error)
#'
#' @param var_or_NULL A variable of any kind or NULL
#'
#' @examples
#' NULL_to_NA(NA) ## NA
#' NULL_to_NA(NULL) ## NA
#' NULL_to_NA("hi") ## "hi"
#'
#' @export
#'
NULL_to_NA = function(var_or_NULL) {
if (is.null(var_or_NULL)) return(NA)
return(var_or_NULL)
}
#'
#' An mzQC-formatted date+time, as required by the mzQC spec doc
#'
#' The format is "%Y-%m-%d %H:%M:%S".
#'
#' @field datetime A correctly formatted date time (use as read-only)
#'
#' @exportClass MzQCDateTime
#' @export MzQCDateTime
#'
#' @examples
#' dt1 = MzQCDateTime$new("1900-01-01")
#' dt2 = MzQCDateTime$new(Sys.time())
#' ## test faulty input
#' ## errors with 'character string is not in a standard unambiguous format'
#' try(MzQCDateTime$new('lala'), silent=TRUE)
#' ## test roundtrip conversion from/to JSON
#' dt2$fromData(jsonlite::fromJSON(jsonlite::toJSON(dt1)))
# dt1$datetime == dt2$datetime ## TRUE
#'
#' @export
#'
MzQCDateTime = setRefClass(
'MzQCDateTime',
fields = list(datetime = 'character'),
methods = list(
initialize = function(date = as.character(Sys.time()))
{
set(date)
},
set = function(.self, date)
{
.self$datetime = format(as.POSIXct(date), "%Y-%m-%dT%H:%M:%S") # using ISO8601 format
},
isValid = function(.self)
{
return(TRUE) ## always valid, because it's designed that way
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
return(jsonlite:::asJSON(.self$datetime, ...))
},
fromData = function(.self, data)
{
.self$set(data)
}
)
)
setMethod('asJSON', 'MzQCDateTime', function(x, ...) x$toJSON(...))
#'
#' An controlled vocabulary document, usually pointing to an .obo file
#'
#' @field name Full name of the controlled vocabulary.
#' @field uri Publicly accessible URI of the controlled vocabulary.
#' @field version [optional] Version of the controlled vocabulary.
#'
#' @export MzQCcontrolledVocabulary
#'
#' @examples
#' MzQCcontrolledVocabulary$new(
#' "Proteomics Standards Initiative Quality Control Ontology",
#' "https://github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo",
#' "1.2.0")
#'
#' @export
#'
MzQCcontrolledVocabulary = setRefClass(
'MzQCcontrolledVocabulary',
fields = list(name = 'character',
uri = 'character',
version = 'character' # optional
),
methods = list(
initialize = function(name = NA_character_, uri = NA_character_, version = NA_character_)
{
.self$name = name
.self$uri = uri
.self$version = version
},
isValid = function(.self) {
if (isUndefined(.self$name, .self$uri)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("name" = .self$name,
"uri" = .self$uri,
"version" = .self$version)
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$name = data$name
.self$uri = data$uri
.self$version = NULL_to_charNA(data$version)
}
)
)
setMethod('asJSON', 'MzQCcontrolledVocabulary', function(x, ...) x$toJSON(...))
#'
#' An controlled vocabulary parameter, as detailed in the OBO file
#'
#' @field accession Accession number identifying the term within its controlled vocabulary (pattern: ^[A-Z]+:[A-Z0-9]+$).
#' @field name Name of the controlled vocabulary term describing the parameter.
#' @field value [optional] Value of the parameter.
#' @field description [optional] Definition of the controlled vocabulary term.
#'
#' @export MzQCcvParameter
#'
#' @examples
#' MzQCcvParameter$new("QC:4000139",
#' "RT acquisition range",
#' c(0.2959, 5969.8172))
#' isValidMzQC(MzQCcvParameter$new("MS:0000000"))
#'
#' @export
#'
MzQCcvParameter = setRefClass(
'MzQCcvParameter',
fields = list(accession = 'character',
name = 'character',
value = 'ANY', # optional
description = 'character' # optional
),
methods = list(
initialize = function(accession = NA_character_, name = NA_character_, value = NA, description = NA_character_)
{
.self$accession = accession
.self$name = name
.self$value = value
.self$description = description
},
isValid = function(.self) {
if (isUndefined(.self$accession, .self$name)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("accession" = .self$accession,
"name" = .self$name)
if (!is.na(.self$description)) r["description"] = .self$description
if (!is.na(.self$value)) r["value"] = .self$value
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$accession = data$accession
.self$name = data$name
.self$description = NULL_to_charNA(data$description)
.self$value = NULL_to_NA(data$value)
}
)
)
setMethod('asJSON', 'MzQCcvParameter', function(x, ...) x$toJSON(...))
