ValidateApi: Validate operations

In lifs-tools/rmzTab-m: R Package Client for mzTab-M Reference Implementation and Validation API

Validate operations

Description

rmzTabM.Validate

Format

An R6Class generator object

Methods

ValidateMzTabFile Validates an mzTab file in XML or JSON representation and reports syntactic, structural, and semantic errors.

• @param mztabfile MzTab

• @param level Enum < [info, warn, error] >

• @param max.errors integer

• @param semantic.validation character

• @returnType list( ValidationMessage )
  

• status code : 200 | Validation Okay

• return type : array[ValidationMessage]

• response headers :

• status code : 415 | Unsupported content type

• response headers :

• status code : 422 | Invalid input

• return type : array[ValidationMessage]

• response headers :

• status code : 0 | Unexpected error

• return type : Error

• response headers :

Public fields

apiClient

Handles the client-server communication.

Methods

Public methods

• ValidateApi$new()

• ValidateApi$ValidateMzTabFile()

• ValidateApi$ValidateMzTabFileWithHttpInfo()

• ValidateApi$clone()

---

Method new()

Create a new ValidateApi object.

Usage

ValidateApi$new(apiClient)

Arguments

apiClient

An initialized ApiClient.

---

Method ValidateMzTabFile()

Validate an MzTab object.

Usage

ValidateApi$ValidateMzTabFile(
  mztabfile,
  level = "info",
  max.errors = 100,
  semantic.validation = FALSE,
  ...
)

Arguments

mztabfile

The MzTab object to validate.

level

The validation level.

max.errors

The maximum number of errors.

semantic.validation

Whether semantic validation should also be performed.

...

local optional variable arguments

---

Method ValidateMzTabFileWithHttpInfo()

Validate an MzTab file but include HTTP response info.

Usage

ValidateApi$ValidateMzTabFileWithHttpInfo(
  mztabfile,
  level = "info",
  max.errors = 100,
  semantic.validation = FALSE,
  ...
)

Arguments

mztabfile

The MzTab object to validate.

level

The validation level.

max.errors

The maximum number of errors.

semantic.validation

Whether semantic validation should also be performed.

...

local optional variable arguments

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ValidateApi$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## Not run: 
####################  ValidateMzTabFile  ####################

library(rmzTabM)
# MzTab | mzTab file that should be validated.
var.mztabfile <- MzTab$new()
# character | The level of errors that should be reported, one of ERROR, WARN, INFO.
var.level <- 'info' 
# integer | The maximum number of errors to return.
var.max.errors <- 100 
# character | Whether a semantic validation against the default rule set should be performed.
var.semantic.validation <- FALSE 

api.instance <- ValidateApi$new()

result <- api.instance$ValidateMzTabFile(var.mztabfile, 
  level=var.level, max.errors=var.max.errors, 
  semantic.validation=var.semantic.validation
)



## End(Not run)

lifs-tools/rmzTab-m documentation built on Jan. 26, 2023, 4:45 p.m.