d2Parser: General purpose parsing function for different formats of...

In jason-p-pickering/datim-validation: External Validation Routines for Data Payloads in DATIM

General purpose parsing function for different formats of DHIS2 data

Description

d2Parser will parse a compliant DHIS2 XML, JSON, or CSV file and transform it into a standard data frame which can be used in subsequent DATIM validation routines.

Usage

d2Parser(
  filename,
  type = "csv",
  datastream = "RESULTS",
  datasets = NA,
  organisationUnit = NA,
  dataElementIdScheme = "id",
  orgUnitIdScheme = "id",
  idScheme = "id",
  invalidData = FALSE,
  hasHeader = TRUE,
  isoPeriod = NA,
  d2session = dynGet("d2_default_session", inherits = TRUE)
)

Arguments

filename	Location of the payload to be imported. Should be a valid import file.
type	Type of the file. Should be one of xml, json or csv.
datastream	One of RESULTS, TARGETS, NARRATIVES or SIMS.
datasets	Should be a character vector of data set UIDs. Alternatively, if left missing, user will be promted to choose from a list.
organisationUnit	Organisation unit ancestor.
dataElementIdScheme	Should be one of either code, name, shortName, or id. If this paramater is "id", then the Data elements are assumed to be already specififed as UIDs.
orgUnitIdScheme	Should be one of either code, name, shortName or id. If this paramater is "id", then the organisation units are assumed to be already specififed as UIDs
idScheme	Remapping scheme for category option combos.
invalidData	Exclude any (NA or missing) data from the parsed file?
hasHeader	TRUE by default. Should be set to FALSE if the file does not contain header information.
isoPeriod	period to be used for date shift boundaries. If not provided, no boundaries are set.
d2session	DHIS2 Session id

Value

A list object consisting of "info", "data" and "tests".

Note

function(filename = "/home/me/foo.xml", type = "xml", dataElementIdScheme = "code", orgUnitIdScheme = "code", idScheme = "id") Note that all values will be returned as characters.

Examples

## Not run: 
    #Be sure to login to DATIM first
    datimutils::loginToDATIM(config_path = "/home/me/datim-test.json")
    #Load a CSV file
    d <- d2Parser("myfile.csv",type="csv",header=TRUE)
    #Load a JSON file
    d <- d2Parser("myfile.json",type="json",dataElementIdScheme="code")
    #Load an XML file
    d <- d2Parser("myfile.xml",type="xml",dataElementIdScheme="name")

## End(Not run)

jason-p-pickering/datim-validation documentation built on April 20, 2023, 5:32 a.m.