#'
#' An inputfile within metadata for a run/setQuality
#'
#' @field name The name MUST uniquely match to a location (specified below) listed in the mzQC file.
#' @field location Unique file location, REQUIRED to be specified as a URI. The file URI is RECOMMENDED to be publicly accessible.
#' @field fileFormat A MzQCcvParameter with 'accession' and 'name'.
#' @field fileProperties An array of MzQCcvParameter, usually with 'accession', 'name' and 'value'. Recommended are at least two entries:
#' a) Completion time of the input file (MS:1000747) and b) Checksum of the input file (any child of: MS:1000561 ! data file checksum type).
#'
#' @export MzQCinputFile
#'
#'
#' @export
#'
MzQCinputFile = setRefClass(
'MzQCinputFile',
fields = list(name = 'character',
location = 'character',
fileFormat = 'MzQCcvParameter',
fileProperties = 'list' # array of MzQCcvParameter, optional
),
methods = list(
# defaults are required, otherwise refClasses do not work.
initialize = function(name = NA_character_, location = NA_character_, fileFormat = MzQCcvParameter$new(), fileProperties = list())
{
.self$name = name
.self$location = location
.self$fileFormat = fileFormat
.self$fileProperties = fileProperties
},
isValid = function(.self)
{
# force evaluation of all fields by '+'
if (isUndefined(.self$name, .self$location) + !.self$fileFormat$isValid()) return(FALSE)
return(isValidMzQC(.self$fileProperties)) ## TRUE for empty list, which is ok
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list(name = .self$name, location = .self$location, fileFormat = .self$fileFormat)
if (length(.self$fileProperties) > 0) r$fileProperties = .self$fileProperties
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$name = data$name
.self$location = data$location
.self$fileFormat$fromData(data$fileFormat)
.self$fileProperties = fromDatatoMzQC(MzQCcvParameter, data$fileProperties) ## for lists, call the free function
}
)
)
setMethod('asJSON', 'MzQCinputFile', function(x, ...) x$toJSON(...))
#
# file_format = MzQCcvParameter$new("MS:1000584", "mzML format")
# nif = MzQCinputFile$new("tmp.mzML", "c:\\", file_format)
# nif
# nif2 = nif
# l2 = list(file_format, file_format)
# nif2$fileProperties = l2
# x = jsonlite::toJSON(nif, pretty = TRUE)
# x
# x2 = jsonlite::toJSON(nif2)
# xdata = jsonlite::fromJSON(x, simplifyDataFrame = FALSE)
# xdata
# inherits(fromDatatoMzQC(MzQCcvParameter, xdata$fileProperties), "list")
# jsonlite::toJSON(xdata, pretty = TRUE, auto_unbox = T)
# isValidMzQC(l2)
# nif$fromData(xdata)
#'
#' Details of the software used to create the QC metrics
#'
#' @field accession Accession number identifying the term within its controlled vocabulary (pattern: ^[A-Z]+:[A-Z0-9]+$).
#' @field name Name of the controlled vocabulary term describing the software tool.
#' @field version Version number of the software tool.
#' @field uri Publicly accessible URI of the software tool or documentation.
#' @field description [optional] Definition of the controlled vocabulary term.
#' @field value [optional] Value of the software tool.
#'
#' @export MzQCanalysisSoftware
#'
#'
#' @export
#'
MzQCanalysisSoftware = setRefClass(
'MzQCanalysisSoftware',
fields = list(accession = 'character',
name = 'character',
version = 'character',
uri = 'character',
description = 'character', # optional
value = 'character' # optional
),
methods = list(
# defaults are required, otherwise refClasses do not work.
initialize = function(accession = NA_character_,
name = NA_character_,
version = NA_character_,
uri = NA_character_,
description = NA_character_, ## optional
value = NA_character_ ## optional
)
{
.self$accession = accession
.self$name = name
.self$version = version
.self$uri = uri
.self$description = description
.self$value = value
},
isValid = function(.self)
{
if (isUndefined(.self$accession, .self$name, .self$version, .self$uri)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("accession" = .self$accession,
"name" = .self$name,
"version" = .self$version,
"uri" = .self$uri)
if (!isUndefined(.self$description)) r$description = .self$description
if (!isUndefined(.self$value)) r$value = .self$value
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$accession = data$accession
.self$name = data$name
.self$version = data$version
.self$uri = data$uri
.self$description = NULL_to_charNA(data$description)
.self$value = NULL_to_charNA(data$value)
}
)
)
setMethod('asJSON', 'MzQCanalysisSoftware', function(x, ...) x$toJSON(...))
#'
#'The metadata for a run/setQuality
#'
#' @field label Unique name for the run (for runQuality) or set (for setQuality).
#' @field inputFiles Array/list of MzQCinputFile objects
#' @field analysisSoftware Array/list of MzQCanalysisSoftware objects
#' @field cvParameters [optional] Array of cvParameters objects
#'
#' @export MzQCmetadata
#'
#' @export
#'
MzQCmetadata = setRefClass(
'MzQCmetadata',
fields = list(label = 'character',
inputFiles = 'list', # array of MzQCinputFile
analysisSoftware = 'list', # array of MzQCanalysisSoftware
cvParameters = 'list' # optional array of MzQCcvParameter
),
methods = list(
initialize = function(label = NA_character_, inputFiles =list(), analysisSoftware = list(), cvParameters = list())
{
.self$label = label
.self$inputFiles = inputFiles
.self$analysisSoftware = analysisSoftware
.self$cvParameters = cvParameters
},
isValid = function(.self)
{
# force evaluation of all fields by '+'
if (isUndefined(.self$label) + !isValidMzQC(.self$inputFiles, .self$analysisSoftware, .self$cvParameters)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("label" = .self$label,
"inputFiles" = .self$inputFiles,
"analysisSoftware" = .self$analysisSoftware)
## only add if present (otherwise leads to 'cvParameters = []')
if (length(.self$cvParameters) > 0 ) r$cvParameters = list(.self$cvParameters) ## extra list for the enclosing '[ ... ]'
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$label = data$label
.self$inputFiles = fromDatatoMzQC(MzQCinputFile, data$inputFiles)
.self$analysisSoftware = fromDatatoMzQC(MzQCanalysisSoftware, data$analysisSoftware)
.self$cvParameters = fromDatatoMzQC(MzQCcvParameter, data$cvParameters)
}
)
)
setMethod('asJSON', 'MzQCmetadata', function(x, ...) x$toJSON(...))
################################################################################################################################
#################################################################################################################################'
#' The central class to store QC information
#'
#' @field accession Accession number identifying the term within its controlled vocabulary (pattern: ^[A-Z]+:[A-Z0-9]+$).
#' @field name Name of the controlled vocabulary element describing the metric.
#' @field description [optional] Definition of the controlled vocabulary term.
#' @field value [optional] Value of the metric (single value, n-tuple, table, matrix).
#' The structure is not checked by our mzQC implementation and must be handled by the caller
#' @field unit [optional] Array of unit(s), stored as MzQcvParameter
#'
#' @export MzQCqualityMetric
#'
MzQCqualityMetric = setRefClass(
'MzQCqualityMetric',
fields = list(accession = 'character',
name = 'character',
description = 'character', # optional
value = 'ANY', # optional value of unspecified type
unit = 'list' # optional array of MzQCcvParameter
),
methods = list(
initialize = function(accession = NA_character_, name = NA_character_, description = NA_character_, value = NA, unit = list())
{
.self$accession = accession
.self$name = name
.self$description = description
if (!missing(value)) .self$value = value else .self$value = NA ## need to set as NA explicitly, because the default value 'uninitialized class ANY' cannot be converted to JSON
.self$unit = unit
},
isValid = function(.self)
{
if (isUndefined(.self$accession, .self$name)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("accession" = .self$accession,
"name" = .self$name,
"description" = .self$description,
"value" = .self$value ## NA is written as "value": [null] and read back as NA
)
if (length(.self$unit) > 0) r$unit = .self$unit ## optional
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$accession = data$accession
.self$name = data$name
.self$description = NULL_to_charNA(data$description)
if (!is.na(data$value)) .self$value = data$value
.self$unit = fromDatatoMzQC(MzQCcvParameter, data$unit) ## if data$unit is empty, or NA, the empty list will be returned
}
)
)
setMethod('asJSON', 'MzQCqualityMetric', function(x, ...) x$toJSON(...))
#a_qc_metric = MzQCqualityMetric$new("acc", "nnam")
#xq = jsonlite::toJSON(a_qc_metric)
#jsonlite::fromJSON(xq)
#'
#' Base class of runQuality/setQuality
#'
#' @field metadata The metadata for this run/setQuality
#' @field qualityMetrics Array of MzQCqualityMetric objects
#'
#' @export MzQCbaseQuality
#'
#'
MzQCbaseQuality = setRefClass(
'MzQCbaseQuality',
fields = list(metadata = 'MzQCmetadata',
qualityMetrics = 'list'), # array of MzQCqualityMetric
methods = list(
initialize = function(metadata = MzQCmetadata$new(), qualityMetrics = list())
{
.self$metadata = metadata
.self$qualityMetrics = qualityMetrics
},
isValid = function(.self)
{
if (!isValidMzQC(.self$metadata, .self$qualityMetrics)) return(FALSE)
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("metadata" = .self$metadata,
"qualityMetrics" = .self$qualityMetrics)
return (jsonlite:::asJSON(r, ...))
},
fromData = function(.self, data)
{
.self$metadata = data$metadata
.self$qualityMetrics = fromDatatoMzQC(MzQCbaseQuality, data$qualityMetrics) ## if data$qualityMetrics is empty, or NA, the empty list will be returned
}
)
)
setMethod('asJSON', 'MzQCbaseQuality', function(x, ...) x$toJSON(...))
MzQCrunQuality = setRefClass(
"MzQCrunQuality",
contains = "MzQCbaseQuality"
)
MzQCsetQuality = setRefClass(
"MzQCsetQuality",
contains = "MzQCbaseQuality"
)
###########################################################################
#' Root element of an mzQC document
#'
#' At least one of runQualities or setQualities MUST be present.
#'
#' @field version Version of the mzQC format.
#' @field creationDate Creation date of the mzQC file.
#' @field contactName Name of the operator/creator of this mzQC file.
#' @field contactAddress Contact address (mail/e-mail or phone)
#' @field description Description and comments about the mzQC file contents.
#' @field runQualities Array of MzQCrunQuality;
#' @field setQualities Array of MzQCsetQuality
#' @field controlledVocabularies Array of CV domains used (obo files)
#'
#' @export MzQCmzQC
#'
#'
MzQCmzQC = setRefClass(
'MzQCmzQC',
fields = list(version = 'character',
creationDate = 'MzQCDateTime',
contactName = 'character', # optional
contactAddress = 'character', # optional
description = 'character', # optional
runQualities = 'list', # array of MzQCrunQuality # hint: at least runQuality or a setQuality must be present
setQualities = 'list', # array of MzQCsetQuality
controlledVocabularies = 'list'), # array of MzQCcontrolledVocabulary
methods = list(
initialize = function(version = NA_character_,
creationDate = MzQCDateTime$new(),
contactName = NA_character_,
contactAddress = NA_character_,
description = NA_character_,
runQualities = list(),
setQualities = list(),
controlledVocabularies = list())
{
.self$version = version
.self$creationDate = creationDate
.self$contactName = contactName
.self$contactAddress = contactAddress
.self$description = description
.self$runQualities = runQualities
.self$setQualities = setQualities
.self$controlledVocabularies = controlledVocabularies
},
isValid = function(.self)
{
# force evaluation using '+'
if (isUndefined(.self$version) +
!isValidMzQC(.self$creationDate, .self$runQualities, .self$setQualities, .self$controlledVocabularies)) return(FALSE)
# at least one must be present
if (length(.self$runQualities) + length(.self$setQualities) == 0)
{
warning("At least one runQuality or setQuality must be present! (currently all empty)", immediate. = TRUE, call. = FALSE)
return(FALSE)
}
return(TRUE)
},
toJSON = function(.self, ...)
{
if (!isValidMzQC(.self)) stop(paste0("Object of class '", class(.self), "' is not in a valid state for writing to JSON"))
r = list("version" = .self$version,
"creationDate" = .self$creationDate)
if (!isUndefined(.self$contactName)) r$contactName = .self$contactName
if (!isUndefined(.self$contactAddress)) r$contactAddress = .self$contactAddress
if (!isUndefined(.self$description)) r$description = .self$description
## do not write them out if they are empty (leads to 'runQuality: []', which is invalid)
if (length(.self$runQualities) > 0) r$runQualities = list(.self$runQualities) ## wrap in extra list for the enclosing '[ { ...} ]'
if (length(.self$setQualities) > 0) r$setQualities = list(.self$setQualities) ## wrap in extra list for the enclosing '[ { ...} ]'
r$controlledVocabularies = .self$controlledVocabularies
return (jsonlite:::asJSON(list("mzQC" = r), ...))
},
fromData = function(.self, data)
{
.self$version = data$version
.self$creationDate = fromDatatoMzQC(MzQCDateTime, data$creationDate)
.self$contactName = NULL_to_charNA(data$contactName)
.self$contactAddress = NULL_to_charNA(data$contactAddress)
.self$description = NULL_to_charNA(data$description)
.self$runQualities = fromDatatoMzQC(MzQCrunQuality, data$runQualities) ## if data$runQualities is empty, or NA, the empty list will be returned
.self$setQualities = fromDatatoMzQC(MzQCsetQuality, data$setQualities) ## if data$setQualities is empty, or NA, the empty list will be returned
.self$controlledVocabularies = fromDatatoMzQC(MzQCcontrolledVocabulary, data$controlledVocabularies) ## if data$controlledVocabularies is empty, or NA, the empty list will be returned
}
)
)
setMethod('asJSON', 'MzQCmzQC', function(x, ...) x$toJSON(...))
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